% This file was created with JabRef 2.3.1.
% Encoding: Cp1252

@ARTICLE{Abedini2006,
  author = {Andisheh Abedini and Daniel P Raleigh},
  title = {Destabilization of human IAPP amyloid fibrils by proline mutations
	outside of the putative amyloidogenic domain: is there a critical
	amyloidogenic domain in human IAPP?},
  journal = {J. Mol. Biol.},
  year = {2006},
  volume = {355},
  pages = {274--281},
  number = {2},
  month = {Jan},
  abstract = {Islet amyloid polypeptide (IAPP; amylin) is responsible for amyloid
	formation in type-2 diabetes. Not all organisms form islet amyloid,
	and amyloid formation correlates strongly with variations in primary
	sequence. Studies of human and rodent IAPP have pointed to the amino
	acid residues 20-29 region as the important amyloid-modulating sequence.
	The rat 20-29 sequence contains three proline residues and does not
	form amyloid, while the human sequence contains no proline and readily
	forms amyloid. This has led to the view that the 20-29 region constitutes
	a critical amyloidogenic domain that dictates the properties of the
	entire sequence. The different behavior of human and rat IAPP could
	be due to differences in the 20-29 region or due simply to the fact
	that multiple proline residues destabilize amyloid fibrils. We tested
	how critical the 20-29 region is by studying a variant identical
	with the human peptide in this segment but with three proline residues
	outside this region. We designed a variant of the amyloidogenic 8-37
	region of human IAPP (hIAPP(8-37) 3xP) with proline substitutions
	at positions 17, 19 and 30. Compared to the wild-type, the 3xP variant
	was much easier to synthesize and had dramatically greater solubility.
	Fourier transform infra red spectroscopy, transmission electron microscopy,
	Congo red staining and thioflavin-T binding indicate that this variant
	has a reduced tendency to form beta-sheet structure and forms deposits
	with much less structural order than the wild-type. Far-UV CD studies
	show that the small amount of beta-sheet structure developed by hIAPP(8-37)
	3xP after long periods of incubation dissociates readily into random-coil
	structure upon dilution into Tris buffer. The observation that proline
	substitutions outside the putative core domain effectively abolish
	amyloid formation indicates that models of IAPP aggregation must
	consider contributions from other regions.},
  file = {aggregations\\IAPP\\j mol biol 2006 destablization of hiapp.pdf:aggregations\\IAPP\\j
	mol biol 2006 destablization of hiapp.pdf:PDF},
  keywords = {Amino Acid Sequence; Amino Acid Substitution; Amyloid; Humans; Molecular
	Sequence Data; Mutation; Proline; Protein Structure, Secondary; Protein
	Structure, Tertiary; Research Support, N.I.H., Extramural; Research
	Support, U.S. Gov't, Non-P.H.S.},
  myid = {6},
  owner = {Gurpreet},
  pii = {S0022-2836(05)01299-4},
  pmid = {16303136},
  timestamp = {2006.12.18 12:00:03}
}

@ARTICLE{Abedini2005,
  author = {Andisheh Abedini and Daniel P Raleigh},
  title = {The role of His-18 in amyloid formation by human islet amyloid polypeptide.},
  journal = {Biochemistry},
  year = {2005},
  volume = {44},
  pages = {16284--16291},
  number = {49},
  month = {Dec},
  abstract = {The 37-residue islet amyloid polypeptide (IAPP) is the major protein
	component of the amyloid deposits found in type-II diabetes. IAPP
	is stored in a relatively low pH environment in the pancreatic secretory
	granules prior to its release to the extracellular environment. Human
	IAPP contains a single histidine at position 18. Aggregation of IAPP
	is considerably faster at a lower pH (4.0 +/- 0.3) than at high pH
	(8.8 +/- 0.3), as judged by turbidity and thioflavine-T fluorescence
	studies. The rate of aggregation at low pH increases drastically
	in the presence of salt. CD experiments show that the conversion
	of largely unstructured monomers to beta-sheet-rich structures is
	faster at high pH. TEM studies show that fibrils are formed at both
	pH values but are more prevalent at pH 8.8 (+/-0.3). Both the free
	N terminus of IAPP and His-18 will titrate over the pH range studied.
	An N-terminal acetylated fragment consisting of residues 8-37 of
	human IAPP was also studied to isolate contributions from the protonation
	of His-18. Previous studies have shown that this fragment forms protofibrils
	that are very similar to those formed by intact IAPP. The effects
	of varying the protonation state of His-18 in the 8-37 analogue indicate
	that the rate of aggregation and fibril formation is noticeably faster
	when His-18 is deprotonated, similar to the wild type. However, the
	pH-dependent effects are larger for full-length IAPP than for the
	disulfide-truncated, acetylated analogue. TEM studies indicate differences
	in the morphology of the deposits formed at high and low pH. These
	results are discussed in light of recent structural models of IAPP
	fibrils.},
  doi = {10.1021/bi051432v},
  file = {aggregations\\IAPP\\biochemistry 2005 the role of his 18 in amyloid
	formation by IAPP.pdf:aggregations\\IAPP\\biochemistry 2005 the role
	of his 18 in amyloid formation by IAPP.pdf:PDF},
  keywords = {Amino Acid Sequence; Amyloid; Histidine; Humans; Hydrogen-Ion Concentration;
	Molecular Sequence Data; Sequence Alignment; Thiazoles},
  myid = {10},
  owner = {Gurpreet},
  pmid = {16331989},
  timestamp = {2006.12.19 10:42:47}
}

@BOOK{Allen1989,
  title = {Computer Simulation of Liquids},
  publisher = {Oxford University Press, USA},
  year = {1989},
  author = {M. P. Allen and D. J. Tildesley},
  owner = {Gurpreet},
  timestamp = {2007.03.22 05:49:11}
}

@ARTICLE{Arakawa1985,
  author = {T. Arakawa and S. N. Timasheff},
  title = {Theory of protein solubility.},
  journal = {Methods Enzymol.},
  year = {1985},
  volume = {114},
  pages = {49--77},
  keywords = {Crystallization; Kinetics; Proteins; Solubility; Solvents; Thermodynamics},
  owner = {singh},
  pmid = {4079776},
  timestamp = {2008.10.15}
}

@ARTICLE{Azriel2001,
  author = {R. Azriel and E. Gazit},
  title = {Analysis of the minimal amyloid-forming fragment of the islet amyloid
	polypeptide. An experimental support for the key role of the phenylalanine
	residue in amyloid formation.},
  journal = {J. Biol. Chem.},
  year = {2001},
  volume = {276},
  pages = {34156--34161},
  number = {36},
  month = {Sep},
  abstract = {The development of type II diabetes was shown to be associated with
	the formation of amyloid fibrils consisted of the islet amyloid polypeptide
	(IAPP or amylin). Recently, a short functional hexapeptide fragment
	of IAPP (NH(2)-NFGAIL-COOH) was found to form fibrils that are very
	similar to those formed by the full-length polypeptide. To better
	understand the specific role of the residues that compose the fragment,
	we performed a systematic alanine scan of the IAPP "basic amyloidogenic
	units." Turbidity assay experiments demonstrated that the wild-type
	peptide and the Asn(1) --> Ala and Gly(3) --> Ala peptides had the
	highest rate of aggregate formation, whereas the Phe(2) --> Ala peptide
	did not form any detectable aggregates. Dynamic light-scattering
	experiments demonstrated that all peptides except the Phe(2) -->
	Ala form large multimeric structures. Electron microscopy and Congo
	red staining confirmed that the structures formed by the various
	peptides are indeed amyloid fibrils. Taken together, the results
	of our study provide clear experimental evidence for the key role
	of phenylalanine residue in amyloid formation by IAPP. In contrast,
	glycine, a residue that was suggested to facilitate amyloid formation
	in other systems, has only a minor role, if any, in this case. Our
	results are discussed in the context of the remarkable occurrence
	of aromatic residues in short functional fragments and potent inhibitors
	of amyloid-related polypeptides. We hypothesize that pi-pi interactions
	may play a significant role in the molecular recognition and self-assembly
	processes that lead to amyloid formation.},
  doi = {10.1074/jbc.M102883200},
  keywords = {Alanine; Amino Acid Sequence; Amyloid; Asparagine; Coloring Agents;
	Congo Red; Glycine; Humans; Kinetics; Light; Microscopy, Electron;
	Models, Chemical; Molecular Sequence Data; Peptides; Phenylalanine;
	Protein Binding; Scattering, Radiation; Sequence Homology, Amino
	Acid; Time Factors},
  owner = {Gurpreet},
  pii = {M102883200},
  pmid = {11445568},
  timestamp = {2008.02.17 03:45:53}
}

@ARTICLE{Balbach2000,
  author = {J. J. Balbach and Y. Ishii and O. N. Antzutkin and R. D. Leapman
	and N. W. Rizzo and F. Dyda and J. Reed and R. Tycko},
  title = {Amyloid fibril formation by A beta 16-22, a seven-residue fragment
	of the Alzheimer's beta-amyloid peptide, and structural characterization
	by solid state NMR.},
  journal = {Biochemistry},
  year = {2000},
  volume = {39},
  pages = {13748--13759},
  number = {45},
  month = {Nov},
  abstract = {The seven-residue peptide N-acetyl-Lys-Leu-Val-Phe-Phe-Ala-Glu-NH(2),
	called A beta(16-22) and representing residues 16-22 of the full-length
	beta-amyloid peptide associated with Alzheimer's disease, is shown
	by electron microscopy to form highly ordered fibrils upon incubation
	of aqueous solutions. X-ray powder diffraction and optical birefringence
	measurements confirm that these are amyloid fibrils. The peptide
	conformation and supramolecular organization in A beta(16-22) fibrils
	are investigated by solid state (13)C NMR measurements. Two-dimensional
	magic-angle spinning (2D MAS) exchange and constant-time double-quantum-filtered
	dipolar recoupling (CTDQFD) measurements indicate a beta-strand conformation
	of the peptide backbone at the central phenylalanine. One-dimensional
	and two-dimensional spectra of selectively and uniformly labeled
	samples exhibit (13)C NMR line widths of <2 ppm, demonstrating that
	the peptide, including amino acid side chains, has a well-ordered
	conformation in the fibrils. Two-dimensional (13)C-(13)C chemical
	shift correlation spectroscopy permits a nearly complete assignment
	of backbone and side chain (13)C NMR signals and indicates that the
	beta-strand conformation extends across the entire hydrophobic segment
	from Leu17 through Ala21. (13)C multiple-quantum (MQ) NMR and (13)C/(15)N
	rotational echo double-resonance (REDOR) measurements indicate an
	antiparallel organization of beta-sheets in the A beta(16-22) fibrils.
	These results suggest that the degree of structural order at the
	molecular level in amyloid fibrils can approach that in peptide or
	protein crystals, suggest how the supramolecular organization of
	beta-sheets in amyloid fibrils can be dependent on the peptide sequence,
	and illustrate the utility of solid state NMR measurements as probes
	of the molecular structure of amyloid fibrils. A beta(16-22) is among
	the shortest fibril-forming fragments of full-length beta-amyloid
	reported to date, and hence serves as a useful model system for physical
	studies of amyloid fibril formation.},
  keywords = {Amyloid beta-Protein; Birefringence; Carbon Isotopes; Humans; Models,
	Chemical; Models, Molecular; Nitrogen Isotopes; Nuclear Magnetic
	Resonance, Biomolecular; Oligopeptides; Peptide Fragments; Protein
	Conformation; Protein Structure, Secondary; X-Ray Diffraction},
  owner = {Gurpreet},
  pii = {bi0011330},
  pmid = {11076514},
  timestamp = {2008.02.17 03:33:53}
}

@ARTICLE{Balbirnie2001,
  author = {M. Balbirnie and R. Grothe and D. S. Eisenberg},
  title = {An amyloid-forming peptide from the yeast prion Sup35 reveals a dehydrated
	beta-sheet structure for amyloid.},
  journal = {Proc. Natl. Acad. Sci. U. S. A.},
  year = {2001},
  volume = {98},
  pages = {2375--2380},
  number = {5},
  month = {Feb},
  abstract = {X-ray diffraction and other biophysical tools reveal features of the
	atomic structure of an amyloid-like crystal. Sup35, a prion-like
	protein in yeast, forms fibrillar amyloid assemblies intrinsic to
	its prion function. We have identified a polar peptide from the N-terminal
	prion-determining domain of Sup35 that exhibits the amyloid properties
	of full-length Sup35, including cooperative kinetics of aggregation,
	fibril formation, binding of the dye Congo red, and the characteristic
	cross-beta x-ray diffraction pattern. Microcrystals of this peptide
	also share the principal properties of the fibrillar amyloid, including
	a highly stable, beta-sheet-rich structure and the binding of Congo
	red. The x-ray powder pattern of the microcrystals, extending to
	0.9-A resolution, yields the unit cell dimensions of the well-ordered
	structure. These dimensions restrict possible atomic models of this
	amyloid-like structure and demonstrate that it forms packed, parallel-stranded
	beta-sheets. The unusually high density of the crystals shows that
	the packed beta-sheets are dehydrated, despite the polar character
	of the side chains. These results suggest that amyloid is a highly
	intermolecularly bonded, dehydrated array of densely packed beta-sheets.
	This dry beta-sheet could form as Sup35 partially unfolds to expose
	the peptide, permitting it to hydrogen-bond to the same peptide of
	other Sup35 molecules. The implication is that amyloid-forming units
	may be short segments of proteins, exposed for interactions by partial
	unfolding.},
  doi = {10.1073/pnas.041617698},
  keywords = {Amino Acid Sequence; Amyloid; Base Sequence; Crystallization; Crystallography,
	X-Ray; DNA Primers; Fungal Proteins; Microscopy, Electron; Prions;
	Protein Conformation; Saccharomyces cerevisiae Proteins; Spectroscopy,
	Fourier Transform Infrared},
  owner = {Gurpreet},
  pii = {041617698},
  pmid = {11226247},
  timestamp = {2008.02.17 03:24:07}
}

@ARTICLE{Ball2008,
  author = {Philip Ball},
  title = {Water as an Active Constituent in Cell Biology},
  journal = {Chemical Reviews},
  year = {2008},
  volume = {108},
  pages = {74--108},
  number = {1}
}

@ARTICLE{Baumketner2005,
  author = {Andrij Baumketner and Joan-Emma Shea},
  title = {The influence of different treatments of electrostatic interactions
	on the thermodynamics of folding of peptides.},
  journal = {J. Phys. Chem. B},
  year = {2005},
  volume = {109},
  pages = {21322--21328},
  number = {45},
  month = {Nov},
  abstract = {Replica exchange molecular dynamics simulations were performed to
	investigate the effects of different electrostatic treatments on
	the structure and thermodynamics of a small beta-hairpin forming
	peptide. Three different electrostatic schemes were considered: regular
	cutoffs, generalized reaction field (GRF), and particle mesh Ewald
	(PME), with the peptide modeled using OPLS/AA all-atom force field
	with explicit TIP3P water. Both the GRF and PME methods yielded results
	consistent with experiment, with free energy surfaces displaying
	a single minimum corresponding to the native beta-hairpin structure.
	In contrast, use of straight cutoffs led to the population of an
	additional local minimum corresponding to nonhairpin conformations
	that compete with the formation of the native beta-hairpin at low
	temperatures. This extra minimum would not be apparent in conventional
	constant-temperature molecular dynamics simulations run for a few
	nanoseconds. This result points to the critical need of careful sampling
	of conformational space to assess the quality of different numerical
	treatments of long-range forces. While differences emerged in the
	nature of the unfolded states populated using PME and GRF approaches,
	simulations on the beta-hairpin forming peptide and on two additional
	control peptides indicate that the GRF treatment of electrostatics
	offers a satisfactory compromise between accuracy and computational
	speed for the identification of low-energy conformations. A GRF-based
	approach emerges as a viable means for treating larger biological
	systems that would be prohibitively costly to simulate using PME
	methods.},
  doi = {10.1021/jp051325a},
  institution = {Department of Chemistry and Biochemistry, University of California
	at Santa Barbara, Santa Barbara, California 93106, USA.},
  keywords = {Computer Simulation; Electrostatics; Models, Molecular; Peptides;
	Protein Folding; Protein Structure, Secondary; Thermodynamics},
  owner = {singh},
  pmid = {16853765},
  timestamp = {2008.10.16}
}

@ARTICLE{Baynes2004,
  author = {Brian M Baynes and Bernhardt L Trout},
  title = {Rational design of solution additives for the prevention of protein
	aggregation.},
  journal = {Biophys. J.},
  year = {2004},
  volume = {87},
  pages = {1631--1639},
  number = {3},
  month = {Sep},
  abstract = {We have developed a statistical-mechanical model of the effect of
	solution additives on protein association reactions. This model incorporates
	solvent radial distribution functions obtained from all-atom molecular
	dynamics simulations of particular proteins into simple models of
	protein interactions. In this way, the effects of additives can be
	computed along the entire association/dissociation reaction coordinate.
	We used the model to test our hypothesis that a class of large solution
	additives, which we term "neutral crowders," can slow protein association
	and dissociation by being preferentially excluded from protein-protein
	encounter complexes, in a manner analogous to osmotic stress. The
	magnitude of this proposed "gap effect" was probed for two simple
	model systems: the association of two spheres and the association
	of two planes. Our results suggest that for a protein of 20 A radius,
	an 8 A additive can increase the free energy barrier for association
	and dissociation by as much as 3-6 kcal/mol. Because the proposed
	gap effect is present only for reactions involving multiple molecules,
	it can be exploited to develop novel additives that affect protein
	association reactions although having little or no effect on unimolecular
	reactions such as protein folding. This idea has many potential applications
	in areas such as the stabilization of proteins against aggregation
	during folding and in pharmaceutical formulations.},
  doi = {10.1529/biophysj.104.042473},
  file = {aggregations\\others\\biophy j 2004 rational design of solution additives.pdf:aggregations\\others\\biophy
	j 2004 rational design of solution additives.pdf:PDF},
  keywords = {Biophysics; Carbonic Anhydrases; Drug Design; Entropy; Interferon
	Type II; Kinetics; Models, Chemical; Models, Statistical; Models,
	Theoretical; Oxidative Stress; Oxygen; Protein Binding; Protein Conformation;
	Protein Denaturation; Protein Folding},
  owner = {Gurpreet},
  pii = {87/3/1631},
  pmid = {15345542},
  timestamp = {2007.03.22 02:51:24}
}

@ARTICLE{Benjwal:06a,
  author = {Sangeeta Benjwal and Shikha Verma and Klaus-Heinrich R�hm and and
	Olga Gursky},
  title = {Monitoring protein aggregation during thermal unfolding in circular
	dichroism experiments},
  journal = {Protein Sci.},
  year = {2006},
  volume = {15},
  pages = {635�639},
  owner = {Brov},
  timestamp = {2008.04.09}
}

@ARTICLE{Berendsen1987,
  author = {Berendsen, H. J. C. and Grigera, J. R. and Straatsma, T. P.},
  title = {The missing term in effective pair potentials.},
  journal = {J. Phys. Chem.},
  year = {1987},
  volume = {91},
  pages = {6269--6271},
  owner = {blake},
  timestamp = {2008.03.14}
}

@ARTICLE{Berendsen1984,
  author = {Berendsen, H. J. C. and Postma, J.P.M. and DiNola, A. and Haak, J.R.},
  title = {Molecular dynamics with coupling to an external bath.},
  journal = {J. Chem. Phys.},
  year = {1984},
  volume = {81},
  pages = {3684--3690}
}

@ARTICLE{Binder:03a,
  author = {Kurt Binder},
  title = {Theory of the evaporation/condensation transition of equilibrium
	droplets in finite volumes},
  journal = {Phys. Acta},
  year = {2003},
  volume = {319},
  pages = {99-114},
  owner = {Brov},
  timestamp = {2008.04.09}
}

@ARTICLE{Blokzijl1993,
  author = {Jan B. F. N. Engberts Wilfried Blokzijl},
  title = {Hydrophobic Effects. Opinions and Facts},
  journal = {Angew. Chem. Int. Ed. Engl.},
  year = {1993},
  volume = {32},
  pages = {1545--1579},
  number = {11}
}

@BOOK{Bower2002,
  title = {An introduction to polymer physics},
  publisher = {Cambridge university press},
  year = {2002},
  author = {David I. Bower},
  owner = {singh},
  timestamp = {2008.07.21}
}

@ARTICLE{Broglia1998,
  author = {R. A. Broglia and G. Tiana and S. Pasquali and H. E. Roman and E.
	Vigezzi},
  title = {Folding and aggregation of designed proteins.},
  journal = {Proc. Natl. Acad. Sci. U. S. A.},
  year = {1998},
  volume = {95},
  pages = {12930--12933},
  number = {22},
  month = {Oct},
  abstract = {Protein aggregation is studied by following the simultaneous folding
	of two designed identical 20-letter amino acid chains within the
	framework of a lattice model and using Monte Carlo simulations. It
	is found that protein aggregation is determined by elementary structures
	(partially folded intermediates) controlled by local contacts among
	some of the most strongly interacting amino acids and formed at an
	early stage in the folding process.},
  institution = {Dipartimento di Fisica Universita di Milano and Istituto Nazionale
	di Fisica Nucleare, I-20133 Milan, Italy.},
  keywords = {Amino Acid Sequence; Kinetics; Models, Chemical; Models, Molecular;
	Molecular Sequence Data; Monte Carlo Method; Peptides; Protein Conformation;
	Protein Folding; Proteins},
  owner = {singh},
  pmid = {9789017},
  timestamp = {2008.10.16}
}

@ARTICLE{Brovchenko:08b,
  author = {I. Brovchenko and R. R. Burri and A. Krukau and A. Oleinikova and
	R. Winter},
  title = {Intrinsic thermal expansivity and hydrational properties of amyloid
	peptide A$\beta$42 in liquid water},
  journal = {J. Chem. Phys.},
  year = {2008},
  volume = {129},
  pages = {(in press)},
  owner = {brov},
  timestamp = {2008.02.15}
}

@ARTICLE{Brovchenko:04a,
  author = {I. Brovchenko and A. Geiger and A. Oleinikova},
  title = {Clustering of water molecules in aqueous solutions: Effect of water-solute
	interaction},
  journal = {Phys. Chem. Chem. Phys.},
  year = {2004},
  volume = {6},
  pages = {1982-1987},
  owner = {Brov},
  timestamp = {2007.09.25}
}

@ARTICLE{Brovchenko:06a,
  author = {Ivan Brovchenko and Aliaksei Krukau and Alla Oleinikova and Alexey
	K. Mazur},
  title = {Water percolation governs polymorphic transitions and conductivity
	of \mbox{DNA}},
  journal = {Phys. Rev. Lett.},
  year = {2006},
  volume = {97},
  pages = {137801},
  number = {13},
  eid = {137801},
  owner = {singh},
  timestamp = {2008.05.01}
}

@ARTICLE{Brovchenko:97a,
  author = {Ivan V. Brovchenko and Alla V. Oleinikova},
  title = {Structural changes of the molecular complexes of pyridines with water
	and demixing phenomena in aqueous solutions},
  journal = {J. Chem. Phys.},
  year = {1997},
  volume = {106},
  pages = {7756-7765},
  number = {18},
  doi = {10.1063/1.473776},
  keywords = {water; organic compounds; solubility; mixing; hydrogen bonds; critical
	phenomena; liquid mixtures; critical mixtures; liquid-liquid transformations},
  owner = {Brov},
  publisher = {AIP},
  timestamp = {2008.04.10}
}

@ARTICLE{Buchete:07a,
  author = {Buchete, Nicolae-Viorel and Hummer, Gerhard},
  title = {Structure and Dynamics of Parallel {beta}-Sheets, Hydrophobic Core,
	and Loops in Alzheimer's A{beta} Fibrils},
  journal = {Biophys. J.},
  year = {2007},
  volume = {92},
  pages = {3032-3039},
  number = {9},
  abstract = {We explore the relative contributions of different structural elements
	to the stability of A{beta} fibrils by molecular-dynamics simulations
	performed over a broad range of temperatures (298 K to 398 K). Our
	fibril structures are based on solid-state nuclear magnetic resonance
	experiments of A{beta}(1-40) peptides, with sheets of parallel {beta}-strands
	connected by loops and stabilized by interior salt bridges. We consider
	models with different interpeptide interfaces, and different staggering
	of the N- and C-terminal {beta}-strands along the fibril axis. Multiple
	10-20 ns molecular-dynamics simulations show that fibril segments
	with 12 peptides are stable at ambient temperature. The different
	models converge toward an interdigitated side-chain packing, and
	present water channels solvating the interior D23/K28 salt bridges.
	At elevated temperatures, we observe the early phases of fibril dissociation
	as a loss of order in the hydrophilic loops connecting the two {beta}-strands,
	and in the solvent-exposed N-terminal {beta}-sheets. As the most
	dramatic structural change, we observe collective sliding of the
	N- and C-terminal {beta}-sheets on top of each other. The interior
	C-terminal {beta}-sheets in the hydrophobic core remain largely intact,
	indicating that their formation and stability is crucial to the dissociation/elongation
	and stability of A{beta} fibrils.},
  owner = {singh},
  timestamp = {2008.05.01}
}

@ARTICLE{Cecchini2004,
  author = {M. Cecchini and F. Rao and M. Seeber and A. Caflisch},
  title = {Replica exchange molecular dynamics simulations of amyloid peptide
	aggregation.},
  journal = {J. Chem. Phys.},
  year = {2004},
  volume = {121},
  pages = {10748--10756},
  number = {21},
  month = {Dec},
  abstract = {The replica exchange molecular dynamics (REMD) approach is applied
	to four oligomeric peptide systems. At physiologically relevant temperature
	values REMD samples conformation space and aggregation transitions
	more efficiently than constant temperature molecular dynamics (CTMD).
	During the aggregation process the energetic and structural properties
	are essentially the same in REMD and CTMD. A condensation stage toward
	disordered aggregates precedes the beta-sheet formation. Two order
	parameters, borrowed from anisotropic fluid analysis, are used to
	monitor the aggregation process. The order parameters do not depend
	on the peptide sequence and length and therefore allow to compare
	the amyloidogenic propensity of different peptides},
  doi = {10.1063/1.1809588},
  institution = {Department of Biochemistry, University of Zurich, Winterthurerstrasse
	190, CH-8057 Zurich, Switzerland.},
  keywords = {Amyloid; Binding Sites; Computer Simulation; Kinetics; Models, Chemical;
	Models, Molecular; Multiprotein Complexes; Protein Binding; Protein
	Conformation},
  owner = {singh},
  pmid = {15549960},
  timestamp = {2008.07.23}
}

@ARTICLE{Chi2003,
  author = {Eva Y Chi and Sampathkumar Krishnan and Theodore W Randolph and John
	F Carpenter},
  title = {Physical stability of proteins in aqueous solution: mechanism and
	driving forces in nonnative protein aggregation.},
  journal = {Pharm. Res.},
  year = {2003},
  volume = {20},
  pages = {1325--1336},
  number = {9},
  month = {Sep},
  abstract = {Irreversible protein aggregation is problematic in the biotechnology
	industry, where aggregation is encountered throughout the lifetime
	of a therapeutic protein, including during refolding, purification,
	sterilization, shipping, and storage processes. The purpose of the
	current review is to provide a fundamental understanding of the mechanisms
	by which proteins aggregate and by which varying solution conditions,
	such as temperature, pH, salt type, salt concentration, cosolutes,
	preservatives, and surfactants, affect this process.},
  institution = {Department of Chemical Engineering, Center for Pharmaceutical Biotechnology,
	ECCH 111, Campus Box 424, University of Colorado, Boulder, Colorado,
	USA.},
  keywords = {Drug Stability; Drug Storage; Hydrogen-Ion Concentration; Pharmaceutical
	Solutions; Protein Conformation; Protein Folding; Proteins; Solvents;
	Surface-Active Agents; Temperature; Water},
  owner = {singh},
  pmid = {14567625},
  timestamp = {2008.12.05}
}

@ARTICLE{Chiti2006,
  author = {Fabrizio Chiti and Christopher M Dobson},
  title = {Protein misfolding, functional amyloid, and human disease.},
  journal = {Annu. Rev. Biochem.},
  year = {2006},
  volume = {75},
  pages = {333--366},
  abstract = {Peptides or proteins convert under some conditions from their soluble
	forms into highly ordered fibrillar aggregates. Such transitions
	can give rise to pathological conditions ranging from neurodegenerative
	disorders to systemic amyloidoses. In this review, we identify the
	diseases known to be associated with formation of fibrillar aggregates
	and the specific peptides and proteins involved in each case. We
	describe, in addition, that living organisms can take advantage of
	the inherent ability of proteins to form such structures to generate
	novel and diverse biological functions. We review recent advances
	toward the elucidation of the structures of amyloid fibrils and the
	mechanisms of their formation at a molecular level. Finally, we discuss
	the relative importance of the common main-chain and side-chain interactions
	in determining the propensities of proteins to aggregate and describe
	some of the evidence that the oligomeric fibril precursors are the
	primary origins of pathological behavior.},
  doi = {10.1146/annurev.biochem.75.101304.123901},
  keywords = {Amino Acid Sequence; Amyloid; Amyloidosis; Humans; Models, Molecular;
	Neurodegenerative Diseases; Polymorphism, Genetic; Protein Conformation;
	Protein Folding},
  owner = {Gurpreet},
  pmid = {16756495},
  timestamp = {2007.11.09 01:56:08}
}

@ARTICLE{Chiti:06a,
  author = {Chiti, F. and Dobson, C. M.},
  title = {Protein misfolding, functional amyloid, and human disease},
  journal = {Ann. Rev. Biochem.},
  year = {2006},
  volume = {75},
  pages = {333-366},
  owner = {Brov},
  timestamp = {2007.09.23}
}

@ARTICLE{Colombo2005,
  author = {Giorgio Colombo and Isabella Daidone and Ehud Gazit and Andrea Amadei
	and Alfredo Di Nola},
  title = {Molecular dynamics simulation of the aggregation of the core-recognition
	motif of the islet amyloid polypeptide in explicit water.},
  journal = {Proteins},
  year = {2005},
  volume = {59},
  pages = {519--527},
  number = {3},
  month = {May},
  abstract = {The formation of amyloid fibrils is associated with major human diseases.
	Nevertheless, the molecular mechanism that directs the nucleation
	of these fibrils is not fully understood. Here, we used molecular
	dynamics simulations to study the initial self-assembly stages of
	the NH2-NFGAIL-COOH peptide, the core-recognition motif of the type
	II diabetes associated islet amyloid polypeptide. The simulations
	were performed using multiple replicas of the monomers in explicit
	water, in a confined box starting from a random distribution of the
	peptides at T = 300 K and T = 340 K. At both temperatures the formation
	of unique clusters was observed after a few nanoseconds. Structural
	analysis of the clusters clearly suggested the formation of "flat"
	ellipsoid-shaped clusters through a preferred locally parallel alignment
	of the peptides. The unique assembly is facilitated by a preference
	for an extended conformation of the peptides and by intermolecular
	aromatic interactions. Taken together, our results may provide a
	description of the molecular recognition determinants involved in
	fibril formation, in terms of the atomic detailed structure of nascent
	aggregates. These observations may yield information on new ways
	to control this process for either materials development or drug
	design.},
  doi = {10.1002/prot.20426},
  institution = {Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy.
	g.colombo@icrm.cnr.it},
  keywords = {Amyloid; Binding Sites; Computer Simulation; Humans; Kinetics; Models,
	Molecular; Protein Conformation; Protein Structure, Secondary; Water},
  owner = {singh},
  pmid = {15778964},
  timestamp = {2008.10.16}
}

@ARTICLE{Cooper1994,
  author = {G. J. Cooper},
  title = {Amylin compared with calcitonin gene-related peptide: structure,
	biology, and relevance to metabolic disease.},
  journal = {Endocr. Rev.},
  year = {1994},
  volume = {15},
  pages = {163--201},
  number = {2},
  month = {Apr},
  keywords = {Amino Acid Sequence; Amyloid; Animals; Calcitonin Gene-Related Peptide;
	Comparative Study; Diabetes Mellitus, Type 1; Diabetes Mellitus,
	Type 2; Humans; Insulin Resistance; Kidney Failure; Molecular Sequence
	Data},
  myid = {3},
  owner = {Gurpreet},
  pmid = {8026387},
  timestamp = {2006.12.18}
}

@ARTICLE{Cubellis2005,
  author = {Maria Vittoria Cubellis and Fabien Cailliez and Simon C Lovell},
  title = {Secondary structure assignment that accurately reflects physical
	and evolutionary characteristics.},
  journal = {BMC Bioinformatics},
  year = {2005},
  volume = {6 Suppl 4},
  pages = {S8},
  month = {Dec},
  abstract = {BACKGROUND: Secondary structure is used in hierarchical classification
	of protein structures, identification of protein features, such as
	helix caps and loops, for fold recognition, and as a precursor to
	ab initio structure prediction. There are several methods available
	for assigning secondary structure if the three-dimensional structure
	of the protein is known. Unfortunately they differ in their definitions,
	particularly in the exact positions of the termini. Additionally,
	most existing methods rely on hydrogen bonding, which means that
	important secondary structural classes, such as isolated beta-strands
	and poly-proline helices cannot be identified as they do not have
	characteristic hydrogen-bonding patterns. For this reason we have
	developed a more accurate method for assigning secondary structure
	based on main chain geometry, which also allows a more comprehensive
	assignment of secondary structure. RESULTS: We define secondary structure
	based on a number of geometric parameters. Helices are defined based
	on whether they fit inside an imaginary cylinder: residues must be
	within the correct radius of a central axis. Different types of helices
	(alpha, 3(10) or pi) are assigned on the basis of the angle between
	successive peptide bonds. beta-strands are assigned based on backbone
	dihedrals and with alternating peptide bonds. Thus hydrogen bonding
	is not required and beta-strands can be within a parallel sheet,
	antiparallel sheet, or can be isolated. Poly-proline helices are
	defined similarly, although with three-fold symmetry. CONCLUSION:
	We find that our method better assigns secondary structure than existing
	methods. Specifically, we find that comparing our methods with those
	of others, amino-acid trends at helix caps are stronger, secondary
	structural elements less likely to be concatenated together and secondary
	structure guided sequence alignment is improved. We conclude, therefore,
	that secondary structure assignments using our method better reflects
	physical and evolutionary characteristics of proteins. The program
	is available from http://www.bioinf.man.ac.uk/~lovell/segno.shtml.},
  doi = {10.1186/1471-2105-6-S4-S8},
  file = {protein properties\\sec str assignment that reflect physical &evolutionary
	caracterstics BMC 2005.pdf:protein properties\\sec str assignment
	that reflect physical &evolutionary caracterstics BMC 2005.pdf:PDF},
  keywords = {Algorithms; Computational Biology; Computer Simulation; Databases,
	Protein; Evolution; Evolution, Molecular; Humans; Hydrogen Bonding;
	Models, Molecular; Models, Theoretical; Peptides; Proline; Protein
	Conformation; Protein Folding; Protein Structure, Secondary; Proteins;
	Sequence Alignment},
  myid = {13},
  owner = {Gurpreet},
  pii = {1471-2105-6-S4-S8},
  pmid = {16351757},
  timestamp = {2006.12.26 05:33:11}
}

@ARTICLE{Czeslik2004,
  author = {Claus Czeslik},
  title = {Factors ruling protein adsorption},
  journal = {Z. Phys. Chem.},
  year = {2004},
  volume = {218},
  pages = {771-801},
  owner = {singh},
  timestamp = {2008.07.03}
}

@MANUAL{D.2005,
  title = {Gromacs User Manual version 3.3},
  author = {D. van der Spoel, E. Lindahl, B. Hess},
  year = {2005},
  owner = {Gurpreet},
  timestamp = {2007.10.18 11:22:26},
  url = {www.gromacs.org}
}

@ARTICLE{Bari08012001,
  author = {Di Bari, M. and Cavatorta, F. and Deriu, A. and Albanese, G.},
  title = {{Mean Square Fluctuations of Hydrogen Atoms and Water-Biopolymer
	Interactions in Hydrated Saccharides}},
  journal = {Biophys. J.},
  year = {2001},
  volume = {81},
  pages = {1190-1194},
  number = {2},
  abstract = {We have used the elastic neutron scattering technique to investigate
	the dynamics of the two main saccharidic components of starch: amylose
	and amylopectin. The measurements were carried out in the temperature
	range of 20 to 320 K and at different hydration levels from the dry
	state up to 0.47 g saccharide/g D2O. In the dry samples, the atomic
	dynamics is harmonic up to approximately 300 K. In the hydrated samples
	a "glass-like" transition leading to an anharmonic dynamics is observed.
	The onset of the anharmonicity occurs at temperatures that increase
	from ~180 K to 260 K upon decreasing hydration from 0.5 to 0.1 g
	saccharide/g D2O. This behavior is qualitatively similar to that
	observed in hydrated globular proteins, but quantitative differences
	are present. Assuming a simple asymmetric double-well potential model,
	the temperature and hydration dependence of the transition have been
	described in terms of few physical parameters.},
  owner = {singh},
  timestamp = {2008.05.01}
}

@ARTICLE{Dima2002,
  author = {R. I. Dima and D. Thirumalai},
  title = {Exploring protein aggregation and self-propagation using lattice
	models: phase diagram and kinetics.},
  journal = {Protein Sci.},
  year = {2002},
  volume = {11},
  pages = {1036--1049},
  number = {5},
  month = {May},
  abstract = {Many seemingly unrelated neurodegenerative disorders, such as amyloid
	and prion diseases, are associated with propagating fibrils whose
	structures are dramatically different from the native states of the
	corresponding monomers. This observation, along with the experimental
	demonstration that any protein can aggregate to form either fibrils
	or amorphous structures (inclusion bodies) under appropriate external
	conditions, suggest that there must be general principles that govern
	aggregation mechanisms. To probe generic aspects of prion-like behavior
	we use the model of Harrison, Chan, Prusiner, and Cohen. In this
	model, aggregation of a structure, that is conformationally distinct
	from the native state of the monomer, occurs by three parallel routes.
	Kinetic partitioning, which leads to parallel assembly pathways,
	occurs early in the aggregation process. In all pathways transient
	unfolding precedes polymerization and self-propagation. Chain polymerization
	is consistent with templated assembly, with the dimer being the minimal
	nucleus. The kinetic effciency of R(n-1) + G --> R(n) (R is the aggregation
	prone state and G is either U, the unfolded state, or N, the native
	state of the monomer) is increased when polymerization occurs in
	the presence of a "seed" (a dimer). These results support the seeded
	nucleated-polymerization model of fibril formation in amyloid peptides.
	To probe generic aspects of aggregation in two-state proteins, we
	use lattice models with side chains. The phase diagram in the (T,C)
	plane (T is the temperature and C is the polypeptide concentration)
	reveals a bewildering array of "phases" or structures. Explicit computations
	for dimers show that there are at least six phases including ordered
	structures and amorphous aggregates. In the ordered region of the
	phase diagram there are three distinct structures. We find ordered
	dimers (OD) in which each monomer is in the folded state and the
	interaction between the monomers occurs via a well-defined interface.
	In the domain-swapped structures a certain fraction of intrachain
	contacts are replaced by interchain contacts. In the parallel dimers
	the interface is stabilized by favorable intermolecular hydrophobic
	interactions. The kinetics of folding to OD shows that aggregation
	proceeds directly from U in a dynamically cooperative manner without
	populating partially structured intermediates. These results support
	the experimental observation that ordered aggregation in the two-state
	folders U1A and CI2 takes place from U. The contrasting aggregation
	processes in the two models suggest that there are several distinct
	mechanisms for polymerization that depend not only on the polypeptide
	sequence but also on external conditions (such as C, T, pH, and salt
	concentration).},
  institution = {Institute for Physical Science and Technology, Department of Chemistry
	and Biochemistry, University of Maryland, College Park, MD 20742,
	USA.},
  keywords = {Dimerization; Kinetics; Models, Molecular; Prions; Protein Binding;
	Protein Conformation; Protein Folding; Proteins},
  owner = {singh},
  pmid = {11967361},
  timestamp = {2008.10.16}
}

@BOOK{Doi1996,
  title = {Introduction to polymer physics},
  publisher = {Oxford science publications},
  year = {1996},
  author = {Masao Doi},
  owner = {singh},
  timestamp = {2008.07.21}
}

@ARTICLE{Dumetz2008,
  author = {Andr� C Dumetz and Aaron M Chockla and Eric W Kaler and Abraham
	M Lenhoff},
  title = {Protein phase behavior in aqueous solutions: crystallization, liquid-liquid
	phase separation, gels, and aggregates.},
  journal = {Biophys. J.},
  year = {2008},
  volume = {94},
  pages = {570--583},
  number = {2},
  month = {Jan},
  abstract = {The aggregates and gels commonly observed during protein crystallization
	have generally been considered disordered phases without further
	characterization. Here their physical nature is addressed by investigating
	protein salting-out in ammonium sulfate and sodium chloride for six
	proteins (ovalbumin, ribonuclease A, soybean trypsin inhibitor, lysozyme,
	and beta-lactoglobulin A and B) at 4 degrees C, 23 degrees C, and
	37 degrees C. When interpreted within the framework of a theoretical
	phase diagram obtained for colloidal particles displaying short-range
	attractive interactions, the results show that the formation of aggregates
	can be interpreted theoretically in terms of a gas-liquid phase separation
	for aggregates that are amorphous or gel-like. A notable additional
	feature is the existence of a second aggregation line observed for
	both ovalbumin and ribonuclease A in ammonium sulfate, interpreted
	theoretically as the spinodal. Further investigation of ovalbumin
	and lysozyme reveals that the formation of aggregates can be interpreted,
	in light of theoretical results from mode-coupling theory, as a kinetically
	trapped state or a gel phase that occurs through the intermediate
	of a gas-liquid phase separation. Despite the limitations of simple
	theoretical models of short-range attractive interactions, such as
	their inability to reproduce the effect of temperature, they provide
	a framework useful to describe the main features of protein phase
	behavior.},
  doi = {10.1529/biophysj.107.116152},
  institution = {Center for Molecular and Engineering Thermodynamics, Department of
	Chemical Engineering, University of Delaware, Newark, Delaware 19716,
	USA.},
  keywords = {Animals; Cattle; Chickens; Crystallization; Gels; Muramidase; Ovalbumin;
	Protein Structure, Quaternary; Proteins; Ribonuclease, Pancreatic;
	Solubility; Solutions; Temperature; Time Factors},
  owner = {singh},
  pii = {94/2/570},
  pmid = {18160663},
  timestamp = {2008.06.16}
}

@ARTICLE{Echeverria:02a,
  author = {Echeverria, V. and Cuello, A. C.},
  title = {Intracellular {A}-beta amyloid, a sign for worse things to come?},
  journal = {Mol. Neurobiol.},
  year = {2002},
  volume = {26},
  pages = {299-316},
  owner = {Brov},
  timestamp = {2007.09.19}
}

@ARTICLE{Engel2006,
  author = {Maarten F M Engel and HaciAli Yigittop and Ronald C Elgersma and
	Dirk T S Rijkers and Rob M J Liskamp and Ben de Kruijff and Jo W
	M H�ppener and J. Antoinette Killian},
  title = {Islet amyloid polypeptide inserts into phospholipid monolayers as
	monomer.},
  journal = {J. Mol. Biol.},
  year = {2006},
  volume = {356},
  pages = {783--789},
  number = {3},
  month = {Feb},
  abstract = {Amyloid deposits in the pancreatic islets of Langerhans are thought
	to be a main factor responsible for death of the insulin-producing
	islet beta-cells in type 2 diabetes. It is hypothesized that beta-cell
	death is related to interaction of the 37 amino acid residue human
	islet amyloid polypeptide (hIAPP), the major constituent of islet
	amyloid, with cellular membranes. However, the mechanism of hIAPP-membrane
	interactions is largely unknown. Here, we study the nature and the
	molecular details of the initial step of hIAPP-membrane interactions
	by using the monolayer technique. It is shown that both freshly dissolved
	hIAPP and the non-amyloidogenic mouse IAPP (mIAPP) have a pronounced
	ability to insert into phospholipid monolayers, even at lipid packing
	conditions that exceed the conditions that occur in biological membranes.
	In contrast, the fibrillar form of hIAPP has lost the ability to
	insert. These results, combined with the observations that both the
	insertion kinetics and the dependence of insertion on the initial
	surface pressure are similar for freshly dissolved hIAPP and mIAPP,
	indicate that hIAPP inserts into phospholipid monolayers most likely
	as a monomer. In addition, our results suggest that the N-terminal
	part of hIAPP, which is nearly identical with that of mIAPP, is largely
	responsible for insertion. This is supported by experiments with
	hIAPP fragments, which show that a peptide consisting of the 19 N-terminal
	residues of hIAPP efficiently inserts into phospholipid monolayers,
	whereas an amyloidogenic decapeptide, consisting of residues 20-29
	of hIAPP, inserts much less efficiently. The results obtained here
	suggest that hIAPP monomers might insert with high efficiency in
	biological membranes in vivo. This process could play an important
	role as a first step in hIAPP-induced membrane damage in type 2 diabetes.},
  doi = {10.1016/j.jmb.2005.12.020},
  institution = {Department of Metabolic and Endocrine Diseases, Division of Biomedical
	Genetics, University Medical Center Utrecht, PO Box 85090, NL-3508
	AB Utrecht, The Netherlands. m.f.m.engel@chem.uu.nl},
  keywords = {Amino Acid Sequence; Amyloid; Animals; Cell Membrane; Diabetes Mellitus,
	Type 2; Electrostatics; Humans; Islets of Langerhans; Mice; Models,
	Biological; Molecular Sequence Data; Peptide Fragments; Phospholipids;
	Structure-Activity Relationship},
  owner = {singh},
  pii = {S0022-2836(05)01580-9},
  pmid = {16403520},
  timestamp = {2008.09.14}
}

@ARTICLE{Enright:05a,
  author = {Matthew B. Enright and David M. Leitner},
  title = {Mass fractal dimension and the compactness of proteins},
  journal = {Phys. Rev. E},
  year = {2005},
  volume = {71},
  pages = {011912},
  number = {1},
  eid = {011912},
  numpages = {9},
  owner = {singh},
  publisher = {APS},
  timestamp = {2008.05.01}
}

@ARTICLE{Essmann1995,
  author = {Ulrich Essmann and Lalith Perera and Max L. Berkowitz andTom Darden
	and Hsing Lee and Lee G. Pedersen},
  title = {A smooth particle mesh Ewald method},
  journal = {J. Chem. Phys.},
  year = {1995},
  volume = {103},
  pages = {8577 -- 8593},
  file = {MDS General\\J Chem phys 1995 A smooth particle mesh ewald method.pdf:MDS
	General\\J Chem phys 1995 A smooth particle mesh ewald method.pdf:PDF},
  myid = {12},
  owner = {Gurpreet},
  timestamp = {2006.12.20 04:27:24}
}

@ARTICLE{Fisher1967,
  author = {M.E Fisher},
  title = {The theory of condensation and critical point},
  journal = {Physics},
  year = {1967},
  volume = {3},
  pages = {255-283},
  owner = {Brov},
  timestamp = {2007.07.30}
}

@ARTICLE{Fisher:67a,
  author = {M. E. Fisher},
  title = {The theory of equilibrium critical phenomena},
  journal = {Rep. Prog. Phys.},
  year = {1967},
  volume = {30},
  pages = {615-730},
  owner = {Brov},
  timestamp = {2007.09.23}
}

@ARTICLE{Foffi2002,
  author = {Giuseppe Foffi and Gavin D McCullagh and Aonghus Lawlor and Emanuela
	Zaccarelli and Kenneth A Dawson and Francesco Sciortino and Piero
	Tartaglia and Davide Pini and George Stell},
  title = {Phase equilibria and glass transition in colloidal systems with short-ranged
	attractive interactions: application to protein crystallization.},
  journal = {Phys. Rev. E},
  year = {2002},
  volume = {65},
  pages = {031407},
  number = {3 Pt 1},
  month = {Mar},
  abstract = {We have studied a model of a complex fluid consisting of particles
	interacting through a hard-core and short-range attractive potential
	of both Yukawa and square-well form. Using a hybrid method, including
	a self-consistent and quite accurate approximation for the liquid
	integral equation in the case of the Yukawa fluid, perturbation theory
	to evaluate the crystal free energies, and mode-coupling theory of
	the glass transition, we determine both the equilibrium phase diagram
	of the system and the lines of equilibrium between the supercooled
	fluid and the glass phases. For these potentials, we study the phase
	diagrams for different values of the potential range, the ratio of
	the range of the interaction to the diameter of the repulsive core
	being the main control parameter. Our arguments are relevant to a
	variety of systems, from dense colloidal systems with depletion forces,
	through particle gels, nanoparticle aggregation, and globular protein
	crystallization.},
  institution = {Irish Centre for Colloid Science and Biomaterials, Department of
	Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.},
  owner = {singh},
  pmid = {11909057},
  timestamp = {2008.06.16}
}

@ARTICLE{Frank1945,
  author = {H. S. Frank and M. W. Evans},
  title = {Free Volume and Entropy in Condensed Systems III. Entropy in Binary
	Liquid Mixtures; Partial Molal Entropy in Dilute Solutions; Structure
	and Thermodynamics in Aqueous Electrolytes},
  journal = {J. Chem. Phys.},
  year = {1945},
  volume = {13},
  pages = {507--532},
  owner = {singh},
  timestamp = {2008.12.06}
}

@BOOK{Smit2001,
  title = {Understanding Molecular Simulation},
  publisher = {Academic Press},
  year = {2001},
  author = {Daan Frenkel and Berend Smit},
  edition = {2nd},
  owner = {Gurpreet},
  timestamp = {2007.11.08 02:21:45}
}

@ARTICLE{Furukawa:82a,
  author = {Furukawa, H. and Binder, K.},
  title = {Two-phase equilibria and nucleation barriers near a critical point},
  journal = {Phys. Rev. A},
  year = {1982},
  volume = {26},
  pages = {556--566},
  number = {1},
  month = {Jul},
  doi = {10.1103/PhysRevA.26.556},
  numpages = {10},
  owner = {singh},
  publisher = {American Physical Society},
  timestamp = {2008.05.01}
}

@ARTICLE{Ghosh:03a,
  author = {Ghosh, T. and Garcia, A.E. and Garde, S.},
  title = {Water-Mediated Three-Particle Interactions between Hydrophobic Solutes:
	Size, Pressure, and Salt Effects},
  journal = {J. Phys. Chem. B},
  year = {2003},
  volume = {107},
  pages = {612-617},
  number = {2},
  affiliation = {Department of Chemical Engineering, Rensselaer Polytechnic Institute,
	Troy, New York 12180 and T-10, Theoretical Biology and Biophysics
	Group, MS K710 Los Alamos National Laboratory, Los Alamos, New Mexico
	87545},
  issn = {1520-6106},
  owner = {singh},
  timestamp = {2008.05.01}
}

@ARTICLE{Glover1997,
  author = {J. R. Glover and A. S. Kowal and E. C. Schirmer and M. M. Patino
	and J. J. Liu and S. Lindquist},
  title = {Self-seeded fibers formed by Sup35, the protein determinant of [PSI+],
	a heritable prion-like factor of S. cerevisiae.},
  journal = {Cell},
  year = {1997},
  volume = {89},
  pages = {811--819},
  number = {5},
  month = {May},
  abstract = {The [PSI+] factor of S. cerevisiae represents a new form of inheritance:
	cytosolic transmission of an altered phenotype is apparently based
	upon inheritance of an altered protein structure rather than an altered
	nucleic acid. The molecular basis of its propagation is unknown.
	We report that purified Sup35 and subdomains that induce [PSI+] elements
	in vivo form highly ordered fibers in vitro. Fibers bind Congo red
	and are rich in beta sheet, characteristics of amyloids found in
	certain human diseases, including the prion diseases. Some fibers
	have distinct structures and these, once initiated, are self-perpetuating.
	Preformed fibers greatly accelerate fiber formation by unpolymerized
	protein. These data support a "protein-only" seeded polymerization
	model for the inheritance of [PSI+].},
  keywords = {Fungal Proteins; Humans; Microscopy, Electron; Prions; Protein Conformation;
	Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins},
  owner = {singh},
  pii = {S0092-8674(00)80264-0},
  pmid = {9182769},
  timestamp = {2008.03.02}
}

@ARTICLE{Green2003,
  author = {Janelle Green and Claire Goldsbury and Thierry Mini and Shabir Sunderji
	and Peter Frey and Joerg Kistler and Garth Cooper and Ueli Aebi},
  title = {Full-length rat amylin forms fibrils following substitution of single
	residues from human amylin.},
  journal = {J. Mol. Biol.},
  year = {2003},
  volume = {326},
  pages = {1147--1156},
  number = {4},
  month = {Feb},
  abstract = {Pancreatic amyloid deposits, composed of the 37 amino acid residue
	peptide amylin, represent an integral part of type 2 diabetes mellitus
	pathology. Human amylin (hA) forms fibrils in vitro and is toxic
	to cultured pancreatic islet beta-cells. In contrast, rat amylin
	(rA) which differs from hA by only six amino acid residues in the
	central region of the peptide, residues 18-29, does not form fibrils
	and is not cytotoxic. To elucidate the role of individual residues
	in fibril formation, we have generated a series of full-length rA
	variants and examined their ability to form fibrils in vitro. Single-residue
	substitutions with amino acids from corresponding positions of the
	hA sequence, i.e. R18H, L23F, or V26I, were sufficient to render
	rA competent for fibril formation albeit at a small yield. Combining
	two or three of these substitutions generally increased the ability
	to produce fibrils. Variant rA fibril morphologies were examined
	by negative stain electron microscopy and found to be similar to
	those generated by hA itself. Bulk assays, i.e. involving thioflavin-T
	fluorescence and sedimentation, showed that the amount of fibril
	formation was relatively small for these rA variants when compared
	to hA under the same conditions. Fibril growth was demonstrated by
	time-lapse atomic force microscopy, and MALDI-TOF mass spectrometry
	was used to verify that fibrils consisted of full-length peptide.
	Our observations confirm previous reports that the three proline
	residues play a dominant negative role in fibril formation. However,
	their presence is not sufficient to completely abolish the ability
	of rA to form fibrils, as each of the other three implicated residues
	(i.e. R18, L23 and V26) also has a dominant modulating effect.},
  file = {aggregations\\IAPP\\j mol biol 2003 326 full length rat amylin forms
	fibrils following substitution of single residue.pdf:aggregations\\IAPP\\j
	mol biol 2003 326 full length rat amylin forms fibrils following
	substitution of single residue.pdf:PDF},
  keywords = {Amino Acid Sequence; Amyloid; Animals; Humans; Microscopy, Atomic
	Force; Molecular Sequence Data; Peptides; Proline; Protein Conformation;
	Rats; Research Support, Non-U.S. Gov't; Sequence Alignment; Spectrometry,
	Mass, Matrix-Assisted Laser Desorption-Ionization},
  myid = {7},
  owner = {Gurpreet},
  pii = {S0022283602013773},
  pmid = {12589759},
  timestamp = {2006.12.18 12:00:04}
}

@ARTICLE{Green2004,
  author = {Janelle D Green and Claire Goldsbury and Joerg Kistler and Garth
	J S Cooper and Ueli Aebi},
  title = {Human amylin oligomer growth and fibril elongation define two distinct
	phases in amyloid formation.},
  journal = {J. Biol. Chem.},
  year = {2004},
  volume = {279},
  pages = {12206--12212},
  number = {13},
  month = {Mar},
  abstract = {Human amylin (hA), a 37-amino-acid polypeptide, is one of a number
	of peptides with the ability to form amyloid fibrils and cause disease.
	It is the main constituent of the pancreatic amyloid deposits associated
	with type 2 diabetes. Increasing interest in early assembly intermediates
	rather than the mature fibrils as the cytotoxic agent has led to
	this study in which the smallest hA oligomers have been captured
	by atomic force microscopy. These are 2.3 +/- 1.9 nm in height, 23
	+/- 14 nm in length, and consist of an estimated 16 hA molecules.
	Oligomers first grow to a height of about 6 nm before they begin
	to significantly elongate into fibrils. Congo red inhibits elongation
	but not the growth in height of hA oligomers. Two distinct phases
	have thus been identified in hA fibrillogenesis: lateral growth of
	oligomers followed by longitudinal growth into mature fibrils. These
	observations suggest that mature fibrils are assembled directly via
	longitudinal growth of full-width oligomers, making assembly by lateral
	association of protofibrils appear less likely.},
  doi = {10.1074/jbc.M312452200},
  institution = {M. E. M�ller Institute for Structural Biology, Biozentrum, University
	of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland.},
  keywords = {Adsorption; Amyloid; Amyloid beta-Protein; Congo Red; Diabetes Mellitus,
	Type 2; Humans; Microscopy, Atomic Force; Peptides; Propanols; Time
	Factors},
  owner = {singh},
  pii = {M312452200},
  pmid = {14704152},
  timestamp = {2008.09.14}
}

@ARTICLE{Green2004a,
  author = {J. D. Green and L. Kreplak and C. Goldsbury and X. Li Blatter and
	M. Stolz and G. S. Cooper and A. Seelig and J. Kistler and U. Aebi},
  title = {Atomic force microscopy reveals defects within mica supported lipid
	bilayers induced by the amyloidogenic human amylin peptide.},
  journal = {J. Mol. Biol.},
  year = {2004},
  volume = {342},
  pages = {877--887},
  number = {3},
  month = {Sep},
  abstract = {To date, over 20 peptides or proteins have been identified that can
	form amyloid fibrils in the body and are thought to cause disease.
	The mechanism by which amyloid peptides cause the cytotoxicity observed
	and disease is not understood. However, one of the major hypotheses
	is that amyloid peptides cause membrane perturbation. Hence, we have
	studied the interaction between lipid bilayers and the 37 amino acid
	residue polypeptide amylin, which is the primary constituent of the
	pancreatic amyloid associated with type 2 diabetes. Using a dye release
	assay we confirmed that the amyloidogenic human amylin peptide causes
	membrane disruption; however, time-lapse atomic force microscopy
	revealed that this did not occur by the formation of defined pores.
	On the contrary, the peptide induced the formation of small defects
	spreading over the lipid surface. We also found that rat amylin,
	which has 84\% identity with human amylin but cannot form amyloid
	fibrils, could also induce similar lesions to supported lipid bilayers.
	The effect, however, for rat amylin but not human amylin, was inhibited
	under high ionic conditions. These data provide an alternative theory
	to pore formation, and how amyloid peptides may cause membrane disruption
	and possibly cytotoxicity.},
  doi = {10.1016/j.jmb.2004.07.052},
  institution = {M.E. M�ller Institute for Structural Biology, Biozentrum, University
	of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland.},
  keywords = {Aluminum Silicates; Amino Acid Sequence; Amyloid; Amyloid beta-Protein;
	Animals; Detergents; Diabetes Mellitus, Type 2; Humans; Islets of
	Langerhans; Lipid Bilayers; Microscopy, Atomic Force; Microscopy,
	Electron; Models, Biological; Molecular Sequence Data; Octoxynol;
	Rats; Recombinant Proteins},
  owner = {singh},
  pii = {S0022-2836(04)00875-7},
  pmid = {15342243},
  timestamp = {2008.09.14}
}

@ARTICLE{Grudzielanek:06a,
  author = {Grudzielanek, S. and Smirnovas, V. and Winter, R.},
  title = {Solvation-assisted Pressure Tuning of Insulin Fibrillation: From
	Novel Aggregation Pathways to Biotechnological Applications},
  journal = {J. Mol. Biol.},
  year = {2006},
  volume = {356},
  pages = {497-509},
  owner = {Brov},
  timestamp = {2007.09.24}
}

@ARTICLE{Gustavsson1991,
  author = {A. Gustavsson and U. Engstr�m and P. Westermark},
  title = {Normal transthyretin and synthetic transthyretin fragments form amyloid-like
	fibrils in vitro.},
  journal = {Biochem. Biophys. Res. Commun.},
  year = {1991},
  volume = {175},
  pages = {1159--1164},
  number = {3},
  month = {Mar},
  abstract = {In two general forms of amyloidosis, senile systemic amyloidosis and
	several familial amyloidoses the amyloid fibrils are built up by
	transthyretin and fragments of the molecule. It has previously been
	demonstrated that other amyloid fibril proteins e.g. atrial natriuretic
	factor and islet amyloid polypeptide form amyloid-like fibrils in
	vitro. In this study we used normal transthyretin and synthetic polypeptides
	corresponding to segments of the transthyretin molecule. We show
	that normal transthyretin and two of our tested polypeptides, which
	corresponded to the beta-strands A and G, easily form amyloid-like
	fibrils in vitro.},
  keywords = {Amino Acid Sequence; Amyloidosis; Humans; Microscopy, Electron; Molecular
	Sequence Data; Oligopeptides; Peptide Fragments; Prealbumin},
  owner = {Gurpreet},
  pmid = {2025248},
  timestamp = {2008.02.17 03:29:17}
}

@ARTICLE{Haass:07a,
  author = {Haass, Christian and Selkoe, Dennis J.},
  title = {Soluble protein oligomers in neurodegeneration: lessons from the
	Alzheimer's amyloid [beta]-peptide},
  journal = {Nat. Rev. Mol. Cell. Biol.},
  year = {2007},
  volume = {8},
  pages = {101-112},
  owner = {Brov},
  timestamp = {2007.09.23}
}

@ARTICLE{Hanabusa:92a,
  author = {Hanabusa, T. and Kubo, K. and Oki, C. and Nakano, Y. and Okai, K.
	and Sanke, T. and Nanjo K.},
  title = {Islet amyloid polypeptide {(IAPP)} secretion from islet cells and
	its plasma concentration in patients with non-insulin-dependent diabetes
	mellitus},
  journal = {Diabetes Res. Clin. Pract.},
  year = {1992},
  volume = {15},
  pages = {89-96},
  owner = {Brov},
  timestamp = {2007.09.19}
}

@ARTICLE{Hansmann:97a,
  author = {U. H. E. Hansmann},
  title = {Parallel temperaing algorithm for conformational studies of biological
	molecules},
  journal = {Chem. Phys. Lett.},
  year = {1997},
  volume = {281},
  pages = {140-150},
  owner = {brov},
  timestamp = {2008.10.17}
}

@ARTICLE{Harper1997,
  author = {J. D. Harper and P. T. Lansbury},
  title = {Models of amyloid seeding in Alzheimer's disease and scrapie: mechanistic
	truths and physiological consequences of the time-dependent solubility
	of amyloid proteins.},
  journal = {Annu. Rev. Biochem.},
  year = {1997},
  volume = {66},
  pages = {385--407},
  abstract = {Ordered protein aggregation in the brain is a hallmark of Alzheimer's
	disease and scrapie. The disease-specific amyloid fibrils comprise
	primarily a single protein, amyloid beta, in Alzheimer's disease,
	and the prion protein in scrapie. These proteins can be induced to
	form aggregates in vitro that are indistinguishable from brain-derived
	fibrils. Consequently, much effort has been invested in the development
	of in vitro model systems to study the details of the aggregation
	processes and the effects of endogenous molecules that have been
	implicated in disease. Selected studies of this type are reviewed
	herein. A simple mechanistic model has emerged for both processes
	that involves a nucleation-dependent polymerization. This mechanism
	dictates that aggregation is dependent on protein concentration and
	time. Furthermore, amyloid formation can be seeded by a preformed
	fibril. The physiological consequences of this mechanism are discussed.},
  doi = {10.1146/annurev.biochem.66.1.385},
  keywords = {Alzheimer Disease; Amino Acid Sequence; Amyloid; Animals; Brain; Humans;
	Molecular Sequence Data; Scrapie; Solubility; Time Factors},
  owner = {Gurpreet},
  pmid = {9242912},
  timestamp = {2007.11.08 02:21:45}
}

@ARTICLE{Harrison1999,
  author = {P. M. Harrison and H. S. Chan and S. B. Prusiner and F. E. Cohen},
  title = {Thermodynamics of model prions and its implications for the problem
	of prion protein folding.},
  journal = {J. Mol. Biol.},
  year = {1999},
  volume = {286},
  pages = {593--606},
  number = {2},
  month = {Feb},
  abstract = {Prion disease is caused by the propagation of a particle containing
	PrPSc, a misfolded form of the normal cellular prion protein (PrPC).
	PrPC can re-fold to form PrPSc with loss of alpha-helical structure
	and formation of extensive beta-sheet structure. Here, we model this
	prion folding problem with a simple, low-resolution lattice model
	of protein folding. If model proteins are allowed to re-fold upon
	dimerization, a minor proportion of them (up to approximately 17\%)
	encrypts an alternative native state as a homodimer. The structures
	in this homodimeric native state re-arrange so that they are very
	different in conformation from the monomeric native state. We find
	that model proteins that are relatively less stable as monomers are
	more susceptible to the formation of alternative native states as
	homodimers. These results suggest that less-stable proteins have
	a greater need for a well-designed energy landscape for protein folding
	to overcome an increased chance of encrypting substantially different
	native conformations stabilized by multimeric interactions. This
	conceptual framework for aberrant folding should be relevant in Alzheimer's
	disease and other disorders associated with protein aggregation.},
  doi = {10.1006/jmbi.1998.2497},
  institution = { Molecular Pharmacology, University of California, San Francisco,
	94143, USA.},
  keywords = {Amino Acid Substitution; Chemistry, Physical; Computer Simulation;
	Dimerization; Humans; Models, Molecular; Point Mutation; PrPC Proteins;
	PrPSc Proteins; Protein Conformation; Protein Folding; Protein Structure,
	Secondary; Recombinant Fusion Proteins; Thermodynamics},
  owner = {singh},
  pii = {S0022-2836(98)92497-4},
  pmid = {9973573},
  timestamp = {2008.10.16}
}

@ARTICLE{Harroun2001,
  author = {T. A. Harroun and J. P. Bradshaw and R. H. Ashley},
  title = {Inhibitors can arrest the membrane activity of human islet amyloid
	polypeptide independently of amyloid formation.},
  journal = {FEBS Lett.},
  year = {2001},
  volume = {507},
  pages = {200--204},
  number = {2},
  month = {Oct},
  abstract = {Human islet amyloid polypeptide (hIAPP), co-secreted with insulin
	from pancreatic beta cells, misfolds to form amyloid deposits in
	non-insulin-dependent diabetes mellitus (NIDDM). Like many amyloidogenic
	proteins, hIAPP is membrane-active: this may be significant in the
	pathogenesis of NIDDM. Non-fibrillar hIAPP induces electrical and
	physical breakdown in planar lipid bilayers, and IAPP inserts spontaneously
	into lipid monolayers, markedly increasing their surface area and
	producing Brewster angle microscopy reflectance changes. Congo red
	inhibits these activities, and they are completely arrested by rifampicin,
	despite continued amyloid formation. Our results support the idea
	that non-fibrillar IAPP is membrane-active, and may have implications
	for therapy and for structural studies of membrane-active amyloid.},
  institution = {Department of Preclinical Veterinary Sciences, University of Edinburgh,
	UK.},
  keywords = {Amyloid; Congo Red; Humans; Lipid Bilayers; Rifampin},
  owner = {singh},
  pii = {S0014-5793(01)02972-6},
  pmid = {11684098},
  timestamp = {2008.09.14}
}

@ARTICLE{Hawley1971,
  author = {S. A. Hawley},
  title = {Reversible pressure--temperature denaturation of chymotrypsinogen.},
  journal = {Biochemistry},
  year = {1971},
  volume = {10},
  pages = {2436--2442},
  number = {13},
  month = {Jun},
  keywords = {Chymotrypsin; Enzyme Precursors; Mathematics; Pressure; Protein Denaturation;
	Ribonucleases; Spectrophotometry; Temperature; Thermodynamics; Ultraviolet
	Rays},
  owner = {singh},
  pmid = {5557794},
  timestamp = {2008.07.03}
}

@ARTICLE{Heremans1998,
  author = {K. Heremans and L. Smeller},
  title = {Protein structure and dynamics at high pressure.},
  journal = {Biochim. Biophys. Acta},
  year = {1998},
  volume = {1386},
  pages = {353--370},
  number = {2},
  month = {Aug},
  abstract = {The effect of pressure on the structure and dynamics of proteins is
	discussed in the framework of the pressure-temperature stability
	phase diagram. The elastic (reversible) properties, thermal expansion,
	compressibility and heat capacity, are correlated with the entropy,
	volume, and the coupling between entropy and volume fluctuations
	respectively. The experimental approaches that can be used to measure
	these quantities are reviewed. The plastic (conformational) changes
	reflect the changes in these properties in the cold, pressure and
	heat denaturation.},
  institution = {Department of Chemistry, Katholieke Universiteit Leuven, Belgium.
	Karel.Heremans@fys.kuleuven.ac.be},
  keywords = {Chemistry, Physical; Elasticity; Hydrostatic Pressure; Protein Conformation;
	Protein Denaturation; Temperature},
  owner = {singh},
  pmid = {9733996},
  timestamp = {2008.06.30}
}

@ARTICLE{Hoover1985,
  author = {Hoover, W.G.},
  title = {Canonical dynamics: equilibrium phase-space distributions.},
  journal = {Phys. Rev. A},
  year = {1985},
  volume = {31},
  pages = {1695--1697}
}

@ARTICLE{Ida:96a,
  author = {Ida, N. and Hartmann, T. and Pantel, J. and Schroder, J. and Zerfass,
	R. and Forstl, H. and Sandbrink, R. and Masters, C.L. and Beyreuther,
	K.},
  title = {Analysis of heterogeneous beta{A}4 peptides in human cerebrospinal
	fluid and blood by a newly developed sensitive Western blot assay},
  journal = {J. Biol. Chem.},
  year = {1996},
  volume = {271},
  pages = {22908-22914},
  owner = {Brov},
  timestamp = {2007.09.19}
}

@ARTICLE{Jaikaran2001,
  author = {E. T. Jaikaran and C. E. Higham and L. C. Serpell and J. Zurdo and
	M. Gross and A. Clark and P. E. Fraser},
  title = {Identification of a novel human islet amyloid polypeptide beta-sheet
	domain and factors influencing fibrillogenesis.},
  journal = {J. Mol. Biol.},
  year = {2001},
  volume = {308},
  pages = {515--525},
  number = {3},
  month = {May},
  abstract = {Human islet amyloid polypeptide (hIAPP) accumulates as pancreatic
	amyloid in type 2 diabetes and readily forms fibrils in vitro. Investigations
	into the mechanism of hIAPP fibril formation have focused largely
	on residues 20 to 29, which are considered to comprise a primary
	amyloidogenic domain. In rodents, proline substitutions within this
	region and the subsequent beta-sheet disruption, prevents fibril
	formation. An additional amyloidogenic fragment within the C-terminal
	sequence, residues 30 to 37, has been identified recently. We have
	extended these observations by examining a series of overlapping
	peptide fragments from the human and rodent sequences. Using protein
	spectroscopy (CD/FTIR), electron microscopy and X-ray diffraction,
	a previously unrecognised amyloidogenic domain was localised within
	residues 8 to 20. Synthetic peptides corresponding to this region
	exhibited a transition from random coil to beta-sheet conformation
	and assembled into fibrils having a typical amyloid-like morphology.
	The comparable rat 8-20 sequence, which contains a single His18Arg
	substitution, was also capable of assembling into amyloid-like fibrils.
	Examination of peptide fragments corresponding to residues 1 to 13
	revealed that the immediate N-terminal region is likely to have only
	a modulating influence on fibril formation or conformational conversion.
	The contributions of charged residues as they relate to the amyloid-forming
	8-20 sequence were also investigated using IAPP fragments and by
	assessing the effects of pH and counterions. The identification of
	these principal amyloidogenic sequences and the effects of associated
	factors provide details on the IAPP aggregation pathway and structure
	of the peptide in its fibrillar state.},
  doi = {10.1006/jmbi.2001.4593},
  file = {aggregations\\IAPP\\j mol biol2001 308 identification of novel IAPP
	beta sheet domain.pdf:aggregations\\IAPP\\j mol biol2001 308 identification
	of novel IAPP beta sheet domain.pdf:PDF},
  keywords = {Amino Acid Sequence; Amino Acid Substitution; Amyloid; Amyloidosis;
	Animals; Circular Dichroism; Comparative Study; Diabetes Mellitus,
	Type 2; Humans; Hydrogen-Ion Concentration; Islets of Langerhans;
	Microscopy, Electron; Molecular Sequence Data; Peptide Fragments;
	Protein Folding; Protein Structure, Secondary; Protein Structure,
	Tertiary; Rats; Research Support, Non-U.S. Gov't; Spectroscopy, Fourier
	Transform Infrared; Thiazoles; X-Ray Diffraction},
  myid = {4},
  owner = {Gurpreet},
  pii = {S0022-2836(01)94593-0},
  pmid = {11327784},
  timestamp = {2006.12.18 12:00:01}
}

@ARTICLE{Jansen:05a,
  author = {Jansen, Ralf and Dzwolak, Wojciech and Winter, Roland},
  title = {Amyloidogenic Self-Assembly of Insulin Aggregates Probed by High
	Resolution Atomic Force Microscopy},
  journal = {Biophys. J.},
  year = {2005},
  volume = {88},
  pages = {1344-1353},
  number = {2},
  abstract = {As the application of high-resolution atomic force microscopy (AFM)
	has led us recently to the discovery of a unique pressure-induced
	circular amyloid, we used the same approach to examine morphological
	events accompanying insulin aggregation under ambient conditions.
	This study presents the multistage, hierarchical character of the
	spontaneous fibrillation of insulin at low pH and at 60 and 70{degrees}C,
	and--due to the marked enhancement of image resolution achieved--brings
	new clues as to the fibrils' ultrastructure and mechanisms of its
	assembly. Specifically, focusing on the prefibrillar amorphous aggregates
	occurring 30 s after elevating temperature to the nucleation-enhancing
	60{degrees}C, revealed the tendency of the globule-shaped oligomers
	to queue and assembly into elongated forms. This suggests that the
	shape of the nuclei itself predetermines--in part--the fibrillar
	architecture of the amyloid. Among first fibrillar features, short
	but relatively thick (8-nm) seedlike forms appeared on a very short
	timescale within the first minute of incubation. It has been shown
	that such fibrils are likely to act as lateral scaffolds for the
	growth of amyloid. By using phase-image AFM as a nanometer-resolved
	probe of visco-elastic surface properties, we were able to show that
	bundles of early protofilaments associated into parallel fibrils
	are capable of a cooperative transformation into twisted, highly
	ordered superhelices of the mature amyloid. Independently from producing
	evidence for the step-resolved character of the process, intermediate
	and morphologically heterogeneous forms were trapped and characterized,
	which yields direct evidence for the multipathway character of the
	amyloidogenesis of insulin. Apart from the faster kinetics, the increased
	temperature of 70{degrees}C leads to a higher degree of morphological
	variability: along straight rods, twisted ribbonlike structures,
	rod bundles, and ropelike structures become prominent in the corresponding
	AFM data.},
  owner = {singh},
  timestamp = {2008.05.01}
}

@ARTICLE{Jarrett1993,
  author = {J. T. Jarrett and P. T. Lansbury},
  title = {Seeding "one-dimensional crystallization" of amyloid: a pathogenic
	mechanism in Alzheimer's disease and scrapie?},
  journal = {Cell},
  year = {1993},
  volume = {73},
  pages = {1055--1058},
  number = {6},
  month = {Jun},
  keywords = {Alzheimer Disease; Amyloid; Animals; Humans; Scrapie},
  owner = {Gurpreet},
  pii = {0092-8674(93)90635-4},
  pmid = {8513491},
  timestamp = {2007.11.09 05:07:08}
}

@ARTICLE{Jarrett:93a,
  author = {Jarrett, J. T. and Lansbury, P. T.},
  title = {Seeding "one-dimensional crystallization" of amyloid: a pathogenic
	mechanism in {A}lzheimer's disease and scrapie?},
  journal = {Cell},
  year = {1993},
  volume = {73},
  pages = {1055-1058},
  owner = {Brov},
  timestamp = {2008.04.10}
}

@ARTICLE{Javid:07a,
  author = {Nadeem Javid and Karsten Vogtt and Christina Krywka and Metin Tolan
	and Roland Winter},
  title = {Capturing the Interaction Potential of Amyloidogenic Proteins},
  journal = {Phys. Rev. Lett.},
  year = {2007},
  volume = {99},
  pages = {028101},
  number = {2},
  eid = {028101},
  keywords = {proteins},
  owner = {singh},
  publisher = {APS},
  timestamp = {2008.05.01}
}

@ARTICLE{Jorgensen:83a,
  author = {Jorgensen, W. L. and Chandreskhar, J. and Madura, J. D. and Impey,
	R. W. and Klein, M. L.},
  journal = {J. Chem. Phys.},
  year = {1983},
  volume = {79},
  pages = {926},
  owner = {Brov},
  timestamp = {2007.04.26}
}

@ARTICLE{Jorgensen1988,
  author = {Jorgensen, William L. and Tirado-Rives, Julian},
  title = {The OPLS [optimized potentials for liquid simulations] potential
	functions for proteins, energy minimizations for crystals of cyclic
	peptides and crambin.},
  journal = {J. Am. Chem. Soc.},
  year = {1988},
  volume = {110},
  pages = {1657-1666},
  number = {6},
  abstract = {no abstract},
  issn = {0002-7863}
}

@ARTICLE{Kaminski2001,
  author = {Kaminski, G.A. and Friesner, R.A. and Tirado-Rives, J. and Jorgensen,
	W.L.},
  title = {Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins
	via Comparison with Accurate Quantum Chemical Calculations on Peptides.},
  journal = {J. Phys. Chem. B},
  year = {2001},
  volume = {105},
  pages = {6474-6487},
  number = {28},
  abstract = {Abstract: We present results of improving the OPLS-AA force field
	for peptides by means of refitting the key Fourier torsional coefficients.
	The fitting technique combines using accurate ab initio data as the
	target, choosing an efficient fitting subspace of the whole potential-energy
	surface, and determining weights for each of the fitting points based
	on magnitudes of the potential-energy gradient. The average energy
	RMS deviation from the LMP2/cc-pVTZ(-f)//HF/6-31G** data is reduced
	by ca. 40% from 0.81 to 0.47 kcal/mol as a result of the fitting
	for the electrostatically uncharged dipeptides. Transferability of
	the parameters is demonstrated by using the same alanine dipeptide-fitted
	backbone torsional parameters for all of the other dipeptides (with
	the appropriate side-chain refitting) and the alanine tetrapeptide.
	Parameters of nonbonded interactions have also been refitted for
	the sulfur-containing dipeptides (cysteine and methionine), and the
	validity of the new Coulombic charges and the van der Waals 's and
	's is proved through reproducing gas-phase energies of complex formation
	heats of vaporization and densities of pure model liquids. Moreover,
	a novel approach to fitting torsional parameters for electrostatically
	charged molecular systems has been presented and successfully tested
	on five dipeptides with charged side chains.},
  affiliation = {Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107},
  issn = {1520-6106}
}

@ARTICLE{Kauzmann1959,
  author = {W. Kauzmann},
  title = {Some Factors in the Interpretation of Protein Denaturation},
  journal = {Adv. Protein Chem.},
  year = {1959},
  volume = {1},
  pages = {1 -- 63},
  owner = {singh},
  timestamp = {2008.12.06}
}

@ARTICLE{Kayed2003,
  author = {Rakez Kayed and Elizabeth Head and Jennifer L Thompson and Theresa
	M McIntire and Saskia C Milton and Carl W Cotman and Charles G Glabe},
  title = {Common structure of soluble amyloid oligomers implies common mechanism
	of pathogenesis.},
  journal = {Science},
  year = {2003},
  volume = {300},
  pages = {486--489},
  number = {5618},
  month = {Apr},
  abstract = {Soluble oligomers are common to most amyloids and may represent the
	primary toxic species of amyloids, like the Abeta peptide in Alzheimer's
	disease (AD). Here we show that all of the soluble oligomers tested
	display a common conformation-dependent structure that is unique
	to soluble oligomers regardless of sequence. The in vitro toxicity
	of soluble oligomers is inhibited by oligomer-specific antibody.
	Soluble oligomers have a unique distribution in human AD brain that
	is distinct from fibrillar amyloid. These results indicate that different
	types of soluble amyloid oligomers have a common structure and suggest
	they share a common mechanism of toxicity.},
  doi = {10.1126/science.1079469},
  institution = {Department of Molecular Biology and Biochemistry, University of California,
	Irvine, CA 92697-3900, USA.},
  keywords = {Aged; Aged, 80 and over; Alzheimer Disease; Amyloid; Amyloid beta-Protein;
	Animals; Antibodies; Antibody Specificity; Biopolymers; Brain; Brain
	Chemistry; Cell Survival; Humans; Microscopy, Confocal; Microscopy,
	Electron; Molecular Mimicry; Neurofibrillary Tangles; Peptide Fragments;
	Protein Conformation; Rabbits; Solubility; Tumor Cells, Cultured},
  owner = {singh},
  pii = {300/5618/486},
  pmid = {12702875},
  timestamp = {2008.09.14}
}

@ARTICLE{Kessler2003,
  author = {Jeffrey C Kessler and Jean-Christophe Rochet and Peter T Lansbury},
  title = {The N-terminal repeat domain of alpha-synuclein inhibits beta-sheet
	and amyloid fibril formation.},
  journal = {Biochemistry},
  year = {2003},
  volume = {42},
  pages = {672--678},
  number = {3},
  month = {Jan},
  abstract = {The conversion of alpha-synuclein into amyloid fibrils in the substantia
	nigra is linked to Parkinson's disease. Alpha-synuclein is natively
	unfolded in solution, but can be induced to form either alpha-helical
	or beta-sheet structure depending on its concentration and the solution
	conditions. The N-terminus of alpha-synuclein comprises seven 11-amino
	acid repeats (XKTKEGVXXXX) which can form an amphipathic alpha-helix.
	Why seven repeats, rather than six or eight, survived the evolutionary
	process is not clear. To probe this question, two sequence variants
	of alpha-synuclein, one with two fewer (del2) and one with two additional
	(plus2) repeats, were studied. As compared to wild-type alpha-synuclein,
	the plus2 variant disfavors the formation of beta-sheet-rich oligomers,
	including amyloid fibrils. In contrast, the truncated variant, del2,
	favors beta-sheet and fibril formation. We propose that the repeat
	number in WT alpha-synuclein represents an evolutionary balance between
	the functional conformer of alpha-synuclein (alpha-helix and/or random
	coil) and its pathogenic beta-sheet conformation. N-terminal truncation
	of alpha-synuclein may promote pathogenesis.},
  doi = {10.1021/bi020429y},
  institution = {Center for Neurologic Diseases, Brigham and Women's Hospital, and
	Department of Neurology, Harvard Medical School, 65 Landsdowne Street,
	Cambridge, Massachusetts 02139, USA.},
  keywords = {Amino Acid Sequence; Amyloid; Circular Dichroism; Cloning, Molecular;
	Humans; Molecular Sequence Data; Nerve Tissue Proteins; Parkinson
	Disease; Peptide Fragments; Propanols; Protein Folding; Protein Isoforms;
	Protein Structure, Secondary; Protein Structure, Tertiary; Repetitive
	Sequences, Amino Acid; Synucleins; alpha-Synuclein},
  owner = {singh},
  pmid = {12534279},
  timestamp = {2008.07.24}
}

@ARTICLE{Kirkitadze2001,
  author = {M. D. Kirkitadze and M. M. Condron and D. B. Teplow},
  title = {Identification and characterization of key kinetic intermediates
	in amyloid beta-protein fibrillogenesis.},
  journal = {J. Mol. Biol.},
  year = {2001},
  volume = {312},
  pages = {1103--1119},
  number = {5},
  month = {Oct},
  abstract = {Amyloid beta-protein (Abeta) assembly into toxic oligomeric and fibrillar
	structures is a seminal event in Alzheimer's disease, therefore blocking
	this process could have significant therapeutic benefit. A rigorous
	mechanistic understanding of Abeta assembly would facilitate the
	targeting and design of fibrillogenesis inhibitors. Prior studies
	have shown that Abeta fibrillogenesis involves conformational changes
	leading to the formation of extended beta-sheets and that an alpha-helix-containing
	intermediate may be involved. However, the significance of this intermediate
	has been a matter of debate. We report here that the formation of
	an oligomeric, alpha-helix-containing assembly is a key step in Abeta
	fibrillogenesis. The generality of this phenomenon was supported
	by conformational studies of 18 different Abeta peptides, including
	wild-type Abeta(1-40) and Abeta(1-42), biologically relevant truncated
	and chemically modified Abeta peptides, and Abeta peptides causing
	familial forms of cerebral amyloid angiopathy. Without exception,
	fibrillogenesis of these peptides involved an oligomeric alpha-helix-containing
	intermediate and the kinetics of formation of the intermediate and
	of fibrils was temporally correlated. The kinetics varied depending
	on amino acid sequence and the extent of peptide N- and C-terminal
	truncation. The pH dependence of helix formation suggested that Asp
	and His exerted significant control over this process and over fibrillogenesis
	in general. Consistent with this idea, Abeta peptides containing
	Asp-->Asn or His-->Gln substitutions showed altered fibrillogenesis
	kinetics. These data emphasize the importance of the dynamic interplay
	between Abeta monomer conformation and oligomerization state in controlling
	fibrillogenesis kinetics.},
  doi = {10.1006/jmbi.2001.4970},
  institution = {Center for Neurologic Diseases, Brigham and Women's Hospital, Boston,
	MA 02115, USA.},
  keywords = {Alzheimer Disease; Amino Acid Sequence; Amyloid beta-Protein; Amyloidosis;
	Asparagine; Aspartic Acid; Chromatography, Gel; Circular Dichroism;
	Histidine; Humans; Hydrogen-Ion Concentration; Kinetics; Microscopy,
	Electron; Molecular Sequence Data; Mutation; Peptide Fragments; Protein
	Folding; Protein Structure, Quaternary; Protein Structure, Secondary},
  owner = {singh},
  pii = {S0022-2836(01)94970-8},
  pmid = {11580253},
  timestamp = {2008.07.24}
}

@ARTICLE{Knight2004,
  author = {Jefferson D Knight and Andrew D Miranker},
  title = {Phospholipid catalysis of diabetic amyloid assembly.},
  journal = {J. Mol. Biol.},
  year = {2004},
  volume = {341},
  pages = {1175--1187},
  number = {5},
  month = {Aug},
  abstract = {Islet amyloid polypeptide (IAPP) is a 37-residue hormone that forms
	cytotoxic amyloid fibers in the endocrine pancreas of patients with
	type II diabetes (NIDDM). A potential origin for cytotoxicity is
	disruption of lipid membranes by IAPP as has been observed in vitro.
	The cause of amyloid formation during NIDDM is not known, nor is
	the mechanism by which membrane disruption occurs in vitro. Here,
	we use kinetic studies in conjunction with assessments of lipid binding
	and electron microscopy to investigate the interactions of IAPP with
	phospholipid bilayers and the morphological effects of membranes
	on IAPP fibers. Fibrillogenesis of IAPP is catalyzed by synthetic
	and human tissue-derived phospholipids, leading to >tenfold increases
	in the rate of fibrillogenesis. The molecular basis of this phenomenon
	includes a strong dependence on the concentration and charge density
	of the membrane. IAPP binds to lipid membranes of mixed anionic (DOPG)
	and zwitterionic (DOPC) content. The transition for binding occurs
	over a physiologically relevant range of anionic content. Membrane
	binding by IAPP occurs on timescales that are short compared to fibrillogenesis
	and results in assembly into preamyloid states via ordered interactions
	at the N but not C terminus of the protein. These assemblies lead
	both to gross morphological changes in liposomes and to alterations
	in the appearance of early fibers when compared to liposome-free
	fibril formation. Intact bilayer surfaces are regenerated upon dissociation
	of fibers from the membrane surface. These findings offer a structural
	mechanism of membrane destabilization and suggest that changes in
	lipid metabolism could induce IAPP fiber formation in NIDDM.},
  doi = {10.1016/j.jmb.2004.06.086},
  institution = {Department of Pharmacology, Yale University, New Haven, CT 06520-8066,
	USA.},
  keywords = {Amino Acid Sequence; Amyloid; Animals; Diabetes Mellitus, Type 2;
	Female; Humans; Lipid Bilayers; Liposomes; Molecular Sequence Data;
	Peptides; Phosphatidylcholines; Phosphatidylglycerols; Protein Binding;
	Sequence Alignment},
  owner = {singh},
  pii = {S0022-2836(04)00798-3},
  pmid = {15321714},
  timestamp = {2008.09.14}
}

@ARTICLE{Krukau2007,
  author = {A. Krukau and I. Brovchenko and A. Geiger},
  title = {Temperature-induced conformational transition of a model elastin-like
	peptide \mbox{GVG(VPGVG)$_3$} in water},
  journal = {Biomacromolecules},
  year = {2007},
  volume = {8},
  pages = {2196-2202},
  owner = {brov},
  timestamp = {2007.06.26}
}

@ARTICLE{Kyte1982,
  author = {J. Kyte and R. F. Doolittle},
  title = {A simple method for displaying the hydropathic character of a protein.},
  journal = {J. Mol. Biol.},
  year = {1982},
  volume = {157},
  pages = {105--132},
  number = {1},
  month = {May},
  keywords = {Amino Acid Sequence; Amino Acids; Animals; Bacteriorhodopsins; Chymotrypsinogen;
	L-Lactate Dehydrogenase; Membrane Proteins; Methods; Proteins; Water},
  owner = {singh},
  pii = {0022-2836(82)90515-0},
  pmid = {7108955},
  timestamp = {2008.12.03}
}

@BOOK{Leach2001,
  title = {Molecular Modelling principles and applications},
  publisher = {Prentice Hall},
  year = {2001},
  author = {Andrew R. Leach},
  owner = {singh},
  timestamp = {2008.07.18}
}

@ARTICLE{Li:07a,
  author = {Je-Luen Li and Roberto Car and Chao Tang and Ned S. Wingreen},
  title = {Hydrophobic interaction and hydrogen-bond network for a methane pair
	in liquid water},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {2007},
  volume = {104},
  pages = {2626-2630},
  owner = {Brov},
  timestamp = {2007.09.23}
}

@ARTICLE{Li:99a,
  author = {Leping Li and Thomas A. Darden and L. Bartolotti and Dorothea Kominos
	and Lee G. Pedersen},
  title = {An Atomic Model for the Pleated beta -Sheet Structure of Abeta Amyloid
	Protofilaments},
  journal = {Biophys. J.},
  year = {1999},
  volume = {76},
  pages = {2871-2878},
  owner = {Brov},
  timestamp = {2007.09.23}
}

@ARTICLE{Lindahl2001,
  author = {Erik Lindahl and Berk Hess and David van der Spoel},
  title = {GROMACS 3.0: a package for molecular simulation and trajectory analysis},
  journal = {J. Mol. Mod.},
  year = {2001},
  volume = {7},
  pages = {306 -- 317},
  myid = {11},
  owner = {Gurpreet},
  timestamp = {2006.12.20 03:32:45}
}

@ARTICLE{Lopes2007,
  author = {D. H J Lopes and A. Meister and A. Gohlke and A. Hauser and A. Blume
	and R. Winter},
  title = {Mechanism of islet amyloid polypeptide fibrillation at lipid interfaces
	studied by infrared reflection absorption spectroscopy.},
  journal = {Biophys. J.},
  year = {2007},
  volume = {93},
  pages = {3132--3141},
  number = {9},
  month = {Nov},
  abstract = {Islet amyloid polypeptide (IAPP) is a pancreatic hormone and one of
	a number of proteins that are involved in the formation of amyloid
	deposits in the islets of Langerhans of type II diabetes mellitus
	patients. Though IAPP-membrane interactions are known to play a major
	role in the fibrillation process, the mechanism and the peptide's
	conformational changes involved are still largely unknown. To obtain
	new insights into the conformational dynamics of IAPP upon its aggregation
	at membrane interfaces and to relate these structures to its fibril
	formation, we studied the association of IAPP at various interfaces
	including neutral as well as charged phospholipids using infrared
	reflection absorption spectroscopy. The results obtained reveal that
	the interaction of human IAPP with the lipid interface is driven
	by the N-terminal part of the peptide and is largely driven by electrostatic
	interactions, as the protein is able to associate strongly with negatively
	charged lipids only. A two-step process is observed upon peptide
	binding, involving a conformational transition from a largely alpha-helical
	to a beta-sheet conformation, finally forming ordered fibrillar structures.
	As revealed by simulations of the infrared reflection absorption
	spectra and complementary atomic force microscopy studies, the fibrillar
	structures formed consist of parallel intermolecular beta-sheets
	lying parallel to the lipid interface but still contain a significant
	number of turn structures. We may assume that these dynamical conformational
	changes observed for negatively charged lipid interfaces play an
	important role as the first steps of IAPP-induced membrane damage
	in type II diabetes.},
  doi = {10.1529/biophysj.107.110635},
  institution = {University of Dortmund, Department of Chemistry, Physical Chemistry
	I-Biophysical Chemistry, D-44227 Dortmund, Germany.},
  keywords = {Adsorption; Amyloid; Animals; Electrostatics; Humans; Phosphatidylcholines;
	Phosphatidylglycerols; Rats; Spectrophotometry, Infrared; Water},
  owner = {singh},
  pii = {biophysj.107.110635},
  pmid = {17660321},
  timestamp = {2008.11.28}
}

@ARTICLE{Lue:99a,
  author = {Lue, Lih-Fen and Kuo, Yu-Min and Roher, Alex E. and Brachova, Libuse
	and Shen, Yong and Sue, Lucia and Beach, Thomas and Kurth, Janice
	H. and Rydel, Russel E. and Rogers, Joseph},
  title = {Soluble Amyloid {beta} Peptide Concentration as a Predictor of Synaptic
	Change in {A}lzheimer's Disease},
  journal = {Am. J. Pathol.},
  year = {1999},
  volume = {155},
  pages = {853-862},
  number = {3},
  abstract = {We have characterized amyloid {beta} peptide (A{beta}) concentration,
	A{beta} deposition, paired helical filament formation, cerebrovascular
	amyloid angiopathy, apolipoprotein E (ApoE) allotype, and synaptophysin
	concentration in entorhinal cortex and superior frontal gyrus of
	normal elderly control (ND) patients, Alzheimer's disease (AD) patients,
	and high pathology control (HPC) patients who meet pathological criteria
	for AD but show no synapse loss or overt antemortem symptoms of dementia.
	The measures of A{beta} deposition, A{beta}-immunoreactive plaques
	with and without cores, thioflavin histofluorescent plaques, and
	concentrations of insoluble A{beta}, failed to distinguish HPC from
	AD patients and were poor correlates of synaptic change. By contrast,
	concentrations of soluble A{beta} clearly distinguished HPC from
	AD patients and were a strong inverse correlate of synapse loss.
	Further investigation revealed that A{beta}40, whether in soluble
	or insoluble form, was a particularly useful measure for classifying
	ND, HPC, and AD patients compared with A{beta}42. A{beta}40 is known
	to be elevated in cerebrovascular amyloid deposits, and A{beta}40
	(but not A{beta}42) levels, cerebrovascular amyloid angiopathy, and
	ApoE4 allele frequency were all highly correlated with each other.
	Although paired helical filaments in the form of neurofibrillary
	tangles or a penumbra of neurites surrounding amyloid cores also
	distinguished HPC from AD patients, they were less robust predictors
	of synapse change compared with soluble A{beta}, particularly soluble
	A{beta}40. Previous experiments attempting to relate A{beta} deposition
	to the neurodegeneration that underlies AD dementia may have failed
	because they assayed the classical, visible forms of the molecule,
	insoluble neuropil plaques, rather than the soluble, unseen forms
	of the molecule.},
  eprint = {http://ajp.amjpathol.org/cgi/reprint/155/3/853.pdf},
  owner = {singh},
  timestamp = {2008.05.01}
}

@ARTICLE{Luna-Barcenas:97a,
  author = {Gabriel Luna-Barcenas and J. Carson Meredith and Isaac C. Sanchez
	and Keith P. Johnston and Dmitry G. Gromov and Juan J. de Pablo},
  title = {Relationship between polymer chain conformation and phase boundaries
	in a supercritical fluid},
  journal = {J. Chem. Phys.},
  year = {1997},
  volume = {107},
  pages = {10782-10792},
  number = {24},
  keywords = {POLYMERS; SUPERCRITICAL STATE; CONFORMATIONAL CHANGES; MONTE CARLO
	METHOD; LENNARD-JONES POTENTIAL; SOLUTIONS; DENSITY; PHASE STUDIES;
	SIMULATION; CRITICAL TEMPERATURE; polymer solutions; solvent effects},
  owner = {Brov},
  publisher = {AIP},
  timestamp = {2008.04.10}
}

@ARTICLE{Ma:02a,
  author = {Ma, Buyong and Nussinov, Ruth},
  title = {Stabilities and conformations of Alzheimer's beta -amyloid peptide
	oligomers (Abeta 16-22, Abeta 16-35, and Abeta 10-35): Sequence effects},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {2002},
  volume = {99},
  pages = {14126-14131},
  number = {22},
  abstract = {Previously, we have studied the minimal oligomer size of an aggregate
	amyloid seed and the mechanism of seed growth with a multilayer {beta}-sheet
	model. Under high temperature simulation conditions, our approach
	can test the stability of possible amyloid forms. Here, we report
	our study of oligomers of Alzheimer's amyloid {beta}-peptide (A{beta})
	fragments 16-22, 16-35, and 10-35 (abbreviated A{beta}16-22, A{beta}16-35,
	and A{beta}10-35, respectively). Our simulations indicate that an
	antiparallel {beta}-sheet orientation is the most stable for the
	A{beta}16-22, in agreement with a solid state NMR-based model [Balbach,
	J. J., Ishii, Y., Antzutkin, O. N., Leapman, R. D., Rizzo, N. W.,
	et al. (2000) Biochemistry 39, 13748-13759]. A model with twenty-four
	A{beta}16-22 strands indicates a highly twisted fibril. Whereas the
	short A{beta}16-22 and A{beta}24-36 may exist in fully extended form,
	the linear parallel {beta}-sheets for A{beta}16-35 appear impossible,
	mainly because of the polar region in the middle of the 16-35 sequence.
	However, a bent double-layered hairpin-like structure (called hook)
	with the polar region at the turn forms parallel {beta}-sheets with
	higher stability. An intra-strand salt-bridge (D23-K28) stabilizes
	the bent hairpin-like hook structure. The bent double-{beta}-sheet
	model for the A{beta}10-35 similarly offers oligomer stability.},
  owner = {singh},
  timestamp = {2008.05.01}
}

@ARTICLE{Macdowell:06a,
  author = {Luis G. MacDowell and Vincent K. Shen and Jeffrey R. Errington},
  title = {Nucleation and cavitation of spherical, cylindrical, and slablike
	droplets and bubbles in small systems},
  journal = {J. Chem. Phys.},
  year = {2006},
  volume = {125},
  pages = {034705},
  owner = {singh},
  timestamp = {2008.05.01}
}

@ARTICLE{Macdowell:04a,
  author = {Luis G. MacDowell and Peter Virnau and Marcus Muller and Kurt Binder},
  title = {The evaporation/condensation transition of liquid droplets},
  journal = {J. Chem. Phys.},
  year = {2004},
  volume = {120},
  pages = {5293-5308},
  number = {11},
  keywords = {evaporation; condensation; drops; surface tension; equations of state;
	chemical potential; Lennard-Jones potential; probability; Laplace
	equations},
  owner = {Brov},
  publisher = {AIP},
  timestamp = {2007.09.19}
}

@ARTICLE{Mackerell2004,
  author = {Alexander D Mackerell},
  title = {Empirical force fields for biological macromolecules: overview and
	issues.},
  journal = {J. Comput. Chem.},
  year = {2004},
  volume = {25},
  pages = {1584--1604},
  number = {13},
  month = {Oct},
  abstract = {Empirical force field-based studies of biological macromolecules are
	becoming a common tool for investigating their structure-activity
	relationships at an atomic level of detail. Such studies facilitate
	interpretation of experimental data and allow for information not
	readily accessible to experimental methods to be obtained. A large
	part of the success of empirical force field-based methods is the
	quality of the force fields combined with the algorithmic advances
	that allow for more accurate reproduction of experimental observables.
	Presented is an overview of the issues associated with the development
	and application of empirical force fields to biomolecular systems.
	This is followed by a summary of the force fields commonly applied
	to the different classes of biomolecules; proteins, nucleic acids,
	lipids, and carbohydrates. In addition, issues associated with computational
	studies on "heterogeneous" biomolecular systems and the transferability
	of force fields to a wide range of organic molecules of pharmacological
	interest are discussed.},
  doi = {10.1002/jcc.20082},
  file = {MDS\\force field\\j comp chem 2004 25 empirical force fields for biological
	macromolecules.pdf:MDS\\force field\\j comp chem 2004 25 empirical
	force fields for biological macromolecules.pdf:PDF},
  keywords = {Algorithms; Carbohydrates; Computer Simulation; Electrostatics; Lipids;
	Macromolecular Substances; Models, Molecular; Nucleic Acids; Proteins;
	Structure-Activity Relationship; Thermodynamics},
  owner = {Gurpreet},
  pmid = {15264253},
  timestamp = {2007.03.25 06:05:01}
}

@ARTICLE{Maeda:01a,
  author = {Maeda, Y. and Nakamura, T. and Ikeda, I.},
  title = {Changes in the hydration states of \mbox{Poly(N-alkylacrylamide)s}
	during their phase transitions in water observed by \mbox{ FTIR}
	spectroscopy},
  journal = {Macromolecules},
  year = {2001},
  volume = {34},
  pages = {1391-1399},
  number = {5},
  affiliation = {Department of Applied Chemistry and Biotechnology, Fukui University,
	Fukui 910-8507, Japan},
  issn = {0024-9297},
  owner = {Brov},
  timestamp = {2008.04.10}
}

@ARTICLE{Marinari:92a,
  author = {E. Marinari and G. Parisi},
  title = {Simulated tempering - a new Monte Carlo scheme},
  journal = {Europhys. Lett.},
  year = {1992},
  volume = {19},
  pages = {451-458},
  owner = {brov},
  timestamp = {2008.10.17}
}

@ARTICLE{Mazor2002,
  author = {Yariv Mazor and Sharon Gilead and Itai Benhar and Ehud Gazit},
  title = {Identification and characterization of a novel molecular-recognition
	and self-assembly domain within the islet amyloid polypeptide.},
  journal = {J. Mol. Biol.},
  year = {2002},
  volume = {322},
  pages = {1013--1024},
  number = {5},
  month = {Oct},
  abstract = {The islet amyloid polypeptide (hIAPP) is a 37 amino acid residue polypeptide
	that was found to accumulate as amyloid fibrils in the pancreas of
	individuals with type II diabetes. Previous studies identified various
	fragments of hIAPP that can form amyloid fibrils in vitro (e.g. hIAPP(8-20),
	hIAPP(23-27), and hIAPP(30-37)). However, no comparative and systematic
	information was available on the role of these structural domains
	(or others) in the process of molecular recognition that mediates
	fibrillization, in the context of the full-length polypeptide. To
	systematically map and compare potential recognition domains, we
	studied the ability of hIAPP to interact with an array of 28 membrane-spotted
	overlapping peptides that span the entire sequence of hIAPP (i.e.
	hIAPP(1-10), hIAPP(2-11...), hIAPP(28-37)). Our study clearly identified
	a major domain of molecular recognition within hIAPP, as the polypeptide
	was found to bind with high affinity to a defined linear group of
	peptides ranging from hIAPP(7-16) to hIAPP(12-21). The maximal binding
	of the full-length polypeptide was to the hIAPP(11-20) peptide fragment
	(with the sequence RLANFLVHSS). In order to define the minimal fragment,
	within this apparent recognition motif, that is capable of self-association
	and thus may serve as the core molecular recognition motif, we examined
	the ability of truncated analogs of the recognition sequence to self-assemble
	into amyloid fibrils. The shortest active fragments capable of self-assembly
	were found to be the pentapeptides FLVHS and NFLVH. The apparent
	role of this motif in the process of hIAPP self-assembly is consistent
	with the profile of the hIAAP-binding distribution to the peptide
	array. The identification of such short recognition motifs is extremely
	useful in the attempts to develop means to block amyloid fibril formation
	by hIAPP. It is worth mentioning that this is only the second time
	in which peptides as short as a pentapeptide were shown to form amyloid
	fibrils (the other pentapeptide is FGAIL).},
  file = {aggregations\\IAPP\\j mol biol2002 322 identification and characterization
	of a novel molecular recognition and self assemly domain within IAPP.pdf:aggregations\\IAPP\\j
	mol biol2002 322 identification and characterization of a novel molecular
	recognition and self assemly domain within IAPP.pdf:PDF},
  keywords = {Amino Acid Motifs; Amino Acid Sequence; Amyloid; Base Sequence; Binding
	Sites; Carrier Proteins; Diabetes Mellitus, Type 2; Humans; Molecular
	Sequence Data; Molecular Structure; Peptide Fragments; Protein Binding;
	Protein Structure, Tertiary; Recombinant Fusion Proteins; Research
	Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.;
	Spectroscopy, Fourier Transform Infrared},
  myid = {8},
  owner = {Gurpreet},
  pii = {S0022283602008872},
  pmid = {12367525},
  timestamp = {2006.12.18 12:00:05}
}

@ARTICLE{Melquiond:07a,
  author = {Adrien Melquiond and Jean-Christophe Gelly and Normand Mousseau and
	Philippe Derreumaux},
  title = {Probing amyloid fibril formation of the NFGAIL peptide by computer
	simulations},
  journal = {J. Chem. Phys.},
  year = {2007},
  volume = {126},
  pages = {065101},
  number = {6},
  eid = {065101},
  keywords = {proteins; macromolecules; molecular biophysics; molecular configurations;
	aggregation; diseases},
  owner = {singh},
  timestamp = {2008.05.01}
}

@ARTICLE{Mirzabekov1996,
  author = {T. A. Mirzabekov and M. C. Lin and B. L. Kagan},
  title = {Pore formation by the cytotoxic islet amyloid peptide amylin.},
  journal = {J. Biol. Chem.},
  year = {1996},
  volume = {271},
  pages = {1988--1992},
  number = {4},
  month = {Jan},
  abstract = {Amylin is a 37-amino acid cytotoxic constituent of amyloid deposits
	found in the islets of Langerhans of patients with type II diabetes.
	Extracellular accumulation of this peptide results in damage to insulin-producing
	beta cell membranes and cell death. We report here that at cytotoxic
	concentrations, amylin forms voltage-dependent, relatively nonselective,
	ion-permeable channels in planar phospholipid bilayer membranes.
	Channel formation is dependent upon lipid membrane composition, ionic
	strength, and membrane potential. At 1-10 microM, cytotoxic human
	amylin dramatically increases the conductance of lipid bilayer membranes,
	while non-cytotoxic rat amylin does not. We suggest that channel
	formation may be the mechanism of cytotoxicity of human amylin.},
  institution = {Department of Psychiatry and Biobehavioral Sciences, UCLA Neuropsychiatric
	Institute, USA.},
  keywords = {Amyloid; Animals; Cell Membrane Permeability; Cytotoxins; Electric
	Conductivity; Humans; Ion Channels; Lipid Bilayers; Membrane Proteins;
	Rats},
  owner = {singh},
  pmid = {8567648},
  timestamp = {2008.09.14}
}

@ARTICLE{Mishra2008,
  author = {Rajesh Mishra and Roland Winter},
  title = {Cold- and pressure-induced dissociation of protein aggregates and
	amyloid fibrils.},
  journal = {Angew. Chem. Int. Ed. Engl.},
  year = {2008},
  volume = {47},
  pages = {6518--6521},
  number = {35},
  doi = {10.1002/anie.200802027},
  institution = {Dortmund University of Technology, Faculty of Chemistry, Physical
	Chemistry-Biophysical Chemistry, Otto-Hahn Strasse 6, 44227 Dortmund,
	Germany.},
  keywords = {Amyloid; Cold; Humans; Pressure; Protein Denaturation; Protein Folding;
	Thermodynamics},
  owner = {singh},
  pmid = {18646033},
  timestamp = {2008.11.28}
}

@ARTICLE{Mitra:08a,
  author = {L. Mitra and A. Oleinikova and R. Winter},
  title = {Intrinsic volumetric properties of trialanine isomers in aqueous
	solution},
  journal = {ChemPhysChem},
  volume = {(in press)},
  owner = {brov},
  timestamp = {2008.03.24}
}

@ARTICLE{Narayanan:94a,
  author = {T. Narayanan and Anil Kumar},
  title = {Reentrant phase transitions in multicomponent liquid mixtures},
  journal = {Phys. Rep.},
  year = {1994},
  volume = {249},
  pages = {135-218},
  owner = {Brov},
  timestamp = {2008.04.09}
}

@ARTICLE{Nguyen2004,
  author = {Hung D Nguyen and Carol K Hall},
  title = {Molecular dynamics simulations of spontaneous fibril formation by
	random-coil peptides.},
  journal = {Proc. Natl. Acad. Sci. U. S. A.},
  year = {2004},
  volume = {101},
  pages = {16180--16185},
  number = {46},
  month = {Nov},
  abstract = {Assembly of normally soluble proteins into amyloid fibrils is a cause
	or associated symptom of numerous human disorders, including Alzheimer's
	and the prion diseases. We report molecular-level simulation of spontaneous
	fibril formation. Systems containing 12-96 model polyalanine peptides
	form fibrils at temperatures greater than a critical temperature
	that decreases with peptide concentration and exceeds the peptide's
	folding temperature, consistent with experimental findings. Formation
	of small amorphous aggregates precedes ordered nucleus formation
	and subsequent rapid fibril growth through addition of beta-sheets
	laterally and monomeric peptides at fibril ends. The fibril's structure
	is similar to that observed experimentally.},
  doi = {10.1073/pnas.0407273101},
  institution = {Department of Chemical and Biomolecular Engineering, North Carolina
	State University, Raleigh, NC 27695-7905, USA.},
  keywords = {Amyloid; Biophysics; Humans; Models, Molecular; Multiprotein Complexes;
	Peptides; Thermodynamics},
  owner = {singh},
  pii = {0407273101},
  pmid = {15534217},
  timestamp = {2008.10.16}
}

@ARTICLE{Nguyen:07a,
  author = {Nguyen, Phuong H. and Li, Mai Suan and Stock, Gerhard and Straub,
	John E. and Thirumalai, D.},
  title = {Monomer adds to preformed structured oligomers of {A}beta-peptides
	by a two-stage dock-lock mechanism},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {2007},
  volume = {104},
  pages = {111-116},
  number = {1},
  abstract = {Nonfibrillar soluble oligomers, which are intermediates in the transition
	from monomers to amyloid fibrils, may be the toxic species in Alzheimer's
	disease. To monitor the early events that direct assembly of amyloidogenic
	peptides we probe the dynamics of formation of (A[beta]16-22)n by
	adding a monomer to a preformed (A[beta]16-22)n-1 (n = 4-6) oligomer
	in which the peptides are arranged in an antiparallel [beta]-sheet
	conformation. All atom molecular dynamics simulations in water and
	multiple long trajectories, for a cumulative time of 6.9 {micro}s,
	show that the oligomer grows by a two-stage dock-lock mechanism.
	The largest conformational change in the added disordered monomer
	occurs during the rapid ({approx}50 ns) first dock stage in which
	the [beta]-strand content of the monomer increases substantially
	from a low initial value. In the second slow-lock phase, the monomer
	rearranges to form in register antiparallel structures. Surprisingly,
	the mobile structured oligomers undergo large conformational changes
	in order to accommodate the added monomer. The time needed to incorporate
	the monomer into the fluid-like oligomer grows even when n = 6, which
	suggests that the critical nucleus size must exceed six. Stable antiparallel
	structure formation exceeds hundreds of nanoseconds even though frequent
	interpeptide collisions occur at elevated monomer concentrations
	used in the simulations. The dock-lock mechanism should be a generic
	mechanism for growth of oligomers of amyloidogenic peptides.},
  owner = {singh},
  timestamp = {2008.05.01}
}

@ARTICLE{Nilsson1999,
  author = {M. R. Nilsson and D. P. Raleigh},
  title = {Analysis of amylin cleavage products provides new insights into the
	amyloidogenic region of human amylin.},
  journal = {J. Mol. Biol.},
  year = {1999},
  volume = {294},
  pages = {1375--1385},
  number = {5},
  month = {Dec},
  abstract = {Human amylin is the primary component of amyloid deposits found in
	the pancreatic beta-cells of patients with type 2 diabetes mellitus.
	Recently, two fragments of amylin have been identified in vivo. One
	fragment contains residues 17 to 37 of human amylin (AMYLIN17-37)
	and the other contains residues 24 to 37 (AMYLIN24-37). The secondary
	structure and amyloid forming ability of each peptide was determined
	at pH 5.5(+/-0.3) and pH 7.4(+/-0.3). Results at these two values
	of pH were very similar. Both peptides are predominantly unstructured
	in solution (CD) but adopt a significant amount of beta-sheet secondary
	structure upon aggregation (FTIR). Transmission electron microscopy
	(TEM) confirmed the presence of amyloid fibrils. AMYLIN24-37 was
	further dissected by studying peptides corresponding to residues
	24 to 29 and 30 to 37. The AMYLIN30-37 peptide forms amyloid deposits.
	Samples of the 24 to 29 fragment which had TFA as the associated
	counterion formed ordered deposits but samples associated with HCl
	did not. Residues 20 to 29 are traditionally thought to be the amyloidogenic
	region of amylin, but this study demonstrates that peptides derived
	from other regions of amylin are capable of forming amyloid, and
	hence indicates that these regions of amylin can play a role in amyloid
	formation.},
  doi = {10.1006/jmbi.1999.3286},
  file = {aggregations\\IAPP\\j mol biol 1999 analysis of amylin cleavage products.pdf:aggregations\\IAPP\\j
	mol biol 1999 analysis of amylin cleavage products.pdf:PDF},
  keywords = {Amino Acid Sequence; Amyloid; Birefringence; Circular Dichroism; Congo
	Red; Humans; Hydrochloric Acid; Hydrogen-Ion Concentration; Microscopy,
	Electron; Molecular Sequence Data; Peptide Fragments; Protein Binding;
	Protein Structure, Secondary; Solutions; Spectrometry, Mass, Matrix-Assisted
	Laser Desorption-Ionization; Spectroscopy, Fourier Transform Infrared;
	Trifluoroacetic Acid},
  myid = {9},
  owner = {Gurpreet},
  pii = {S0022-2836(99)93286-2},
  pmid = {10600392},
  timestamp = {2006.12.19 10:18:52}
}

@ARTICLE{Nose1984,
  author = {Nose, S.},
  title = {A molecular dynamics method for simulations in the canonical ensemble.},
  journal = {Mol. Phys.},
  year = {1984},
  volume = {52},
  pages = {255--268}
}

@ARTICLE{Nussbaumer:08a,
  author = {A. Nu{\ss}baumer and E. Bittner and W. Janke},
  title = {Monte {C}arlo study of the droplet formation-dissolution transition
	on different two-dimensional lattices},
  journal = {Phys. Rev. E},
  year = {2008},
  volume = {77},
  pages = {041109},
  number = {4},
  keywords = {dissolving; drops; Ising model; lattice theory; magnetisation; Monte
	Carlo methods},
  numpages = {13},
  owner = {singh},
  publisher = {APS},
  timestamp = {2008.05.01}
}

@ARTICLE{Nussbaumer:06a,
  author = {A. Nu{\ss}baumer and E. Bittner and T. Neuhaus and W. Janke},
  title = {Monte {C}arlo study of the evaporation/condensation transition of
	{I}sing droplets},
  journal = {Europhys. Lett.},
  year = {2006},
  volume = {75},
  pages = {716-722},
  owner = {Brov},
  timestamp = {2007.09.23}
}

@ARTICLE{Nemethy1981,
  author = {G. N�methy and W. J. Peer and H. A. Scheraga},
  title = {Effect of protein-solvent interactions on protein conformation.},
  journal = {Annu. Rev. Biophys. Bioeng.},
  year = {1981},
  volume = {10},
  pages = {459--497},
  doi = {10.1146/annurev.bb.10.060181.002331},
  keywords = {Amino Acids; Chemistry, Physical; Molecular Weight; Peptides; Protein
	Conformation; Proteins; Solvents; Water},
  owner = {singh},
  pmid = {7020582},
  timestamp = {2008.07.21}
}

@ARTICLE{Oddo:06a,
  author = {Oddo, S. and Caccamo, A. and Smith, A. F. and Green, K. N. and LaFerla,
	F. M.},
  title = {A Dynamic Relationship between Intracellular and Extracellular Pools
	of {A}beta},
  journal = {Am. J. Pathol.},
  year = {2006},
  volume = {168},
  pages = {184-194},
  owner = {Brov},
  timestamp = {2007.09.19}
}

@ARTICLE{Oleinikova:06d,
  author = {A. Oleinikova and I. Brovchenko},
  title = {Percolating networks and liquid-liquid transitions in supercooled
	water},
  journal = {J. Phys.: Condens. Matt.},
  year = {2006},
  volume = {18},
  pages = {S2247-S2259},
  owner = {brov},
  timestamp = {2007.06.04}
}

@ARTICLE{Oleinikova:02a,
  author = {A. Oleinikova and I. Brovchenko and A. Geiger and B. Guillot},
  title = {Percolation of water in aqueous solution and liquid--liquid immiscibility},
  journal = {J. Chem. Phys.},
  year = {2002},
  volume = {117},
  pages = {3296-3304},
  number = {7},
  keywords = {percolation; water; solubility; liquid-liquid transformations; hydrogen
	bonds; Monte Carlo methods},
  owner = {Brov},
  publisher = {AIP},
  timestamp = {2008.04.10}
}

@ARTICLE{Oleinikova:05b,
  author = {A. Oleinikova and I. Brovchenko and N. Smolin and A. Krukau and A.
	Geiger and R. Winter},
  title = {Percolation transition of hydration water: from planar hydrophilic
	surfaces to proteins},
  journal = {Phys. Rev. Lett.},
  year = {2005},
  volume = {95},
  pages = {247802},
  number = {24},
  eid = {247802},
  keywords = {solvation; percolation; water; hydrogen bonds; proteins; molecular
	biophysics},
  owner = {singh},
  timestamp = {2008.05.01}
}

@ARTICLE{Onuchic1997,
  author = {J. N. Onuchic and Z. Luthey-Schulten and P. G. Wolynes},
  title = {Theory of protein folding: the energy landscape perspective.},
  journal = {Annu. Rev. Phys. Chem.},
  year = {1997},
  volume = {48},
  pages = {545--600},
  abstract = {The energy landscape theory of protein folding is a statistical description
	of a protein's potential surface. It assumes that folding occurs
	through organizing an ensemble of structures rather than through
	only a few uniquely defined structural intermediates. It suggests
	that the most realistic model of a protein is a minimally frustrated
	heteropolymer with a rugged funnel-like landscape biased toward the
	native structure. This statistical description has been developed
	using tools from the statistical mechanics of disordered systems,
	polymers, and phase transitions of finite systems. We review here
	its analytical background and contrast the phenomena in homopolymers,
	random heteropolymers, and protein-like heteropolymers that are kinetically
	and thermodynamically capable of folding. The connection between
	these statistical concepts and the results of minimalist models used
	in computer simulations is discussed. The review concludes with a
	brief discussion of how the theory helps in the interpretation of
	results from fast folding experiments and in the practical task of
	protein structure prediction.},
  doi = {10.1146/annurev.physchem.48.1.545},
  institution = {Department of Physics, University of California at San Diego, La
	Jolla 92093-0319, USA.},
  keywords = {Amino Acid Sequence; Computer Simulation; Models, Molecular; Molecular
	Sequence Data; Polymers; Protein Folding; Sequence Homology, Amino
	Acid; Thermodynamics},
  owner = {singh},
  pmid = {9348663},
  timestamp = {2008.11.27}
}

@ARTICLE{Padrick:02a,
  author = {Padrick, S.B. and Miranker, A.D.},
  title = {Islet Amyloid: Phase Partitioning and Secondary Nucleation Are Central
	to the Mechanism of Fibrillogenesis},
  journal = {Biochemistry},
  year = {2002},
  volume = {41},
  pages = {4694-4703},
  number = {14},
  affiliation = {Department of Molecular Biophysics and Biochemistry, Yale University,
	260 Whitney Avenue, New Haven, Connecticut 06520-8114},
  issn = {0006-2960},
  owner = {singh},
  timestamp = {2008.05.01}
}

@ARTICLE{Pangali:79a,
  author = {C. Pangali and M. Rao and B. J. Berne},
  title = {A {M}onte {C}arlo simulation of the hydrophobic interaction},
  journal = {J. Chem. Phys.},
  year = {1979},
  volume = {71},
  pages = {2975-2981},
  number = {7},
  owner = {singh},
  publisher = {AIP},
  timestamp = {2008.05.01}
}

@MANUAL{Paschek,
  title = {Volume,Temperature-Replica Exchange Molecular Dynamics with the GROMACS
	3.2.1 Simulation Package. RPMDRUN - A mini-HOWTO},
  author = {Dietmar Paschek},
  owner = {singh},
  timestamp = {2008.07.22},
  url = {http://ganter.chemie.uni-dortmund.de/�pas}
}

@ARTICLE{Porat2003,
  author = {Yair Porat and Sofiya Kolusheva and Raz Jelinek and Ehud Gazit},
  title = {The human islet amyloid polypeptide forms transient membrane-active
	prefibrillar assemblies.},
  journal = {Biochemistry},
  year = {2003},
  volume = {42},
  pages = {10971--10977},
  number = {37},
  month = {Sep},
  abstract = {The formation of amyloid fibrils by the human islet amyloid polypeptide
	is associated with type II diabetes. While it was previously suggested
	that the formed fibrils are toxic to pancreatic beta-cells due to
	membrane permeation activity, more recent studies suggested that
	protofibrillar assemblies have significantly higher potency in permeating
	lipid bilayers. Here, we specifically studied the membrane interaction
	activity of soluble and insoluble islet amyloid polypeptide assemblies
	at high temporal resolution. A colorimetric analysis using lipid/polydiacetylene
	(PDA) biomimetic vesicles clearly demonstrated the transient formation
	of soluble assemblies that strongly interact with the lipid vesicles.
	A peak in the level of membrane binding of the soluble fraction,
	as reflected by the colorimetric assay, was observed after incubation
	for approximately 1 h, followed by a decrease in the level of membrane
	interaction of the assemblies. The transient nature of the membrane-active
	assemblies was independently confirmed by a fluorescence quenching
	assay. Ultrastructural analysis using transmission electron microscopy
	provided morphological evidence of prefibrillar assemblies, supported
	the transient existence of membrane interacting soluble species,
	and facilitated observation of the non-membrane-active filaments
	in the solution. Taken together, our results provide experimental
	evidence for the formation of transient soluble prefibrillar assemblies
	which are highly membrane-active. The implications of these observations
	are discussed in light of designed fibrillization inhibitors.},
  doi = {10.1021/bi034889i},
  institution = {Department of Molecular Microbiology and Biotechnology, George S.
	Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978,
	Israel.},
  keywords = {Amyloid; Cell Membrane; Circular Dichroism; Diabetes Mellitus, Type
	2; Humans; Islets of Langerhans; Lipid Bilayers; Lipids; Microscopy,
	Electron; Peptides; Spectrometry, Fluorescence; Time Factors},
  owner = {singh},
  pmid = {12974632},
  timestamp = {2008.09.14}
}

@ARTICLE{Prausnitz:03a,
  author = {John M. Prausnitz},
  title = {Molecular thermodynamics for some applications in biotechnology},
  journal = {J. Chem. Thermod.},
  year = {2003},
  volume = {35},
  pages = {21-39},
  owner = {Brov},
  timestamp = {2008.04.10}
}

@ARTICLE{Pullara:07a,
  author = {Pullara, F. and Emanuele, A. and Palma-Vittorelli, M. B. and Palma,
	M. U.},
  title = {Protein Aggregation/Crystallization and Minor Structural Changes:
	Universal versus Specific Aspects},
  journal = {Biophys. J.},
  year = {2007},
  volume = {93},
  pages = {3271-3278},
  number = {9},
  abstract = {Protein association covers wide interests in biophysics, protein science,
	and biotechnologies, and it is often viewed as governed by conformation
	details. More recently, the existence of a universal physical principle
	governing aggregation/crystallization processes has been suggested
	by a series of experiments and shown to be linked to the universal
	scaling properties of concentration fluctuations occurring in the
	proximity of a phase transition (spinodal demixing in the specific
	case). Such properties have provided a quantitative basis for capturing
	kinetic association data on a universal master curve, ruled by the
	normalized distance of the state of the system from its instability
	region. Here we report new data on lysozyme crystal nucleation. They
	strengthen the evidence in favor of universality and show that the
	system enters the region of universal behavior in a stepwise manner
	as a result of minor conformation changes. Results also show that
	the link between conformation details and universal behavior is actuated
	by interactions mediated by the solvent. Outside the region of universal
	behavior, nucleation rates become unpredictable and undetectably
	long.},
  eprint = {http://www.biophysj.org/cgi/reprint/93/9/3271.pdf},
  owner = {singh},
  timestamp = {2008.05.01}
}

@ARTICLE{Quist2005,
  author = {Arjan Quist and Ivo Doudevski and Hai Lin and Rushana Azimova and
	Douglas Ng and Blas Frangione and Bruce Kagan and Jorge Ghiso and
	Ratnesh Lal},
  title = {Amyloid ion channels: a common structural link for protein-misfolding
	disease.},
  journal = {Proc. Natl. Acad. Sci. U. S. A.},
  year = {2005},
  volume = {102},
  pages = {10427--10432},
  number = {30},
  month = {Jul},
  abstract = {Protein conformational diseases, including Alzheimer's, Huntington's,
	and Parkinson's diseases, result from protein misfolding, giving
	a distinct fibrillar feature termed amyloid. Recent studies show
	that only the globular (not fibrillar) conformation of amyloid proteins
	is sufficient to induce cellular pathophysiology. However, the 3D
	structural conformations of these globular structures, a key missing
	link in designing effective prevention and treatment, remain undefined
	as of yet. By using atomic force microscopy, circular dichroism,
	gel electrophoresis, and electrophysiological recordings, we show
	here that an array of amyloid molecules, including amyloid-beta(1-40),
	alpha-synuclein, ABri, ADan, serum amyloid A, and amylin undergo
	supramolecular conformational change. In reconstituted membranes,
	they form morphologically compatible ion-channel-like structures
	and elicit single ion-channel currents. These ion channels would
	destabilize cellular ionic homeostasis and hence induce cell pathophysiology
	and degeneration in amyloid diseases.},
  doi = {10.1073/pnas.0502066102},
  institution = {Neuroscience Research Institute, University of California, Santa
	Barbara, CA 93106, USA.},
  keywords = {Amyloid; Amyloidosis; Circular Dichroism; Electrophoresis; Electrophysiology;
	Ion Channels; Microscopy, Atomic Force; Protein Conformation; Protein
	Folding},
  owner = {singh},
  pii = {0502066102},
  pmid = {16020533},
  timestamp = {2008.09.14}
}

@ARTICLE{Raschke:01a,
  author = {Raschke, Tanya M. and Tsai, Jerry and Levitt, Michael},
  title = {Quantification of the hydrophobic interaction by simulations of the
	aggregation of small hydrophobic solutes in water},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {2001},
  volume = {98},
  pages = {5965-5969},
  number = {11},
  owner = {singh},
  timestamp = {2008.05.01}
}

@ARTICLE{Rhoades:00a,
  author = {E. Rhoades and J. Agarwal and A. Gafni},
  title = {Aggregation of an amyloidogenic fragment of human islet amyloid polypeptide},
  journal = {Biochim. Biophys. Acta},
  year = {2000},
  volume = {1476},
  pages = {230-238},
  owner = {Brov},
  timestamp = {2008.04.22}
}

@ARTICLE{Rohrig:06a,
  author = {Rohrig, Ute F. and Laio, Alessandro and Tantalo, Nazario and Parrinello,
	Michele and Petronzio, Roberto},
  title = {Stability and Structure of Oligomers of the {A}lzheimer Peptide {A}beta16-22:
	From the Dimer to the 32-Mer},
  journal = {Biophys. J.},
  year = {2006},
  volume = {91},
  pages = {3217-3229},
  number = {9},
  owner = {singh},
  timestamp = {2008.05.01}
}

@ARTICLE{Serpell:00a,
  author = {L. C. Serpell},
  title = {Alzheimer's amyloid fibrils: structure and assembly.},
  journal = {Biochim Biophys Acta},
  year = {2000},
  volume = {1502},
  pages = {16--30},
  number = {1},
  month = {Jul},
  abstract = {Structural studies of Alzheimer's amyloid fibrils have revealed information
	about the structure at different levels. The amyloid-beta peptide
	has been examined in various solvents and conditions and this has
	led to a model by which a conformational switching occurs from alpha-helix
	or random coil, to a beta-sheet structure. Amyloid fibril assembly
	proceeds by a nucleation dependent pathway leading to elongation
	of the fibrils. Along this pathway small oligomeric intermediates
	and short fibrillar structures (protofibrils) have been observed.
	In cross-section the fibril appears to be composed of several subfibrils
	or protofilaments. Each of these protofilaments is composed of beta-sheet
	structure in which hydrogen bonding occurs along the length of the
	fibre and the beta-strands run perpendicular to the fibre axis. This
	hierarchy of structure is discussed in this review.},
  institution = {Neurobiology Division, MRC Centre, Cambridge, UK. serpell@mrc-lmb.cam.ac.uk},
  keywords = {Alzheimer Disease; Amyloid beta-Protein; Animals; Congo Red; Humans;
	Microscopy, Atomic Force; Molecular Structure; Neurons; Peptide Fragments;
	Protein Conformation; Protein Structure, Secondary; Senile Plaques;
	Solubility; X-Ray Diffraction},
  owner = {singh},
  pii = {S0925-4439(00)00029-6},
  pmid = {10899428},
  timestamp = {2008.12.18}
}

@ARTICLE{Shao1999,
  author = {H. Shao and S. Jao and K. Ma and M. G. Zagorski},
  title = {Solution structures of micelle-bound amyloid beta-(1-40) and beta-(1-42)
	peptides of Alzheimer's disease.},
  journal = {J. Mol. Biol.},
  year = {1999},
  volume = {285},
  pages = {755--773},
  number = {2},
  month = {Jan},
  abstract = {The amyloid beta-peptide is the major protein constituent of neuritic
	plaques in Alzheimer's disease. The beta-peptide varies slightly
	in length and exists in two predominant forms: (1) the shorter, 40
	residue beta-(1-40), found mainly in cerebrovascular amyloid; and
	(2) the longer, 42 residue beta-(1-42), which is the major component
	in amyloid plaque core deposits. We report here that the sodium dodecyl
	sulphate (SDS) micelle, a membrane-mimicking system for biophysical
	studies, prevents aggregation of the beta-(1-40) and the beta-(1-42)
	into the neurotoxic amyloid-like, beta-pleated sheet structure, and
	instead encourages folding into predominantly alpha-helical structures
	at pH 7.2. Analysis of the nuclear Overhauser enhancement (NOE) and
	the alphaH NMR chemical shift data revealed no significant structural
	differences between the beta-(1-40) and the beta-(1-42). The NMR-derived,
	three-dimensional structure of the beta-(1-42) consists of an extended
	chain (Asp1-Gly9), two alpha-helices (Tyr10-Val24 and Lys28-Ala42),
	and a looped region (Gly25-Ser26-Asn27). The most stable alpha-helical
	regions reside at Gln15-Val24 and Lys28-Val36. The majority of the
	amide (NH) temperature coefficients were less than 5, indicative
	of predominately strong NH backbone bonding. The lack of a persistent
	region with consistently low NH coefficients, together with the rapid
	NH exchange rates in deuterated water and spin-labeled studies, suggests
	that the beta-peptide is located at the lipid-water interface of
	the micelle and does not become inbedded within the hydrophobic interior.
	This result has implications for the circulation of membrane-bound
	beta-peptide in biological fluids, and may also facilitate the design
	of amyloid inhibitors to prevent an alpha-helix-->beta-sheet conversion
	in Alzheimer's disease.},
  institution = {Department of Chemistry, Case Western Reserve University, Cleveland,
	OH, 44106, USA.},
  keywords = {Alzheimer Disease; Amino Acid Sequence; Amyloid beta-Protein; Humans;
	Hydrogen; Micelles; Molecular Sequence Data; Peptide Fragments; Peptides;
	Protein Structure, Secondary; Solutions; Spin Labels; Temperature},
  owner = {singh},
  pii = {S0022283698923488},
  pmid = {9878442},
  timestamp = {2008.07.24}
}

@ARTICLE{Simmerling2002,
  author = {Carlos Simmerling and Bentley Strockbine and Adrian E Roitberg},
  title = {All-atom structure prediction and folding simulations of a stable
	protein.},
  journal = {J. Am. Chem. Soc.},
  year = {2002},
  volume = {124},
  pages = {11258--11259},
  number = {38},
  month = {Sep},
  file = {MDS\\force field\\simmerling.pdf:MDS\\force field\\simmerling.pdf:PDF},
  keywords = {Amino Acid Sequence; Computer Simulation; Models, Chemical; Models,
	Molecular; Molecular Sequence Data; Nuclear Magnetic Resonance, Biomolecular;
	Oligopeptides; Protein Folding; Thermodynamics},
  owner = {Gurpreet},
  pii = {ja0273851},
  pmid = {12236726},
  timestamp = {2007.04.05 02:09:52}
}

@INPROCEEDINGS{Singh:07a,
  author = {Singh, G. and Brovchenko, I. and Oleinikova, A and Winter, R.},
  title = {{Aggregation of Fragments of the Islet Amyloid Polypeptide as a Phase
	Transition: A Cluster Analysis}},
  booktitle = {{From Computational Biophysics to Systems Biology (CBSB07)}, Vol.
	36,},
  year = {2007},
  series = {John von Neumann Institute for Computing, Julich, NIC Series},
  pages = {275-278},
  owner = {Brov},
  timestamp = {2008.04.24}
}

@ARTICLE{Sipe1992,
  author = {J. D. Sipe},
  title = {Amyloidosis.},
  journal = {Annu. Rev. Biochem.},
  year = {1992},
  volume = {61},
  pages = {947--975},
  doi = {10.1146/annurev.bi.61.070192.004503},
  file = {aggregations\\review\\ann rev biochem amyloidosis.pdf:aggregations\\review\\ann
	rev biochem amyloidosis.pdf:PDF},
  keywords = {Amyloid; Amyloidosis; Animals; Humans; Protein Precursors; Protein
	Processing, Post-Translational},
  myid = {1},
  owner = {gurpreet},
  pmid = {1497327},
  timestamp = {2006.12.09 12:00:00}
}

@ARTICLE{Sipe2000,
  author = {J. D. Sipe and A. S. Cohen},
  title = {Review: history of the amyloid fibril.},
  journal = {J. Struct. Biol.},
  year = {2000},
  volume = {130},
  pages = {88--98},
  number = {2-3},
  month = {Jun},
  abstract = {Rudolph Virchow, in 1854, introduced and popularized the term amyloid
	to denote a macroscopic tissue abnormality that exhibited a positive
	iodine staining reaction. Subsequent light microscopic studies with
	polarizing optics demonstrated the inherent birefringence of amyloid
	deposits, a property that increased intensely after staining with
	Congo red dye. In 1959, electron microscopic examination of ultrathin
	sections of amyloidotic tissues revealed the presence of fibrils,
	indeterminate in length and, invariably, 80 to 100 A in width. Using
	the criteria of Congophilia and fibrillar morphology, 20 or more
	biochemically distinct forms of amyloid have been identified throughout
	the animal kingdom; each is specifically associated with a unique
	clinical syndrome. Fibrils, also 80 to 100 A in width, have been
	isolated from tissue homogenates using differential sedimentation
	or solubility. X-ray diffraction analysis revealed the fibrils to
	be ordered in the beta pleated sheet conformation, with the direction
	of the polypeptide backbone perpendicular to the fibril axis (cross
	beta structure). Because of the similar dimensions and tinctorial
	properties of the fibrils extracted from amyloid-laden tissues and
	amyloid fibrils in tissue sections, they have been assumed to be
	identical. However, the spatial relationship of proteoglycans and
	amyloid P component (AP), common to all forms of amyloid, to the
	putative protein only fibrils in tissues, has been unclear. Recently,
	it has been suggested that, in situ, amyloid fibrils are composed
	of proteoglycans and AP as well as amyloid proteins and thus resemble
	connective tissue microfibrils. Chemical and physical definition
	of the fibrils in tissues will be needed to relate the in vitro properties
	of amyloid protein fibrils to the pathogenesis of amyloid fibril
	formation in vivo.},
  doi = {10.1006/jsbi.2000.4221},
  keywords = {Amyloid; Amyloidosis; Animals; History, 20th Century; Humans; Protein
	Structure, Secondary; Serum Amyloid A Protein},
  owner = {Gurpreet},
  pii = {S1047-8477(00)94221-7},
  pmid = {10940217},
  timestamp = {2007.11.06 04:47:11}
}

@ARTICLE{Smeller2002,
  author = {L. Smeller},
  title = {Pressure-temperature phase diagrams of biomolecules.},
  journal = {Biochim. Biophys. Acta},
  year = {2002},
  volume = {1595},
  pages = {11--29},
  number = {1-2},
  month = {Mar},
  abstract = {The pressure-temperature phase diagram of various biomolecules is
	reviewed. Special attention is focused on the elliptic phase diagram
	of proteins. The phenomenological thermodynamic theory describing
	this diagram explains the heat, cold and pressure denaturations in
	a unified picture. The limitations and possible developments of this
	theory are discussed as well. It is pointed out that a more complex
	diagram can be obtained when the intermolecular interactions are
	also taken into account. In this case metastable states appear on
	the pressure-temperature (p-T) diagram due to intermolecular interactions.
	Pressure-temperature phase diagrams of other biopolymers are also
	discussed. While the p-T diagrams of helix-coil transition of nucleic
	acids and of gel-liquid crystal transition of lipid bilayers are
	non-elliptical, those of gelatinization of starch and of phase separation
	of some synthetic polymers show an elliptic profile, similar to that
	of proteins. Finally, the p-T diagram of bacterial inactivation is
	shown to be elliptic. From the point of view of basic science, this
	fact shows that the key factor of inactivation should be the protein
	type, and from the viewpoint of practical applications, it serves
	as the theoretical basis of pressure treatment of biosystems.},
  institution = {Department of Biophysics and Radiation Biology, Semmelweis University,
	Budapest, Hungary. smeller@puskin.sote.hu},
  keywords = {Animals; Humans; Polymers; Pressure; Protein Denaturation; Proteins;
	Temperature; Water},
  owner = {singh},
  pii = {S0167483801003326},
  pmid = {11983384},
  timestamp = {2008.07.03}
}

@ARTICLE{Smith:93a,
  author = {David E. Smith and A. D. J. Haymet},
  title = {Free energy, entropy, and internal energy of hydrophobic interactions:
	Computer simulations},
  journal = {J. Chem. Phys.},
  year = {1993},
  volume = {98},
  pages = {6445-6454},
  number = {8},
  owner = {singh},
  publisher = {AIP},
  timestamp = {2008.05.01}
}

@ARTICLE{Sparr2004,
  author = {Emma Sparr and Maarten F M Engel and Dmitri V Sakharov and Mariette
	Sprong and Jet Jacobs and Ben de Kruijff and Jo W M H�ppener and
	J. Antoinette Killian},
  title = {Islet amyloid polypeptide-induced membrane leakage involves uptake
	of lipids by forming amyloid fibers.},
  journal = {FEBS Lett.},
  year = {2004},
  volume = {577},
  pages = {117--120},
  number = {1-2},
  month = {Nov},
  abstract = {Fibril formation of islet amyloid polypeptide (IAPP) is associated
	with cell death of the insulin-producing pancreatic beta-cells in
	patients with Type 2 Diabetes Mellitus. A likely cause for the cytotoxicity
	of human IAPP is that it destroys the barrier properties of the cell
	membrane. Here, we show by fluorescence confocal microscopy on lipid
	vesicles that the process of hIAPP amyloid formation is accompanied
	by a loss of barrier function, whereby lipids are extracted from
	the membrane and taken up in the forming amyloid deposits. No membrane
	interaction was observed when preformed fibrils were used. It is
	proposed that lipid uptake from the cell membrane is responsible
	for amyloid-induced membrane damage and that this represents a general
	mechanism underlying the cytotoxicity of amyloid forming proteins.},
  doi = {10.1016/j.febslet.2004.09.075},
  institution = {Department Biochemistry of Membranes, Centre of Biomembranes and
	Lipid Enzymology, Institute of Biomembranes, Utrecht University,
	Padualaan 8, NL-3584 CH Utrecht, The Netherlands. emma.sparr@fkem1.lu.se},
  keywords = {Amino Acid Sequence; Amyloid; Animals; Cell Membrane; Fluorescent
	Dyes; Lipid Metabolism; Microscopy, Confocal; Molecular Sequence
	Data; Rats},
  owner = {singh},
  pii = {S0014579304012074},
  pmid = {15527771},
  timestamp = {2008.09.14}
}

@BOOK{Stauffer:92a,
  title = {Introduction to Percolation Theory},
  publisher = {Taylor and Francis, London},
  year = {1992},
  author = {D. Stauffer and A. Aharony},
  owner = {Brov},
  timestamp = {2007.09.19}
}

@BOOK{Stryer1996,
  title = {Biochemistry},
  publisher = {W. H. Freeman and Company},
  year = {1996},
  author = {Stryer, L.},
  edition = {4th},
  owner = {Gurpreet},
  timestamp = {2007.03.22 02:17:54}
}

@ARTICLE{Sugita1999,
  author = {Sugita, Y.
	
	Okamoto, Y.},
  title = {Replica-exchange molecular dynamics method for protein folding},
  journal = {Chem. Phys. Lett.},
  year = {1999},
  volume = {314},
  pages = {141-151},
  owner = {Gurpreet},
  timestamp = {2007.11.08 02:21:45}
}

@ARTICLE{Sunde1997,
  author = {M. Sunde and L. C. Serpell and M. Bartlam and P. E. Fraser and M.
	B. Pepys and C. C. Blake},
  title = {Common core structure of amyloid fibrils by synchrotron X-ray diffraction.},
  journal = {J. Mol. Biol.},
  year = {1997},
  volume = {273},
  pages = {729--739},
  number = {3},
  month = {Oct},
  abstract = {Tissue deposition of normally soluble proteins as insoluble amyloid
	fibrils is associated with serious diseases including the systemic
	amyloidoses, maturity onset diabetes, Alzheimer's disease and transmissible
	spongiform encephalopathy. Although the precursor proteins in different
	diseases do not share sequence homology or related native structure,
	the morphology and properties of all amyloid fibrils are remarkably
	similar. Using intense synchrotron sources we observed that six different
	ex vivo amyloid fibrils and two synthetic fibril preparations all
	gave similar high-resolution X-ray fibre diffraction patterns, consistent
	with a helical array of beta-sheets parallel to the fibre long axis,
	with the strands perpendicular to this axis. This confirms that amyloid
	fibrils comprise a structural superfamily and share a common protofilament
	substructure, irrespective of the nature of their precursor proteins.},
  doi = {10.1006/jmbi.1997.1348},
  file = {aggregations\\review\\j mol biol common core structure of amyloid
	fibrils by synchroton xray diffraction.pdf:aggregations\\review\\j
	mol biol common core structure of amyloid fibrils by synchroton xray
	diffraction.pdf:PDF},
  keywords = {Amyloid; Humans; Models, Molecular; Protein Conformation; X-Ray Diffraction},
  myid = {2},
  owner = {Gurpreet},
  pii = {S0022-2836(97)91348-6},
  pmid = {9356260},
  timestamp = {2006.12.15}
}

@ARTICLE{Swendsen:86a,
  author = {R. Swendsen and J. Wang},
  title = {Replica Monte Carlo of spin-glasses},
  journal = {Phys. Rev. Lett.},
  year = {1986},
  volume = {57},
  pages = {2607-2609},
  owner = {brov},
  timestamp = {2008.10.17}
}

@BOOK{Tanford2001,
  title = {Nature's Robots: A History of Proteins.},
  publisher = {Oxford University Press, USA},
  year = {2001},
  author = {C. Tanford and J. A. Reynolds},
  owner = {singh},
  timestamp = {2008.10.15}
}

@ARTICLE{Tenidis2000,
  author = {K. Tenidis and M. Waldner and J. Bernhagen and W. Fischle and M.
	Bergmann and M. Weber and M. L. Merkle and W. Voelter and H. Brunner
	and A. Kapurniotu},
  title = {Identification of a penta- and hexapeptide of islet amyloid polypeptide
	(IAPP) with amyloidogenic and cytotoxic properties.},
  journal = {J. Mol. Biol.},
  year = {2000},
  volume = {295},
  pages = {1055--1071},
  number = {4},
  month = {Jan},
  abstract = {Pancreatic amyloid is found in more than 95 \% of type II diabetes
	patients. Pancreatic amyloid is formed by the aggregation of islet
	amyloid polypeptide (hIAPP or amylin), which is a 37-residue peptide.
	Because pancreatic amyloid is cytotoxic, it is believed that its
	formation is directly associated with the development of the disease.
	We recently showed that hIAPP amyloid formation follows the nucleation-dependent
	polymerization mechanism and proceeds via a conformational transition
	of soluble hIAPP into aggregated beta-sheets. Here, we report that
	the penta- and hexapeptide sequences, hIAPP(23-27) (FGAIL) and hIAPP(22-27)
	(NFGAIL) of hIAPP are sufficient for the formation of beta-sheet-containing
	amyloid fibrils. Although these two peptides differ by only one amino
	acid residue, they aggregate into completely different fibrillar
	assemblies. hIAPP(23-27) (FGAIL) fibrils self-assemble laterally
	into unusually broad ribbons, whereas hIAPP(22-27) (NFGAIL) fibrils
	coil around each other in a typical amyloid fibril morphology. hIAPP(20-27)
	(SNNFGAIL) also aggregates into beta-sheet-containing fibrils, whereas
	no amyloidogenicity is found for hIAPP(24-27) (GAIL), indicating
	that hIAPP(23-27) (FGAIL) is the shortest fibrillogenic sequence
	of hIAPP. Insoluble amyloid formation by the partial hIAPP sequences
	followed kinetics that were consistent with a nucleation-dependent
	polymerization mechanism. hIAPP(22-27) (NFGAIL), hIAPP(20-27) (SNNFGAIL),
	and also the known fibrillogenic sequence, hIAPP(20-29) (SNNFGAILSS)
	exhibited significantly lower kinetic and thermodynamic solubilities
	than the pentapeptide hIAPP(23-27) (FGAIL). Fibrils formed by all
	short peptide sequences and also by hIAPP(20-29) were cytotoxic towards
	the pancreatic cell line RIN5fm, whereas no cytotoxicity was observed
	for the soluble form of the peptides, a notion that is consistent
	with hIAPP cytotoxicity. Our results suggest that a penta- and hexapeptide
	sequence of an appropriate amino acid composition can be sufficient
	for beta-sheet and amyloid fibril formation and cytotoxicity and
	may assist in the rational design of inhibitors of pancreatic amyloid
	formation or other amyloidosis-related diseases.},
  doi = {10.1006/jmbi.1999.3422},
  file = {aggregations\\IAPP\\j mol bio identification of penta and hexapeptide
	of IAAP with amyloidogenic and cytotoxic properties.pdf:aggregations\\IAPP\\j
	mol bio identification of penta and hexapeptide of IAAP with amyloidogenic
	and cytotoxic properties.pdf:PDF},
  keywords = {Amino Acid Sequence; Amyloid; Animals; Cell Line; Cell Survival; Humans;
	Insulinoma; Kinetics; Microscopy, Atomic Force; Microscopy, Electron;
	Molecular Sequence Data; Pancreatic Neoplasms; Peptide Fragments;
	Protein Conformation; Protein Structure, Secondary; Rats; Research
	Support, Non-U.S. Gov't; Spectroscopy, Fourier Transform Infrared;
	Tumor Cells, Cultured},
  myid = {5},
  owner = {Gurpreet},
  pii = {S0022-2836(99)93422-8},
  pmid = {10656810},
  timestamp = {2006.12.18 12:00:02}
}

@ARTICLE{Thirumalai2003,
  author = {D. Thirumalai and D. K. Klimov and R. I. Dima},
  title = {Emerging ideas on the molecular basis of protein and peptide aggregation.},
  journal = {Curr. Opin. Struct. Biol.},
  year = {2003},
  volume = {13},
  pages = {146--159},
  number = {2},
  month = {Apr},
  abstract = {Several neurodegenerative diseases are associated with the unfolding
	and subsequent fibrillization of proteins. Although neither the assembly
	mechanism nor the atomic structures of the amyloid fibrils are known,
	recent experimental and computational studies suggest that a few
	general principles that govern protein aggregation may exist. Analysis
	of the results of several important recent studies has led to a set
	of tentative ideas concerning the oligomerization of proteins and
	peptides. General rules have been described that may be useful in
	predicting regions of known proteins (prions and transthyretin) that
	are susceptible to fluctuations, which give rise to structures that
	can aggregate by the nucleation-growth mechanism. Despite large variations
	in the sequence-dependent polymerization kinetics of several structurally
	unrelated proteins, there appear to be only a few plausible scenarios
	for protein and peptide aggregation.},
  file = {aggregations\\review\\curr opin str biol emerging ideas on molecular
	basis of protein and peptide aggregation.pdf:aggregations\\review\\curr
	opin str biol emerging ideas on molecular basis of protein and peptide
	aggregation.pdf:PDF},
  keywords = {Alzheimer Disease; Amyloid beta-Protein; Binding Sites; Dimerization;
	Humans; Macromolecular Substances; Models, Molecular; Neurodegenerative
	Diseases; Peptides; PrPC Proteins; Prealbumin; Prions; Protein Binding;
	Protein Conformation; Protein Folding; Protein Structure, Secondary;
	Protein Structure, Tertiary; Proteins; Structure-Activity Relationship},
  myid = {14},
  owner = {Gurpreet},
  pii = {S0959440X03000320},
  pmid = {12727507},
  timestamp = {2007.02.19 12:45:37}
}

@ARTICLE{Tienari:97a,
  author = {Tienari, P. J. and Ida, N. and Ikonen, E. and Simons, M. and Weidemann,
	A. and Multhaup, G. and Masters, C. L. and Dotti, C. G. and Beyreuther,
	K.},
  title = {Intracellular and secreted {A}lzheimer beta-amyloid species are generated
	by distinct mechanisms in cultured hippocampal neurons},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {1997},
  volume = {94},
  pages = {4125-4130},
  owner = {Brov},
  timestamp = {2007.09.19}
}

@INBOOK{Timasheff:81a,
  pages = {315-335},
  title = {Protein-Protein Interactions, The self-assembly of long rodlike structures,
	{Frieden C. and Nichol L. W.}, eds.},
  publisher = {John Wiley and Sons, New York},
  year = {1981},
  editor = {Frieden, C. and Nichol, L. W., eds.},
  author = {Timasheff, S.},
  owner = {singh},
  timestamp = {2008.05.01}
}

@ARTICLE{Tsai2005,
  author = {Hui-Hsu Gavin Tsai and Meital Reches and Chung-Jung Tsai and Kannan
	Gunasekaran and Ehud Gazit and Ruth Nussinov},
  title = {Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering
	molecular dynamics simulation: significant role of Asn ladder.},
  journal = {Proc. Natl. Acad. Sci. U. S. A.},
  year = {2005},
  volume = {102},
  pages = {8174--8179},
  number = {23},
  month = {Jun},
  abstract = {Recent evidence suggests that amyloidogenic oligomers may be the toxic
	species in cell cultures. Thus, it is crucial to understand their
	structure and oligomerization mechanism in atomistic detail. By employing
	tens of fast central processing units and an advanced phase-space
	sampling algorithm, parallel-tempering molecular dynamics, we have
	explored the energy landscape of amyloidogenic peptide oligomerization
	in explicit water. A pentapeptide, DFNKF, derived from human calcitonin
	and its mutant, DFAKF, was simulated with a total simulation time
	of approximately 500 ns. The detailed oligomerization process of
	a DFNKF parallel beta-sheet formation at 300 K has been characterized.
	The assembly of a parallel beta-sheet from the amorphous state mainly
	occurs via a "bottleneck" channel where the interstrand Asn-Asn stacking
	is the major interaction. The interactions of Asn-Asn stacking include
	both backbone and side-chain hydrogen bonds. The Asn-Asn interactions
	work like "glue" by sticking the DFNKF strands together and assist
	the "on-pathway" oligomerization. The Asn-Asn stacking observed here
	is similar to the Asn ladder commonly found in globular beta-helix
	proteins. A control run shows that when Asn is mutated to Ala, the
	stability and population of the DFAKF parallel beta-sheet is decreased.
	Furthermore, our in vitro mutagenesis experiments show that the ability
	of DFAKF peptides to form amyloid fibrils is significantly reduced,
	in agreement with the simulations. Knowledge of the energy landscape
	of oligomerization may provide hints for rational drug design, preventing
	amyloid-associated diseases.},
  doi = {10.1073/pnas.0408653102},
  institution = {ational Cancer Institute, Building 469, Room 145, Frederick, MD 21702,
	USA. tsaih@ncifcrf.gov},
  keywords = {Algorithms; Amino Acid Sequence; Amyloid; Asparagine; Computer Simulation;
	Humans; Hydrogen Bonding; Mutation; Peptides; Protein Structure,
	Quaternary; Protein Structure, Secondary; Temperature; Thermodynamics},
  owner = {singh},
  pii = {0408653102},
  pmid = {15923262},
  timestamp = {2008.10.17}
}

@ARTICLE{Wallqvist:91a,
  author = {Wallqvist, Anders},
  title = {Molecular dynamics study of a hydrophobic aggregate in an aqueous
	solution of methane},
  journal = {J. Phys. Chem.},
  year = {1991},
  volume = {95},
  pages = {8921-8927},
  number = {22},
  issn = {0022-3654},
  owner = {singh},
  timestamp = {2008.05.01}
}

@ARTICLE{Westermark1990,
  author = {P. Westermark and U. Engstr�m and K. H. Johnson and G. T. Westermark
	and C. Betsholtz},
  title = {Islet amyloid polypeptide: pinpointing amino acid residues linked
	to amyloid fibril formation.},
  journal = {Proc. Natl. Acad. Sci. U. S. A.},
  year = {1990},
  volume = {87},
  pages = {5036--5040},
  number = {13},
  month = {Jul},
  abstract = {Islet amyloid polypeptide (IAPP), a putative polypeptide hormone,
	is a product of pancreatic beta-cells and the major constituent of
	the amyloid deposits seen mainly in islets of type 2 diabetic humans
	and diabetic cats. The connection between IAPP amyloid formation
	and diabetes is unknown, but a limited segment of the IAPP molecule,
	positions 20-29, seems responsible for the aggregation to fibrils.
	Differences in the amino acid sequence of this region probably determine
	whether or not islet amyloid can develop in a particular species.
	Amyloid fibril formation can be mimicked in vitro with the aid of
	synthetic peptides. With this technique we show that peptides corresponding
	to IAPP positions 20-29 of human and cat, species that develop IAPP-derived
	islet amyloid, form amyloid-like fibrils in vitro. The corresponding
	IAPP segment from three rodent species that do not develop IAPP-derived
	amyloid did not give rise to fibrils. Substitution of the human IAPP-(20-29)
	decapeptide with one or two amino acid residues from species without
	islet amyloid generally reduced the capacity to form fibrils. We
	conclude that the sequence Ala-Ile-Leu-Ser-Ser, corresponding to
	positions 25-29 of human IAPP, is strongly amyloidogenic and that
	a proline-for-serine substitution in position 28, as in several rodents,
	almost completely inhibits formation of amyloid fibrils.},
  keywords = {Amino Acid Sequence; Amyloid; Amyloidosis; Animals; Cats; Cricetinae;
	Diabetes Mellitus, Type 2; Humans; Islets of Langerhans; Microscopy,
	Electron; Molecular Sequence Data; Mutation; Protein Precursors;
	Rats; Sequence Homology, Nucleic Acid; Species Specificity},
  owner = {Gurpreet},
  pmid = {2195544},
  timestamp = {2008.02.17 03:37:48}
}

@ARTICLE{Williamson2007,
  author = {Jessica A Williamson and Andrew D Miranker},
  title = {Direct detection of transient alpha-helical states in islet amyloid
	polypeptide.},
  journal = {Protein Sci.},
  year = {2007},
  volume = {16},
  pages = {110--117},
  number = {1},
  month = {Jan},
  abstract = {The protein islet amyloid polypeptide (IAPP) is a glucose metabolism
	associated hormone cosecreted with insulin by the beta-cells of the
	pancreas. In humans with type 2 diabetes, IAPP deposits as amyloid
	fibers. The assembly intermediates of this process are associated
	with beta-cell death. Here, we examine the rat IAPP sequence variant
	under physiological solution conditions. Rat IAPP is mechanistically
	informative for fibrillogenesis, as it samples intermediate-like
	states but does not progress to form amyloid. A central challenge
	was the development of a bacterial expression system to generate
	isotopically labeled IAPP without terminal tags, but which does include
	a eukaryotic post-translational modification. While optical spectroscopy
	shows IAPP to be natively unfolded, NMR chemical shifts of backbone
	and beta-carbon resonances reveal the sampling of alpha-helical states
	across a continuous stretch comprising approximately 40\% of the
	protein. In addition, the manifestation of nonrandom coil chemical
	shifts is confirmed by the relative insensitivity of the amide proton
	chemical shifts to alterations in temperature. Intriguingly, the
	residues displaying helical propensity are conserved with the human
	sequence, suggesting a functional role for this conformational bias.
	The inability of rat IAPP to self assemble can be ascribed, in part,
	to several slowly exchanging conformations evident as multiple chemical
	shift assignments in the immediate vicinity of three proline residues
	residing outside of this helical region.},
  doi = {10.1110/ps.062486907},
  institution = {Department of Molecular Biophysics and Biochemistry, Yale University,
	New Haven, CT 06520-8114, USA.},
  keywords = {Amino Acid Sequence; Amyloid; Animals; Humans; Molecular Sequence
	Data; Nuclear Magnetic Resonance, Biomolecular; Protein Structure,
	Secondary; Rats; Recombinant Proteins; Sequence Homology, Amino Acid;
	Thermodynamics},
  owner = {singh},
  pii = {ps.062486907},
  pmid = {17123962},
  timestamp = {2008.07.24}
}

@ARTICLE{Wilson:99a,
  author = {Wilson, C. A. and Doms, R. and Lee, V. M.-Y.},
  title = {Intracellular {APP} processing and {A}beta production in {A}lzheimer
	disease},
  journal = {J. Neuropathol. Exp. Neurol.},
  year = {1999},
  volume = {58},
  pages = {787-794},
  owner = {Brov},
  timestamp = {2007.09.19}
}

@ARTICLE{Winnik:90a,
  author = {Winnik, Francoise M.},
  title = {Fluorescence studies of aqueous solutions of \mbox{poly(N-isopropylacrylamide)}
	below and above their \mbox{LCST}},
  journal = {Macromolecules},
  year = {1990},
  volume = {23},
  pages = {233-242},
  number = {1},
  issn = {0024-9297},
  owner = {Brov},
  timestamp = {2008.04.10}
}

@ARTICLE{Wu2005,
  author = {Chun Wu and Hongxing Lei and Yong Duan},
  title = {Elongation of ordered peptide aggregate of an amyloidogenic hexapeptide
	NFGAIL observed in molecular dynamics simulations with explicit solvent.},
  journal = {J. Am. Chem. Soc.},
  year = {2005},
  volume = {127},
  pages = {13530--13537},
  number = {39},
  month = {Oct},
  abstract = {The mechanisms by which amyloidogenic peptides and proteins form soluble
	toxic oligomers remain elusive. We have studied the formation of
	partially ordered tetramers and well-ordered octamers of an amyloidogenic
	hexapeptide NFGAIL (residues 22-27 of the human islet amyloid polypeptide)
	in our previous work. Continuing the effort, we here probe the beta-sheet
	elongation process by a combined total of 2.0 micros molecular dynamics
	simulations with explicit solvent. In a set of 10 simulations with
	the peptides restrained to the extended conformation, we observed
	that the main growth mode was elongation along the beta-sheet hydrogen
	bonds through primarily a two-stage process. Driven by hydrophobic
	forces, the peptides initially attached to the surface of the ordered
	oligomer, moved quickly to the beta-sheet edges, and formed stable
	beta-sheet hydrogen bonds. Addition of peptides to the existing oligomer
	notably improved the order of the peptide aggregate in which labile
	outer layer beta-sheets were stabilized, which provides good templates
	for further elongation. These simulations suggested that elongation
	along the beta-sheet hydrogen bonds occurs at the intermediate stage
	when low-weight oligomers start to form. We did not observe significant
	preference toward either parallel or antiparallel beta-sheets at
	the elongation stage for this peptide. In another set of 10 unrestrained
	simulations, the dominant growth mode was disordered aggregation.
	Taken together, these results offered a glimpse at the molecular
	events leading to the formation of ordered and disordered low-weight
	oligomers.},
  doi = {10.1021/ja050767x},
  institution = {Department of Chemistry and Biochemistry, University of Delaware,
	Newark, Delaware 19716, USA.},
  keywords = {Amyloid; Models, Molecular; Oligopeptides; Solvents},
  owner = {singh},
  pmid = {16190716},
  timestamp = {2008.10.16}
}

@ARTICLE{Wu:05a,
  author = {Wu, C. and Lei, H. and Duan, Y.},
  title = {Elongation of Ordered Peptide Aggregate of an Amyloidogenic Hexapeptide
	NFGAIL Observed in Molecular Dynamics Simulations with Explicit Solvent},
  journal = {J. Amer. Chem. Soc.},
  year = {2005},
  volume = {127},
  pages = {13530-13537},
  number = {39},
  affiliation = {Contribution from the Department of Chemistry and Biochemistry, University
	of Delaware, Newark, Delaware 19716, and UC Davis Genome Center and
	Department of Applied Science, University of California, Davis, California
	95616},
  owner = {singh},
  timestamp = {2008.05.01}
}

@ARTICLE{Wu2004,
  author = {Chun Wu and Hongxing Lei and Yong Duan},
  title = {Formation of partially ordered oligomers of amyloidogenic hexapeptide
	(NFGAIL) in aqueous solution observed in molecular dynamics simulations.},
  journal = {Biophys. J.},
  year = {2004},
  volume = {87},
  pages = {3000--3009},
  number = {5},
  month = {Nov},
  abstract = {A combined total of more than 600.0 ns molecular dynamics simulations
	with explicit solvent have been carried on systems containing either
	four peptides or a single peptide to investigate the early-stage
	aggregation process of an amyloidogenic hexapeptide, NFGAIL (residues
	22-27 of the human islet amyloid polypeptide). Direct observation
	of the aggregation process was made possible by placing four peptides
	in a box of water with an effective concentration of 158 mg/ml to
	enhance the rate of aggregation. Partially ordered oligomers containing
	multistrand beta-sheets were observed which could be the precursory
	structures leading to the amyloid-forming embryonic nuclei. Comparative
	simulations on a single peptide suggested that the combined effect
	of higher peptide concentration and periodic boundary condition promoted
	compact monomers and the short-range interpeptide interactions favored
	the beta-extended conformation. Of particular interest was the persistent
	fluctuation of the size of the aggregates throughout the simulations,
	suggesting that dissociation of peptides from the disordered aggregates
	was an obligatory step toward the formation of ordered oligomers.
	Although 95\% of peptides formed oligomers and 44\% were in beta-extended
	conformations, only 16\% of peptides formed multistrand beta-sheets.
	The disordered aggregates were mainly stabilized by hydrophobic interactions
	while cross-strand main-chain hydrogen bonds manifested the ordered
	oligomers. The transition to the beta-extended conformation was mildly
	cooperative due to short-range interactions between beta-extended
	peptides. Taken together, we propose that the role of hydrophobic
	interaction in the early stage of aggregation is to promote disordered
	aggregates and disfavor the formation of ordered nuclei and dissociation
	of the disordered oligomers could be the rate-limiting step at the
	initiation stage.},
  doi = {10.1529/biophysj.104.047076},
  keywords = {Amyloid; Binding Sites; Dimerization; Models, Chemical; Models, Molecular;
	Motion; Multiprotein Complexes; Oligopeptides; Protein Binding; Protein
	Conformation; Protein Structure, Secondary; Solutions; Water},
  owner = {Gurpreet},
  pii = {biophysj.104.047076},
  pmid = {15326028},
  timestamp = {2007.11.08 02:21:45}
}

@ARTICLE{Yeh1999,
  author = {ln-Chul Yeh and Max L. Berkowitz},
  title = {Ewald summation for systems with slab geometry},
  journal = {J. Chem. Phys.},
  year = {1999},
  volume = {111},
  pages = {3155},
  file = {MDS General\\J Chem phys 1995 A smooth particle mesh ewald method.pdf:MDS
	General\\J Chem phys 1995 A smooth particle mesh ewald method.pdf:PDF},
  myid = {12},
  owner = {Gurpreet},
  timestamp = {2006.12.20 04:27:24}
}

@ARTICLE{Zangi:06a,
  author = {Zangi, R. and Berne, B.J.},
  title = {Aggregation and Dispersion of Small Hydrophobic Particles in Aqueous
	Electrolyte Solutions},
  journal = {J. Phys. Chem. B},
  year = {2006},
  volume = {110},
  pages = {22736-22741},
  number = {45},
  affiliation = {Department of Chemistry and Center for Biomolecular Simulations, Columbia
	University, 3000 Broadway, New York, New York 10027},
  issn = {1520-6106},
  owner = {singh},
  timestamp = {2008.05.01}
}

@ARTICLE{Zanuy2003,
  author = {David Zanuy and Buyong Ma and Ruth Nussinov},
  title = {Short peptide amyloid organization: stabilities and conformations
	of the islet amyloid peptide NFGAIL.},
  journal = {Biophys. J.},
  year = {2003},
  volume = {84},
  pages = {1884--1894},
  number = {3},
  month = {Mar},
  abstract = {Experimentally, short peptides have been shown to form amyloids similar
	to those of their parent proteins. Consequently, they present useful
	systems for studies of amyloid conformation. Here we simulate extensively
	the NFGAIL peptide, derived from the human islet amyloid polypeptide
	(residues 22-27). We simulate different possible strand/sheet organizations,
	from dimers to nonamers. Our simulations indicate that the most stable
	conformation is an antiparallel strand orientation within the sheets
	and parallel between sheets. Consistent with the alanine mutagenesis,
	we find that the driving force is the hydrophobic effect. Whereas
	the NFGAIL forms stable oligomers, the NAGAIL oligomer is unstable,
	and disintegrates very quickly after the beginning of the simulation.
	The simulations further identify a minimal seed size. Combined with
	our previous simulations of the prion-derived AGAAAAGA peptide, AAAAAAAA,
	and the Alzheimer Abeta fragments 16-22, 24-36, 16-35, and 10-35,
	and the solid-state NMR data for Abeta fragments 16-22, 10-35, and
	1-40, some insight into the length and the sequence matching effects
	may be obtained.},
  institution = {Laboratory of Experimental and Computational Biology, National Cancer
	Institute-Frederick Cancer Research and Development Center, Frederick,
	Maryland 21702, USA.},
  keywords = {Amino Acid Sequence; Amyloid; Computer Simulation; Drug Stability;
	Humans; Hydrophobicity; Macromolecular Substances; Models, Molecular;
	Molecular Sequence Data; Oligopeptides; Protein Conformation; Protein
	Folding; Protein Structure, Secondary; Protein Subunits; Reproducibility
	of Results; Sensitivity and Specificity},
  owner = {singh},
  pmid = {12609890},
  timestamp = {2008.10.16}
}

@ARTICLE{Zanuy2003a,
  author = {David Zanuy and Ruth Nussinov},
  title = {The sequence dependence of fiber organization. A comparative molecular
	dynamics study of the islet amyloid polypeptide segments 22-27 and
	22-29.},
  journal = {J. Mol. Biol.},
  year = {2003},
  volume = {329},
  pages = {565--584},
  number = {3},
  month = {Jun},
  abstract = {Amyloid fiber formation and the possible polymorphism of molecular
	arrangements depend on the polypeptide length and composition. Here,
	we seek the chemical clues underlying these processes. Our starting
	point is based on the experimental observation that some short peptide
	segments are able to develop fibers that are very similar to those
	of their original parent proteins. We focus our study on the NFGAILSS
	peptide, derived from the human islet amyloid polypeptide (residues
	22-29). This peptide turned out to be a perfect example, illustrating
	the fact that the amyloid microscopic organization is highly complex,
	rather than simply involving hydrogen bond formation. Furthermore,
	obtaining a reliable molecular model has allowed us to analyze the
	differences between the amyloid structure we have obtained for this
	peptide and that obtained for the previously studied, two residues
	shorter, segment (residues 22-27, NFGAIL). This comparative study
	yields some clues about chemical events that govern the aggregation
	of proteins into oriented fibers, such as molecular packing between
	sheets and the degree of interaction specificity. We characterize
	the important role played by the hydrophobic and aromatic residues
	in the inter-sheet association and present new approaches toward
	the understanding of the nature of events that are likely to take
	place during fibril formation. These include analysis of interaction
	patterns derived from specific sheet-associated packing.},
  institution = {Laboratory of Experimental and Computational Biology, NCI-Frederick,
	Bldg 469, Rm 151, Frederick, MD 21702, USA.},
  keywords = {Amino Acid Sequence; Amyloid; Humans; Hydrogen Bonding; Hydrophobicity;
	Models, Molecular; Peptide Fragments; Protein Binding; Protein Structure,
	Quaternary; Structure-Activity Relationship; Thermodynamics},
  owner = {singh},
  pii = {S0022283603004911},
  pmid = {12767835},
  timestamp = {2008.10.16}
}

@ARTICLE{Zheng:06a,
  author = {Zheng, Jie and Ma, Buyong and Tsai, Chung-Jung and Nussinov, Ruth},
  title = {{Structural Stability and Dynamics of an Amyloid-Forming Peptide
	GNNQQNY from the Yeast Prion Sup-35}},
  journal = {Biophys. J.},
  year = {2006},
  volume = {91},
  pages = {824-833},
  number = {3},
  abstract = {A seven amino acid yeast prion sup-35 fragment (GNNQQNY) forms amyloid
	fibrils. The availability of its detailed atomic oligomeric structure
	makes it a good model for studying the early stage of aggregation.
	Here we perform long all-atom explicit solvent molecular simulations
	of various sizes and arrangements of oligomer seeds of the wild-type
	and its mutants to study its stability and dynamics. Previous studies
	have suggested that the early stage rate-limiting step of oligomer
	formation occurs in high-order oligomers. Our simulations show that
	with the increase in the number of strands even from a dimer to a
	trimer, oligomer stability increases dramatically. This suggests
	that the minimal nucleus seed for GNNQQNY fibril formation could
	be small and is likely three or four peptides, in agreement with
	experiment, and that higher-order oligomers do not dissociate quickly
	since they have small diffusion coefficients and thus slow kinetics.
	Further, for the hydrophilic polar GNNQQNY, there are no hydrogen
	bonds and no hydrophobic interactions between adjacent {beta}-sheets.
	Simulations suggest that within the sheet, the driving forces to
	associate and stabilize are interstrand backbone-backbone and side
	chain-side chain hydrogen bonds, whereas between the sheets, shape-complementary
	by the dry polar steric zipper via the side chains of Asn-2, Gln-4,
	and Asn-6 holds the sheets together, as proposed in an earlier study.
	Since the polar side chains of Asn-2, Gln-4, and Asn-6 act as a hook
	to bind two neighboring sheets together, these geometric restraints
	reduce the conformational search for the correct side chain packing
	to a two-dimensional problem of intersheet side chain interactions.
	Mutant simulations show that substitution of Asn-2, Gln-4, or Asn-6
	by Ala would disrupt this steric zipper, leading to unstable oligomers.},
  eprint = {http://www.biophysj.org/cgi/reprint/91/3/824.pdf},
  owner = {singh},
  timestamp = {2008.05.01}
}

@BOOK{Malmsten2003,
  title = {Biopolymers at interfaces},
  publisher = {Marcel Dekker, Inc},
  year = {2003},
  editor = {Martin Malmsten},
  owner = {singh},
  timestamp = {2008.07.03}
}

@BOOK{Oren2001,
  title = {Computational Biochemistry and Biophysics},
  publisher = {CRC},
  year = {2001},
  editor = {Oren M. Becker, Benoit Roux, Masakatsu Watanabe},
  file = {General\\bks\\Biophysics\\Computational Biochemistry and Biophysics
	- Oren M. Becker.pdf:General\\bks\\Biophysics\\Computational Biochemistry
	and Biophysics - Oren M. Becker.pdf:PDF},
  owner = {Gurpreet},
  timestamp = {2007.04.01 03:09:58}
}

@ARTICLE{2005a,
  title = {So much more to know.},
  journal = {Science},
  year = {2005},
  volume = {309},
  pages = {78--102},
  number = {5731},
  month = {Jul},
  keywords = {Knowledge; Science},
  owner = {singh},
  pii = {309/5731/78b},
  pmid = {15994524},
  timestamp = {2008.07.21}
}

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