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Butler","year":"2004","journal-title":"Diabetes"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1093\/ilar.47.3.225","article-title":"Islet amyloid polypeptide (IAPP) transgenic rodents as models for type 2 diabetes","volume":"47","author":"AV Matveyenko","year":"2006","journal-title":"ILAR J"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"1279","DOI":"10.2337\/diab.45.9.1279","article-title":"Missense Mutation of Amylin Gene (S20G) in Japanese NIDDM Patients","volume":"45","author":"S Sakagashira","year":"1996","journal-title":"Diabetes"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"2101","DOI":"10.1016\/S0002-9440(10)64848-1","article-title":"S20G Mutant Amylin Exhibits Increased in Vitro Amyloidogenicity and Increased Intracellular Cytotoxicity Compared to Wild-Type Amylin","volume":"157","author":"S Sakagashira","year":"2000","journal-title":"The American Journal of 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Shim","year":"2009","journal-title":"PNAS"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"9900","DOI":"10.1021\/bi800828u","article-title":"Amylin Proprotein Processing Generates Progressively More Amyloidogenic Peptides that Initially Sample the Helical State\u2020","volume":"47","author":"IT Yonemoto","year":"2008","journal-title":"Biochemistry"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"11982","DOI":"10.1074\/jbc.M809085200","article-title":"Dynamic \u03b1-Helix Structure of Micelle-bound Human Amylin","volume":"284","author":"SM Patil","year":"2009","journal-title":"J Biol Chem"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"2337","DOI":"10.1016\/j.bbamem.2011.06.012","article-title":"Structure and membrane orientation of IAPP in its natively amidated form at physiological pH in a membrane environment","volume":"1808","author":"RPR Nanga","year":"2011","journal-title":"Biochimica et Biophysica Acta (BBA)\u2014Biomembranes"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"17205","DOI":"10.1074\/jbc.M801383200","article-title":"Structure of \u03b1-Helical Membrane-bound Human Islet Amyloid Polypeptide and Its Implications for Membrane-mediated Misfolding","volume":"283","author":"M Apostolidou","year":"2008","journal-title":"J Biol Chem"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1016\/j.jmb.2005.12.020","article-title":"Islet Amyloid Polypeptide Inserts into Phospholipid Monolayers as Monomer","volume":"356","author":"MFM Engel","year":"2006","journal-title":"Journal of Molecular Biology"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1016\/j.bpj.2012.01.039","article-title":"How Type II Diabetes-Related Islet Amyloid Polypeptide Damages Lipid Bilayers","volume":"102","author":"C-C Lee","year":"2012","journal-title":"Biophysical Journal"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"E1656","DOI":"10.1152\/ajpendo.00318.2007","article-title":"Induction of Endoplasmic Reticulum Stress-Induced B-Cell Apoptosis and Accumulation of Polyubiquitinated Proteins by Human Islet Amyloid Polypeptide","volume":"293","author":"C-J Huang","year":"2007","journal-title":"Am J Physiol Endocrinol Metab"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1016\/0196-9781(91)90038-Q","article-title":"Syntheses, structures and anorectic effects of human and rat amylin","volume":"12","author":"A Balasubramaniam","year":"1991","journal-title":"Peptides"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"8252","DOI":"10.1021\/ja9010095","article-title":"Three-Dimensional Structure and Orientation of Rat Islet Amyloid Polypeptide Protein in a Membrane Environment by Solution NMR Spectroscopy","volume":"131","author":"RPR Nanga","year":"2009","journal-title":"J Am Chem Soc"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1038\/nchem.1293","article-title":"Two-dimensional infrared spectroscopy reveals the complex behaviour of an amyloid fibril inhibitor","volume":"4","author":"CT Middleton","year":"2012","journal-title":"Nat Chem"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1021\/ct700301q","article-title":"GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation","volume":"4","author":"B Hess","year":"2008","journal-title":"Journal of Chemical Theory and Computation"},{"key":"ref95","first-page":"126","article-title":"Canonical sampling through velocity rescaling RID A-1776-2009 RID C-6971-2008","author":"G Bussi","year":"2007","journal-title":"J Chem Phys"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"7182","DOI":"10.1063\/1.328693","article-title":"Polymorphic transitions in single crystals: A new molecular dynamics method","volume":"52","author":"M Parrinello","year":"1981","journal-title":"Journal of Applied Physics"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1080\/00268978300102851","article-title":"Constant pressure molecular dynamics for molecular systems","volume":"50","author":"S Nos\u00e9","year":"1983","journal-title":"Molecular Physics"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle mesh Ewald: An N\u22c5log(N) method for Ewald sums in large systems","volume":"98","author":"T Darden","year":"1993","journal-title":"J Chem Phys"},{"key":"ref99","doi-asserted-by":"crossref","first-page":"8577","DOI":"10.1063\/1.470117","article-title":"A smooth particle mesh Ewald method","volume":"103","author":"U Essmann","year":"1995","journal-title":"J Chem Phys"},{"key":"ref100","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H","article-title":"LINCS: A linear constraint solver for molecular simulations","volume":"18","author":"B Hess","year":"1997","journal-title":"J Comput Chem"},{"key":"ref101","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1080\/00268978400101201","article-title":"A molecular dynamics method for simulations in the canonical ensemble","volume":"52","author":"S Nos\u00e9","year":"1984","journal-title":"Molecular Physics"},{"key":"ref102","doi-asserted-by":"crossref","first-page":"1695","DOI":"10.1103\/PhysRevA.31.1695","article-title":"Canonical dynamics: Equilibrium phase-space distributions","volume":"31","author":"WG Hoover","year":"1985","journal-title":"Phys Rev A"},{"key":"ref103","doi-asserted-by":"crossref","first-page":"2197","DOI":"10.1021\/ct900202f","article-title":"A Collective Variable for the Efficient Exploration of Protein Beta-Sheet Structures: Application to SH3 and GB1","volume":"5","author":"F Pietrucci","year":"2009","journal-title":"Journal of Chemical Theory and Computation"},{"key":"ref104","doi-asserted-by":"crossref","first-page":"1961","DOI":"10.1016\/j.cpc.2009.05.011","article-title":"PLUMED: A portable plugin for free-energy calculations with molecular dynamics","volume":"180","author":"M Bonomi","year":"2009","journal-title":"Computer Physics Communications"},{"key":"ref105","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1007\/s10858-011-9478-4","article-title":"SHIFTX2: significantly improved protein chemical shift prediction","volume":"50","author":"B Han","year":"2011","journal-title":"J Biomol NMR"},{"key":"ref106","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1110\/ps.062486907","article-title":"Direct detection of transient \u03b1-helical states in islet amyloid polypeptide","volume":"16","author":"JA Williamson","year":"2007","journal-title":"Protein Science"},{"key":"ref107","doi-asserted-by":"crossref","first-page":"7079","DOI":"10.1021\/ja900285z","article-title":"Association of Highly Compact Type II Diabetes Related Islet Amyloid Polypeptide Intermediate Species at Physiological Temperature Revealed by Diffusion NMR Spectroscopy","volume":"131","author":"R Soong","year":"2009","journal-title":"J Am Chem Soc"},{"key":"ref108","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1002\/bip.360221211","article-title":"Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features","volume":"22","author":"W Kabsch","year":"1983","journal-title":"Biopolymers"},{"key":"ref109","doi-asserted-by":"crossref","first-page":"D411","DOI":"10.1093\/nar\/gkq1105","article-title":"A series of PDB related databases for everyday needs","volume":"39","author":"RP Joosten","year":"2011","journal-title":"Nucl Acids Res"},{"key":"ref110","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1007\/s10858-010-9433-9","article-title":"SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network","volume":"48","author":"Y Shen","year":"2010","journal-title":"J Biomol NMR"},{"key":"ref111","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1146\/annurev.bi.47.070178.001343","article-title":"Empirical predictions of protein conformation","volume":"47","author":"PY Chou","year":"1978","journal-title":"Annu Rev Biochem"},{"key":"ref112","doi-asserted-by":"crossref","first-page":"015005","DOI":"10.1088\/1478-3975\/6\/1\/015005","article-title":"A role for helical intermediates in amyloid formation by natively unfolded polypeptides?","volume":"6","author":"A Abedini","year":"2009","journal-title":"Phys Biol"},{"key":"ref113","doi-asserted-by":"crossref","first-page":"13505","DOI":"10.1021\/bi701427q","article-title":"Peptide Conformation and Supramolecular Organization in Amylin Fibrils: Constraints from Solid-State NMR\u2020","volume":"46","author":"S Luca","year":"2007","journal-title":"Biochemistry"},{"key":"ref114","doi-asserted-by":"crossref","first-page":"19285","DOI":"10.1073\/pnas.1314481110","article-title":"Mechanism of IAPP amyloid fibril formation involves an intermediate with a transient \u03b2-sheet","volume":"110","author":"LE Buchanan","year":"2013","journal-title":"PNAS"},{"key":"ref115","doi-asserted-by":"crossref","first-page":"155101","DOI":"10.1063\/1.4798460","article-title":"\u03b1-helix to \u03b2-hairpin transition of human amylin monomer","volume":"138","author":"S Singh","year":"2013","journal-title":"The Journal of Chemical Physics"},{"key":"ref116","doi-asserted-by":"crossref","first-page":"3787","DOI":"10.1021\/ja209931w","article-title":"Structure and Dynamics of an Unfolded Protein Examined by Molecular Dynamics Simulation","volume":"134","author":"K Lindorff-Larsen","year":"2012","journal-title":"J Am Chem Soc"}],"container-title":["PLOS 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