Insights into the structural stability and possible aggregation pathways of the LYQLEN peptides derived from human insulin

Andersen, 1983, Rattle: A “Velocity” Version of the Shake Algorithm for Molecular Dynamics Calculations, J. Comput. Phys., 52, 24, 10.1016/0021-9991(83)90014-1 Arora, 2004, Insulin Amyloid Fibrillation at above 100 {degrees} C: New Insights into Protein Folding under Extreme Temperatures, Protein Sci., 13, 2429, 10.1110/ps.04823504 Bader, 2006, Probing the Mechanism of Amyloidogenesis Through a Tandem Repeat of the PI3-SH3 Domain Suggests a Generic Model for Protein Aggregation and Fibril Formation, J. Mol. Biol., 356, 189, 10.1016/j.jmb.2005.11.034 Bouchard, 2000, Formation of Insulin Amyloid Fibrils Followed by FTIR Simultaneously with CD and Electron Microscopy, Protein Sci., 9, 1960, 10.1110/ps.9.10.1960 Chang, 2009, Molecular Dynamics Simulations to Investigate the Structural Stability and Aggregation Behavior of the GGVVIA Oligomers Derived from Amyloid beta Peptide, J. Biomol. Struct. Dyn., 26, 731, 10.1080/07391102.2009.10507285 Chothia, 1973, Conformation of Twisted Beta-pleated Sheets in Proteins, J. Mol. Biol., 75, 295, 10.1016/0022-2836(73)90022-3 Cohen, 1982, Electron Microscopy of Amyloid, Electron Microsc. Proteins, 3, 165 Colombo, 2007, Peptide Self-assembly at the Nanoscale: a Challenging Target for Computational and Experimental Biotechnology, Trends Biotechnol., 25, 211, 10.1016/j.tibtech.2007.03.004 De Simone, 2008, Insights into Stability and Toxicity of Amyloid-like Oligomers by Replica Exchange Molecular Dynamics Analyses, Biophys. J., 95, 1965, 10.1529/biophysj.108.129213 De Simone, 2008, Structure, Dynamics, and Stability of Assemblies of the Human Prion Fragment SNQNNF, Biochem. Biophys. Res. Commun., 366, 800, 10.1016/j.bbrc.2007.12.047 Devlin, 2006, The Component Polypeptide Chains of Bovine Insulin Nucleate or Inhibit Aggregation of the Parent Protein in a Conformation-dependent Manner, J. Mol. Biol., 360, 497, 10.1016/j.jmb.2006.05.007 Dobson, 1999, Protein Misfolding, Evolution and Disease, Trends Biochem. Sci., 24, 329, 10.1016/S0968-0004(99)01445-0 Dobson, 2003, Protein Folding and Disease: A View from the First Horizon Symposium, Nat. Rev. Drug Discov., 2, 154, 10.1038/nrd1013 Dobson, 2006, Protein Aggregation and Its Consequences for Human Disease, Protein Pept. Lett., 13, 219, 10.2174/092986606775338362 Dunn, 2005, Zinc-ligand Interactions Modulate Assembly and Stability of the Insulin Hexamer–A Review, Biometals, 18, 295, 10.1007/s10534-005-3685-y Esposito, 2006, Molecular Dynamics Analyses of Cross-beta-spine Steric Zipper Models: Beta-sheet Twisting and Aggregation, Proc. Natl. Acad. Sci. U.S.A., 103, 11533, 10.1073/pnas.0602345103 Fandrich, 2007, On the Structural Definition of Amyloid Fibrils and Other Polypeptide Aggregates, Cell Mol. Life Sci., 64, 2066, 10.1007/s00018-007-7110-2 Fandrich, 2001, Amyloid Fibrils from Muscle Myoglobin, Nature, 410, 165, 10.1038/35065514 Gibson, 2006, Inhibition of Insulin Fibrillogenesis with Targeted Peptides, Protein Sci., 15, 1133, 10.1110/ps.051879606 Groenning, 2007, Binding Mode of Thioflavin T in Insulin Amyloid Fibrils, J. Struct. Biol., 159, 483, 10.1016/j.jsb.2007.06.004 Guijarro, 1998, Amyloid Fibril Formation by an SH3 Somain, Proc. Natl. Acad. Sci. U.S.A., 95, 4224, 10.1073/pnas.95.8.4224 Ha, 2005, Template-directed Self-assembly and Growth of Insulin Amyloid Fibrils, Biotechnol. Bioeng., 90, 848, 10.1002/bit.20486 Haspel, 2005, A Comparative Study of Amyloid Fibril Formation by Residues 15–19 of the Human Calcitonin Hormone: A Single Beta-sheet Model with a Small Hydrophobic Core, J. Mol. Biol., 345, 1213, 10.1016/j.jmb.2004.11.002 Hong, 2006, Fibrillation of Human Insulin A and B Chains, Biochemistry, 45, 9342, 10.1021/bi0604936 Hong, 2005, Independent Heterologous Fibrillation of Insulin and Its B-chain Peptide, Biochemistry, 44, 16701, 10.1021/bi051658y Hua, 2004, Mechanism of Insulin Fibrillation: the Structure of Insulin under Amyloidogenic Conditions Resembles a Protein-folding Intermediate, J. Biol. Chem., 279, 21449, 10.1074/jbc.M314141200 Hwang, 1998, Derivation of Class II Force Fields. VI. Carbohydrate Compounds and Anomeric Effects, Biopolymers, 45, 435, 10.1002/(SICI)1097-0282(199805)45:6<435::AID-BIP3>3.0.CO;2-Q Ivanova, 2006, A Systematic Screen of Beta2-microglobulin and Insulin for Amyloid-like Segments, Proc. Natl. Acad. Sci. U.S.A., 103, 4079, 10.1073/pnas.0511298103 Jarrett, 1992, Amyloid Fibril Formation Requires a Chemically Discriminating Nucleation Event: Studies of an Amyloidogenic Sequence from the Bacterial Protein OsmB, Biochemistry, 31, 12345, 10.1021/bi00164a008 Jimenez, 2002, The Protofilament Structure of Insulin Amyloid Fibrils, Proc. Natl. Acad. Sci. U.S.A., 99, 9196, 10.1073/pnas.142459399 Knott, 2004, Energetics of Protein Thermodynamic Cooperativity: Contributions of Local and Nonlocal Interactions, Polymer, 45, 623, 10.1016/j.polymer.2003.10.068 Konno, 2001, Multistep Nucleus Formation and a Separate Subunit Contribution of the Amyloidgenesis of Heat-denatured Monellin, Protein Sci., 10, 2093, 10.1110/ps.20201 Konno, 1999, Amyloid-like Aggregates of a Plant Protein: A Case of a Sweet-tasting Protein, Monellin, FEBS Lett., 454, 122, 10.1016/S0014-5793(99)00789-9 Li, 2008, Formation and Growth of Oligomers: A Monte Carlo Study of an Amyloid Tau Fragment, PLoS Comput. Biol., 4, e1000238, 10.1371/journal.pcbi.1000238 Lin, 2010, “Structural Stability and Aggregation Behavior of the VEALYL Peptide Derived from Human Insulin: A Molecular Dynamics Simulation Study, Biopolymers, 94, 269, 10.1002/bip.21322 Nielsen, 2001, Probing the Mechanism of Insulin Fibril Formation with Insulin Mutants, Biochemistry, 40, 8397, 10.1021/bi0105983 Nielsen, 2001, Effect of Environmental Factors on the Kinetics of Insulin Fibril Formation: Elucidation of the Molecular Mechanism, Biochemistry, 40, 6036, 10.1021/bi002555c Periole, 2009, Factors that Affect the Degree of Twist in Beta-sheet Structures: a Molecular Dynamics Simulation Study of a Cross-beta Filament of the GNNQQNY Peptide, J. Phys. Chem. B, 113, 1728, 10.1021/jp8078259 Rochet, 2000, Amyloid Fibrillogenesis: Themes and Variations, Curr. Opin. Struct. Biol., 10, 60, 10.1016/S0959-440X(99)00049-4 Sawaya, 2007, Atomic Structures of Amyloid Cross-beta Spines Reveal Varied Steric Zippers, Nature, 447, 453, 10.1038/nature05695 Selkoe, 2004, Cell Biology of Protein Misfolding: the Examples of Alzheimer's and Parkinson's Diseases, Nat. Cell Biol., 6, 1054, 10.1038/ncb1104-1054 Serpell, 2000, The Protofilament Substructure of Amyloid Fibrils, J. Mol. Biol., 300, 1033, 10.1006/jmbi.2000.3908 Sunde, 1997, Common Core Structure of Amyloid Fibrils by Synchrotron X-ray Diffraction, J. Mol. Biol., 273, 729, 10.1006/jmbi.1997.1348 Thirumalai, 2003, Emerging Ideas on the Molecular Basis of Protein and Peptide Aggregation, Curr. Opin. Struct. Biol., 13, 146, 10.1016/S0959-440X(03)00032-0 Tsai, 2005, Energy Landscape of Amyloidogenic Peptide Oligomerization by Parallel-tempering Molecular Dynamics Simulation: Significant Role of Asn Ladder, Proc. Natl. Acad. Sci. U.S.A., 102, 8174, 10.1073/pnas.0408653102 Tsai, 2004, The Stability and Dynamics of the Human Calcitonin Amyloid Peptide DFNKF, Biophys. J., 87, 146, 10.1529/biophysj.104.040352 Ventura, 2004, Short Amino Acid Stretches Can Mediate Amyloid Formation in Globular Proteins: the Src Homology 3 (SH3) Case, Proc. Natl. Acad. Sci. U.S.A., 101, 7258, 10.1073/pnas.0308249101 Wang, 2005, Protein Aggregation and Its Inhibition in Biopharmaceutics, Int. J. Pharm., 289, 1, 10.1016/j.ijpharm.2004.11.014 Wang, 2005, A Twisted Four-sheeted Model for an Amyloid Fibril, Structure, 13, 1279, 10.1016/j.str.2005.06.010 Zheng, 2006, Structural Stability and Dynamics of an Amyloid-forming Peptide GNNQQNY from the Yeast Prion Sup-35, Biophys. J., 91, 824, 10.1529/biophysj.106.083246