title: Folding molecular dynamics simulations accurately predict the effect of mutations on the stability and structure of a vammin-derived peptide.
abstract: Folding molecular dynamics simulations amounting to a grand total of 4 μs of simulation time were performed on two peptides (with native and mutated sequences) derived from loop 3 of the vammin protein and the results compared with the experimentally known peptide stabilities and structures. The simulations faithfully and accurately reproduce the major experimental findings and show that (a) the native peptide is mostly disordered in solution, (b) the mutant peptide has a well-defined and stable structure, and (c) the structure of the mutant is an irregular β-hairpin with a non-glycine β-bulge, in excellent agreement with the peptide's known NMR structure. Additionally, the simulations also predict the presence of a very small β-hairpin-like population for the native peptide but surprisingly indicate that this population is structurally more similar to the structure of the native peptide as observed in the vammin protein than to the NMR structure of the isolated mutant peptide. We conclude that, at least for the given system, force field, and simulation protocol, folding molecular dynamics simulations appear to be successful in reproducing the experimentally accessible physical reality to a satisfactory level of detail and accuracy.
authors.affiliation: Department of Molecular Biology and Genetics, Democritus University of Thrace , University campus, 68100 Alexandroupolis, Greece.
authors.forename: Panagiotis I
authors.initials: PI
authors.lastname: Koukos
authors.forename: Nicholas M
authors.initials: NM
authors.lastname: Glykos
mesh_terms: D003198:Computer Simulation; D006860:Hydrogen Bonding; D008962:Models, Theoretical; D056004:Molecular Dynamics Simulation; D009154:Mutation / Q000235:genetics*; D010446:Peptide Fragments / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013816:Thermodynamics; D042461:Vascular Endothelial Growth Factor A / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D014757:Viper Venoms / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D010446:Peptide Fragments; D042461:Vascular Endothelial Growth Factor A; D014757:Viper Venoms; C519402:vammin protein, Vipera ammodytes ammodytes