Paper Citing NAMD - Abstract
Koukos, Panagiotis I.; Glykos, Nicholas M.
Folding Molecular Dynamics Simulations Accurately Predict the Effect of Mutations on the Stability and Structure of a Vammin-Derived Peptide
JOURNAL OF PHYSICAL CHEMISTRY B, 118:10076-10084, AUG 28 2014
Folding molecular dynamics simulations amounting to a grand total of 4 mu s 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 beta-hairpin with a non-glycine beta-bulge, in excellent agreement with the peptide's known NMR structure. Additionally, the simulations also predict the presence of a very small beta-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.
