Starting-structure dependence of nanosecond timescale intersubstate transitions and reproducibility of MD-derived order parameters.

ABSTRACT: Factors affecting the accuracy of molecular dynamics (MD) simulations are investigated by comparing generalized order parameters for backbone NH vectors of the B3 immunoglobulin-binding domain of streptococcal protein G (GB3) derived from simulations with values obtained from NMR spin relaxation (Yao L, Grishaev A, Cornilescu G, Bax A, J Am Chem Soc 2010;132:4295-4309.). Choices for many parameters of the simulations, such as buffer volume, water model, or salt concentration, have only minor influences on the resulting order parameters. In contrast, seemingly minor conformational differences in starting structures, such as orientations of sidechain hydroxyl groups, resulting from applying different protonation algorithms to the same structure, have major effects on backbone dynamics. Some,

SUBMITTER: Zeiske T 

PROVIDER: S-EPMC3557728 | biostudies-literature | 2013 Mar

REPOSITORIES: biostudies-literature