Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation.

ABSTRACT: Molecular dynamics (MD) simulations and nuclear magnetic resonance spin-relaxation measurements provide detailed insights into ps-ns structural dynamics of proteins. An analysis of discrepancies between the two methods is presented for the B3 immunoglobulin-binding domain of streptococcal protein G. MD simulations using three MD force fields (OPLS-AA, AMBER ff99SB, and AMBER ff03) overestimate the flexibility of backbone N--H vectors at the borders of secondary structure and in loops when compared with experimentally determined backbone amide generalized order parameters (Hall and Fushman, J Am Chem Soc 2006; 12:7855-7870). Comparison with a previous study of residual dipolar coupling constants (Bouvignies et al., Proc Natl Acad Sci USA 2005;102:13885-13890) indicates that slower timescale

SUBMITTER: Trbovic N 

PROVIDER: S-EPMC2750878 | biostudies-literature | 2008 May

REPOSITORIES: biostudies-literature