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, 7 ). Comparison with a previous study of residual dipolar coupling constants (Bouvignies et al., 8 ) indicates that slower timescale motions do not account for the discrepancies. Structural analysis reveals that relative imbalance between the description of hydrogen bonding and other terms of modern force fields may be responsible for disagreement. Proteins 2008.