Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation.
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 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.
Trbovic
Nikola
N
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.
Kim
Byungchan
B
Friesner
Richard A
RA
Palmer
Arthur G
AG
D001426:Bacterial Proteins / Q000737:chemistry; D019295:Computational Biology; D003198:Computer Simulation; D006860:Hydrogen Bonding; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
D001426:Bacterial Proteins; C034284:IgG Fc-binding protein, Streptococcus