Structural dynamics of protein backbone phi angles: extended molecular dynamics simulations versus experimental (3) J scalar couplings.
(3)J scalar couplings report on the conformational averaging of backbone phi angles in peptides and proteins, and therefore represent a potentially powerful tool for studying the details of both structure and dynamics in solution. We have compared an extensive experimental dataset with J-couplings predicted from unrestrained molecular dynamics simulation using enhanced sampling available from accelerated molecular dynamics or using long timescale trajectories (200 ns). The dynamic fluctuations predicted to be present along the backbone, in agreement with residual dipolar coupling analysis, are compatible with the experimental (3)J scalar couplings providing a slightly better reproduction of these experimental parameters than a high-resolution static structure.
Markwick
Phineus R L
PR
Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel UMR 5075, CNRS/CEA/UJF, 41 Rue Jules Horowitz, Grenoble, France.
Showalter
Scott A
SA
Bouvignies
Guillaume
G
Brüschweiler
Rafael
R
Blackledge
Martin
M
D003198:Computer Simulation; D008956:Models, Chemical; D009419:Nerve Tissue Proteins / Q000737:chemistry; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D025801:Ubiquitin / Q000737:chemistry
C029152:G-substrate; D009419:Nerve Tissue Proteins; D011506:Proteins; D025801:Ubiquitin