Recent improvements of the protein backbone force-field parameters in AMBER99SB have allowed accurate simulation of backbone dynamics, but the consequences for side-chain dynamics have been unclear. It is demonstrated for Ca2+-bound calbindin D9k and ubiquitin that the methyl group dynamics, as assessed by deuterium relaxation measurements of 13CH2D groups, is well-reproduced across the protein by molecular dynamics (MD) simulation. Direct analysis of simulated spectral density functions and fitted S2 order parameters yield remarkably good agreement. These results provide important benchmarks for amino acid specific improvements of side-chain force fields.
All Science Journal Classification (ASJC) codes
- Colloid and Surface Chemistry