Toward quantitative interpretation of methyl side-chain dynamics from NMR by molecular dynamics simulations

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 D-9k and ubiquitin that the methyl group dynamics, as assessed by deuterium relaxation measurements of (CH2D)-C-13 groups, is well-reproduced across the protein by molecular dynamics (MD) simulation. Direct analysis of simulated spectral density functions and fitted S (2) order parameters yield remarkably good agreement. These results provide important benchmarks for amino acid specific improvements of side-chain force fields.