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 Ca 2+ -bound calbindin D 9k and ubiquitin that the methyl group dynamics, as assessed by deuterium relaxation measurements of 13 CH 2 D 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.
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Showalter et al. (2007) studied this question.