Abstract
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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 14146-14147 |
| Number of pages | 2 |
| Journal | Journal of the American Chemical Society |
| Volume | 129 |
| Issue number | 46 |
| DOIs | |
| State | Published - Nov 21 2007 |
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All Science Journal Classification (ASJC) codes
- Catalysis
- Chemistry(all)
- Biochemistry
- Colloid and Surface Chemistry
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Toward quantitative interpretation of methyl side-chain dynamics from NMR by molecular dynamics simulations. / Showalter, Scott A.; Johnson, Eric; Rance, Mark; Brüschweiler, Rafael.
In: Journal of the American Chemical Society, Vol. 129, No. 46, 21.11.2007, p. 14146-14147.Research output: Contribution to journal › Article
TY - JOUR
T1 - Toward quantitative interpretation of methyl side-chain dynamics from NMR by molecular dynamics simulations
AU - Showalter, Scott A.
AU - Johnson, Eric
AU - Rance, Mark
AU - Brüschweiler, Rafael
PY - 2007/11/21
Y1 - 2007/11/21
N2 - 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.
AB - 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.
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U2 - 10.1021/ja075976r
DO - 10.1021/ja075976r
M3 - Article
VL - 129
SP - 14146
EP - 14147
JO - Journal of the American Chemical Society
JF - Journal of the American Chemical Society
SN - 0002-7863
IS - 46
ER -