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

Scott A. Showalter; Eric Johnson; Mark Rance; Rafael Brüschweiler

doi:10.1021/ja075976r

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

Scott A. Showalter, Eric Johnson, Mark Rance, Rafael Brüschweiler

Research output: Contribution to journal › Article › peer-review

62 Scopus citations

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 D_9k 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	https://doi.org/10.1021/ja075976r
State	Published - Nov 21 2007

All Science Journal Classification (ASJC) codes

Catalysis
Chemistry(all)
Biochemistry
Colloid and Surface Chemistry

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10.1021/ja075976r

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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.",

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

Abstract

All Science Journal Classification (ASJC) codes

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