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 journalArticle

57 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)14146-14147
Number of pages2
JournalJournal of the American Chemical Society
Volume129
Issue number46
DOIs
StatePublished - Nov 21 2007

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Molecular Dynamics Simulation
Molecular dynamics
Nuclear magnetic resonance
Calbindins
Benchmarking
Deuterium
Computer simulation
Ubiquitin
Proteins
Spectral density
Amino Acids
Probability density function
Amino acids

All Science Journal Classification (ASJC) codes

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

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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 journalArticle

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