The effect of motional averaging on the calculation of NMR-derived structural properties

Daura, Xavier, Antes, Iris, van Gunsteren, Wilfred F, Thiel, Walter and Mark, Alan E. (1999) The effect of motional averaging on the calculation of NMR-derived structural properties. Proteins: Structure, Function, and Bioinformatics, 36 4: 542-555. doi:10.1002/(SICI)1097-0134(19990901)36:4<542::AID-PROT17>3.0.CO;2-M

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Author Daura, Xavier
Antes, Iris
van Gunsteren, Wilfred F
Thiel, Walter
Mark, Alan E.
Title The effect of motional averaging on the calculation of NMR-derived structural properties
Journal name Proteins: Structure, Function, and Bioinformatics   Check publisher's open access policy
ISSN 0887-3585
Publication date 1999-09-01
Sub-type Article (original research)
DOI 10.1002/(SICI)1097-0134(19990901)36:4<542::AID-PROT17>3.0.CO;2-M
Open Access Status File (Author Post-print)
Volume 36
Issue 4
Start page 542
End page 555
Total pages 14
Place of publication Hoboken, NJ, United States
Publisher John Wiley & Sons
Language eng
Formatted abstract
The effect of motional averaging when relating structural properties inferred from nuclear magnetic resonance (NMR) experiments to molecular dynamics simulations of peptides is considered. In particular, the effect of changing populations of conformations, the extent of sampling, and the sampling frequency on the estimation of nuclear Overhauser effect (NOE) inter-proton distances, vicinal 3J-coupling constants, and chemical shifts are investigated. The analysis is based on 50-ns simulations of a β- heptapeptide in methanol at 298 K, 340 K, 350 K, and 360 K. This peptide undergoes reversible folding and samples a significant proportion of the available conformational space during the simulations, with at 298 K being predominantly folded and at 360 K being predominantly unfolded. The work highlights the fact that when motional averaging is included, NMR data has only limited capacity to distinguish between a single fully folded peptide conformation and various mixtures of folded and unfolded conformations.
Keyword 3J-coupling constant
Chemical shift
Computer simulation
Molecular dynamics
NMR
NOE distance
Peptides
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown
Additional Notes Variant title Proteins : Structure, Function and Genetics

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Chemistry and Molecular Biosciences
 
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Created: Wed, 30 Mar 2011, 11:21:05 EST by Professor Alan Mark on behalf of School of Chemistry & Molecular Biosciences