A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides

Feenstra, K. A., Peter, C., Scheek, R. M., van Gunsteren, W. F. and Mark, A. E. (2002) A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides. Journal of Biomolecular Nmr, 23 3: 181-194.

Author Feenstra, K. A.
Peter, C.
Scheek, R. M.
van Gunsteren, W. F.
Mark, A. E.
Title A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides
Journal name Journal of Biomolecular Nmr   Check publisher's open access policy
Publication date 2002
Sub-type Article
Volume number 23
Issue number 3
ISSN 0925-2738
Start page 181
End page 194
Total pages 14
Place of publication Dordrecht
Publisher Kluwer Academic Publ
Language eng
Abstract Three methods for calculating nuclear magnetic resonance cross-relaxation rates from molecular dynamics simulations of small flexible molecules have been compared in terms of their ability to reproduce relaxation data obtained experimentally and to produce consistent descriptions of the system. The importance of the accuracy of the simulation versus the amount of sampling of phase space has also been assessed by comparing different length simulations performed with different time step schemes. A nine-residue peptide from the protein HPr of index. E. Coli was used as a test system. The work shows that, in this case, single conformations or a limited ensemble of configurations are insufficient to properly describe the behavior of the peptide and that different approaches to incorporate molecular motions lead to significant differences in the cross-relaxation rates calculated. The correlation between the cross-relaxation rates calculated from simulations performed with different time step schemes was high and increased with increasing simulation length indicating that the extent of sampling is more important than the details of the atomic motion.
Keyword Biochemistry & Molecular Biology
Spectroscopy
conformational dynamics
large time-scale dynamics
molecular dynamics
peptide nmr
Nuclear-magnetic-resonance
Molecular-dynamics Simulations
Escherichia-coli
Spectroscopy
Distances
Molscript
Accuracy
Program
Motion
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article
Collections: Excellence in Research Australia (ERA) - Collection
School of Chemistry and Molecular Biosciences
 
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Created: Wed, 19 Sep 2007, 15:34:04 EST