Orientation restraints in molecular dynamics simulations using time and ensemble averaging

Journal of Magnetic Resonance

Volumn 164, Issue 1, 2003, Pages 19-27

  Hess, B ^a   Scheek, R M ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

Chemical shift anisotropies; Molecular dynamics; Residual dipolar couplings; Restraints; Time and ensemble averaging

Indexed keywords

ANISOTROPY; MOLECULAR DYNAMICS; MOLECULAR ORIENTATION; TENSORS; VECTORS;

RESIDUAL DIPOLAR COUPLINGS;

PROTEINS;

BACTERIAL PROTEIN; PHOSPHOCARRIER PROTEIN HPR; PHOSPHOENOLPYRUVATE SUGAR PHOSPHOTRANSFERASE;

ALGORITHM; ANISOTROPY; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; EVALUATION; MECHANICAL STRESS; METHODOLOGY; MOTION; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; STATISTICAL MODEL;

ALGORITHMS; ANISOTROPY; BACTERIAL PROTEINS; COMPUTER SIMULATION; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MODELS, STATISTICAL; MOTION; PHOSPHOENOLPYRUVATE SUGAR PHOSPHOTRANSFERASE SYSTEM; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; STRESS, MECHANICAL;

EID: 0041467255     PISSN: 10907807     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1090-7807(03)00178-2     Document Type: Article

References (13)

1. Bayer P., Varani L., Varani G. Refinement of the structure of protein-RNA complexes by residual dipolar coupling analysis. J. Biomol. NMR. 14:1999;149-155.
2. Clore G.M., Garrett D.S. r -factor, free r, and complete cross-validation for dipolar coupling refinement of NMR structures J. Am. Chem. Soc. 121:1999;9008-9012.
3. Schwalbe H., Grimshaw S.B., Spencer A., Buck M., Boyd J., Dobson C.M., Redfield C., Smith L.J. A refined structure of hen lysozyme determined using residual dipolar coupling data. Protein Sci. 10:2001;677-688.
4. Colombo G., Roccatano D., Mark A.E. Folding and stability of the three-stranded β-sheet peptide betanova: insights from molecular dynamics. Proteins. 46:2002;380-392.
5. Tolman J.R., Al-Hashimi H.M., Kay L.E., Prestegard J.H. Structural and dynamic analysis of residual dipolar coupling data for proteins. J. Am. Chem. Soc. 123:2001;1416-1424.
6. Peti W., Meiler J., Brüschwieler R., Griesinger C. Model-free analysis of protein backbone motion from residual dipolar couplings. J. Am. Chem. Soc. 124:2002;5822-5833.
7. Tolman J.R. A novel approach to the retrieval of structural and dynamic information from residual dipolar couplings using several oriented media in biomolecular NMR spectroscopy. J. Am. Chem. Soc. 124:2002;12020-12030.
8. Feenstra A.K., Hess B., Berendsen H.J.C. Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. J. Comput. Chem. 20(8):1999;786-798.
9. Lindahl E., Hess B., van der Spoel D. Gromacs 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Mod. 7:2001;306-317.
10. van Lune F., Manning L., Dijkstra K., Berendsen H.J.C., Scheek R.M. Order-parameter tensor description of HPr in a medium of oriented bicelles. J. Biomol. NMR. 23:2002;169-179.
11. van Gunsteren W.F., Billeter S.R., Eising A.A., Hünenberger P.H., Krüger P., Mark A.E., Scott W.R.P., Tironi I.G. Biomolecular Simulation: GROMOS96 Manual and User Guide. 1996;BIOMOS b.v. Zürich, Groningen.
12. Jia Z., Quail J.W., Waygood E.B., Delbaere L.T.J. The 2.0. Å-resolution structure of Escherichia coli histidine-containing phosphocarrier protein HPr. A redetermination J. Biol. Chem. 268:1993;22490-22501.
13. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., Hermans J. Interaction models for water in relation to protein hydration. Pullman B. Intermolecular Forces. 1981;331-342 Reidel, Dordrecht.