Model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins.

Meiler J, Prompers JJ, Peti W, Griesinger C, Br├╝schweiler R
J Am Chem Soc. 2001 123 (25): 6098-107

PMID: 11414844 · DOI:10.1021/ja010002z

The effects of internal motions on residual dipolar NMR couplings of proteins partially aligned in a liquid-crystalline environment are analyzed using a 10 ns molecular dynamics (MD) computer simulation of ubiquitin. For a set of alignment tensors with different orientations and rhombicities, MD-averaged dipolar couplings are determined and subsequently interpreted for different scenarios in terms of effective alignment tensors, average orientations of dipolar vectors, and intramolecular reorientational vector distributions. Analytical relationships are derived that reflect similarities and differences between motional scaling of dipolar couplings and scaling of dipolar relaxation data (NMR order parameters). Application of the self-consistent procedure presented here to dipolar coupling measurements of biomolecules aligned in different liquid-crystalline media should allow one to extract in a "model-free" way average orientations of dipolar vectors and specific aspects of their motions.

MeSH Terms (7)

Computer Simulation Electrochemistry Kinetics Nuclear Magnetic Resonance, Biomolecular Protein Conformation Proteins Ubiquitins

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