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Explicit treatment of force contribution from alignment tensor using overdetermined linear equations and its application in NMR structure determination
Article first published online: 2 APR 2007
DOI: 10.1002/jcc.20712
Copyright © 2007 Wiley Periodicals, Inc.
1096-987X/asset/cover.gif?v=1&s=4429aac2462ebd499c13b3d7fe983679c5767778 "Journal of Computational Chemistry")
Additional Information
How to Cite
Rathinavelan, T. and Im, W. (2007), Explicit treatment of force contribution from alignment tensor using overdetermined linear equations and its application in NMR structure determination. Journal of Computational Chemistry, 28: 1858–1864. doi: 10.1002/jcc.20712
Publication History
- Issue published online: 8 JUN 2007
- Article first published online: 2 APR 2007
- Manuscript Accepted: 29 JAN 2007
- Manuscript Revised: 12 JAN 2007
- Manuscript Received: 8 SEP 2006
Keywords:
- residual dipolar coupling (RDC);
- singular value decomposition (SVD);
- replica exchange molecular dynamics (REX-MD);
- root mean square deviation (RMSD);
- β-hairpin;
- protein G
Graphical Abstract
Abstract
Residual dipolar coupling (RDC) provides valuable information about the orientation of each internuclear vector in a macromolecule with respect to the static magnetic field. However, structure determination utilizing RDC still remains challenging without additional restraints such as NOE. In this context, a novel approach has been developed to efficiently extract structural information from RDC by successive application of singular value decomposition (SVD) method in the course of NMR structure determination. Force contribution from the alignment tensor is rigorously formulated in the context of SVD, and assessments have been made to verify its numerical accuracy. The efficacy of this approach is illustrated by showing that RDC restraints alone can restore a distorted β-hairpin to native-like structure using the replica-exchange molecular dynamics simulations. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007