Combining NMR Relaxation with Chemical Shift Perturbation Data to Drive Protein–protein Docking
- 1 April 2006
- journal article
- research article
- Published by Springer Science and Business Media LLC in Journal of Biomolecular NMR
- Vol. 34 (4), 237-244
- https://doi.org/10.1007/s10858-006-0024-8
Abstract
The modeling of biomolecular complexes by computational docking using the known structures of their constituents is developing rapidly to become a powerful tool in structural biology. It is especially useful in combination with even limited experimental information describing the interface. Here we demonstrate for the first time the use of diffusion anisotropy in combination with chemical shift perturbation data to drive protein–protein docking. For validation purposes we make use of simulated diffusion anisotropy data. Inclusion of this information, which can be derived from NMR relaxation rates and reports on the orientation of the components of a complex with respect to the rotational diffusion tensor, substantially improves the docking results.Keywords
This publication has 25 references indexed in Scilit:
- Weak alignment NMR: a hawk-eyed view of biomolecular structureCurrent Opinion in Structural Biology, 2005
- Filtering and selection of structural models: Combining docking and NMRProteins-Structure Function and Bioinformatics, 2003
- Docking of Protein−Protein Complexes on the Basis of Highly Ambiguous Intermolecular Distance Restraints Derived from1HN/15N Chemical Shift Mapping and Backbone15N−1H Residual Dipolar Couplings Using Conjoined Rigid Body/Torsion Angle DynamicsJournal of the American Chemical Society, 2003
- HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical InformationJournal of the American Chemical Society, 2003
- Combined Use of NMR Relaxation Measurements and Hydrodynamic Calculations To Study Protein Association. Evidence for Tetramers of Low Molecular Weight Protein Tyrosine Phosphatase in SolutionJournal of the American Chemical Society, 2002
- HYDRONMR: Prediction of NMR Relaxation of Globular Proteins from Atomic-Level Structures and Hydrodynamic CalculationsJournal of Magnetic Resonance, 2000
- Crystallography & NMR System: A New Software Suite for Macromolecular Structure DeterminationActa Crystallographica Section D-Biological Crystallography, 1998
- Long-Range Motional Restrictions in a Multidomain Zinc-Finger Protein from Anisotropic TumblingScience, 1995
- Mapping of the binding interfaces of the proteins of the bacterial phosphotransferase system, HPr and IIAglcBiochemistry, 1993
- Backbone dynamics of calmodulin studied by nitrogen-15 relaxation using inverse detected two-dimensional NMR spectroscopy: the central helix is flexibleBiochemistry, 1992