Combining NMR relaxation with chemical shift perturbation data to drive protein-protein docking.

Journal of Biomolecular NMR
Aalt D J van DijkAlexandre M J J Bonvin

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.

References

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Citations

Jun 7, 2007·Journal of the American Chemical Society·Yaroslav Ryabov, David Fushman
May 1, 2010·Nature Protocols·Sjoerd J de VriesAlexandre M J J Bonvin
Mar 23, 2010·Molecular & Cellular Proteomics : MCP·Ezgi KaracaAlexandre M J J Bonvin
Dec 18, 2012·Molecular & Cellular Proteomics : MCP·Edward S C Shih, Ming-Jing Hwang
Jul 18, 2012·BMC Structural Biology·Dina Schneidman-DuhovnyAndrej Sali
Feb 10, 2012·Journal of Biomedicine & Biotechnology·Olivier FisetteSébastien Morin
Jun 14, 2014·Progress in Nuclear Magnetic Resonance Spectroscopy·Christoph GöblMichael Sattler
Apr 25, 2013·Progress in Nuclear Magnetic Resonance Spectroscopy·Lu-Yun Lian
Apr 1, 2008·Bioorganic & Medicinal Chemistry·Guoyun BaiMichael Shapiro
Sep 7, 2007·Proteins·Sjoerd J de VriesAlexandre M J J Bonvin
Sep 28, 2015·Journal of Molecular Biology·G C P van ZundertA M J J Bonvin
Apr 7, 2016·Acta Crystallographica. Section D, Structural Biology·Galina A StepanyukJames R Williamson
Nov 16, 2010·Journal of Structural Biology·Tobias MadlMichael Sattler
Aug 29, 2012·Molecular Biology International·Jaroslav KubrychtPavel Souček
Aug 28, 2021·International Journal of Molecular Sciences·Aljaž Gaber, Miha Pavšič

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