Determination of the rotational diffusion tensor of macromolecules in solution from nmr relaxation data with a combination of exact and approximate methods--application to the determination of interdomain orientation in multidomain proteins

Journal of Magnetic Resonance
R GhoseD Cowburn

Abstract

In this paper we present a method for determining the rotational diffusion tensor from NMR relaxation data using a combination of approximate and exact methods. The approximate method, which is computationally less intensive, computes values of the principal components of the diffusion tensor and estimates the Euler angles, which relate the principal axis frame of the diffusion tensor to the molecular frame. The approximate values of the principal components are then used as starting points for an exact calculation by a downhill simplex search for the principal components of the tensor over a grid of the space of Euler angles relating the diffusion tensor frame to the molecular frame. The search space of Euler angles is restricted using the tensor orientations calculated using the approximate method. The utility of this approach is demonstrated using both simulated and experimental relaxation data. A quality factor that determines the extent of the agreement between the measured and predicted relaxation data is provided. This approach is then used to estimate the relative orientation of SH3 and SH2 domains in the SH(32) dual-domain construct of Abelson kinase complexed with a consolidated ligand.

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Citations

Jun 7, 2007·Journal of the American Chemical Society·Yaroslav Ryabov, David Fushman
Mar 31, 2006·Proceedings of the National Academy of Sciences of the United States of America·David AchilaDavid L Huffman
Feb 16, 2016·Structure·Carlos A CastañedaDavid Fushman
Jul 17, 2010·Progress in Nuclear Magnetic Resonance Spectroscopy·Matthew P NicholasRanajeet Ghose
Nov 17, 2009·Journal of Molecular Biology·Andrea PiserchioRanajeet Ghose
Jul 24, 2008·Journal of Molecular Biology·Ertan EryilmazRanajeet Ghose
Apr 18, 2008·Journal of Magnetic Resonance·Fabien FerrageRanajeet Ghose
Sep 27, 2005·Journal of Molecular Biology·Valerie NogueraJean-Marc Lancelin
Jun 14, 2014·Progress in Nuclear Magnetic Resonance Spectroscopy·Christoph GöblMichael Sattler
Oct 1, 2015·Physical Chemistry Chemical Physics : PCCP·Carlos A CastañedaDavid Fushman
Nov 13, 2018·Physical Chemistry Chemical Physics : PCCP·Antonino Polimeno, Mirco Zerbetto
Jul 24, 2013·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Pieter E S SmithLucio Frydman
Aug 15, 2006·The Journal of Biological Chemistry·Aswin NatarajanJustine M Hill
Oct 31, 2013·Journal of Biomolecular NMR·Konstantin BerlinDavid Fushman
Jul 19, 2017·Proceedings of the National Academy of Sciences of the United States of America·Andrea PiserchioRanajeet Ghose
Jun 2, 2018·Methods : a Companion to Methods in Enzymology·Sebastien Alphonse, Ranajeet Ghose
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Jun 19, 2002·Accounts of Chemical Research·David A Case
May 21, 2013·Progress in Biophysics and Molecular Biology·Yury E Shapiro
May 25, 2021·Physical Chemistry Chemical Physics : PCCP·Christoph WiedemannFrank Bordusa
Dec 4, 2002·Journal of Molecular Biology·Ranjani VaradanDavid Fushman
Jul 27, 2021·Journal of Biomolecular Structure & Dynamics·Gouri S JasKrzysztof Kuczera
Jan 3, 2018·Journal of Chemical Theory and Computation·Po-Chia ChenJanosch Hennig
Feb 1, 2018·The Journal of Physical Chemistry. B·Max LinkeGerhard Hummer
Dec 7, 2007·The Journal of Physical Chemistry. B·Vance Wong, David A Case

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