Analysis of self-associating proteins by singular value decomposition of solution scattering data.

Biophysical Journal
Tim E WilliamsonAlan M Friedman

Abstract

We describe a method by which a single experiment can reveal both association model (pathway and constants) and low-resolution structures of a self-associating system. Small-angle scattering data are collected from solutions at a range of concentrations. These scattering data curves are mass-weighted linear combinations of the scattering from each oligomer. Singular value decomposition of the data yields a set of basis vectors from which the scattering curve for each oligomer is reconstructed using coefficients that depend on the association model. A search identifies the association pathway and constants that provide the best agreement between reconstructed and observed data. Using simulated data with realistic noise, our method finds the correct pathway and association constants. Depending on the simulation parameters, reconstructed curves for each oligomer differ from the ideal by 0.05-0.99% in median absolute relative deviation. The reconstructed scattering curves are fundamental to further analysis, including interatomic distance distribution calculation and low-resolution ab initio shape reconstruction of each oligomer in solution. This method can be applied to x-ray or neutron scattering data from small angles to moderat...Continue Reading

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Citations

May 2, 2013·Acta Crystallographica. Section D, Biological Crystallography·Ezgi Karaca, Alexandre M J J Bonvin
Apr 20, 2010·Journal of Bioinformatics and Computational Biology·Paritosh A KavathekarDevin J Balkcom
Jul 18, 2012·BMC Structural Biology·Dina Schneidman-DuhovnyAndrej Sali
Nov 12, 2015·Computational and Structural Biotechnology Journal·Xiaojun XuIvaylo Ivanov
Mar 5, 2014·The FEBS Journal·Anne T Tuukkanen, Dmitri I Svergun
Dec 18, 2014·Protein Science : a Publication of the Protein Society·Barnali N Chaudhuri
Sep 20, 2008·Current Opinion in Structural Biology·H Tsuruta, T C Irving
Aug 26, 2015·Journal of Applied Crystallography·Andrew W MalabyDavid G Lambright
Aug 31, 2017·Journal of Chemical Information and Modeling·Pernille SønderbyGünther H J Peters
Nov 3, 2020·The Journal of Physical Chemistry. B·Maelenn ChevreuilGuillaume Tresset

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