Normal Mode Flexible Fitting of High-Resolution Structures of Biological Molecules Toward SAXS Data.

Bioinformatics and Biology Insights
Christian Gorba, Florence Tama

Abstract

We present a method to reconstruct a three-dimensional protein structure from an atomic pair distribution function derived from the scattering intensity profile from SAXS data by flexibly fitting known x-ray structures. This method uses a linear combination of low-frequency normal modes from an elastic network description of the molecule in an iterative manner to deform the structure to conform optimally to the target pair distribution function derived from SAXS data. For computational efficiency, the protein and water molecules included in the protein first hydration shell are coarse-grained. In this paper, we demonstrate the validity of our coarse-graining approach to study SAXS data. Illustrative results of our flexible fitting studies on simulated SAXS data from five different proteins are presented.

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Citations

Sep 21, 2010·Journal of Structural Biology·Osamu MiyashitaFlorence Tama
May 21, 2015·Biophysical Journal·Robert P Rambo, John A Tainer
May 23, 2015·IUCrJ·Erik MalmerbergPetrus H Zwart
Nov 27, 2018·Frontiers in Molecular Biosciences·Slavica JonicIsabelle Callebaut
Mar 19, 2013·Annual Review of Biophysics·Robert P Rambo, John A Tainer
Feb 18, 2020·Journal of Molecular Biology·Ashutosh SrivastavaFlorence Tama
Jan 7, 2015·Archives of Biochemistry and Biophysics·Swapnil Mahajan, Yves-Henri Sanejouand
Jan 23, 2019·The Journal of Physical Chemistry. B·Elisa Frezza, Richard Lavery
Oct 9, 2012·Journal of Chemical Theory and Computation·G Jeschke
Aug 24, 2021·Frontiers in Molecular Biosciences·Bhaskar DasguptaFlorence Tama
Oct 3, 2021·Journal of Computational Chemistry·Yves-Henri Sanejouand

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Methods Mentioned

BETA
X-ray
Fluorescence
NMR
Intensity Scattering

Software Mentioned

Gnom
NMA
Crysol
Solvate

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