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Obtaining tertiary protein structures by the ab-initio interpretation of small angle X-ray scattering data

Lookup NU author(s): Dr Owen Davies

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Abstract

Small angle X-ray scattering (SAXS) is an important tool for investigating the structure of proteins in solution. We present a novel ab-initio method representing polypeptide chains as discrete curves used to derive a meaningful three-dimensional model from \textbf{only} the primary sequence and SAXS data. High resolution structures were used to generate probability density functions for each common secondary structural element found in proteins, which are used to place realistic restraints on the model curve's geometry. This is coupled with a novel explicit hydration shell model in order derive physically meaningful 3D models by optimizing against experimental SAXS data. The efficacy of this model is verified on an established benchmark protein set, then it is used to predict the Lysozyme structure using only its primary sequence and SAXS data. The method is used to generate a biologically plausible model of the coiled-coil component of the human synaptonemal complex central element protein.

Publication metadata

Author(s): Prior C, Davies OR, Bruce D, Pohl E

Publication type: Article

Publication status: Published

Journal: Journal of Chemical Theory and Computation

Year: 2020

Volume: 16

Issue: 3

Pages: 1985-2001

Print publication date: 10/03/2020

Online publication date: 05/02/2020

Acceptance date: 05/02/2020

ISSN (print): 1549-9618

ISSN (electronic): 1549-9626

Publisher: American Chemical Society

URL: https://doi.org/10.1021/acs.jctc.9b01010

DOI: 10.1021/acs.jctc.9b01010

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