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Obtaining Tertiary Protein Structures by the ab Initio Interpretation of Small Angle X-ray Scattering Data

Prior, Christopher; Davies, Owen R.; Bruce, Daniel; Pohl, Ehmke

Obtaining Tertiary Protein Structures by the ab Initio Interpretation of Small Angle X-ray Scattering Data Thumbnail


Authors

Owen R. Davies

Daniel Bruce



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 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 to derive physically meaningful three-dimensional models by optimizing against experimental SAXS data. The efficacy of this model is verified on an established benchmark protein set, and 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.

Citation

Prior, C., Davies, O. R., Bruce, D., & Pohl, E. (2020). Obtaining Tertiary Protein Structures by the ab Initio Interpretation of Small Angle X-ray Scattering Data. Journal of Chemical Theory and Computation, 16(3), 1985-2001. https://doi.org/10.1021/acs.jctc.9b01010

Journal Article Type Article
Online Publication Date Feb 5, 2020
Publication Date Mar 10, 2020
Deposit Date Mar 12, 2020
Publicly Available Date Feb 5, 2021
Journal Journal of Chemical Theory and Computation
Print ISSN 1549-9618
Electronic ISSN 1549-9626
Publisher American Chemical Society
Peer Reviewed Peer Reviewed
Volume 16
Issue 3
Pages 1985-2001
DOI https://doi.org/10.1021/acs.jctc.9b01010

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Copyright Statement
This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of chemical theory and computation copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acs.jctc.9b01010







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