Prediction of allosteric sites and signalling: insights from benchmarking datasets
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Published version
Author(s)
Wu, Nan
Stromich, Leonie
Yaliraki, Sophia N
Type
Journal Article
Abstract
Allostery is a pervasive mechanism that regulates protein activity through ligand binding at a site different from the orthosteric site. The universality of allosteric regulation complemented by the benefits of highly specific and potentially non-toxic allosteric drugs makes uncovering allosteric sites invaluable. However, there are few computational methods to effectively predict them. Bond-to-bond propensity analysis has successfully predicted allosteric sites in 19 of 20 cases using an energy-weighted atomistic graph. We here extended the analysis onto 432 structures of 146 proteins from two benchmarking datasets for allosteric proteins: ASBench and CASBench. We further introduced two statistical measures to account for the cumulative effect of high-propensity residues and the crucial residues in a given site. The allosteric site is recovered for 127 of 146 proteins (407 of 432 structures) knowing only the orthosteric sites or ligands. The quantitative analysis using a range of statistical measures enables better characterization of potential allosteric sites and mechanisms involved.
Date Issued
2022-01-14
Date Acceptance
2021-11-15
Citation
Patterns, 2022, 3 (1), pp.1-12
ISSN
2666-3899
Publisher
Cell Press
Start Page
1
End Page
12
Journal / Book Title
Patterns
Volume
3
Issue
1
Copyright Statement
© 2021 The Authors. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
License URL
Sponsor
Engineering & Physical Science Research Council (EPSRC)
Identifier
https://www.sciencedirect.com/science/article/pii/S2666389921002828
Grant Number
EP/N014529/1
Publication Status
Published
Date Publish Online
2021-12-09