Water networks can determine the affinity of ligand binding to proteins

John Fintan Darby, Adam Hopkins, Roderick Eliot Hubbard, Shirley M. Roberts, Seishi Shimizu, James A. Brannigan, Johan Turkenburg, Gavin Hugh Thomas, Marcus Fischer

Research output: Contribution to journalArticlepeer-review

Abstract

Solvent organization is a key but underexploited contributor to the thermodynamics of protein–ligand recognition, with implications for ligand discovery, drug resistance and protein engineering. Here, we explore the contribution of solvent to ligand binding in the Haemophilus influenzae virulence protein SiaP. By introducing a single mutation without direct ligand contacts, we observed a >1000-fold change in sialic acid binding affinity. Crystallographic and calorimetric data of wild-type and mutant SiaP showed that this change results from an enthalpically unfavourable perturbation of the solvent network. This disruption is reflected by changes in the normalized atomic displacement parameters of crystallographic water molecules. In SiaP’s enclosed cavity, relative differences in water-network dynamics serve as a simple predictor of changes in the free energy of binding upon changing protein, ligand or both. This suggests that solvent structure is an evolutionary con-straint on protein sequence that contributes to ligand affinity and selectivity.
Original languageEnglish
Pages (from-to)15818-15826
Number of pages9
JournalJournal of the American Chemical Society
Volume141
Issue number40
Early online date13 Sep 2019
DOIs
Publication statusPublished - 9 Oct 2019

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