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Water networks can determine the affinity of ligand binding to proteins

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JournalJournal of the American Chemical Society
DateAccepted/In press - 13 Sep 2019
DateE-pub ahead of print - 13 Sep 2019
DatePublished (current) - 9 Oct 2019
Issue number40
Number of pages9
Pages (from-to)15818-15826
Early online date13/09/19
Original languageEnglish


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.

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