Download MendeleyWater networks can determine the affinity of ligand binding to proteins.
Darby, J.F., Hopkins, A.P., Shimizu, S., Roberts, S.M., Brannigan, J.A., Turkenburg, J.P., Thomas, G.H., Hubbard, R.E., Fischer, M.(2019) J Am Chem Soc
- PubMed: 31518131
- DOI: https://doi.org/10.1021/jacs.9b06275
- Primary Citation of Related Structures:
2V4C, 2WX9, 2WYK, 2WYP, 2XA5, 6H75, 6H76 - PubMed 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 unfavorable 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 constraint on protein sequence that contributes to ligand affinity and selectivity.
Organizational Affiliation:
Demuris Ltd., The Biosphere , Draymans Way, Newcastle Helix , Newcastle upon Tyne NE4 5BX , United Kingdom.
