2WYK image
Entry Detail
PDB ID:
2WYK
Title:
SiaP in complex with Neu5Gc
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2009-11-16
Release Date:
2011-01-26
Method Details:
Experimental Method:
Resolution:
1.50 Å
R-Value Free:
0.17
R-Value Work:
0.13
R-Value Observed:
0.13
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:SIALIC ACID-BINDING PERIPLASMIC PROTEIN SIAP
Chain IDs:A
Chain Length:308
Number of Molecules:1
Biological Source:HAEMOPHILUS INFLUENZAE
Primary Citation
Water networks can determine the affinity of ligand binding to proteins.
J.Am.Chem.Soc. ? ? ? (2019)
PMID: 31518131 DOI: 10.1021/jacs.9b06275

Abstact

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.

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