Open AccessQuantification of the Effects of Ionic Strength, Viscosity, and Hydrophobicity on Protein–Ligand Binding Affinity
Author(s) -
Christos Papaneophytou,
Asterios I. Grigoroudis,
Campbell McInnes,
George Kontopidis
Publication year - 2014
Publication title -
acs medicinal chemistry letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.065
H-Index - 66
ISSN - 1948-5875
DOI - 10.1021/ml500204e
Subject(s) - ionic strength , dissociation constant , ligand (biochemistry) , chemistry , macromolecule , solvent , dissociation (chemistry) , viscosity , protein ligand , organic chemistry , biochemistry , aqueous solution , thermodynamics , receptor , physics
In order to quantify the interactions between molecules of biological interest, the determination of the dissociation constant (K d) is essential. Estimation of the binding affinity in this way is routinely performed in "favorable" conditions for macromolecules. Crucial data for ligand-protein binding elucidation is mainly derived from techniques (e.g., macromolecular crystallography) that require the addition of high concentration of salts and/or other additives. In this study we have evaluated the effect of temperature, ionic strength, viscosity, and hydrophobicity on the K d of three previously characterized protein-ligand systems, based on variation in their binding sites, in order to provide insight into how these often overlooked unconventional circumstances impact binding affinity. Our conclusions are as follows: (1) increasing solvent viscosity in general is detrimental to ligand binding, (2) moderate increases in temperature have marginal effects on the dissociation constant, and (3) the degree of hydrophobicity of the ligand and the binding site determines the extent of the influence of cosolvents and salt concentration on ligand binding affinity.