Van der Waals Interactions Dominate Ligand-Protein Association in a Protein Binding Site Occluded from Solvent Water

Elizabeth Barratt, Richard J. Bingham, Daniel J. Warner, Charles A. Laughton, Simon E V Phillips, Steve W. Homans

Research output: Contribution to journalArticle

115 Citations (Scopus)

Abstract

In the present study we examine the enthalpy of binding of 2-methoxy-3-isobutylpyrazine (IBMP) to the mouse major urinary protein (MUP), using a combination of isothermal titration calorimetry (ITC), NMR, X-ray crystallography, all-atom molecular dynamics simulations, and site-directed mutagenesis. Global thermodynamics data derived from ITC indicate that binding is driven by favorable enthalpic contributions, rather than a classical entropy-driven signature that might be expected given that the binding pocket of MUP-1 is very hydrophobic. The only ligand-protein hydrogen bond is formed between the side-chain hydroxyl of Tyr120 and the ring nitrogen of the ligand in the wild-type protein. ITC measurements on the binding of IBMP to the Y120F mutant demonstrate a reduced enthalpy of binding, but nonetheless binding is still enthalpy dominated. A combination of solvent isotopic substitution ITC measurements and all-atom molecular dynamics simulations with explicit inclusion of solvent water suggests that solvation is not a major contributor to the overall binding enthalpy. Moreover, hydrogen/deuterium exchange measurements suggest that there is no significant contribution to the enthalpy of binding derived from "tightening" of the protein structure. Data are consistent with binding thermodynamics dominated by favorable dispersion interactions, arising from the inequality of solvent-solute dispersion interactions before complexation versus solute-solute dispersion interactions after complexation, by virtue of poor solvation of the binding pocket.

LanguageEnglish
Pages11827-11834
Number of pages8
JournalJournal of the American Chemical Society
Volume127
Issue number33
DOIs
Publication statusPublished - 24 Aug 2005
Externally publishedYes

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Calorimetry
Binding sites
Protein Binding
Enthalpy
Titration
Binding Sites
Ligands
Proteins
Water
Molecular Dynamics Simulation
Thermodynamics
Deuterium Exchange Measurement
Solvation
Complexation
Molecular dynamics
X Ray Crystallography
Entropy
Site-Directed Mutagenesis
Atoms
Mutagenesis

Cite this

Barratt, Elizabeth ; Bingham, Richard J. ; Warner, Daniel J. ; Laughton, Charles A. ; Phillips, Simon E V ; Homans, Steve W. / Van der Waals Interactions Dominate Ligand-Protein Association in a Protein Binding Site Occluded from Solvent Water. In: Journal of the American Chemical Society. 2005 ; Vol. 127, No. 33. pp. 11827-11834.
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Van der Waals Interactions Dominate Ligand-Protein Association in a Protein Binding Site Occluded from Solvent Water. / Barratt, Elizabeth; Bingham, Richard J.; Warner, Daniel J.; Laughton, Charles A.; Phillips, Simon E V; Homans, Steve W.

In: Journal of the American Chemical Society, Vol. 127, No. 33, 24.08.2005, p. 11827-11834.

Research output: Contribution to journalArticle

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