Ligand escape pathways and (un)binding free energy calculations for the hexameric insulin-phenol complex

Biophys J. 2008 Nov 1;95(9):4193-204. doi: 10.1529/biophysj.108.139675. Epub 2008 Aug 1.

Abstract

Cooperative binding of phenolic species to insulin hexamers is known to stabilize pharmaceutical preparations of the hormone. Phenol dissociation is rapid on hexamer dissolution timescales, and phenol unbinding upon dilution is likely the first step in the conversion of (pharmaceutical) hexameric insulin to the active monomeric form upon injection. However, a clear understanding of the determinants of the rates of phenol unbinding remains obscure, chiefly because residues implicated in phenol exchange as determined by NMR are not all associated with likely unbinding routes suggested by the best-resolved hexamer structures. We apply random acceleration molecular dynamics simulation to identify potential escape routes of phenol from hydrophobic cavities in the hexameric insulin-phenol complex. We find three major pathways, which provide new insights into (un)binding mechanisms for phenol. We identify several residues directly participating in escape events that serve to resolve ambiguities from recent NMR experiments. Reaction coordinates for dissociation of phenol are developed based on these exit pathways. Potentials of mean force along the reaction coordinate for each pathway are resolved using multiple independent steered molecular dynamics simulations with second-order cumulant expansion of Jarzynski's equality. Our results for DeltaF agree reasonably well within the range of known experimental and previous simulation magnitudes of this quantity. Based on structural analysis and energetic barriers for each pathway, we suggest a plausible preferred mechanism of phenolic exchange that differs from previous mechanisms. Several weakly-bound metastable states are also observed for the first time in the phenol dissociation reaction.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Insulin / chemistry*
  • Insulin / metabolism*
  • Ligands
  • Models, Molecular
  • Molecular Conformation
  • Phenol / chemistry*
  • Phenol / metabolism
  • Protein Binding
  • Protein Multimerization*
  • Protein Structure, Quaternary
  • Surface Properties
  • Thermodynamics

Substances

  • Insulin
  • Ligands
  • Phenol