Journal article
Ligand Escape Pathways and (Un)Binding Free Energy Calculations for the Hexameric Insulin-Phenol Complex
Biophysical journal, v 95(9), pp 4193-4204
01 Nov 2008
PMID: 18676643
Featured in Collection : UN Sustainable Development Goals @ Drexel
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 Δ
F
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.
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Details
- Title
- Ligand Escape Pathways and (Un)Binding Free Energy Calculations for the Hexameric Insulin-Phenol Complex
- Creators
- Harish Vashisth - Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PennsylvaniaCameron F Abrams - Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania
- Publication Details
- Biophysical journal, v 95(9), pp 4193-4204
- Publisher
- The Biophysical Society
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Chemical and Biological Engineering
- Web of Science ID
- WOS:000260072600013
- Scopus ID
- 2-s2.0-58149144258
- Other Identifier
- 991014878154304721
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- Web of Science research areas
- Biophysics