Works (1)
Updated: July 5th, 2023 15:39
2016 journal article
Steered molecular dynamics study of inhibitor binding in the internal binding site in dehaloperoxidase-hemoglobin
BIOPHYSICAL CHEMISTRY, 211, 28–38.
author keywords: Binding pathway; Potential of mean force; Protein-ligand interaction; Michaelis-menten kinetics; Steered molecular dynamics; Jarzynski equality
MeSH headings : Binding Sites; Enzyme Inhibitors / chemistry; Enzyme Inhibitors / pharmacology; Hemoglobins / antagonists & inhibitors; Hemoglobins / chemistry; Hemoglobins / metabolism; Models, Molecular; Molecular Dynamics Simulation; Molecular Structure; Peroxidases / antagonists & inhibitors; Peroxidases / chemistry; Peroxidases / metabolism; Phenols / chemistry; Phenols / pharmacology
TL;DR:
The binding free energy of 4-bromophenol (4-BP), an inhibitor that binds in the internal binding site in dehaloperoxidase-hemoglobin (DHP) was calculated using Molecular Dynamics methods combined with pulling or umbrella sampling and the effects of systematic changes in the pulling speed, pulling force constant and restraint force constant on the calculated potential of mean force (PMF) are presented.
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open access via manuscript.elsevier.com (publisher PDF)
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Added: August 6, 2018
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