Qing W. Zhou

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. (via Semantic Scholar)