title: Steered molecular dynamics study of inhibitor binding in the internal binding site in dehaloperoxidase-hemoglobin.
abstract: 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 (MD) methods combined with pulling or umbrella sampling. 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 in this study. The PMFs calculated using steered molecular dynamics (SMD) were validated by umbrella sampling (US) in the strongly restrained regime. A series of restraint force constants ranging from 1000 down to 5 kJ/(mol nm(2)) were used in SMD simulations. This range was validated using US, however noting that weaker restraints give rise to a broader sampling of configurations. This comparison was further tested by a pulling simulation conducted without any restraints, which was observed to have a value closest to the experimentally measured free energy for binding of 4-BP to DHP based on ultraviolet-visible (UV-vis) and resonance Raman spectroscopies. The protein-inhibitor system is well suited for fundamental study of free energy calculations because the DHP protein is relatively small and the inhibitor is quite rigid. Simulation configuration structures are compared to the X-ray crystallography structures of the binding site of 4-BP in the distal pocket above the heme.
authors.affiliation: Research Institute for Soft Matter and Biomimetics, Department of Physics, Xiamen University, 361005 Xiamen, People's Republic of China.
authors.forename: Zhisen
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Department of Chemistry, North Carolina State University, Raleigh, NC 27695.
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Santos
authors.affiliation: Department of Chemistry, North Carolina State University, Raleigh, NC 27695.
authors.forename: Qing
authors.initials: Q
authors.lastname: Zhou
authors.affiliation: Soft Matter Research Center and Department of Chemistry, Zhejiang University, 310003 Hangzhou, Peoples Republic of China.
authors.forename: Lijun
authors.initials: L
authors.lastname: Liang
authors.affiliation: Soft Matter Research Center and Department of Chemistry, Zhejiang University, 310003 Hangzhou, Peoples Republic of China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Soft Matter Research Center and Department of Chemistry, Zhejiang University, 310003 Hangzhou, Peoples Republic of China. Electronic address: tao_wu@zju.edu.cn.
authors.forename: Tao
authors.initials: T
authors.lastname: Wu
authors.affiliation: Soft Matter Research Center and Department of Chemistry, Zhejiang University, 310003 Hangzhou, Peoples Republic of China; Department of Chemistry, North Carolina State University, Raleigh, NC 27695. Electronic address: Franzen@ncsu.edu.
authors.forename: Stefan
authors.initials: S
authors.lastname: Franzen
mesh_terms: D001665:Binding Sites; D004791:Enzyme Inhibitors / Q000737:chemistry* / Q000494:pharmacology; D006454:Hemoglobins / Q000037:antagonists & inhibitors* / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D010544:Peroxidases / Q000037:antagonists & inhibitors* / Q000737:chemistry* / Q000378:metabolism; D010636:Phenols / Q000737:chemistry* / Q000494:pharmacology
chemical_list: D004791:Enzyme Inhibitors; D006454:Hemoglobins; D010636:Phenols; C098661:DHP I dehaloperoxidase; D010544:Peroxidases; C032037:4-bromophenol
keywords: Binding pathway; Jarzynski equality; Michaelis–menten kinetics; Potential of mean force; Protein-ligand interaction; Steered molecular dynamics