引用本文:
【打印本页】   【HTML】   【下载PDF全文】   View/Add Comment  【EndNote】   【RefMan】   【BibTex】
过刊浏览    高级检索
本文已被:浏览 49次   下载 55  
分享到: 微信 更多
Ab Initio QM/MM Molecular Dynamics Simulation of CO in the Heme Distal Pocket of Myoglobin
Xiao He
Author NameAffiliationE-mail
Xiao He College of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China xiaohe@phy.ecnu.edu.cn 
Abstract:
Myoglobin has important biological functions in storing and transporting small diatomic molecules in human body. Two possible orientations of carbon monoxide (CO) in the heme distal pocket (named B1 and B2 states) of myoglobin have been experimentally indicated. In this study, ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation of CO in myoglobin was carried out to investigate the two possible B states. Our results demonstrate that the B1 and B2 states correspond to Fe?CO (with carbon atom closer to iron center of heme) and Fe?OC (with oxygen atom closer to Fe), by comparing with the experimental infrared spectrum. QM electrostatic polarization effect on CO brought from the protein and solvent environment is the main driving force, which anchors CO in two distinctive orientations and hinders its rotation. The calculated vibrational frequency shift between the state B1 and B2 is 13.1 cm-1, which is in good agreement with experimental value of 11.5 cm-1. This study also shows that the electric field produced by the solvent plays an important role in assisting protein functions by exerting directional electric field at the active site of the protein. From residue-based electric field decomposition, several residues were found to have most contributions to the total electric field at the CO center, including a few charged residues and three adjacent uncharged polar residues (namely, HIS64, ILE107 and PHE43). This study provides new physical insights on rational design of enzyme with higher electric field at the active site.
Key words:  vibrational Stark shift, electric field, solvation effect
FundProject:
Ab Initio QM/MM Molecular Dynamics Simulation of CO in the Heme Distal Pocket of Myoglobin
Xiao He
摘要:
Myoglobin has important biological functions in storing and transporting small diatomic molecules in human body. Two possible orientations of carbon monoxide (CO) in the heme distal pocket (named B1 and B2 states) of myoglobin have been experimentally indicated. In this study, ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation of CO in myoglobin was carried out to investigate the two possible B states. Our results demonstrate that the B1 and B2 states correspond to Fe?CO (with carbon atom closer to iron center of heme) and Fe?OC (with oxygen atom closer to Fe), by comparing with the experimental infrared spectrum. QM electrostatic polarization effect on CO brought from the protein and solvent environment is the main driving force, which anchors CO in two distinctive orientations and hinders its rotation. The calculated vibrational frequency shift between the state B1 and B2 is 13.1 cm-1, which is in good agreement with experimental value of 11.5 cm-1. This study also shows that the electric field produced by the solvent plays an important role in assisting protein functions by exerting directional electric field at the active site of the protein. From residue-based electric field decomposition, several residues were found to have most contributions to the total electric field at the CO center, including a few charged residues and three adjacent uncharged polar residues (namely, HIS64, ILE107 and PHE43). This study provides new physical insights on rational design of enzyme with higher electric field at the active site.
关键词:  vibrational Stark shift, electric field, solvation effect
DOI:
分类号: