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CO分子在肌红蛋白结合口袋的QM/MM动力学模拟
王宪位,张增辉,何晓*
作者单位E-mail
王宪位 浙江工业大学理学院, 杭州 310023;华东师范大学化学与分子工程学院, 上海 200062;浙江省高端激光制造装备协同创新中心, 杭州 310014  
张增辉 华东师范大学化学与分子工程学院, 上海 200062;上海纽约大学计算化学中心, 上海 200062;纽约大学化学系, 纽约 10003  
何晓* 华东师范大学化学与分子工程学院, 上海 200062;上海纽约大学计算化学中心, 上海 200062 xiaohe@phy.ecnu.edu.cn 
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DOI:10.1063/1674-0068/30/cjcp1709169
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基金项目:This work was supported by the National Key R&D Program of China (No.2016YFA0501700), the National Natural Science Foundation of China (No.21673074, No.21433004, and No.11547164), Zhejiang Provincial Natural Science Foundation (No.LY17B030008), Youth Top-Notch Talent Support Program of Shanghai, NYUECNU Center for Computational Chemistry at NYU Shanghai, Shanghai Putuo District (No.2014-A-02), and NYU Global Seed Grant for Collaborative Research.
Ab initio Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulation of CO in the Heme Distal Pocket of Myoglobin
Xian-wei Wang,John Z. H. Zhang,Xiao He*
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 as 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:  QM/MM simulation  Stark shift  Electrostatic polarization effect  Electric field