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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*
Author NameAffiliationE-mail
Xian-wei Wang College of Science, Zhejiang University of Technology, Hangzhou 310023, China;College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China;Zhejiang Provincial Collaborative Innovation Center of High-end Laser Manufacturing Equipment, Hangzhou 310014, China  
John Z. H. Zhang College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China;NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China;Department of Chemistry, New York University, New York 10003, USA  
Xiao He* College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China;NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 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 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
FundProject: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.
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*
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DOI:10.1063/1674-0068/30/cjcp1709169
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