Ab initio Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulation of CO in the Heme Distal Pocket of Myoglobin  

CO分子在肌红蛋白结合口袋的QM／MM动力学模拟

作　　者：王宪位 张增辉 何晓[2,4] 

机构地区：[1]浙江工业大学理学院,杭州310023 [2]华东师范大学化学与分子工程学院,上海200062 [3]浙江省高端激光制造装备协同创新中心,杭州310014 [4]上海纽约大学计算化学中心,上海200062 [5]纽约大学化学系,纽约10003

出　　处：《Chinese Journal of Chemical Physics》2017年第6期705-716,I0002,共13页化学物理学报（英文）

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 as BI 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：QM/MM simulation Stark shift Electrostatic polarization effect Electric field 

分 类 号：O[理学]