高等学校化学学报2017，Vol.38Issue(10)：1813-1821,9.DOI:10.7503/cjcu20170202
喹啉加氧酶中氧气扩散的通道分析
Theoretical Analysis of Oxygen Diffusion in the Micro-channels of Quinoline Oxygenase
摘要
Abstract
Oxygen diffusion pathways of quinoline oxygenase ( HOD ) were investigated by bioinformatics analysis, quantum chemical optimization, CAVER and MD pocket prediction, random accelerated molecular dynamics simulations and umbrella sampling. The results show that the pre-reaction site of oxygen does locate inside the active pocket, and there exists several possible oxygen tunnels in HOD, in which the one with shortest length has the highest priority. Random accelerated molecular dynamics proved that oxygen has the highest probability to exit from this tunnel, and umbrella sampling further verified its free energy for oxygen passing by is the lowest. The tunnel ended at the binding site of oxygen located on the Re-face of the substrate, which is consistent with previous studies. These results better illuminate the kinetics and the stereo-selectivity of the catalytic reaction in HOD, and also provide theoretical guidance to further experimentally improve the efficiency of oxygen usage by enzyme.关键词
喹啉加氧酶/氧气扩散/随机加速分子动力学/伞状抽样Key words
Quinoline oxygenase/Oxygendiffusion/Random accelerated molecular dynamics/Umbrella sampling分类
化学化工引用本文复制引用
周超,石婷,赵一雷,王晓雷..喹啉加氧酶中氧气扩散的通道分析[J].高等学校化学学报,2017,38(10):1813-1821,9.基金项目
国家自然科学基金(批准号:21377085, 21303101)、中国博士后科学基金(批准号:2014T70413, 2014M561463)和上海交通大学高性能计算中心资助.Supported by the National Natural Science Foundation of China(Nos.21377085, 21303101), the China Postdoctoral Science Foundation ( Nos.2014T70413, 2014M561463) and the Center for High Performance Computing of Shanghai Jiaotong University, China. （批准号:21377085, 21303101）
