颗粒型甲烷单加氧酶（Particulate methane monooxygenase,PMMO）是一个与细胞膜结合的金属酶,能将烷烃生物催化为醇.研究PMMO与烷烃的结合模式及催化机制将有利于设计合成一个新的模拟酶,进而有效地利用烷烃作为新能源.用分子对接方法获得了PMMO单体与一系列烷烃的结合模式,并对PMMO单体和PMMO-戊烷复合物进行了6 ns的分子动力学模拟,最后对复合物进行了构象成簇及结合能分析.结果表明,戊烷结合到靠近Zn2＋的疏水口袋中,该口袋由pmoA亚基的M45～W60和R190～T193以及pmoC亚基的Q161’三个片段组成.动力学结果表明,与PMMO单体比,PMMO-戊烷复合物保持着相近的运动模式,但幅度更明显,另外,戊烷在疏水口袋中的大幅度运动对于PMMO发挥催化作用是必须的.结合能计算揭示疏水相互作用是戊烷与PMMO稳定识别的主要驱动力,所有模拟结果与实验数据吻合较好.%Particulate methane monooxygenase（PMMO） is an membrane-bound metalloenzyme that catalyses the biological conversion of alkane to alcohol.The study on the binding modes between alkane and the catalytic mechanism of PMMO may aid the design of a new synthetic catalyst,which uses alkane as an alternative new energy source.The binding modes of PMMO with a series of alkanes were obtained via molecular docking method,then two 6 ns molecular dynamics simulations were performed for both PMMO and PMMO-pentane complex systems.Finally,conformation cluster and binding energy analysis were implemented for the complex systems.The results show that pentane binds to the hydrophobic pocket near the zinc ion,which is comprised by three segments（i.e.,the residues from M45 to W60,R190 to T193 in pmoA subunit and Q161＇ in pmoC subunit）.Compared with PMMO,PMMO-pentane complex maintains a similar motive mode but a more remarkable motive extent.Additionally,large-scale motion of pentane in the hydrophobic pocket is important for the catalysis of PMMO.The results of binding energy computations still revealed that the stable recognition of PMMO by pentane was mainly driven by the hydrophobic interactions.All the simulation results agree well with experimental data.
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