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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 a metallo-enzyme that binds to the cell membrane and catalyzes the biocatalysis of alkanes to alcohols.Study on the binding mode and catalytic mechanism of PMMO with alkanes will be helpful to design and synthesize a new simulation Enzyme, and then effectively utilize alkane as a new energy source.The binding mode between PMMO monomer and a series of alkanes was obtained by molecular docking method, and the molecular dynamics simulation of PMMO monomer and PMMO-pentane complex was performed for 6 ns, Finally, the conformational clustering and binding energy analysis of the complexes were carried out. The results showed that pentane binds to the hydrophobic pocket close to Zn2 +, consisting of the pmoA subunits M45 ~ W60 and R190 ~ T193 and the pmoC subunit Q161 ’ The kinetic results show that the PMMO-pentane complex maintains a similar kinetic pattern compared to the PMMO monomer, but the magnitude is more pronounced, and the substantial movement of pentane in the hydrophobic pocket plays a catalytic role for PMMO It is necessary to reveal the hydrophobic interaction with energy calculation, which is the main driving force for the stable identification of pentane and PMMO. All simulation results are in good agreement with the experimental data.