Lid Closure Mechanism of Yarrowia lipolytica Lipase in Methanol Investigated by Molecular Dynamics Simulation

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• 作者：Yang Jiang ; Lingli Li ; Haiyang Zhang ; Wei Feng ; Tianwei Tan
• 刊名：Journal of Chemical Information and Modeling
• 出版年：2014
• 出版时间：July 28, 2014
• 年：2014
• 卷：54
• 期：7
• 页码：2033-2041
• 全文大小：456K
• ISSN：1549-960X

文摘

In nonaqueous organic solvents, lipases can catalyze esterification reactions, which increase their application value. Yarrowia lipolytica Lipase (Lip2) possesses potential values in medicine and industrial production. In order to investigate its lid closure mechanism in methanol we performed molecular dynamics (MD) simulations of the open conformation of Lip2 in methanol and hexane, respectively. Simulation results indicated that Lip2 undergoes a greater conformational change in methanol. Principle component analysis showed Lip2 has 鈥渄ouble-domain鈥?and 鈥渢orsion鈥?motion modes in hexane and methanol. By analyzing B-factor and dynamical cross-correlation, region Ser274-Asn288, region Thr106-His126, and region Asp61-Asp67 were found to interact with the lid region (Thr88-Leu105). Furthermore, local restricted MD simulations showed that closure mechanism of Lip2 is 鈥渄ouble-lid movement鈥?which is also observed in Pseudomonas aeruginosa Lipase (PAL), and we detected two interaction propagation pathways in Lip2 driven by the interaction between Ser274-Asn288 and methanol.