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Analysis of the Conformational Stability and Activity of Lipase by Molecular Dynamics Simulation

Author: LiCong
Tutor: TanTianWei
School: Beijing University of Chemical Technology
Course: Chemical Engineering and Technology
Keywords: lipase molecular dynamics simulation lipase inactivation thermal stability
CLC: Q55
Type: Master's thesis
Year: 2010
Downloads: 409
Quote: 5
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Abstract

In this study, molecular dynamics simulation was used to investigate lipase conformation change and activity change. The work consists of three parts:(1)Investigating the conformation changes of Candida antarctica lipase B (CALB) in several polar and non-polar organic solvents by molecular dynamics simulation. The conformation changes of CALB in the polar and non-polar solvents were examined in three aspects:the overall conformation changes, the local conformation changes and the conformation changes of the active site.The simulation results show that both the overall conformation and local conformation of CALB are very stable in all organic solvents, but the conformation of the active site shows differences between polar and non-polar organic solvents.In non-polar organic solvents, the conformation of active site keeps stable, while in polar organic solvents, several molecules reach into the active site and interact intensively with the active site, which destroys the hydrogen bond between SER105 (OG) and HIS224 (NE2).The activation energy of CALB and the activation energy of the active site region in different solvents were further simulated by QM/MM simulation.The results indicate that the changes in the active site region in different solvents are the main factor that affects the activity of the CALB.(2)Investigating the conformation changes of Candida antarctica lipase B (CALB)in methanol-water mixed solvents by molecular dynamics simulation. The crystal structure of CALB was solved into five methanol-water mixed solvents box with different methanol concentration (Vmethanol/Vsolvents):1%,10%,20%,30%,50%.Then molecular dynamics simulations of the lipase-solvents system were performed.The simulation results show that when the methanol concentration is more that 20%,some methanol molecules approach the active site region of CALB and destroy the key hydrogen bond of the active site, which results in the inactivation of CALB。(3)Investigating the protective effect of olive oil on the thermal stability of Candida rugosa lipase (CRL) by molecular dynamics simulation.The crystal structure of CRL was solved into two solvents box:water solution, water solution with 60 olive oil molecules. Molecular dynamics simulations of the lipase-solvent system were performed under five temperature:300K,310K, 320K,330K, and 340K. The simulation results show that the olive oil molecules can interact strongly with CRL through hydrophobic effect in water solution. The overall structure and theα-helix structure of CRL is more stable in the water solution with olive oil molecules than that in the solution with water molecules alone,when the temperature increases from 300K to 340K.

Analysis of the Conformational Stability and Activity of Lipase by Molecular Dynamics Simulation

Abstract

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