Simulated Protein Thermal Detection (SPTD) for Enzyme Thermostability Study and an Application Example for Pullulanase from Bacillus deramificans

Title:Simulated Protein Thermal Detection (SPTD) for Enzyme Thermostability Study and an Application Example for Pullulanase from Bacillus deramificans

Volume: 24 Issue: 34

Author(s): Jian-Xiu Li, Shu-Qing Wang, Qi-Shi Du*, Hang Wei, Xiao-Ming Li, Jian-Zong Meng, Qing-Yan Wang, Neng-Zhong Xie*, Ri-Bo Huang* Kuo-Chen Chou

Affiliation:

• State Key Laboratory of Biomass Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007,China

• State Key Laboratory of Biomass Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007,China

• State Key Laboratory of Biomass Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007,China

Keywords: Simulated protein thermal detection, B-factors, thermal stability, protein engineering, site-directed mutation, pullulanase, molecular dynamics.

Abstract: Background: The relationship between protein structure and its bioactivity is one of the fundamental problems for protein engineering and pharmaceutical design.

Method: A new method, called SPTD (Simulated Protein Thermal Detection), was proposed for studying and improving the thermal stability of enzymes. The method was based on the evidence observed by conducting the MD (Molecular Dynamics) simulation for all the atoms of an enzyme vibrating from the velocity at a room temperature (e.g., 25°C) to the desired working temperature (e.g., 65°C). According to the recorded MD trajectories and the coordinate deviations of the constituent residues under the two different temperatures, some new strategies have been found that are useful for both drug delivery and starch industry.

Conclusion: The SPTD technique presented in this paper may become a very useful tool for pharmaceutical design and protein engineering.

Cite this article as:

Li Jian-Xiu , Wang Shu-Qing , Du Qi-Shi*, Wei Hang , Li Xiao-Ming , Meng Jian-Zong , Wang Qing-Yan , Xie Neng-Zhong *, Huang Ri-Bo *, Chou Kuo-Chen , Simulated Protein Thermal Detection (SPTD) for Enzyme Thermostability Study and an Application Example for Pullulanase from Bacillus deramificans, Current Pharmaceutical Design 2018; 24 (34) . https://dx.doi.org/10.2174/1381612824666181113120948