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Insight into the structural stability of wild type and mutants of the tobacco etch virus protease with molecular dynamics simulations

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Abstract

The efficiency and high specificity of tobacco etch virus protease (TEVp) has made it widely used for cleavage of recombinant fusion proteins. However, TEVp suffers from a few intrinsic defects such as self-cleavage, poorly expressed in E. coli and less soluble. So some mutants were designed to improve it, such as S219V, T17S/N68D/I77V and L56V/S135G etc. MD simulations for the WT TEVp and its mutants were performed to explore the underlying dynamic effects of mutations on TEVp. Although the globular domains are fairly conserved, the three mutations have diverse effects on the dynamics properties of TEVp, including the elongation of β-sheet, conversion of loop to helix and the flexibility of active core. Our present study indicates that the three mutants for TEVp can change their secondary structure and tend to form more helixes and sheets to improve stability. The study also helps us to understand the effects of some mutations on TEVp, provides us insights into the change of them at the atomic level and gives a potential rational method to design an improved protein.

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Abbreviations

TEVp:

Tobacco etch virus protease

MD:

Molecular dynamics

WT:

Wild type

SASA:

Solvent accessible surface area

DCCM:

Dynamic cross correlation map

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Acknowledgments

This work was financially supported by the National Key Technology R&D program of China (2009BAK61B04, 2006BAF07B01) and Science & Technology Foundation of Sichuan Province (2011JTD0026). NAMD and VMD were developed by the Theoretical Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign, USA.

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Authors and Affiliations

  1. Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, People’s Republic of China

    Yu Wang, Guo-Fei Zhu, Si-Yan Ren, Yong-Guang Han, Yue Luo & Lin-Fang Du

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  1. Yu Wang
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  2. Guo-Fei Zhu
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Correspondence to Lin-Fang Du.

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Wang, Y., Zhu, GF., Ren, SY. et al. Insight into the structural stability of wild type and mutants of the tobacco etch virus protease with molecular dynamics simulations. J Mol Model 19, 4865–4875 (2013). https://doi.org/10.1007/s00894-013-1930-9

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  • DOI: https://doi.org/10.1007/s00894-013-1930-9

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