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

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.

Tobacco etch virus (TEV) protease with multiple mutations to improve solubility and reduce self‐cleavage exhibits enhanced enzymatic activity

“…In this study, we tried to introduce two types of mutations into TEV protease simultaneously to improve solubility and to protect against self‐cleavage. The S219 mutation that provides protection against self‐cleavage [18] was introduced into a background of T17S, N68D, and I77V mutations, which increase the solubility and stability of the protease [14,15], and the enzyme kinetics of both engineered TEV proteases was analyzed and compared.…”

“…The T17S/N68D/I77V mutant TEV protease was generated by random mutagenesis, and these mutations improve the solubility and yield of TEV protease effectively because they are located at or near the surface of TEV protease [14]. Additionally, the T17S/N68D/I77V mutant is more stable than the wild‐type protease because the mutations result in more rigid secondary structure elements, such as helices and sheets [15].…”

Structural basis of valmerins as dual inhibitors of GSK3β/CDK5

“…A total of 100 snapshots were extracted from the 30-50 ns MD trajectory with an equal interval to calculate binding free energy (ΔG binding ) between GSK3β/CDK5 and valmerin-19 using the MM-PBSA method [32][33][34][35]. ΔG binding was calculated using Eq.…”

Insight into the structural stability of wild-type and histidine mutants in Pin1 by experimental and computational methods

“…We calculated the distances changes in the hydrogen bond network between partial atom pairs along with the 20 ns simulation time 32 . The Cys113: SG forms a hydrogen bond with His59: NE2, His59: ND1 forms a hydrogen bond with His157: ND1, and His157:NE2 forms a hydrogen bond with Thr152: OG1.…”