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Improving the thermostability and activity of Paenibacillus pasadenensis chitinase through semi-rational design. Int J Biol Macromol 2020; 150:9-15. [PMID: 32035157 DOI: 10.1016/j.ijbiomac.2020.02.033] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 02/04/2023]
Abstract
Chitinase is a promising biocatalyst for chitin biotransformation in the field of recalcitrant biomass degradation. Excellent catalytic performance is conducive to its commercial utilization. In this work, sequence- and structure-based semi-rational design was performed to evolve the thermostability and activity of a previously identified chitinase PpChi1 from Paenibacillus pasadenensis CS0611. After combinational mutagenesis, the mutant S244C-I319C/T259P with disulfide bond introduction and proline substitution exhibited higher specific activity at higher temperature, 26.3-fold in half-life value at 50 °C, and a 7.9 °C rise in half-inactivation temperature T1/215min compared to the wild-type enzyme. The optimal reaction temperature of the mutant was shifted from 45 °C to 52.5 °C. Molecular dynamic simulation and structure analysis confirmed that these improvements of the mutant were attributed to its stabilized folding form, possibly caused by the decreased entropy of unfolding. This work gives an initial insight into the effect of conserved proline residues in thermostable chitinases and proposes a feasible approach for improving chitinase thermostability to facilitate its application in chitin hydrolysis to valuable oligosaccharides.
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Schmidt A, Shvetsov A, Soboleva E, Kil Y, Sergeev V, Surzhik M. Thermostability improvement of Aspergillus awamori glucoamylase via directed evolution of its gene located on episomal expression vector in Pichia pastoris cells. Protein Eng Des Sel 2019; 32:251-259. [DOI: 10.1093/protein/gzz048] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 11/21/2019] [Accepted: 11/30/2019] [Indexed: 11/13/2022] Open
Abstract
AbstractNovel thermostable variants of glucoamylase (GA) from filamentous fungus Aspergillus awamori X100 were constructed using the directed evolution approach based on random mutagenesis by error-prone PCR of the catalytic domain region of glucoamylase gene located on a new episomal expression vector pPEHα in Pichia pastoris cells. Out of 3000 yeast transformants screened, six new thermostable GA variants with amino acid substitutions Val301Asp, Thr390Ala, Thr390Ala/Ser436Pro, Leu7Met/His391Tyr, Asn9His/Ile82Phe and Ser8Arg/Gln338Leu were identified and studied. To estimate the effect of each substitution in the double mutants, we have constructed the relevant single mutants of GA by site-directed mutagenesis and analyzed their thermal properties. Results of the analysis showed that only Ile82Phe and Ser8Arg substitutions by themselves increased enzyme thermostability. While the substitutions Leu7Met, Asn9His and Gln338Leu decreased the thermal stability of GA, the synergistic effect of double mutant variants Leu7Met/His391Tyr, Asn9His/Ile82Phe and Ser8Arg/Gln338Leu resulted in significant thermostability improvement as compared to the wild type GA. Thr390Ala and Thr390Ala/Ser436Pro mutant variants revealed the highest thermostability with free activation energy changes ΔΔG of 2.99 and 3.1 kJ/mol at 80°C, respectively.
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Affiliation(s)
- Alexander Schmidt
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Centre “Kurchatov Institute”, Orlova Roscha 1, Postal Code 188300, Gatchina, Russia
- BioMedical Technology Department, Kurchatov Institute, Akademika Kurchatova square 1, Postal Code 123182, Moscow, Russia
| | - Alexey Shvetsov
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Centre “Kurchatov Institute”, Orlova Roscha 1, Postal Code 188300, Gatchina, Russia
- BioMedical Technology Department, Kurchatov Institute, Akademika Kurchatova square 1, Postal Code 123182, Moscow, Russia
- Institute of Physics, Nanotechnology and Telecommunications, Peter the Great Saint-Petersburg Polytechnic University, Polytechnicheskaya 29, Postal Code 195251, St. Petersburg, Russia
| | - Elena Soboleva
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Centre “Kurchatov Institute”, Orlova Roscha 1, Postal Code 188300, Gatchina, Russia
- Institute of Physics, Nanotechnology and Telecommunications, Peter the Great Saint-Petersburg Polytechnic University, Polytechnicheskaya 29, Postal Code 195251, St. Petersburg, Russia
| | - Yury Kil
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Centre “Kurchatov Institute”, Orlova Roscha 1, Postal Code 188300, Gatchina, Russia
| | - Vladimir Sergeev
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Centre “Kurchatov Institute”, Orlova Roscha 1, Postal Code 188300, Gatchina, Russia
- Institute of Physics, Nanotechnology and Telecommunications, Peter the Great Saint-Petersburg Polytechnic University, Polytechnicheskaya 29, Postal Code 195251, St. Petersburg, Russia
| | - Marina Surzhik
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Centre “Kurchatov Institute”, Orlova Roscha 1, Postal Code 188300, Gatchina, Russia
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Abstract
Using structure and sequence based analysis we can engineer proteins to increase their thermal stability.
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Affiliation(s)
- H. Pezeshgi Modarres
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - M. R. Mofrad
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - A. Sanati-Nezhad
- BioMEMS and Bioinspired Microfluidic Laboratory
- Department of Mechanical and Manufacturing Engineering
- University of Calgary
- Calgary
- Canada
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Yin X, Hu D, Li JF, He Y, Zhu TD, Wu MC. Contribution of Disulfide Bridges to the Thermostability of a Type A Feruloyl Esterase from Aspergillus usamii. PLoS One 2015; 10:e0126864. [PMID: 25969986 PMCID: PMC4429965 DOI: 10.1371/journal.pone.0126864] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 04/08/2015] [Indexed: 11/18/2022] Open
Abstract
The contribution of disulfide bridges to the thermostability of a type A feruloyl esterase (AuFaeA) from Aspergillus usamii E001 was studied by introducing an extra disulfide bridge or eliminating a native one from the enzyme. MODIP and DbD, two computational tools that can predict the possible disulfide bridges in proteins for thermostability improvement, and molecular dynamics (MD) simulations were used to design the extra disulfide bridge. One residue pair A126-N152 was chosen, and the respective amino acid residues were mutated to cysteine. The wild-type AuFaeA and its variants were expressed in Pichia pastoris GS115. The temperature optimum of the recombinant (re-) AuFaeAA126C-N152C was increased by 6°C compared to that of re-AuFaeA. The thermal inactivation half-lives of re-AuFaeAA126C-N152C at 55 and 60°C were 188 and 40 min, which were 12.5- and 10-folds longer than those of re-AuFaeA. The catalytic efficiency (kcat/Km) of re-AuFaeAA126C-N152C was similar to that of re-AuFaeA. Additionally, after elimination of each native disulfide bridge in AuFaeA, a great decrease in expression level and at least 10°C decrease in thermal stability of recombinant AuEaeA variants were also observed.
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Affiliation(s)
- Xin Yin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Die Hu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jian-Fang Li
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yao He
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Tian-Di Zhu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Min-Chen Wu
- Wuxi Medical School, Jiangnan University, Wuxi, China
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