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Thermostability Improvement of L-Asparaginase from Acinetobacter soli via Consensus-Designed Cysteine Residue Substitution. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196670. [PMID: 36235209 PMCID: PMC9572581 DOI: 10.3390/molecules27196670] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/05/2022]
Abstract
To extend the application range of L-asparaginase in food pre-processing, the thermostability improvement of the enzyme is essential. Herein, two non-conserved cysteine residues with easily oxidized free sulfhydryl groups, Cys8 and Cys283, of Acinetobacter soli L-asparaginase (AsA) were screened out via consensus design. After saturation mutagenesis and combinatorial mutation, the mutant C8Y/C283Q with highly improved thermostability was obtained with a half-life of 361.6 min at 40 °C, an over 34-fold increase compared with that of the wild-type. Its melting temperature (Tm) value reaches 62.3 °C, which is 7.1 °C higher than that of the wild-type. Molecular dynamics simulation and structure analysis revealed the formation of new hydrogen bonds of Gln283 and the aromatic interaction of Tyr8 formed with adjacent residues, resulting in enhanced thermostability. The improvement in the thermostability of L-asparaginase could efficiently enhance its effect on acrylamide inhibition; the contents of acrylamide in potato chips were efficiently reduced by 86.50% after a mutant C8Y/C283Q treatment, which was significantly higher than the 59.05% reduction after the AsA wild-type treatment. In addition, the investigation of the mechanism behind the enhanced thermostability of AsA could further direct the modification of L-asparaginases for expanding their clinical and industrial applications.
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Nezhad NG, Rahman RNZRA, Normi YM, Oslan SN, Shariff FM, Leow TC. Thermostability engineering of industrial enzymes through structure modification. Appl Microbiol Biotechnol 2022; 106:4845-4866. [PMID: 35804158 DOI: 10.1007/s00253-022-12067-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/25/2022] [Accepted: 07/02/2022] [Indexed: 01/14/2023]
Abstract
Thermostability is an essential requirement of enzymes in the industrial processes to catalyze the reactions at high temperatures; thus, enzyme engineering through directed evolution, semi-rational design and rational design are commonly employed to construct desired thermostable mutants. Several strategies are implemented to fulfill enzymes' thermostability demand including decreasing the entropy of the unfolded state through substitutions Gly → Xxx or Xxx → Pro, hydrogen bond, salt bridge, introducing two different simultaneous interactions through single mutant, hydrophobic interaction, filling the hydrophobic cavity core, decreasing surface hydrophobicity, truncating loop, aromatic-aromatic interaction and introducing positively charged residues to enzyme surface. In the current review, horizons about compatibility between secondary structures and substitutions at preferable structural positions to generate the most desirable thermostability in industrial enzymes are broadened. KEY POINTS: • Protein engineering is a powerful tool for generating thermostable industrial enzymes. • Directed evolution and rational design are practical approaches in enzyme engineering. • Substitutions in preferable structural positions can increase thermostability.
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Affiliation(s)
- Nima Ghahremani Nezhad
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Yahaya M Normi
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Fairolniza Mohd Shariff
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia. .,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia. .,Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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3
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Thompson MK, Shay MR, de Serrano V, Dumarieh R, Ghiladi RA, Franzen S. A new inhibition mechanism in the multifunctional catalytic hemoglobin dehaloperoxidase as revealed by the DHP A(V59W) mutant: A spectroscopic and crystallographic study. J PORPHYR PHTHALOCYA 2021. [DOI: 10.1142/s1088424621500826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
As multifunctional catalytic hemoglobins, dehaloperoxidase isoenzymes A and B (DHP A and B) are among the most versatile hemoproteins in terms of activities displayed. The ability of DHP to bind over twenty different substrates in the distal pocket might appear to resemble the promiscuousness of monooxygenase enzymes, yet there are identifiable substrate-specific interactions that can steer the type of oxidation (O-atom vs. electron transfer) that occurs inside the DHP distal pocket. Here, we have investigated the DHP A(V59W) mutant in order to probe the limits of conformational flexibility in the distal pocket as it relates to the genesis of this substrate-dependent activity differentiation. The X-ray crystal structure of the metaquo DHP A(V59W) mutant (PDB 3K3U) and the V59W mutant in complex with fluoride [denoted as DHP A(V59W-F)] (PDB 7MNH) show significant mobility of the tryptophan in the distal pocket, with two parallel conformations having W59-N[Formula: see text] H-bonded to a heme-bound ligand (H2O or F[Formula: see text], and another conformation [observed only in DHP A(V59W-F)] that brings W59 sufficiently close to the heme as to preclude axial ligand binding. UV-vis and resonance Raman spectroscopic studies show that DHP A(V59W) is 5-coordinate high spin (5cHS) at pH 5 and 6-coordinate high spin (6cHS) at pH 7, whereas DHP A(V59W-F) is 6cHS from pH 5 to 7. Enzyme assays confirm robust peroxidase activity at pH 5, but complete loss of activity at pH 7. We find no evidence that tryptophan plays a role in the oxidation mechanism ([Formula: see text]. radical formation). Instead, the data reveal a new mechanism of DHP inhibition, namely a shift towards a non-reactive form by OH[Formula: see text] ligation to the heme-Fe that is strongly stabilized (presumably through H-bonding interactions) by the presence of W59 in the distal cavity.
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Affiliation(s)
- Matthew K. Thompson
- Department of Chemistry & Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Madeline R. Shay
- Department of Chemistry & Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Vesna de Serrano
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Rania Dumarieh
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Reza A. Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
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Li S, Yang Q, Tang B. Improving the thermostability and acid resistance of Rhizopus oryzae α-amylase by using multiple sequence alignment based site-directed mutagenesis. Biotechnol Appl Biochem 2020; 67:677-684. [PMID: 32133700 DOI: 10.1002/bab.1907] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 02/25/2020] [Indexed: 12/14/2022]
Abstract
Higher thermostability or acid resistance for fungal α-amylase will help to improve the sugar-making process and cut down the production costs. Here, the thermostability or acid resistance of Rhizopus oryzae α-amylase (ROAmy) was significantly enhanced by site-directed evolution based on multiple sequence alignment (MSA) method. For instance, compared with the wild-type ROAmy, the optimum temperature of mutants G136D and A144Y was increased from 50 to 55 °C, whereas for mutants V174R and I276P, the optimum temperature was increased from 50 to 60 °C. The optimum pH of mutants G136D and A144Y shifted from 5.5 to 5.0, whereas for mutants V174R and T253E, the optimum pH changed from 5.5 to 4.5. The results showed that mutant V174R had a 2.52-fold increase in half-life at 55 °C, a 2.55-fold increase in half-life at pH 4.5, and a 1.61-fold increase in catalytic efficiency (kcat /Km ) on soluble starch. The three-dimensional model simulation revealed that changes of hydrophilicity, hydrogen bond, salt bridge, or rigidity observed in mutants might mainly account for the improvement of thermostability and acid resistance. The mutants with improved catalytic properties attained in this work may render an accessible and operable approach for directed evolution of fungal α-amylase aimed at interesting functions.
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Affiliation(s)
- Song Li
- School of Biological and Chemical Engineering, Anhui Polytechnic University, Central Beijing Road, Wuhu, China
| | - Qian Yang
- School of Biological and Chemical Engineering, Anhui Polytechnic University, Central Beijing Road, Wuhu, China
| | - Bin Tang
- School of Biological and Chemical Engineering, Anhui Polytechnic University, Central Beijing Road, Wuhu, China
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5
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Xu Z, Cen YK, Zou SP, Xue YP, Zheng YG. Recent advances in the improvement of enzyme thermostability by structure modification. Crit Rev Biotechnol 2019; 40:83-98. [DOI: 10.1080/07388551.2019.1682963] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Zhe Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Ke Cen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Shu-Ping Zou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
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Bashirova A, Pramanik S, Volkov P, Rozhkova A, Nemashkalov V, Zorov I, Gusakov A, Sinitsyn A, Schwaneberg U, Davari MD. Disulfide Bond Engineering of an Endoglucanase from Penicillium verruculosum to Improve Its Thermostability. Int J Mol Sci 2019; 20:E1602. [PMID: 30935060 PMCID: PMC6479618 DOI: 10.3390/ijms20071602] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/25/2019] [Accepted: 03/27/2019] [Indexed: 01/29/2023] Open
Abstract
Endoglucanases (EGLs) are important components of multienzyme cocktails used in the production of a wide variety of fine and bulk chemicals from lignocellulosic feedstocks. However, a low thermostability and the loss of catalytic performance of EGLs at industrially required temperatures limit their commercial applications. A structure-based disulfide bond (DSB) engineering was carried out in order to improve the thermostability of EGLII from Penicillium verruculosum. Based on in silico prediction, two improved enzyme variants, S127C-A165C (DSB2) and Y171C-L201C (DSB3), were obtained. Both engineered enzymes displayed a 15⁻21% increase in specific activity against carboxymethylcellulose and β-glucan compared to the wild-type EGLII (EGLII-wt). After incubation at 70 °C for 2 h, they retained 52⁻58% of their activity, while EGLII-wt retained only 38% of its activity. At 80 °C, the enzyme-engineered forms retained 15⁻22% of their activity after 2 h, whereas EGLII-wt was completely inactivated after the same incubation time. Molecular dynamics simulations revealed that the introduced DSB rigidified a global structure of DSB2 and DSB3 variants, thus enhancing their thermostability. In conclusion, this work provides an insight into DSB protein engineering as a potential rational design strategy that might be applicable for improving the stability of other enzymes for industrial applications.
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Affiliation(s)
- Anna Bashirova
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Subrata Pramanik
- Institute of Biotechnology, RWTH Aachen University, Aachen 52074, Worringerweg 3, Germany.
| | - Pavel Volkov
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Aleksandra Rozhkova
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Vitaly Nemashkalov
- G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142292, Moscow region, Russia.
| | - Ivan Zorov
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
- Department of Chemistry, M.V.Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Alexander Gusakov
- Department of Chemistry, M.V.Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Arkady Sinitsyn
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
- Department of Chemistry, M.V.Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Aachen 52074, Worringerweg 3, Germany.
- DWI-Leibniz Institut für Interaktive Materialien, Forckenbeckstrasse 50, Aachen 52056, Germany.
| | - Mehdi D Davari
- Institute of Biotechnology, RWTH Aachen University, Aachen 52074, Worringerweg 3, Germany.
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Li G, Chen Y, Fang X, Su F, Xu L, Yan Y. Identification of a hot-spot to enhance Candida rugosa lipase thermostability by rational design methods. RSC Adv 2018; 8:1948-1957. [PMID: 35542566 PMCID: PMC9077275 DOI: 10.1039/c7ra11679a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/02/2018] [Indexed: 11/21/2022] Open
Abstract
Lipase is one of the most widely used classes of enzymes in biotechnological applications and organic chemistry. Candida rugosa lipases (CRL) can catalyze hydrolysis, esterification and transesterification with high regio-, stereo- and enantio-selectivity. However, thermal inactivation above 45 °C limits CRL's applications. Studies on improving the thermal stability of CRL are often limited by its slow-growing eukaryotic expression host, which is not suitable for large-scale screening. Identification of thermally stable mutants by rational design, regarded as an efficient substitution of experimental efforts, would provide a method for site-directed improvement of CRL. In this study, mutation-induced stability changes in CRL Lip1 were predicted by three rational design methods. Followed by conservative analyses and functional region exclusion, five mutants of a hot-spot, Asp457Phe, Asp457Trp, Asp457Met, Asp457Leu, and Asp457Tyr, were identified and prepared for enzymatic characterization. These five mutants increased the apparent melting temperature of Lip1 from 7.4 °C to 9.3 °C, with the most thermostable mutant, Asp457Phe, exhibiting a 5.5-fold longer half-life at 50 °C and a 10 °C increase in optimum temperature. Furthermore, pH stability of Lip1 was also enhanced due to the introduction of Asp457Phe mutation. The study demonstrates that thermally stable mutants of CRL could be identified with limited experimental efforts using rational design methods. The thermostability of Candida rugosa lipase expressed in a eukaryotic host is enhanced with limited experimental effort based on rational design methods.![]()
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Affiliation(s)
- Guanlin Li
- Key Laboratory of Molecular Biophysics
- The Ministry of Education
- College of Life Science and Technology
- Huazhong University of Science and Technology
- Wuhan 430074
| | - Yuan Chen
- Key Laboratory of Molecular Biophysics
- The Ministry of Education
- College of Life Science and Technology
- Huazhong University of Science and Technology
- Wuhan 430074
| | - Xingrong Fang
- Key Laboratory of Molecular Biophysics
- The Ministry of Education
- College of Life Science and Technology
- Huazhong University of Science and Technology
- Wuhan 430074
| | - Feng Su
- Key Laboratory of Molecular Biophysics
- The Ministry of Education
- College of Life Science and Technology
- Huazhong University of Science and Technology
- Wuhan 430074
| | - Li Xu
- Key Laboratory of Molecular Biophysics
- The Ministry of Education
- College of Life Science and Technology
- Huazhong University of Science and Technology
- Wuhan 430074
| | - Yunjun Yan
- Key Laboratory of Molecular Biophysics
- The Ministry of Education
- College of Life Science and Technology
- Huazhong University of Science and Technology
- Wuhan 430074
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Zhang XF, Yang GY, Zhang Y, Xie Y, Withers SG, Feng Y. A general and efficient strategy for generating the stable enzymes. Sci Rep 2016; 6:33797. [PMID: 27667190 PMCID: PMC5036031 DOI: 10.1038/srep33797] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 08/31/2016] [Indexed: 11/09/2022] Open
Abstract
The local flexibility of an enzyme's active center plays pivotal roles in catalysis, however, little is known about how the flexibility of these flexible residues affects stability. In this study, we proposed an active center stabilization (ACS) strategy to improve the kinetic thermostability of Candida rugosa lipase1. Based on the B-factor ranking at the region ~10 Å within the catalytic Ser209, 18 residues were selected for site-saturation mutagenesis. Based on three-tier high-throughput screening and ordered recombination mutagenesis, the mutant VarB3 (F344I/F434Y/F133Y/F121Y) was shown to be the most stable, with a 40-fold longer in half-life at 60 °C and a 12.7 °C higher Tm value than that of the wild type, without a decrease in catalytic activity. Further analysis of enzymes with different structural complexities revealed that focusing mutations on the flexible residues within around 10 Å of the catalytic residue might increase the success rate for enzyme stabilization. In summary, this study identifies a panel of flexible residues within the active center that affect enzyme stability. This finding not only provides clues regarding the molecular evolution of enzyme stability but also indicates that ACS is a general and efficient strategy for exploring the functional robustness of enzymes for industrial applications.
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Affiliation(s)
- Xiao-Fei Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guang-Yu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuan Xie
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Stephen G. Withers
- Department of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Structural traits and catalytic versatility of the lipases from the Candida rugosa-like family: A review. Biotechnol Adv 2016; 34:874-885. [DOI: 10.1016/j.biotechadv.2016.05.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/06/2016] [Accepted: 05/13/2016] [Indexed: 11/23/2022]
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