1
|
Qiao J, Sheng Y, Wang M, Li A, Li X, Huang H. Evolving Robust and Interpretable Enzymes for the Bioethanol Industry. Angew Chem Int Ed Engl 2023; 62:e202300320. [PMID: 36701239 DOI: 10.1002/anie.202300320] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/19/2023] [Accepted: 01/26/2023] [Indexed: 01/27/2023]
Abstract
Obtaining a robust and applicable enzyme for bioethanol production is a dream for biorefinery engineers. Herein, we describe a general method to evolve an all-round and interpretable enzyme that can be directly employed in the bioethanol industry. By integrating the transferable protein evolution strategy InSiReP 2.0 (In Silico guided Recombination Process), enzymatic characterization for actual production, and computational molecular understanding, the model cellulase PvCel5A (endoglucanase II Cel5A from Penicillium verruculosum) was successfully evolved to overcome the remaining challenges of low ethanol and temperature tolerance, which primarily limited biomass transformation and bioethanol yield. Remarkably, application of the PvCel5A variants in both first- and second-generation bioethanol production processes (i. Conventional corn ethanol fermentation combined with the in situ pretreatment process; ii. cellulosic ethanol fermentation process) resulted in a 5.7-10.1 % increase in the ethanol yield, which was unlikely to be achieved by other optimization techniques.
Collapse
Affiliation(s)
- Jie Qiao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Yijie Sheng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Minghui Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Anni Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China.,School of Pharmaceutical Science, Nanjing Tech University, Nanjing, 211816, China
| |
Collapse
|
2
|
Community evolution and frequent subgraph patterns affect the thermostability of B. subtilis lipase A. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.100984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
3
|
Cui H, Eltoukhy L, Zhang L, Markel U, Jaeger K, Davari MD, Schwaneberg U. Less Unfavorable Salt Bridges on the Enzyme Surface Result in More Organic Cosolvent Resistance. Angew Chem Int Ed Engl 2021; 60:11448-11456. [PMID: 33687787 PMCID: PMC8252522 DOI: 10.1002/anie.202101642] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Indexed: 11/06/2022]
Abstract
Biocatalysis for the synthesis of fine chemicals is highly attractive but usually requires organic (co-)solvents (OSs). However, native enzymes often have low activity and resistance in OSs and at elevated temperatures. Herein, we report a smart salt bridge design strategy for simultaneously improving OS resistance and thermostability of the model enzyme, Bacillus subtilits Lipase A (BSLA). We combined comprehensive experimental studies of 3450 BSLA variants and molecular dynamics simulations of 36 systems. Iterative recombination of four beneficial substitutions yielded superior resistant variants with up to 7.6-fold (D64K/D144K) improved resistance toward three OSs while exhibiting significant thermostability (thermal resistance up to 137-fold, and half-life up to 3.3-fold). Molecular dynamics simulations revealed that locally refined flexibility and strengthened hydration jointly govern the highly increased resistance in OSs and at 50-100 °C. The salt bridge redesign provides protein engineers with a powerful and likely general approach to design OSs- and/or thermal-resistant lipases and other α/β-hydrolases.
Collapse
Affiliation(s)
- Haiyang Cui
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- DWI Leibniz-Institute for Interactive MaterialsForckenbeckstrasse 5052074AachenGermany
| | - Lobna Eltoukhy
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Lingling Zhang
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesWest 7th Avenue 32, Tianjin Airport Economic Area300308TianjinChina
| | - Ulrich Markel
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme TechnologyHeinrich Heine University DüsseldorfWilhelm Johnen Strasse52426JülichGermany
- Institute of Bio-and Geosciences IBG 1: BiotechnologyForschungszentrum Jülich GmbHWilhelm Johnen Strasse52426JülichGermany
| | - Mehdi D. Davari
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
| | - Ulrich Schwaneberg
- Institute of BiotechnologyRWTH Aachen UniversityWorringer Weg 352074AachenGermany
- DWI Leibniz-Institute for Interactive MaterialsForckenbeckstrasse 5052074AachenGermany
| |
Collapse
|
4
|
Cui H, Eltoukhy L, Zhang L, Markel U, Jaeger K, Davari MD, Schwaneberg U. Less Unfavorable Salt Bridges on the Enzyme Surface Result in More Organic Cosolvent Resistance. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Haiyang Cui
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
- DWI Leibniz-Institute for Interactive Materials Forckenbeckstrasse 50 52074 Aachen Germany
| | - Lobna Eltoukhy
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
| | - Lingling Zhang
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences West 7th Avenue 32, Tianjin Airport Economic Area 300308 Tianjin China
| | - Ulrich Markel
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme Technology Heinrich Heine University Düsseldorf Wilhelm Johnen Strasse 52426 Jülich Germany
- Institute of Bio-and Geosciences IBG 1: Biotechnology Forschungszentrum Jülich GmbH Wilhelm Johnen Strasse 52426 Jülich Germany
| | - Mehdi D. Davari
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology RWTH Aachen University Worringer Weg 3 52074 Aachen Germany
- DWI Leibniz-Institute for Interactive Materials Forckenbeckstrasse 50 52074 Aachen Germany
| |
Collapse
|
5
|
Li G, Qin Y, Fontaine NT, Ng Fuk Chong M, Maria‐Solano MA, Feixas F, Cadet XF, Pandjaitan R, Garcia‐Borràs M, Cadet F, Reetz MT. Machine Learning Enables Selection of Epistatic Enzyme Mutants for Stability Against Unfolding and Detrimental Aggregation. Chembiochem 2021; 22:904-914. [PMID: 33094545 PMCID: PMC7984044 DOI: 10.1002/cbic.202000612] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/22/2020] [Indexed: 12/15/2022]
Abstract
Machine learning (ML) has pervaded most areas of protein engineering, including stability and stereoselectivity. Using limonene epoxide hydrolase as the model enzyme and innov'SAR as the ML platform, comprising a digital signal process, we achieved high protein robustness that can resist unfolding with concomitant detrimental aggregation. Fourier transform (FT) allows us to take into account the order of the protein sequence and the nonlinear interactions between positions, and thus to grasp epistatic phenomena. The innov'SAR approach is interpolative, extrapolative and makes outside-the-box, predictions not found in other state-of-the-art ML or deep learning approaches. Equally significant is the finding that our approach to ML in the present context, flanked by advanced molecular dynamics simulations, uncovers the connection between epistatic mutational interactions and protein robustness.
Collapse
Affiliation(s)
- Guangyue Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety Ministry of Agriculture, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100081P. R. China
| | - Youcai Qin
- State Key Laboratory for Biology of Plant Diseases and Insect Pests Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety Ministry of Agriculture, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100081P. R. China
| | - Nicolas T. Fontaine
- PEACCELArtificial Intelligence Department6 Square Albin Cachot, Box 4275013ParisFrance) .
| | - Matthieu Ng Fuk Chong
- PEACCELArtificial Intelligence Department6 Square Albin Cachot, Box 4275013ParisFrance) .
| | - Miguel A. Maria‐Solano
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de Girona Campus Montilivi17003Girona, CataloniaSpain) .
| | - Ferran Feixas
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de Girona Campus Montilivi17003Girona, CataloniaSpain) .
| | - Xavier F. Cadet
- PEACCELArtificial Intelligence Department6 Square Albin Cachot, Box 4275013ParisFrance) .
| | - Rudy Pandjaitan
- PEACCELArtificial Intelligence Department6 Square Albin Cachot, Box 4275013ParisFrance) .
| | - Marc Garcia‐Borràs
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de Girona Campus Montilivi17003Girona, CataloniaSpain) .
| | - Frederic Cadet
- PEACCELArtificial Intelligence Department6 Square Albin Cachot, Box 4275013ParisFrance) .
| | - Manfred T. Reetz
- Department of ChemistryPhilipps-Universität35032MarburgGermany) .
- Max-Planck-Institut fuer Kohlenforschung45470MülheimGermany
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences32 West 7th Avenue, Tianjin Airport Economic Area300308TianjinP. R. China
| |
Collapse
|
6
|
Sisila V, Puhazhselvan P, Aarthy M, Sakkeeshyaa G, Saravanan P, Kamini NR, Ayyadurai N. Esterification of Polymeric Carbohydrate Through Congener Cutinase-Like Biocatalyst. Appl Biochem Biotechnol 2020; 193:19-32. [PMID: 32808247 DOI: 10.1007/s12010-020-03415-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 08/12/2020] [Indexed: 11/29/2022]
Abstract
Cutinase-like enzymes (CLEs) are bi-functional hydrolases, which share the conserved catalytic site of lipase and consensus pentapeptide sequence of cutinase. Here, we have genetically replaced the canonical amino acids (CAA) by their non-canonical fluorinated surrogates to biosynthesize a novel class of congener biocatalyst for esterification of polymeric carbohydrate with long-chain fatty acid. It is a new enzyme-engineering approach used to manipulate industrially relevant biocatalyst through genetic incorporation of new functionally encoded non-canonical amino acids (NCAA). Global fluorination of CLE improved its catalytic, functional, and structural stability. Molecular docking studies confirmed that the fluorinated CLE (FCLE) had developed a binding affinity towards different fatty acids compared with the parent CLE. Importantly, FCLE could catalyze starch oleate synthesis in 24 h with a degree of substitution of 0.3 ± 0.001. Biophysical and microscopic analysis substantiated the efficient synthesis of the ester by FCLE. Our data represent the first step in the generation of an industrially relevant fluorous multifunctional enzyme for facile synthesis of high fatty acid starch esters.
Collapse
Affiliation(s)
- Valappil Sisila
- Division of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR), Central Leather Research Institute (CLRI), Chennai, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Puhazhendi Puhazhselvan
- Division of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR), Central Leather Research Institute (CLRI), Chennai, India
| | - Mayilvahanan Aarthy
- Division of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR), Central Leather Research Institute (CLRI), Chennai, India
| | | | - Perisamy Saravanan
- Department of Biotechnology, Rajalakshmi Engineering College, Chennai, India
| | - Numbi Ramudu Kamini
- Division of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR), Central Leather Research Institute (CLRI), Chennai, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Niraikulam Ayyadurai
- Division of Biochemistry and Biotechnology, Council of Scientific and Industrial Research (CSIR), Central Leather Research Institute (CLRI), Chennai, India. .,Academy of Scientific and Innovative Research, Ghaziabad, India.
| |
Collapse
|
7
|
The additive mutational effects from surface charge engineering: A compromise between enzyme activity, thermostability and ionic liquid tolerance. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2018.07.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|
8
|
Xia Q, Ding Y. Thermostability of Lipase A and Dynamic Communication Based on Residue Interaction Network. Protein Pept Lett 2019; 26:702-716. [PMID: 31215367 DOI: 10.2174/0929866526666190617091812] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/10/2019] [Accepted: 04/25/2019] [Indexed: 11/22/2022]
Abstract
OBJECTIVE Dynamic communication caused by mutation affects protein stability. The main objective of this study is to explore how mutations affect communication and to provide further insight into the relationship between heat resistance and signal propagation of Bacillus subtilis lipase (Lip A). METHODS The relationship between dynamic communication and Lip A thermostability is studied by long-time MD simulation and residue interaction network. The Dijkstra algorithm is used to get the shortest path of each residue pair. Subsequently, time-series frequent paths and spatio-temporal frequent paths are mined through an Apriori-like algorithm. RESULTS Time-series frequent paths show that the communication between residue pairs, both in wild-type lipase (WTL) and mutant 6B, becomes chaotic with an increase in temperature; however, more residues in 6B can maintain stable communication at high temperature, which may be associated with the structural rigidity. Furthermore, spatio-temporal frequent paths reflect the interactions among secondary structures. For WTL at 300K, β7, αC, αB, the longest loop, αA and αF contact frequently. The 310-helix between β3 and αA is penetrated by spatio-temporal frequent paths. At 400K, only αC can be frequently transmitted. For 6B, when at 300K, αA and αF are in more tight contact by spatio-temporal frequent paths though I157M and N166Y. Moreover, the rigidity of the active site His156 and the C-terminal of Lip A are increased, as reflected by the spatio-temporal frequent paths. At 400K, αA and αF, 310-helix between β3 and αA, the longest loop, and the loop where the active site Asp133 is located can still maintain stable communication. CONCLUSION From the perspective of residue dynamic communication, it is obviously found that mutations cause changes in interactions between secondary structures and enhance the rigidity of the structure, contributing to the thermal stability and functional activity of 6B.
Collapse
Affiliation(s)
- Qian Xia
- Laboratory of Media Design and Software Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Yanrui Ding
- Laboratory of Media Design and Software Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.,Key Laboratory of Industrial Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| |
Collapse
|
9
|
Zhou Y, Jones NC, Nedergaard Pedersen J, Pérez B, Vrønning Hoffmann S, Vang Petersen S, Skov Pedersen J, Perriman A, Kristensen P, Gao R, Guo Z. Insight into the Structure and Activity of Surface-Engineered Lipase Biofluids. Chembiochem 2019; 20:1266-1272. [PMID: 30624001 DOI: 10.1002/cbic.201800819] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Indexed: 11/07/2022]
Abstract
Despite a successful application of solvent-free liquid protein (biofluids) concept to a number of commercial enzymes, the technical advantages of enzyme biofluids as hyperthermal stable biocatalysts cannot be fully utilized as up to 90-99% of native activities are lost when enzymes were made into biofluids. With a two-step strategy (site-directed mutagenesis and synthesis of variant biofluids) on Bacillus subtilis lipase A (BsLA), we elucidated a strong dependency of structure and activity on the number and distribution of polymer surfactant binding sites on BsLA surface. Here, it is demonstrated that improved BsLA variants can be engineered via site-mutagenesis by a rational design, either with enhanced activity in aqueous solution in native form, or with improved physical property and increased activity in solvent-free system in the form of a protein liquid. This work answered some fundamental questions about the surface characteristics for construction of biofluids, useful for identifying new strategies for developing advantageous biocatalysts.
Collapse
Affiliation(s)
- Ye Zhou
- Key Laboratory for Molecular Enzymology and Engineering, Ministry of Education, School of Life Sciences, Jilin University, No. 2699, Qianjin Street, Changchun, 130012, China
- Department of Engineering, Aarhus University, Gustav Wieds Vej 10, Aarhus, 8000, Denmark
| | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, Aarhus, 8000, Denmark
| | - Jannik Nedergaard Pedersen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus, 8000, Denmark
| | - Bianca Pérez
- Eknologisk institut, Kongsvang Allé 29, Aarhus, 8000, Denmark
| | - Søren Vrønning Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, Aarhus, 8000, Denmark
| | - Steen Vang Petersen
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 4, Aarhus, 8000, Denmark
| | - Jan Skov Pedersen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus, 8000, Denmark
| | - Adam Perriman
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol, BS8 1TS, UK
| | - Peter Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Frederik Bayers Vej 7H, Aalborg, 9220, Denmark
| | - Renjun Gao
- Key Laboratory for Molecular Enzymology and Engineering, Ministry of Education, School of Life Sciences, Jilin University, No. 2699, Qianjin Street, Changchun, 130012, China
| | - Zheng Guo
- Department of Engineering, Aarhus University, Gustav Wieds Vej 10, Aarhus, 8000, Denmark
| |
Collapse
|
10
|
Sun Z, Liu Q, Qu G, Feng Y, Reetz MT. Utility of B-Factors in Protein Science: Interpreting Rigidity, Flexibility, and Internal Motion and Engineering Thermostability. Chem Rev 2019; 119:1626-1665. [PMID: 30698416 DOI: 10.1021/acs.chemrev.8b00290] [Citation(s) in RCA: 280] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Chemistry Department, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| |
Collapse
|
11
|
Javed S, Azeem F, Hussain S, Rasul I, Siddique MH, Riaz M, Afzal M, Kouser A, Nadeem H. Bacterial lipases: A review on purification and characterization. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 132:23-34. [DOI: 10.1016/j.pbiomolbio.2017.07.014] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 07/18/2017] [Accepted: 07/27/2017] [Indexed: 11/16/2022]
|
12
|
Structural and functional insights into thermostable and organic solvent stable variant Pro247-Ser of Bacillus lipase. Int J Biol Macromol 2017; 108:845-852. [PMID: 29101046 DOI: 10.1016/j.ijbiomac.2017.10.176] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 10/14/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Thermostability of enzymes is an important issue in protein engineering and has been studied in detail. Still there is no hard and fast rule to define the conditions which will provide thermal stability. Understanding the various factors and mechanism responsible for thermal stability will add on new insights into our present knowledge in this area. Pro247-Ser variant was constructed based on homology modelling and rational design. It exhibited 60 fold increase in thermal stability at 60°C and+0.7M shift in C1/2 value for urea denaturation as compared to WT. Variant displayed noticeable tolerance to organic solvents. With decrease in Km, catalytic efficiency of Pro247-Ser variant was increased by 12 fold. The activity and stability assay including circular dichroism and fluorescence spectroscopy favoured increased thermal performance of variant. Hydrolytic activity of variant was found to be high in comparison to control for all p-nitrophenol esters investigated. The immobilized variant enzyme demonstrated nearly two fold enhanced conversion of methyl oleate than WT enzyme. The additional molecular interactions of variant residue might contribute to increased thermostability of lipase. The homology modeling predicted formation of additional hydrogen bonds between Ser247/O-Thr251/OG1 as well as Ser247/O-Glu250/N.
Collapse
|
13
|
Hermans SM, Pfleger C, Nutschel C, Hanke CA, Gohlke H. Rigidity theory for biomolecules: concepts, software, and applications. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1311] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Susanne M.A. Hermans
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Christopher Pfleger
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Christina Nutschel
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Christian A. Hanke
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| |
Collapse
|
14
|
Ali Z, Tian L, Zhang B, Ali N, khan M, Zhang Q. Synthesis of paramagnetic dendritic silica nanomaterials with fibrous pore structure (Fe3O4@KCC-1) and their application in immobilization of lipase from Candida rugosa with enhanced catalytic activity and stability. NEW J CHEM 2017. [DOI: 10.1039/c7nj01912b] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Paramagnetic mesoporous fibrous silica (Fe3O4@KCC-1) was prepared and its surface was functionalized with 3-aminopropyltriethoxysilane (APTES).
Collapse
Affiliation(s)
- Zafar Ali
- The Key Laboratory of Space Applied Physics and Chemistry
- School of Science
- Northwestern Polytechnical University
- Xi'an
- China
| | - Lei Tian
- The Key Laboratory of Space Applied Physics and Chemistry
- School of Science
- Northwestern Polytechnical University
- Xi'an
- China
| | - Baoliang Zhang
- The Key Laboratory of Space Applied Physics and Chemistry
- School of Science
- Northwestern Polytechnical University
- Xi'an
- China
| | - Nisar Ali
- The Key Laboratory of Space Applied Physics and Chemistry
- School of Science
- Northwestern Polytechnical University
- Xi'an
- China
| | - Muhammad khan
- The Key Laboratory of Space Applied Physics and Chemistry
- School of Science
- Northwestern Polytechnical University
- Xi'an
- China
| | - Qiuyu Zhang
- The Key Laboratory of Space Applied Physics and Chemistry
- School of Science
- Northwestern Polytechnical University
- Xi'an
- China
| |
Collapse
|
15
|
Effects of point mutations on the thermostability of B. subtilis lipase: investigating nonadditivity. J Comput Aided Mol Des 2016; 30:899-916. [DOI: 10.1007/s10822-016-9978-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/22/2016] [Indexed: 11/26/2022]
|
16
|
Ahmad S, Pecqueur L, Dreier B, Hamdane D, Aumont-Nicaise M, Plückthun A, Knossow M, Gigant B. Destabilizing an interacting motif strengthens the association of a designed ankyrin repeat protein with tubulin. Sci Rep 2016; 6:28922. [PMID: 27380724 PMCID: PMC4933879 DOI: 10.1038/srep28922] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/13/2016] [Indexed: 01/10/2023] Open
Abstract
Affinity maturation by random mutagenesis and selection is an established technique to make binding molecules more suitable for applications in biomedical research, diagnostics and therapy. Here we identified an unexpected novel mechanism of affinity increase upon in vitro evolution of a tubulin-specific designed ankyrin repeat protein (DARPin). Structural analysis indicated that in the progenitor DARPin the C-terminal capping repeat (C-cap) undergoes a 25° rotation to avoid a clash with tubulin upon binding. Additionally, the C-cap appears to be involved in electrostatic repulsion with tubulin. Biochemical and structural characterizations demonstrated that the evolved mutants achieved a gain in affinity through destabilization of the C-cap, which relieves the need of a DARPin conformational change upon tubulin binding and removes unfavorable interactions in the complex. Therefore, this specific case of an order-to-disorder transition led to a 100-fold tighter complex with a subnanomolar equilibrium dissociation constant, remarkably associated with a 30% decrease of the binding surface.
Collapse
Affiliation(s)
- Shoeb Ahmad
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Ludovic Pecqueur
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Magali Aumont-Nicaise
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Marcel Knossow
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Benoît Gigant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| |
Collapse
|
17
|
Rathi PC, Fulton A, Jaeger KE, Gohlke H. Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis. PLoS Comput Biol 2016; 12:e1004754. [PMID: 27003415 PMCID: PMC4803202 DOI: 10.1371/journal.pcbi.1004754] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/14/2016] [Indexed: 11/29/2022] Open
Abstract
Protein thermostability is a crucial factor for biotechnological enzyme applications. Protein engineering studies aimed at improving thermostability have successfully applied both directed evolution and rational design. However, for rational approaches, the major challenge remains the prediction of mutation sites and optimal amino acid substitutions. Recently, we showed that such mutation sites can be identified as structural weak spots by rigidity theory-based thermal unfolding simulations of proteins. Here, we describe and validate a unique, ensemble-based, yet highly efficient strategy to predict optimal amino acid substitutions at structural weak spots for improving a protein’s thermostability. For this, we exploit the fact that in the majority of cases an increased structural rigidity of the folded state has been found as the cause for thermostability. When applied prospectively to lipase A from Bacillus subtilis, we achieved both a high success rate (25% over all experimentally tested mutations, which raises to 60% if small-to-large residue mutations and mutations in the active site are excluded) in predicting significantly thermostabilized lipase variants and a remarkably large increase in those variants’ thermostability (up to 6.6°C) based on single amino acid mutations. When considering negative controls in addition and evaluating the performance of our approach as a binary classifier, the accuracy is 63% and increases to 83% if small-to-large residue mutations and mutations in the active site are excluded. The gain in precision (predictive value for increased thermostability) over random classification is 1.6-fold (2.4-fold). Furthermore, an increase in thermostability predicted by our approach significantly points to increased experimental thermostability (p < 0.05). These results suggest that our strategy is a valuable complement to existing methods for rational protein design aimed at improving thermostability. Protein thermostability is a crucial factor for biotechnological enzyme applications. However, performance studies of computational approaches for predicting effects of mutations on protein (thermo)stability have suggested that there is still room for improvement. We describe and validate a novel and unique strategy to predict optimal amino acid substitutions at structural weak spots. At variance with other rational approaches, we exploit the fact that in the majority of cases an increased structural rigidity of the folded state is the underlying cause for thermostability. When applied prospectively on lipase LipA from Bacillus subtilis, a high success rate in predicting thermostabilized lipase variants and a remarkably large increase in their thermostability is achieved. This demonstrates the value of the novel strategy, which extends the existing portfolio of methods for rational protein design.
Collapse
Affiliation(s)
- Prakash Chandra Rathi
- Institute for Pharmaceutical and Medicinal Chemistry, Department of Mathematics and Natural Sciences, Heinrich-Heine-University, Düsseldorf, Germany
| | - Alexander Fulton
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University, Düsseldorf, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- * E-mail: (KEJ); (HG)
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Department of Mathematics and Natural Sciences, Heinrich-Heine-University, Düsseldorf, Germany
- * E-mail: (KEJ); (HG)
| |
Collapse
|
18
|
Zhang X, Yan S, Tyagi RD. Strategies of preserving lipids in microorganism after fermentation. BIORESOURCE TECHNOLOGY 2015; 192:718-725. [PMID: 26101961 DOI: 10.1016/j.biortech.2015.06.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 06/10/2015] [Accepted: 06/11/2015] [Indexed: 06/04/2023]
Abstract
Microbial oil is accumulated by microorganisms as stored energy during cultivation, and will be degraded to generate energy when they are not able to obtain external energy source. As the lipid is the desired production, the in situ degradation of oil by microorganisms after fermentation or during downstream processing has to be prevented. This study investigated the effect of pH, thermal, salinity, bead milling, ultrasonication, and microwave treatment on the viability of Trichosporon oleaginosus when it was used for lipid production. The cells in broth were completely inactivated with the treatment of pH 1 and 2 for 1h, temperature 80 °C for 10 min, ultrasonication for 8 min, and microwave for 6 min, respectively. It was observed that these treatments had no impact on final product (biodiesel) composition and were considered as safe and efficient methods to preserve lipid in cells.
Collapse
Affiliation(s)
- Xiaolei Zhang
- INRS Eau, Terre et Environnement, 490, rue de la Couronne, Québec G1K 9A9, Canada
| | - Song Yan
- INRS Eau, Terre et Environnement, 490, rue de la Couronne, Québec G1K 9A9, Canada
| | | |
Collapse
|
19
|
Rathi PC, Jaeger KE, Gohlke H. Structural Rigidity and Protein Thermostability in Variants of Lipase A from Bacillus subtilis. PLoS One 2015; 10:e0130289. [PMID: 26147762 PMCID: PMC4493141 DOI: 10.1371/journal.pone.0130289] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 05/18/2015] [Indexed: 11/24/2022] Open
Abstract
Understanding the origin of thermostability is of fundamental importance in protein biochemistry. Opposing views on increased or decreased structural rigidity of the folded state have been put forward in this context. They have been related to differences in the temporal resolution of experiments and computations that probe atomic mobility. Here, we find a significant (p = 0.004) and fair (R2 = 0.46) correlation between the structural rigidity of a well-characterized set of 16 mutants of lipase A from Bacillus subtilis (BsLipA) and their thermodynamic thermostability. We apply the rigidity theory-based Constraint Network Analysis (CNA) approach, analyzing directly and in a time-independent manner the statics of the BsLipA mutants. We carefully validate the CNA results on macroscopic and microscopic experimental observables and probe for their sensitivity with respect to input structures. Furthermore, we introduce a robust, local stability measure for predicting thermodynamic thermostability. Our results complement work that showed for pairs of homologous proteins that raising the structural stability is the most common way to obtain a higher thermostability. Furthermore, they demonstrate that related series of mutants with only a small number of mutations can be successfully analyzed by CNA, which suggests that CNA can be applied prospectively in rational protein design aimed at higher thermodynamic thermostability.
Collapse
Affiliation(s)
- Prakash Chandra Rathi
- Institute of Pharmaceutical and Medical Chemistry, Heinrich-Heine-University, Düsseldorf, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University, Düsseldorf, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Research Centre Jülich, Jülich, Germany
| | - Holger Gohlke
- Institute of Pharmaceutical and Medical Chemistry, Heinrich-Heine-University, Düsseldorf, Germany
- * E-mail:
| |
Collapse
|
20
|
Frauenkron-Machedjou VJ, Fulton A, Zhu L, Anker C, Bocola M, Jaeger KE, Schwaneberg U. Towards Understanding Directed Evolution: More than Half of All Amino Acid Positions Contribute to Ionic Liquid Resistance ofBacillus subtilisLipase A. Chembiochem 2015; 16:937-45. [DOI: 10.1002/cbic.201402682] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Indexed: 01/17/2023]
|
21
|
Singh B, Bulusu G, Mitra A. Understanding the thermostability and activity of Bacillus subtilis lipase mutants: insights from molecular dynamics simulations. J Phys Chem B 2015; 119:392-409. [PMID: 25495458 DOI: 10.1021/jp5079554] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Improving the thermostability of industrial enzymes is an important protein engineering challenge. Point mutations, induced to increase thermostability, affect the structure and dynamics of the target protein in several ways and thus can also affect its activity. There appears to be no general rules for improving the thermostabilty of enzymes without adversely affecting their enzymatic activity. We report MD simulations, of wild type Bacillus subtilis lipase (WT) and its six progressively thermostable mutants (2M, 3M, 4M, 6M, 9M, and 12M), performed at different temperatures, to address this issue. Less thermostable mutants (LTMs), 2M to 6M, show WT-like dynamics at all simulation temperatures. However, the two more thermostable mutants (MTMs) show the required flexibility at appropriate temperature ranges and maintain conformational stability at high temperature. They show a deep and rugged free-energy landscape, confining them within a near-native conformational space by conserving noncovalent interactions, and thus protecting them from possible aggregation. In contrast, the LTMs having marginally higher thermostabilities than WT show greater probabilities of accessing non-native conformations, which, due to aggregation, have reduced possibilities of reverting to their respective native states under refolding conditions. Our analysis indicates the possibility of nonadditive effects of point mutations on the conformational stability of LTMs.
Collapse
Affiliation(s)
- Bipin Singh
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology Hyderabad (IIIT-H) , Gachibowli, Hyderabad, 500032, India
| | | | | |
Collapse
|
22
|
Stability and Activity of Porcine Lipase Against Temperature and Chemical Denaturants. Appl Biochem Biotechnol 2014; 174:2711-24. [DOI: 10.1007/s12010-014-1220-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 09/02/2014] [Indexed: 10/24/2022]
|
23
|
Abedi Karjiban R, Lim WZ, Basri M, Abdul Rahman MB. Molecular Dynamics of Thermoenzymes at High Temperature and Pressure: A Review. Protein J 2014; 33:369-76. [DOI: 10.1007/s10930-014-9568-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
24
|
Hwang HT, Qi F, Yuan C, Zhao X, Ramkrishna D, Liu D, Varma A. Lipase-catalyzed process for biodiesel production: Protein engineering and lipase production. Biotechnol Bioeng 2013; 111:639-53. [PMID: 24284881 DOI: 10.1002/bit.25162] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/16/2013] [Accepted: 11/20/2013] [Indexed: 01/05/2023]
Affiliation(s)
- Hyun Tae Hwang
- School of Chemical Engineering; Purdue University; 480 Stadium Mall Drive West Lafayette Indiana 47907
| | - Feng Qi
- Department of Chemical Engineering; Institute of Applied Chemistry; Tsinghua University; Beijing China
| | - Chongli Yuan
- School of Chemical Engineering; Purdue University; 480 Stadium Mall Drive West Lafayette Indiana 47907
| | - Xuebing Zhao
- Department of Chemical Engineering; Institute of Applied Chemistry; Tsinghua University; Beijing China
| | - Doraiswami Ramkrishna
- School of Chemical Engineering; Purdue University; 480 Stadium Mall Drive West Lafayette Indiana 47907
| | - Dehua Liu
- Department of Chemical Engineering; Institute of Applied Chemistry; Tsinghua University; Beijing China
| | - Arvind Varma
- School of Chemical Engineering; Purdue University; 480 Stadium Mall Drive West Lafayette Indiana 47907
| |
Collapse
|
25
|
Yun HS, Park HJ, Joo JC, Yoo YJ. Thermostabilization of Bacillus subtilis lipase A by minimizing the structural deformation caused by packing enhancement. ACTA ACUST UNITED AC 2013; 40:1223-9. [DOI: 10.1007/s10295-013-1330-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 08/06/2013] [Indexed: 11/24/2022]
Abstract
Abstract
Enzyme thermostabilization is a critical research topic due to potential industrial benefits. Among the various reasons to increase enzyme thermostability, enhancement of residual packing at the core of the enzyme structure has been commonly accepted as a successful strategy. However, structural changes that occur with residual packing enhancement may decrease enzyme activity. In this study, a strategy to minimize structural deformation by calculating the overlapping packing volume of a single-point mutation followed by applying a double-point mutation was suggested. Four double mutants, A38V_K23A, A75V_T83A, G80A_N106A, and G172A_V100A, were selected for the in vitro experiment; three of the four showed enhancements in both thermostability and catalytic activity. In particular, G80A_N106A showed 2.78 times higher catalytic activity compared with wild type.
Collapse
Affiliation(s)
- Hong Seung Yun
- grid.31501.36 0000000404705905 School of Chemical and Biological Engineering Seoul National University 151-742 Seoul Korea
| | - Hyun June Park
- grid.31501.36 0000000404705905 Graduate Program of Bioengineering Seoul National University 151-742 Seoul Korea
| | - Jeong Chan Joo
- grid.31501.36 0000000404705905 School of Chemical and Biological Engineering Seoul National University 151-742 Seoul Korea
| | - Young Je Yoo
- grid.31501.36 0000000404705905 School of Chemical and Biological Engineering Seoul National University 151-742 Seoul Korea
- grid.31501.36 0000000404705905 Graduate Program of Bioengineering Seoul National University 151-742 Seoul Korea
- grid.31501.36 0000000404705905 Bio-Max Institute Seoul National University 151-742 Seoul Korea
| |
Collapse
|
26
|
Pfleger C, Gohlke H. Efficient and robust analysis of biomacromolecular flexibility using ensembles of network topologies based on fuzzy noncovalent constraints. Structure 2013; 21:1725-34. [PMID: 23994009 DOI: 10.1016/j.str.2013.07.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 07/04/2013] [Accepted: 07/17/2013] [Indexed: 11/19/2022]
Abstract
We describe an approach (ENT(FNC)) for performing rigidity analyses of biomacromolecules on ensembles of network topologies (ENT) generated from a single input structure. The ENT is based on fuzzy noncovalent constraints, which considers thermal fluctuations of biomacromolecules without actually sampling conformations. Definitions for fuzzy noncovalent constraints were derived from persistency data from molecular dynamics (MD) simulations. A very good agreement between local flexibility and rigidity characteristics from ENT(FNC) and MD simulations-generated ensembles is found. Regarding global characteristics, convincing results were obtained when relative thermostabilities of citrate synthase and lipase A structures were computed. The ENT(FNC) approach significantly improves the robustness of rigidity analyses, is highly efficient, and does not require a protein-specific parameterization. Its low computational demand makes it especially valuable for the analysis of large data sets, e.g., for data-driven protein engineering.
Collapse
Affiliation(s)
- Christopher Pfleger
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | | |
Collapse
|
27
|
Tao Q, Li A, Liu X, Gao H, Zhang Z, Ma R, An Y, Shi L. Improved thermal stability of lipase in W/O microemulsion by temperature-sensitive polymers. Colloids Surf B Biointerfaces 2013; 111:587-93. [PMID: 23907047 DOI: 10.1016/j.colsurfb.2013.06.055] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Revised: 06/26/2013] [Accepted: 06/30/2013] [Indexed: 11/16/2022]
Abstract
Lipase is active at the water-oil interface and thus very useful for many applications in non-aqueous media. However, the use of lipase is often limited due to the heat inactivation which is mainly caused by the irreversible aggregation among lipase molecules. The temperature-sensitive polymers can spontaneously form complexes with lipases at higher temperature in the confined spaces of the water in oil microemulsion. With cooling, lipases are released from the complexes and refold into the native state. In this way, the thermal stability of lipase in a microemulsion is effectively improved, and so is the stability of lipase at ambient temperature. Apart from proving the effectiveness and generality of this method, the temperature-sensitive polymers/lipase microemulsion represents a simple and efficient system which could be used in practical applications, since lipase retains the interfacial activity in this system. Moreover, the influences of some factors on the improvement are discussed and the mechanism of this method is suggested after exploring the process by dynamic light scattering and fluorescence measurements.
Collapse
Affiliation(s)
- Qian Tao
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Ang Li
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xue Liu
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hongjun Gao
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhenkun Zhang
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Rujiang Ma
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yingli An
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Linqi Shi
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
| |
Collapse
|
28
|
Role of active site rigidity in activity: MD simulation and fluorescence study on a lipase mutant. PLoS One 2012; 7:e35188. [PMID: 22514720 PMCID: PMC3325981 DOI: 10.1371/journal.pone.0035188] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 03/09/2012] [Indexed: 11/19/2022] Open
Abstract
Relationship between stability and activity of enzymes is maintained by underlying conformational flexibility. In thermophilic enzymes, a decrease in flexibility causes low enzyme activity while in less stable proteins such as mesophiles and psychrophiles, an increase in flexibility is associated with enhanced enzyme activity. Recently, we identified a mutant of a lipase whose stability and activity were enhanced simultaneously. In this work, we probed the conformational dynamics of the mutant and the wild type lipase, particularly flexibility of their active site using molecular dynamic simulations and time-resolved fluorescence techniques. In contrast to the earlier observations, our data show that active site of the mutant is more rigid than wild type enzyme. Further investigation suggests that this lipase needs minimal reorganization/flexibility of active site residues during its catalytic cycle. Molecular dynamic simulations suggest that catalytically competent active site geometry of the mutant is relatively more preserved than wild type lipase, which might have led to its higher enzyme activity. Our study implies that widely accepted positive correlation between conformation flexibility and enzyme activity need not be stringent and draws attention to the possibility that high enzyme activity can still be accomplished in a rigid active site and stable protein structures. This finding has a significant implication towards better understanding of involvement of dynamic motions in enzyme catalysis and enzyme engineering through mutations in active site.
Collapse
|
29
|
Augustyniak W, Brzezinska AA, Pijning T, Wienk H, Boelens R, Dijkstra BW, Reetz MT. Biophysical characterization of mutants of Bacillus subtilis lipase evolved for thermostability: factors contributing to increased activity retention. Protein Sci 2012; 21:487-97. [PMID: 22267088 DOI: 10.1002/pro.2031] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 12/14/2011] [Accepted: 01/08/2012] [Indexed: 11/10/2022]
Abstract
Previously, Lipase A from Bacillus subtilis was subjected to in vitro directed evolution using iterative saturation mutagenesis, with randomization sites chosen on the basis of the highest B-factors available from the crystal structure of the wild-type (WT) enzyme. This provided mutants that, unlike WT enzyme, retained a large part of their activity after heating above 65 °C and cooling down. Here, we subjected the three best mutants along with the WT enzyme to biophysical and biochemical characterization. Combining thermal inactivation profiles, circular dichroism, X-ray structure analyses and NMR experiments revealed that mutations of surface amino acid residues counteract the tendency of Lipase A to undergo precipitation under thermal stress. Reduced precipitation of the unfolding intermediates rather than increased conformational stability of the evolved mutants seems to be responsible for the activity retention.
Collapse
Affiliation(s)
- Wojciech Augustyniak
- Max-Planck-Institut fur Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mulheim an der Ruhr, Germany
| | | | | | | | | | | | | |
Collapse
|
30
|
Ahmad S, Kumar V, Ramanand KB, Rao NM. Probing protein stability and proteolytic resistance by loop scanning: a comprehensive mutational analysis. Protein Sci 2012; 21:433-46. [PMID: 22246996 DOI: 10.1002/pro.2029] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 12/23/2011] [Accepted: 01/06/2012] [Indexed: 11/07/2022]
Abstract
Improvement in protein thermostability was often found to be associated with increase in its proteolytic resistance as revealed by comparative studies of homologous proteins from extremophiles or mutational studies. Structural elements of protein responsible for this association are not firmly established although loops are implicated indirectly due to their structural role in protein stability. To get a better insight, a detailed study of protein wide mutants and their influence on stability and proteolytic resistance would be helpful. To generate such a data set, a model protein, Bacillus subtilis lipase was subjected to loop scanning site-saturation mutagenesis on 86 positions spanning all loops including termini. Upon screening of ~16,000 clones, 17 single mutants with improved thermostability were identified with increment in apparent melting temperature (Tm(app) ) by 1-6°C resulting in an increase in free energy of unfolding (ΔG(unf) ) by 0.04-1.16 kcal/mol. Proteolytic resistance of all single mutants upon incubation with nonspecific protease, Subtilisin A, was determined. Upon comparison, post-proteolysis residual activities as well as kinetics of proteolysis of mutants showed excellent correlation with ΔG(unf) , (r > 0.9), suggesting that proteolysis was strongly correlated with the global stability of this protein. This significant correlation in this set, with least possible sequence changes (single aa substitution), while covering >60% of protein surface strongly argues for the covariance of these two variables. Compared to studies from extremophiles, with large sequence heterogeneity, the observed correlation in such a narrow sequence space (ΔΔG(unf) = 1.57 kcal⁻¹) justifies the robustness of this relation.
Collapse
Affiliation(s)
- Shoeb Ahmad
- Centre for Cellular and Molecular Biology (Council of Scientific and Industrial Research), Uppal Road, Hyderabad 500007, India
| | | | | | | |
Collapse
|
31
|
Gumulya Y, Reetz MT. Enhancing the Thermal Robustness of an Enzyme by Directed Evolution: Least Favorable Starting Points and Inferior Mutants Can Map Superior Evolutionary Pathways. Chembiochem 2011; 12:2502-10. [DOI: 10.1002/cbic.201100412] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Indexed: 12/22/2022]
|
32
|
Kamal MZ, Ahmad S, Molugu TR, Vijayalakshmi A, Deshmukh MV, Sankaranarayanan R, Rao NM. In vitro evolved non-aggregating and thermostable lipase: structural and thermodynamic investigation. J Mol Biol 2011; 413:726-41. [PMID: 21925508 DOI: 10.1016/j.jmb.2011.09.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Revised: 08/02/2011] [Accepted: 09/02/2011] [Indexed: 11/27/2022]
Abstract
Rational and in vitro evolutionary approaches to improve either protein stability or aggregation resistance were successful, but empirical rules for simultaneous improvement of both stability and aggregation resistance under denaturing conditions are still to be ascertained. We have created a robust variant of a lipase from Bacillus subtilis named "6B" using multiple rounds of in vitro evolution. T(m) and optimum activity temperature of 6B is 78 °C and 65 °C, respectively, which is ~22 °C and 30 °C higher than that of wild-type lipase. Most significantly, 6B does not aggregate upon heating. Physical basis of remarkable thermostability and non-aggregating behavior of 6B was explored using X-ray crystallography, NMR and differential scanning calorimetry. Our structural investigations highlight the importance of tightening of mobile regions of the molecule such as loops and helix termini to attain higher thermostability. Accordingly, NMR studies suggest a very rigid structure of 6B lipase. Further investigation suggested that reduction/perturbation of the large hydrophobic patches present in the wild-type protein structure, decreased propensity of amino acid sequence for aggregation and absence of aggregation-prone intermediate during thermal unfolding of 6B can account for its resistance to aggregation. Overall, our study suggest that better anchoring of the loops with the rest of the protein molecule through mutations particularly on the sites that perturb/disturb the exposed hydrophobic patches can simultaneously increase protein stability and aggregation resistance.
Collapse
Affiliation(s)
- Md Zahid Kamal
- Centre for Cellular and Molecular Biology (Council of Scientific and Industrial Research), Hyderabad 500007, India
| | | | | | | | | | | | | |
Collapse
|
33
|
Kamal MZ, Ahmad S, Yedavalli P, Rao NM. Stability curves of laboratory evolved thermostable mutants of a Bacillus subtilis lipase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1850-6. [PMID: 20599630 DOI: 10.1016/j.bbapap.2010.06.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 06/14/2010] [Accepted: 06/17/2010] [Indexed: 11/26/2022]
Abstract
Shape of the protein stability curves changes to achieve higher melting temperature. Broadly, these changes have been classified as upward shift (increased G(s)), rightward shift (increase in T(s)) and flattening of the stability curves (decrease in C(p)). Comparative studies on homologous mesophilic-thermophilic protein pairs highlighted the differential contribution of these three strategies amongst proteins. But unambiguous way of identification of the strategies, which will be preferred for a protein, is still not achieved. We have performed comparative thermodynamic studies using differential scanning calorimeter (DSC) on thermostable variants of a lipase from Bacillus subtilis. These variants are products of 1, 2, 3 and 4 rounds of directed evolution and harbor mutations having definite contribution in thermostability unlike natural thermophilic proteins. We have shown that upward and rightward shift in stability curves are prime strategies in this lipase. Our results along with that from the other study on laboratory evolved xylanase A suggest that optimization of suboptimal thermodynamic parameters is having a dominant influence in selection of thermodynamic strategies for higher thermostability.
Collapse
Affiliation(s)
- Md Zahid Kamal
- Centre for Cellular and Molecular Biology, Council for Scientific and Industrial research, Uppal Road, Hyderabad-500007, India
| | | | | | | |
Collapse
|