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Ivanović M, Knez Ž, Leitgeb M. Influence of Supercritical Carbon Dioxide on the Activity and Conformational Changes of α-Amylase, Lipase, and Peroxidase in the Solid State Using White Wheat Flour as an Example. Foods 2023; 12:4499. [PMID: 38137304 PMCID: PMC10743174 DOI: 10.3390/foods12244499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Green technologies using renewable and alternative sources, including supercritical carbon dioxide (sc-CO2), are becoming a priority for researchers in a variety of fields, including the control of enzyme activity which, among other applications, is extremely important in the food industry. Namely, extending shelf life of e.g., flour could be reached by tuning the present enzymes activity. In this study, the effect of different sc-CO2 conditions such as temperature (35-50 °C), pressure (200 bar and 300 bar), and exposure time (1-6 h) on the inactivation and structural changes of α-amylase, lipase, and horseradish peroxidase (POD) from white wheat flour and native enzymes was investigated. The total protein (TPC) content and residual activities of the enzymes were determined by standard spectrophotometric methods, while the changes in the secondary structures of the enzymes were determined by circular dichroism spectrometry (CD). The present work is therefore concerned for the first time with the study of the stability and structural changes of the enzyme molecules dominant in white wheat flour under sc-CO2 conditions at different pressures and temperatures. In addition, the changes in aggregation or dissociation of the enzyme molecules were investigated based on the changes in particle size distribution and ζ-potential. The results of the activity assays showed a decrease in the activity of native POD and lipase under optimal exposure conditions (6 h and 50 °C; and 1 h and 50 °C) by 22% and 16%, respectively. In contrast, no significant changes were observed in α-amylase activity. Consequently, analysis of the CD spectra of POD and lipase confirmed a significant effect on secondary structure damage (changes in α-helix, β-sheet, and β-turn content), whereas the secondary structure of α-amylase retained its original configuration. Moreover, the changes in particle size distribution and ζ-potential showed a significant effect of sc-CO2 treatment on the aggregation and dissociation of the selected enzymes. The results of this study confirm that sc-CO2 technology can be effectively used as an environmentally friendly technology to control the activity of major flour enzymes by altering their structures.
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Affiliation(s)
- Milena Ivanović
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia; (M.I.); (Ž.K.)
| | - Željko Knez
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia; (M.I.); (Ž.K.)
- Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia
| | - Maja Leitgeb
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia; (M.I.); (Ž.K.)
- Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia
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van der Ent F, Skagseth S, Lund BA, Sǒan J, Griese JJ, Brandsdal BO, Åqvist J. Computational design of the temperature optimum of an enzyme reaction. SCIENCE ADVANCES 2023; 9:eadi0963. [PMID: 37379391 DOI: 10.1126/sciadv.adi0963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/23/2023] [Indexed: 06/30/2023]
Abstract
Cold-adapted enzymes are characterized both by a higher catalytic activity at low temperatures and by having their temperature optimum down-shifted, compared to mesophilic orthologs. In several cases, the optimum does not coincide with the onset of protein melting but reflects some other type of inactivation. In the psychrophilic α-amylase from an Antarctic bacterium, the inactivation is thought to originate from a specific enzyme-substrate interaction that breaks around room temperature. Here, we report a computational redesign of this enzyme aimed at shifting its temperature optimum upward. A set of mutations designed to stabilize the enzyme-substrate interaction were predicted by computer simulations of the catalytic reaction at different temperatures. The predictions were verified by kinetic experiments and crystal structures of the redesigned α-amylase, showing that the temperature optimum is indeed markedly shifted upward and that the critical surface loop controlling the temperature dependence approaches the target conformation observed in a mesophilic ortholog.
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Affiliation(s)
- Florian van der Ent
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Susann Skagseth
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N9037 Tromsø, Norway
| | - Bjarte A Lund
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N9037 Tromsø, Norway
| | - Jaka Sǒan
- National Institute of Chemistry, SI-1001 Ljubljana, Slovenia
| | - Julia J Griese
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Bjørn O Brandsdal
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N9037 Tromsø, Norway
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N9037 Tromsø, Norway
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Gricajeva A, Kalėdienė L. Investigation of amino acids related to Staphylococcus saprophyticus AG1 EstAG1 carboxylesterase catalytic function revealed a new family of bacterial lipolytic enzymes. Int J Biol Macromol 2023; 235:123791. [PMID: 36828093 DOI: 10.1016/j.ijbiomac.2023.123791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/07/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023]
Abstract
Most of the lipolytic enzymes (carboxylesterases, EC 3.1.1.1 and triacylglycerol acylhydrolases, EC 3.1.1.3) originate from bacteria and form a large group of functionally important enzymes that are also well known for their use in multiple biotechnology sectors. Rapid and increasing amount of bacterial lipolytic enzymes being discovered and characterized led to a necessity to classify them. More than twenty years ago bacterial lipolytic enzymes were originally classified into eight families and six true lipase sub-families based on the differences in their amino acid sequences and biochemical properties. Later, this classification was comprehensively updated to 19 families with eight subfamilies, and more recently, employing deeper comparative analysis methods, classification expanded to 35 families and 11 subfamilies. Bacterial lipolytic enzymes that cannot be classified into currently existing families are still being discovered. This work provides site-directed mutagenesis and differential scanning fluorimetry based investigation of catalytic function-related amino acids of previously discovered and characterized EstAG1 carboxylesterase from Staphylococcus saprophyticus AG1. Experimental results obtained in this work revealed that EstAG1 carboxylesterase can be placed into a new family of bacterial lipolytic enzymes.
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Affiliation(s)
- Alisa Gricajeva
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania.
| | - Lilija Kalėdienė
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
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Öten AM, Atak E, Taktak Karaca B, Fırtına S, Kutlu A. Discussing the roles of proline and glycine from the perspective of cold adaptation in lipases and cellulases. BIOCATAL BIOTRANSFOR 2022. [DOI: 10.1080/10242422.2022.2124111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Ahmet Melih Öten
- Biology Education Center, Faculty of Science and Technology, Uppsala University, Uppsala, Sweden
| | - Evren Atak
- Bioinformatics and System Biology, Bioengineering Department, Gebze Technical University, Kocaeli, Turkey
| | - Banu Taktak Karaca
- Molecular Biology & Genetics Department, Faculty of Natural Science and Engineering, Atlas University, Istanbul, Turkey
| | - Sinem Fırtına
- Bioinformatics & Genetics, Faculty of Natural Science and Engineering, İstinye University, Istanbul, Turkey
| | - Aslı Kutlu
- Bioinformatics & Genetics, Faculty of Natural Science and Engineering, İstinye University, Istanbul, Turkey
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5
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van der Ent F, Lund BA, Svalberg L, Purg M, Chukwu G, Widersten M, Isaksen GV, Brandsdal BO, Åqvist J. Structure and Mechanism of a Cold-Adapted Bacterial Lipase. Biochemistry 2022; 61:933-942. [PMID: 35503728 PMCID: PMC9118546 DOI: 10.1021/acs.biochem.2c00087] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structural origin of enzyme cold-adaptation has been the subject of considerable research efforts in recent years. Comparative studies of orthologous mesophilic-psychrophilic enzyme pairs found in nature are an obvious strategy for solving this problem, but they often suffer from relatively low sequence identity of the enzyme pairs. Small bacterial lipases adapted to distinctly different temperatures appear to provide an excellent model system for these types of studies, as they may show a very high degree of sequence conservation. Here, we report the first crystal structures of lipase A from the psychrophilic bacterium Bacillus pumilus, which confirm the high structural similarity to the mesophilic Bacillus subtilis enzyme, as indicated by their 81% sequence identity. We further employ extensive QM/MM calculations to delineate the catalytic reaction path and its energetics. The computational prediction of a rate-limiting deacylation step of the enzymatic ester hydrolysis reaction is verified by stopped-flow experiments, and steady-state kinetics confirms the psychrophilic nature of the B. pumilus enzyme. These results provide a useful benchmark for examining the structural basis of cold-adaptation and should now make it possible to disentangle the effects of the 34 mutations between the two enzymes on catalytic properties and thermal stability.
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Affiliation(s)
- Florian van der Ent
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden
| | - Bjarte A Lund
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden.,Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø─The Arctic University of Norway, N9037 Tromsø, Norway
| | - Linn Svalberg
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden
| | - Miha Purg
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden
| | - Ghislean Chukwu
- Department of Chemistry─BMC, Uppsala University, Biomedical Center, SE-751 23 Uppsala, Sweden
| | - Mikael Widersten
- Department of Chemistry─BMC, Uppsala University, Biomedical Center, SE-751 23 Uppsala, Sweden
| | - Geir V Isaksen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø─The Arctic University of Norway, N9037 Tromsø, Norway
| | - Bjørn O Brandsdal
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø─The Arctic University of Norway, N9037 Tromsø, Norway
| | - Johan Åqvist
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden.,Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø─The Arctic University of Norway, N9037 Tromsø, Norway
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6
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Carretas-Valdez MI, Moreno-Cordova EN, Ibarra-Hernandez BG, Cinco-Moroyoqui FJ, Castillo-Yañez FJ, Casas-Flores S, Osuna-Amarillas PS, Islas-Osuna MA, Arvizu-Flores AA. Characterization of the trypsin-III from Monterey sardine (Sardinops caeruleus): Insights on the cold-adaptation from the A236N mutant. Int J Biol Macromol 2020; 164:2701-2710. [PMID: 32827617 DOI: 10.1016/j.ijbiomac.2020.08.136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 02/07/2023]
Abstract
Trypsins (E.C. 3.4.21.4) are digestive enzymes that catalyze the hydrolysis of peptide bonds containing arginine and lysine residues. Some trypsins from fish species are active at temperatures just above freezing, and for that are called cold-adapted enzymes, having many biotechnological applications. In this work, we characterized a recombinant trypsin-III from Monterey sardine (Sardinops caeruleus) and studied the role of a single residue on its cold-adapted features. The A236N mutant from sardine trypsin-III showed higher activation energy for the enzyme-catalyzed reaction, it was more active at higher temperatures, and exhibited a higher thermal stability than the wild-type enzyme, suggesting a key role of this residue. The thermodynamic activation parameters revealed an increase in the activation enthalpy for the A236N mutant, suggesting the existence of more intramolecular contacts during the activation step. Molecular models for both enzymes suggest that a hydrogen-bond involving N236 may contact the C-terminal α-helix to the vicinity of the active site, thus affecting the biochemical and thermodynamic properties of the enzyme.
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Affiliation(s)
- Manuel I Carretas-Valdez
- Universidad de Sonora, Departamento de Investigación y Posgrado en Alimentos, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Elena N Moreno-Cordova
- Universidad de Sonora, Departamento de Ciencias Químico-Biológicas, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Brisa G Ibarra-Hernandez
- Universidad de Sonora, Departamento de Investigación y Posgrado en Alimentos, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Francisco J Cinco-Moroyoqui
- Universidad de Sonora, Departamento de Investigación y Posgrado en Alimentos, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Francisco J Castillo-Yañez
- Universidad de Sonora, Departamento de Ciencias Químico-Biológicas, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Sergio Casas-Flores
- IPICYT, División de Biología Molecular, Camino a la Presa San José 2055, Col. Lomas 4a sección, San Luis Potosí, San Luis Potosí 78216, Mexico
| | - Pablo S Osuna-Amarillas
- Universidad Estatal de Sonora, Carretera Navojoa-Huatabampo km 5, Navojoa, Sonora 85874, Mexico
| | - Maria A Islas-Osuna
- Centro de Investigación en Alimentación y Desarrollo, Laboratorio de Genética y Biología Molecular de Plantas, Carr. Gustavo Enrique Astiazarán Rosas, N0. 46. Col. La Victoria, Hermosillo, Sonora 83304, Mexico.
| | - Aldo A Arvizu-Flores
- Universidad de Sonora, Departamento de Ciencias Químico-Biológicas, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico.
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7
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Cui H, Stadtmüller THJ, Jiang Q, Jaeger K, Schwaneberg U, Davari MD. How to Engineer Organic Solvent Resistant Enzymes: Insights from Combined Molecular Dynamics and Directed Evolution Study. ChemCatChem 2020. [DOI: 10.1002/cctc.202000422] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Haiyang Cui
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Tom H. J. Stadtmüller
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Qianjia Jiang
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme Technology Heinrich Heine University Düsseldorf and Research Center Jülich Wilhelm Johnen Strasse 52426 Jülich Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
- DWI-Leibniz Institute for Interactive Materials Forckenbeckstraße 50 52074 Aachen Germany
| | - Mehdi D. Davari
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
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Martínez R, Bernal C, Álvarez R, Concha C, Araya F, Cabrera R, Dhoke GV, Davari MD. Deletion and Randomization of Structurally Variable Regions in B. subtilis Lipase A (BSLA) Alter Its Stability and Hydrolytic Performance Against Long Chain Fatty Acid Esters. Int J Mol Sci 2020; 21:ijms21061990. [PMID: 32183336 PMCID: PMC7139672 DOI: 10.3390/ijms21061990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 12/16/2022] Open
Abstract
The continuous search for novel enzyme backbones and the engineering of already well studied enzymes for biotechnological applications has become an increasing challenge, especially by the increasing potential diversity space provided by directed enzyme evolution approaches and the demands of experimental data generated by rational design of enzymes. In this work, we propose a semi-rational mutational strategy focused on introducing diversity in structurally variable regions in enzymes. The identified sequences are subjected to a progressive deletion of two amino acids and the joining residues are subjected to saturation mutagenesis using NNK degenerate codons. This strategy offers a novel library diversity approach while simultaneously decreasing enzyme size in the variable regions. In this way, we intend to identify and reduce variable regions found in enzymes, probably resulting from neutral drift evolution, and simultaneously studying the functional effect of said regions. This strategy was applied to Bacillus. subtilis lipase A (BSLA), by selecting and deleting six variable enzyme regions (named regions 1 to 6) by the deletion of two amino acids and additionally randomizing the joining amino acid residues. After screening, no active variants were found in libraries 1% and 4%, 15% active variants were found in libraries 2% and 3%, and 25% for libraries 5 and 6 (n = 3000 per library, activity detected using tributyrin agar plates). Active variants were assessed for activity in microtiter plate assay (pNP-butyrate), thermal stability, substrate preference (pNP-butyrate, -palmitate), and compared to wildtype BSLA. From these analyses, variant P5F3 (F41L-ΔW42-ΔD43-K44P), from library 3 was identified, showing increased activity towards longer chain p-nitrophenyl fatty acid esters, when compared to BSLA. This study allowed to propose the targeted region 3 (positions 40-46) as a potential modulator for substrate specificity (fatty acid chain length) in BSLA, which can be further studied to increase its substrate spectrum and selectivity. Additionally, this variant showed a decreased thermal resistance but interestingly, higher isopropanol and Triton X-100 resistance. This deletion-randomization strategy could help to expand and explore sequence diversity, even in already well studied and characterized enzyme backbones such as BSLA. In addition, this strategy can contribute to investigate and identify important non-conserved regions in classic and novel enzymes, as well as generating novel biocatalysts with increased performance in specific processes, such as enzyme immobilization.
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Affiliation(s)
- Ronny Martínez
- Departamento de Ingeniería en Alimentos, Instituto de Investigación Multidisciplinaria en Ciencia y Tecnología, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena 1720010, Chile; (C.B.); (R.Á.); (C.C.)
- Correspondence: ; Tel.: +56-51-2334661; Fax: +56-51-2204446
| | - Claudia Bernal
- Departamento de Ingeniería en Alimentos, Instituto de Investigación Multidisciplinaria en Ciencia y Tecnología, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena 1720010, Chile; (C.B.); (R.Á.); (C.C.)
| | - Rodrigo Álvarez
- Departamento de Ingeniería en Alimentos, Instituto de Investigación Multidisciplinaria en Ciencia y Tecnología, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena 1720010, Chile; (C.B.); (R.Á.); (C.C.)
- Escuela de Tecnología Médica, Facultad de Salud, Sede La Serena, Universidad Santo Tomás, La Serena 1710172, Chile
| | - Christopher Concha
- Departamento de Ingeniería en Alimentos, Instituto de Investigación Multidisciplinaria en Ciencia y Tecnología, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena 1720010, Chile; (C.B.); (R.Á.); (C.C.)
| | - Fernando Araya
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile; (F.A.); (R.C.)
| | - Ricardo Cabrera
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile; (F.A.); (R.C.)
| | - Gaurao V. Dhoke
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany; (G.V.D.); (M.D.D.)
| | - Mehdi D. Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany; (G.V.D.); (M.D.D.)
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Kumar R, Goomber S, Kaur J. Engineering lipases for temperature adaptation: Structure function correlation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140261. [PMID: 31401312 DOI: 10.1016/j.bbapap.2019.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 01/13/2023]
Abstract
Bacillus lipases are industrially attractive enzymes due to their broad substrate specificity and optimum alkaline pH. However, narrow temperature range of action and low thermostability restrain their optimal use and thus, necessitate attention. Several laboratories are engaged in protein engineering of Bacillus lipases to generate variants with improved attributes for decades using techniques such as directed evolution or rational design. This review summarizes the effect of mutations on the conformational changes through in silico modeling and their manifestation with respect to various biochemical parameters. Various studies have been put together to develop a perspective on the molecular basis of biocatalysis of lipases holding industrial importance.
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Affiliation(s)
- Rakesh Kumar
- Department of Biotechnology, Panjab University, Chandigarh 160014, India; Department of Microbiology and Cell Biology, Indian Institute Of Science, Bangalore, Karnataka 560012, India
| | - Shelly Goomber
- Department of Biotechnology, Panjab University, Chandigarh 160014, India; National Institute of Malaria Research, Dwarka, New Delhi, Delhi 110077, India
| | - Jagdeep Kaur
- Department of Biotechnology, Panjab University, Chandigarh 160014, India.
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Solvent stable microbial lipases: current understanding and biotechnological applications. Biotechnol Lett 2018; 41:203-220. [PMID: 30535639 DOI: 10.1007/s10529-018-02633-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/30/2018] [Indexed: 01/10/2023]
Abstract
OBJECTIVE This review examines on our current understanding of microbial lipase solvent tolerance, with a specific focus on the molecular strategies employed to improve lipase stability in a non-aqueous environment. RESULTS It provides an overview of known solvent tolerant lipases and of approaches to improving solvent stability such as; enhancing stabilising interactions, modification of residue flexibility and surface charge alteration. It shows that judicious selection of lipase source supplemented by appropriate enzyme stabilisation, can lead to a wide application spectrum for lipases. CONCLUSION Organic solvent stable lipases are, and will continue to be, versatile and adaptable biocatalytic workhorses commonly employed for industrial applications in the food, pharmaceutical and green manufacturing industries.
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de Almeida JM, Moure VR, Müller-Santos M, de Souza EM, Pedrosa FO, Mitchell DA, Krieger N. Tailoring recombinant lipases: keeping the His-tag favors esterification reactions, removing it favors hydrolysis reactions. Sci Rep 2018; 8:10000. [PMID: 29968752 PMCID: PMC6030132 DOI: 10.1038/s41598-018-27579-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 06/04/2018] [Indexed: 12/19/2022] Open
Abstract
We determined the effect of the His-tag on the structure, activity, stability and immobilization of LipC12, a highly active lipase from a metagenomic library. We purified LipC12 with a N-terminal His-tag and then removed the tag using tobacco etch virus (TEV) protease. Circular dichroism analysis showed that the overall structure of LipC12 was largely unaffected by His-tag removal. The specific hydrolytic activities against natural and artificial substrates were significantly increased by the removal of the His-tag. On the other hand, His-tagged LipC12 was significantly more active and stable in the presence of polar organic solvents than untagged LipC12. The immobilization efficiency on Immobead 150 was 100% for both forms of LipC12 and protein desorption studies confirmed that the His-tag does not participate in the covalent binding of the enzyme. In the case of immobilized LipC12, the His-tag negatively influenced the hydrolytic activity, as it had for the free lipase, however, it positively influenced the esterification activity. These results raise the possibility of tailoring recombinant lipases for different applications, where the His-tag may be retained or removed, as appropriate for the desired activity.
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Affiliation(s)
- Janaina Marques de Almeida
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx.P. 19046 Centro Politécnico, Curitiba, 81531-980, Paraná, Brazil
| | - Vivian Rotuno Moure
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx.P. 19046 Centro Politécnico, Curitiba, 81531-980, Paraná, Brazil
| | - Marcelo Müller-Santos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx.P. 19046 Centro Politécnico, Curitiba, 81531-980, Paraná, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx.P. 19046 Centro Politécnico, Curitiba, 81531-980, Paraná, Brazil
| | - Fábio Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx.P. 19046 Centro Politécnico, Curitiba, 81531-980, Paraná, Brazil
| | - David Alexander Mitchell
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Cx.P. 19046 Centro Politécnico, Curitiba, 81531-980, Paraná, Brazil
| | - Nadia Krieger
- Departamento de Química, Universidade Federal do Paraná, Cx.P. 19081 Centro Politécnico, Curitiba, 81531-980, Paraná, Brazil.
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Fulton A, Hayes MR, Schwaneberg U, Pietruszka J, Jaeger KE. High-Throughput Screening Assays for Lipolytic Enzymes. Methods Mol Biol 2018; 1685:209-231. [PMID: 29086311 DOI: 10.1007/978-1-4939-7366-8_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Screening is defined as the identification of hits within a large library of variants of an enzyme or protein with a predefined property. In theory, each variant present in the respective library needs to be assayed; however, to save time and consumables, many screening regimes involve a primary round to identify clones producing active enzymes. Such primary or prescreenings for lipolytic enzyme activity are often carried out on agar plates containing pH indicators or substrates as triolein or tributyrin. Subsequently, high-throughput screening assays are usually performed in microtiter plate (MTP) format using chromogenic or fluorogenic substrates and, if available, automated liquid handling robotics. Here, we describe different assay systems to determine the activity and enantioselectivity of lipases and esterases as well as the synthesis of several substrates. We also report on the construction of a complete site saturation library derived from lipase A of Bacillus subtilis and its testing for detergent tolerance. This approach allows for the identification of amino acids affecting sensitivity or resistance against different detergents.
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Affiliation(s)
- Alexander Fulton
- Institute of Molecular Enzyme Technology, Heinrich-Heine - Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany
- Novozymes A/S, Krogshoejvej 36, 2880, Bagsvaerd, Denmark
| | - Marc R Hayes
- Institute of Bioorganic Chemistry, Heinrich-Heine - Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, 52074, Aachen, Germany
- DWI Leibniz-Institute for Interactive Materials at RWTH Aachen University, 52056, Aachen, Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry, Heinrich-Heine - Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine - Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany.
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany.
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Yaacob N, Ahmad Kamarudin NH, Leow ATC, Salleh AB, Raja Abd Rahman RNZ, Mohamad Ali MS. The Role of Solvent-Accessible Leu-208 of Cold-Active Pseudomonas fluorescens Strain AMS8 Lipase in Interfacial Activation, Substrate Accessibility and Low-Molecular Weight Esterification in the Presence of Toluene. Molecules 2017; 22:E1312. [PMID: 28805665 PMCID: PMC6152135 DOI: 10.3390/molecules22081312] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 07/31/2017] [Accepted: 08/04/2017] [Indexed: 11/23/2022] Open
Abstract
The alkaline cold-active lipase from Pseudomonas fluorescens AMS8 undergoes major structural changes when reacted with hydrophobic organic solvents. In toluene, the AMS8 lipase catalytic region is exposed by the moving hydrophobic lid 2 (Glu-148 to Gly-167). Solvent-accessible surface area analysis revealed that Leu-208, which is located next to the nucleophilic Ser-207 has a focal function in influencing substrate accessibility and flexibility of the catalytic pocket. Based on molecular dynamic simulations, it was found that Leu-208 strongly facilitates the lid 2 opening via its side-chain. The KM and Kcat/KM of L208A mutant were substrate dependent as it preferred a smaller-chain ester (pNP-caprylate) as compared to medium (pNP-laurate) or long-chain (pNP-palmitate) esters. In esterification of ethyl hexanoate, L208A promotes a higher ester conversion rate at 20 °C but not at 30 °C, as a 27% decline was observed. Interestingly, the wild-type (WT) lipase's conversion rate was found to increase with a higher temperature. WT lipase AMS8 esterification was higher in toluene as compared to L208A. Hence, the results showed that Leu-208 of AMS8 lipase plays an important role in steering a broad range of substrates into its active site region by regulating the flexibility of this region. Leu-208 is therefore predicted to be crucial for its role in interfacial activation and catalysis in toluene.
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Affiliation(s)
- Norhayati Yaacob
- Enzyme Technology/Molecular Biomedicine Laboratory, Enzyme and Microbial Technology Research Centre, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Malaysia.
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 Serdang, Malaysia.
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Department of Cell Biology and Molecule, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Malaysia.
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology Research Centre, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Malaysia.
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Malaysia.
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Malaysia.
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Deleting the Ig-Like Domain of Alicyclobacillus acidocaldarius Endoglucanase Cel9A Causes a Simultaneous Increase in the Activity and Stability. Mol Biotechnol 2016; 58:12-21. [PMID: 26537871 DOI: 10.1007/s12033-015-9900-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Endoglucanase Cel9A from Alicyclobacillus acidocaldarius (AaCel9A) is a monomeric enzyme with 537 residues. This enzyme has an Ig-like domain in the N-terminus of the catalytic domain. In this study, the role of the Ig-like domain on the activity, stability, and structural rigidity of AaCel9A and the effect of calcium on enzyme activity and stability were examined by comparing a truncated enzyme with deletion of the Ig-like domain (AaCel9AΔN) to the wild-type enzyme. Our results showed that the deletion of the Ig-like domain increased the catalytic efficiency of the truncated enzyme up to threefold without any significant changes in the K m of the enzyme. Furthermore, pH and temperature optimum for activity were shifted from 6.5 to 7.5 and from 65 to 60 °C, respectively, by deletion of the Ig-like domain. The thermal stability and fluorescence quenching results indicated that the stability and rigidity of the truncated enzyme have been more than that of the wild-type enzyme. Calcium similarly increased the catalytic efficiency of the enzymes (up to 40 %) and remarkably raised the stability of the AaCel9A compared to the AaCel9AΔN. This shows that Ig-like domain has a role in the increase of the enzyme stability by calcium in the wild-type enzyme.
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Santiago M, Ramírez-Sarmiento CA, Zamora RA, Parra LP. Discovery, Molecular Mechanisms, and Industrial Applications of Cold-Active Enzymes. Front Microbiol 2016; 7:1408. [PMID: 27667987 PMCID: PMC5016527 DOI: 10.3389/fmicb.2016.01408] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 08/25/2016] [Indexed: 11/17/2022] Open
Abstract
Cold-active enzymes constitute an attractive resource for biotechnological applications. Their high catalytic activity at temperatures below 25°C makes them excellent biocatalysts that eliminate the need of heating processes hampering the quality, sustainability, and cost-effectiveness of industrial production. Here we provide a review of the isolation and characterization of novel cold-active enzymes from microorganisms inhabiting different environments, including a revision of the latest techniques that have been used for accomplishing these paramount tasks. We address the progress made in the overexpression and purification of cold-adapted enzymes, the evolutionary and molecular basis of their high activity at low temperatures and the experimental and computational techniques used for their identification, along with protein engineering endeavors based on these observations to improve some of the properties of cold-adapted enzymes to better suit specific applications. We finally focus on examples of the evaluation of their potential use as biocatalysts under conditions that reproduce the challenges imposed by the use of solvents and additives in industrial processes and of the successful use of cold-adapted enzymes in biotechnological and industrial applications.
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Affiliation(s)
- Margarita Santiago
- Department of Chemical Engineering and Biotechnology, Centre for Biochemical Engineering and Biotechnology, Universidad de ChileSantiago, Chile
| | - César A. Ramírez-Sarmiento
- Schools of Engineering, Medicine and Biological Sciences, Institute for Biological and Medical Engineering, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Ricardo A. Zamora
- Departamento de Biología, Facultad de Ciencias, Universidad de ChileSantiago, Chile
| | - Loreto P. Parra
- Schools of Engineering, Medicine and Biological Sciences, Institute for Biological and Medical Engineering, Pontificia Universidad Católica de ChileSantiago, Chile
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de ChileSantiago, Chile
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Point Mutation Ile137-Met Near Surface Conferred Psychrophilic Behaviour and Improved Catalytic Efficiency to Bacillus Lipase of 1.4 Subfamily. Appl Biochem Biotechnol 2015; 178:753-65. [DOI: 10.1007/s12010-015-1907-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
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Borrelli GM, Trono D. Recombinant Lipases and Phospholipases and Their Use as Biocatalysts for Industrial Applications. Int J Mol Sci 2015; 16:20774-840. [PMID: 26340621 PMCID: PMC4613230 DOI: 10.3390/ijms160920774] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 07/17/2015] [Accepted: 08/11/2015] [Indexed: 11/29/2022] Open
Abstract
Lipases and phospholipases are interfacial enzymes that hydrolyze hydrophobic ester linkages of triacylglycerols and phospholipids, respectively. In addition to their role as esterases, these enzymes catalyze a plethora of other reactions; indeed, lipases also catalyze esterification, transesterification and interesterification reactions, and phospholipases also show acyltransferase, transacylase and transphosphatidylation activities. Thus, lipases and phospholipases represent versatile biocatalysts that are widely used in various industrial applications, such as for biodiesels, food, nutraceuticals, oil degumming and detergents; minor applications also include bioremediation, agriculture, cosmetics, leather and paper industries. These enzymes are ubiquitous in most living organisms, across animals, plants, yeasts, fungi and bacteria. For their greater availability and their ease of production, microbial lipases and phospholipases are preferred to those derived from animals and plants. Nevertheless, traditional purification strategies from microbe cultures have a number of disadvantages, which include non-reproducibility and low yields. Moreover, native microbial enzymes are not always suitable for biocatalytic processes. The development of molecular techniques for the production of recombinant heterologous proteins in a host system has overcome these constraints, as this allows high-level protein expression and production of new redesigned enzymes with improved catalytic properties. These can meet the requirements of specific industrial process better than the native enzymes. The purpose of this review is to give an overview of the structural and functional features of lipases and phospholipases, to describe the recent advances in optimization of the production of recombinant lipases and phospholipases, and to summarize the information available relating to their major applications in industrial processes.
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Affiliation(s)
- Grazia M Borrelli
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per la Cerealicoltura, S.S. 673 Km 25, 200-71122 Foggia, Italy.
| | - Daniela Trono
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per la Cerealicoltura, S.S. 673 Km 25, 200-71122 Foggia, Italy.
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Zhao J, Jia N, Jaeger KE, Bocola M, Schwaneberg U. Ionic liquid activatedBacillus subtilislipase A variants through cooperative surface substitutions. Biotechnol Bioeng 2015; 112:1997-2004. [DOI: 10.1002/bit.25617] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 03/27/2015] [Accepted: 04/06/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Jing Zhao
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3; 52074 Aachen Germany
| | - Ning Jia
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3; 52074 Aachen Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology; Heinrich-Heine-University Düsseldorf; Forschungszentrum Jülich; 52426 Jülich Germany
| | - Marco Bocola
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3; 52074 Aachen Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie; RWTH Aachen University; Worringerweg 3; 52074 Aachen Germany
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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]
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Bhanuramanand K, Ahmad S, Rao NM. Engineering deamidation-susceptible asparagines leads to improved stability to thermal cycling in a lipase. Protein Sci 2014; 23:1479-90. [PMID: 25043738 DOI: 10.1002/pro.2516] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 01/15/2023]
Abstract
At high temperatures, protein stability is influenced by chemical alterations; most important among them is deamidation of asparagines. Deamidation kinetics of asparagines depends on the local sequence, solvent, pH, temperature, and the tertiary structure. Suitable replacement of deamidated asparagines could be a viable strategy to improve deamidation-mediated loss in protein properties, specifically protein thermostability. In this study, we have used nano RP-HPLC coupled ESI MS/MS approach to identify residues susceptible to deamidation in a lipase (6B) on heat treatment. Out of 15 asparagines and six glutamines in 6B, only five asparagines were susceptible to deamidation at temperatures higher than 75°C. These five positions were subjected to site saturation mutagenesis followed by activity screen to identify the most suitable substitutions. Only three of the five asparagines were found to be tolerant to substitutions. Best substitutions at these positions were combined into a mutant. The resultant lipase (mutC) has near identical secondary structure and improved thermal tolerance as compared to its parent. The triple mutant has shown almost two-fold higher residual activity compared to 6B after four cycles at 90°C. MutC has retained more than 50% activity even after incubation at 100°C. Engineering asparagines susceptible to deamidation would be a potential strategy to improve proteins to withstand very high temperatures.
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Affiliation(s)
- K Bhanuramanand
- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, 500007, India
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