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Regassa H, Bose D, Mukherjee A. Review of Microorganisms and Their Enzymatic Products for Industrial Bioprocesses. Ind Biotechnol (New Rochelle N Y) 2021. [DOI: 10.1089/ind.2021.0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Hailemeleak Regassa
- Faculty of Applied Sciences & Biotechnology, Shoolini University of Biotechnology & Management Sciences, Solan, Himachal Pradesh, India
| | - Debajyoti Bose
- Faculty of Applied Sciences & Biotechnology, Shoolini University of Biotechnology & Management Sciences, Solan, Himachal Pradesh, India
| | - Alivia Mukherjee
- Department of Chemical and Biological Engineering, University of Saskatchewan, Saskatoon, SK, Canada
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2
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Joondan N, Angundhooa HD, Bhowon MG, Caumul P, Laulloo SJ. Detergent Properties of Coconut Oil Derived N-Acyl Prolinate Surfactant and the In silico Studies on its Effectiveness Against SARS-CoV-2 (COVID-19). TENSIDE SURFACT DET 2020. [DOI: 10.3139/113.110705] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Abstract
In this work, we report the application of coconut oil derived N-acyl prolinate surfactant as a potential ingredient in laundry detergent formulation using biological, physicochemical and molecular docking approach. The properties of the sodium cocyl prolinate surfactant 2 were compared with those of sodium cocoate surfactant 1, a sodium salt of fatty acids from coconut oil, as well as the conventional surfactant sodium dodecyl sulphate (SDS) which is commonly used in the detergent industry. Sodium cocyl prolinate surfactant 2 showed a lower foaming ability compared to SDS and was found to exert a better detergency at a much lower temperature (25°C) compared to surfactant 1 and SDS. The coconut oil based surfactants 1 and 2 displayed a better antibacterial activity against gram positive strains compared to SDS. In view of studying the effectiveness of the surfactants against the severe acute respiratory syndrome corona virus 2, SARS-CoV-2 (COVID-19) which might remain on the surface of contaminated clothes, molecular docking of surfactants 1 and 2 with the spike protein of SARS-CoV-2 was carried out. Surfactant 2 showed an optimum interaction with the amino acid residues of the spike protein which is responsible for the binding of the virus with the host receptors. Molecular docking with savinase, an enzyme used in laundry formulation showed that sodium cocyl prolinate surfactant 2 and SDS displayed comparable interactions with the enzyme. Overall, this study has shown that sodium cocyl prolinate surfactant 2 can be a potential candidate in laundry detergent formulation for machine washing due to its relatively low foaming ability and good detergency properties at a much lower temperature (25°C), making it more energy-efficient. Surfactant 2 was also found to be a promising antimicrobial agent in laundry detergent due to its moderate antibacterial activity and its interaction with the spike protein of SARS-CoV-2, which can help to reduce the spread of any epidemic or pandemic diseases.
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3
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Zhang Y, Xia Y, Liu X, Xiong Z, Wang S, Zhang N, Ai L. High-Level Expression and Substrate-Binding Region Modification of a Novel BL312 Milk-Clotting Enzyme To Enhance the Ratio of Milk-Clotting Activity to Proteolytic Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:13684-13693. [PMID: 31742396 DOI: 10.1021/acs.jafc.9b06114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A novel BL312 milk-clotting enzyme (MCE) exhibited high-level expression and remarkable milk-clotting activity (MCA) (865 ± 20 SU/mL) that was 3.3-fold higher than the control by optimizing induction conditions in recombinant Escherichia. coli harboring pET24a-proMCE. Through substrate-binding region analyses and modification, MCE-G165A was identified from nine mutants and showed a proteolytic activity of 49.4 ± 2.4 U/mL and an MCA/PA ratio of 18.2, which were respectively 1.9-fold lower and 2.0-fold higher than those of the control. The purified MCE-G165A (28 kDa) exhibited weak αs-casein, β-casein, and strong κ-casein (κ-CN) hydrolysis levels as assessed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and reversed-phase high-performance liquid chromatography. The milk-clotting mechanism for MCE-G165A was the primary hydrolysis of Met106-Ala107 and Asn123-Thr124 bonds in κ-CN, as determined by mass spectrometry. MCE-G165A showed different hydrolysis sites in casein, leading to various functional peptides. Feasible methods for obtaining MCEs suitable as calf rennet substitutes are presented.
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Affiliation(s)
- Yao Zhang
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering , University of Shanghai for Science and Technology , Shanghai 200093 , China
| | - Yongjun Xia
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering , University of Shanghai for Science and Technology , Shanghai 200093 , China
| | - Xiaofeng Liu
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering , University of Shanghai for Science and Technology , Shanghai 200093 , China
| | - Zhiqiang Xiong
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering , University of Shanghai for Science and Technology , Shanghai 200093 , China
| | - Shijie Wang
- Shijiazhuang Junlebao Dairy Co., Ltd. , Shijiazhuang , Hebei 050221 , China
| | - Na Zhang
- Key Laboratory of Food Science and Engineering of Heilongjiang Province , Harbin University of Commerce , Harbin 150076 , China
| | - Lianzhong Ai
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering , University of Shanghai for Science and Technology , Shanghai 200093 , China
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4
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Xu Z, Cen YK, Zou SP, Xue YP, Zheng YG. Recent advances in the improvement of enzyme thermostability by structure modification. Crit Rev Biotechnol 2019; 40:83-98. [DOI: 10.1080/07388551.2019.1682963] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Zhe Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Ke Cen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Shu-Ping Zou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
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5
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Chang Z. The 2018 Nobel Prize in Chemistry: Engineering proteins (enzymes/peptide/antibodies) towards desired properties via the construction of random libraries. SCIENCE CHINA-LIFE SCIENCES 2019; 62:713-724. [PMID: 30931497 DOI: 10.1007/s11427-019-9498-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/01/2019] [Indexed: 10/27/2022]
Affiliation(s)
- Zengyi Chang
- School of Life Sciences, State Key Laboratory of Protein and Plant Engineering Research, Center for Protein Science, Center of History and Philosophy of Science, Peking University, Beijing, 100871, China.
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6
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Bjerga GEK, Larsen Ø, Arsın H, Williamson A, García-Moyano A, Leiros I, Puntervoll P. Mutational analysis of the pro-peptide of a marine intracellular subtilisin protease supports its role in inhibition. Proteins 2018; 86:965-977. [PMID: 29907987 PMCID: PMC6220982 DOI: 10.1002/prot.25528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/09/2018] [Accepted: 05/16/2018] [Indexed: 11/06/2022]
Abstract
Intracellular subtilisin proteases (ISPs) have important roles in protein processing during the stationary phase in bacteria. Their unregulated protein degrading activity may have adverse effects inside a cell, but little is known about their regulatory mechanism. Until now, ISPs have mostly been described from Bacillus species, with structural data from a single homolog. Here, we study a marine ISP originating from a phylogenetically distinct genus, Planococcus sp. The enzyme was successfully overexpressed in E. coli, and is active in presence of calcium, which is thought to have a role in minor, but essential, structural rearrangements needed for catalytic activity. The ISP operates at alkaline pH and at moderate temperatures, and has a corresponding melting temperature around 60 °C. The high-resolution 3-dimensional structure reported here, represents an ISP with an intact catalytic triad albeit in a configuration with an inhibitory pro-peptide bound. The pro-peptide is removed in other homologs, but the removal of the pro-peptide from the Planococcus sp. AW02J18 ISP appears to be different, and possibly involves several steps. A first processing step is described here as the removal of 2 immediate N-terminal residues. Furthermore, the pro-peptide contains a conserved LIPY/F-motif, which was found to be involved in inhibition of the catalytic activity.
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Affiliation(s)
- Gro E K Bjerga
- Uni Research, Center for Applied Biotechnology, Thormøhlens gate 55, Bergen, 5006, Norway
| | - Øivind Larsen
- Uni Research, Center for Applied Biotechnology, Thormøhlens gate 55, Bergen, 5006, Norway
| | - Hasan Arsın
- Department of Biological Sciences, University of Bergen, Thormøhlens gate 53, Bergen, 5006, Norway
| | - Adele Williamson
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, Tromsø, 9037, Norway
| | - Antonio García-Moyano
- Uni Research, Center for Applied Biotechnology, Thormøhlens gate 55, Bergen, 5006, Norway
| | - Ingar Leiros
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, Tromsø, 9037, Norway
| | - Pål Puntervoll
- Uni Research, Center for Applied Biotechnology, Thormøhlens gate 55, Bergen, 5006, Norway
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7
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Williams PD, Pollock DD, Goldstein RA. Functionality and the Evolution of Marginal Stability in Proteins: Inferences from Lattice Simulations. Evol Bioinform Online 2017. [DOI: 10.1177/117693430600200013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
It has been known for some time that many proteins are marginally stable. This has inspired several explanations. Having noted that the functionality of many enzymes is correlated with subunit motion, flexibility, or general disorder, some have suggested that marginally stable proteins should have an evolutionary advantage over proteins of differing stability. Others have suggested that stability and functionality are contradictory qualities, and that selection for both criteria results in marginally stable proteins, optimised to satisfy the competing design pressures. While these explanations are plausible, recent research simulating the evolution of model proteins has shown that selection for stability, ignoring any aspects of functionality, can result in marginally stable proteins because of the underlying makeup of protein sequence-space. We extend this research by simulating the evolution of proteins, using a computational protein model that equates functionality with binding and catalysis. In the model, marginal stability is not required for ligand-binding functionality and we observe no competing design pressures. The resulting proteins are marginally stable, again demonstrating that neutral evolution is sufficient for explaining marginal stability in observed proteins.
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Affiliation(s)
- Paul D. Williams
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - David D. Pollock
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Richard A. Goldstein
- Mathematical Biology, National Institute for Medical Sciences, The Ridgeway, Mill Hill, London MW7 1AA, UK
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8
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Sotokawauchi A, Kato-Murayama M, Murayama K, Hosaka T, Maeda I, Onjo M, Ohsawa N, Kato DI, Arima K, Shirouzu M. Structural basis of cucumisin protease activity regulation by its propeptide. J Biochem 2016; 161:45-53. [DOI: 10.1093/jb/mvw053] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/27/2016] [Indexed: 01/13/2023] Open
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9
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Wolski PW, Dana CM, Clark DS, Blanch HW. Engineering ionic liquid-tolerant cellulases for biofuels production. Protein Eng Des Sel 2016; 29:117-22. [DOI: 10.1093/protein/gzv066] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 12/07/2015] [Indexed: 12/22/2022] Open
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10
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Suplatov D, Voevodin V, Švedas V. Robust enzyme design: bioinformatic tools for improved protein stability. Biotechnol J 2014; 10:344-55. [PMID: 25524647 DOI: 10.1002/biot.201400150] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/30/2014] [Accepted: 11/04/2014] [Indexed: 01/22/2023]
Abstract
The ability of proteins and enzymes to maintain a functionally active conformation under adverse environmental conditions is an important feature of biocatalysts, vaccines, and biopharmaceutical proteins. From an evolutionary perspective, robust stability of proteins improves their biological fitness and allows for further optimization. Viewed from an industrial perspective, enzyme stability is crucial for the practical application of enzymes under the required reaction conditions. In this review, we analyze bioinformatic-driven strategies that are used to predict structural changes that can be applied to wild type proteins in order to produce more stable variants. The most commonly employed techniques can be classified into stochastic approaches, empirical or systematic rational design strategies, and design of chimeric proteins. We conclude that bioinformatic analysis can be efficiently used to study large protein superfamilies systematically as well as to predict particular structural changes which increase enzyme stability. Evolution has created a diversity of protein properties that are encoded in genomic sequences and structural data. Bioinformatics has the power to uncover this evolutionary code and provide a reproducible selection of hotspots - key residues to be mutated in order to produce more stable and functionally diverse proteins and enzymes. Further development of systematic bioinformatic procedures is needed to organize and analyze sequences and structures of proteins within large superfamilies and to link them to function, as well as to provide knowledge-based predictions for experimental evaluation.
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Affiliation(s)
- Dmitry Suplatov
- Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
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11
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Li Z, Roccatano D, Lorenz M, Martinez R, Schwaneberg U. Insights on activity and stability of subtilisin E towards guanidinium chloride and sodium dodecylsulfate. J Biotechnol 2014; 169:87-94. [DOI: 10.1016/j.jbiotec.2013.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 10/17/2013] [Accepted: 11/03/2013] [Indexed: 11/25/2022]
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12
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Reetz MT. Biocatalysis in organic chemistry and biotechnology: past, present, and future. J Am Chem Soc 2013; 135:12480-96. [PMID: 23930719 DOI: 10.1021/ja405051f] [Citation(s) in RCA: 522] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Enzymes as catalysts in synthetic organic chemistry gained importance in the latter half of the 20th century, but nevertheless suffered from two major limitations. First, many enzymes were not accessible in large enough quantities for practical applications. The advent of recombinant DNA technology changed this dramatically in the late 1970s. Second, many enzymes showed a narrow substrate scope, often poor stereo- and/or regioselectivity and/or insufficient stability under operating conditions. With the development of directed evolution beginning in the 1990s and continuing to the present day, all of these problems can be addressed and generally solved. The present Perspective focuses on these and other developments which have popularized enzymes as part of the toolkit of synthetic organic chemists and biotechnologists. Included is a discussion of the scope and limitation of cascade reactions using enzyme mixtures in vitro and of metabolic engineering of pathways in cells as factories for the production of simple compounds such as biofuels and complex natural products. Future trends and problems are also highlighted, as is the discussion concerning biocatalysis versus nonbiological catalysis in synthetic organic chemistry. This Perspective does not constitute a comprehensive review, and therefore the author apologizes to those researchers whose work is not specifically treated here.
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Affiliation(s)
- Manfred T Reetz
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein Strasse, 35032 Marburg, Germany.
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13
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Liu B, Zhang J, Fang Z, Gu L, Liao X, Du G, Chen J. Enhanced thermostability of keratinase by computational design and empirical mutation. J Ind Microbiol Biotechnol 2013; 40:697-704. [PMID: 23619970 DOI: 10.1007/s10295-013-1268-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 04/01/2013] [Indexed: 11/25/2022]
Abstract
Keratinases are proteolytic enzymes capable of degrading insoluble keratins. The importance of these enzymes is being increasingly recognized in fields as diverse as animal feed production, textile processing, detergent formulation, leather manufacture, and medicine. To enhance the thermostability of Bacillus licheniformis BBE11-1 keratinase, the PoPMuSiC algorithm was applied to predict the folding free energy change (ΔΔG) of amino acid substitutions. Use of the algorithm in combination with molecular modification of homologous subtilisin allowed the introduction of four amino acid substitutions (N122Y, N217S, A193P, N160C) into the enzyme by site-directed mutagenesis, and the mutant genes were expressed in Bacillus subtilis WB600. The quadruple mutant displayed synergistic or additive effects with an 8.6-fold increase in the t 1/2 value at 60 °C. The N122Y substitution also led to an approximately 5.6-fold increase in catalytic efficiency compared to that of the wild-type keratinase. These results provide further insight into the thermostability of keratinase and suggest further potential industrial applications.
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Affiliation(s)
- Baihong Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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14
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Reetz MT. Gerichtete Evolution stereoselektiver Enzyme: Eine ergiebige Katalysator‐Quelle für asymmetrische Reaktionen. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000826] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Manfred T. Reetz
- Max‐Planck‐Institut für Kohlenforschung, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Deutschland), Fax: (+49) 208‐306‐2985 http://www.mpi‐muelheim.mpg.de/mpikofo_home.html
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15
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Reetz MT. Laboratory Evolution of Stereoselective Enzymes: A Prolific Source of Catalysts for Asymmetric Reactions. Angew Chem Int Ed Engl 2010; 50:138-74. [DOI: 10.1002/anie.201000826] [Citation(s) in RCA: 441] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Manfred T. Reetz
- Max‐Planck‐Institut für Kohlenforschung, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Germany), Fax: (+49) 208‐306‐2985 http://www.mpi‐muelheim.mpg.de/mpikofo_home.html
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16
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Martinez P, Van Dam ME, Robinson AC, Chen K, Arnold FH. Stabilization of substilisin E in organic solvents by site-directed mutagenesis. Biotechnol Bioeng 2010; 39:141-7. [PMID: 18600924 DOI: 10.1002/bit.260390204] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Subtilisin E was rationally engineered to improve its stability in polar organic solvents such as dimethylformamide (DMF). A charged surface residue, Asp248, was substituted by three amino acids of increasing hydrophobicity, Asn, Ala, and Leu; all three variants were stabilized with respect to wild type in 80% DMF. This stabilization was only observed in the presence of high concentrations of the organic solvent: no stability enhancements were observed in 40% DMF. In contrast, the mutation Asn218 --> Ser alters internal hydrogen bonding interactions and stabilizes subtilisin E in both 40% and 80% DMF. This study provides additional evidence that substitution of surface-charged residues is a generally useful mechanism for stabilizing enzymes in organic media and that the stabilizing effects of such substitutions are unique to highly altered solvent environments. The effects of the single amino acid substitutions on free energies of stabilization are additive in the Asp248 --> Asn + Asn218 --> Ser combination variant, yielding an enzyme that is 3.4 times more stable than wild type in 80% DMF.
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Affiliation(s)
- P Martinez
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, Pasadena, California 91125, USA
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17
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Zhong CQ, Song S, Fang N, Liang X, Zhu H, Tang XF, Tang B. Improvement of low-temperature caseinolytic activity of a thermophilic subtilase by directed evolution and site-directed mutagenesis. Biotechnol Bioeng 2009; 104:862-70. [PMID: 19609954 DOI: 10.1002/bit.22473] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
By directed evolution and subsequent site-directed mutagenesis, cold-adapted variants of WF146 protease, a thermophilic subtilase, have been successfully engineered. A four-amino acid substitution variant RTN29 displayed a sixfold increase in caseinolytic activity in the temperature range of 15-25 degrees C, a down-shift of optimum temperature by approximately 15 degrees C, as well as a decrease in thermostability, indicating it follows the general principle of trade-off between activity and stability. Nevertheless, to some extent RTN29 remained its thermophilic nature, and no loss of activity was observed after heat-treatment at 60 degrees C for 2 h. Notably, RTN29 exhibited a lower hydrolytic activity toward suc-AAPF-pNA, due to an increase in K(m) and a decrease in k(cat), in contrast to other artificially cold-adapted subtilases with increased low-temperature activity toward small synthetic substrates. All mutations (S100P, G108S, D114G, M137T, T153A, and S246N) identified in the cold-adapted variants occurred within or near the substrate-binding region. None of these mutations, however, match the corresponding sites in naturally psychrophilic and other artificially cold-adapted subtilases, implying there are multiple routes to cold adaptation. Homology modeling and structural analysis demonstrated that these mutations led to an increase in mobility of substrate-binding region and a modulation of substrate specificity, which seemed to account for the improvement of the enzyme's catalytic activity toward macromolecular substrates at lower temperatures. Our study may provide valuable information needed to develop enzymes coupling high stability and high low-temperature activity, which are highly desired for industrial use.
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Affiliation(s)
- Chuan-Qi Zhong
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072
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18
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Reetz MT, Carballeira JD, Vogel A. Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability. Angew Chem Int Ed Engl 2007; 45:7745-51. [PMID: 17075931 DOI: 10.1002/anie.200602795] [Citation(s) in RCA: 369] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim/Ruhr, Germany.
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19
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Pulido MA, Koga Y, Takano K, Kanaya S. Directed evolution of Tk-subtilisin from a hyperthermophilic archaeon: identification of a single amino acid substitution responsible for low-temperature adaptation. Protein Eng Des Sel 2007; 20:143-53. [PMID: 17351019 DOI: 10.1093/protein/gzm006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Tk-subtilisin from the hyperthermophilic archaeon Thermococcus kodakaraensis is synthesized in a prepro-form (prepro-Tk-subtilisin), secreted in a pro-form (pro-Tk-subtilisin), and matured to an active form (mat-Tk-subtilisin*; a Ca(2+)-bound active form of matured domain of Tk-subtilisin) upon autoprocessing and degradation of the propeptide [Tk-propeptide; propeptide of Tk-subtilisin (Gly1-Leu69)]. Pro-Tk-subtilisin exhibited halo-forming activity only at 80 degrees C, but not at 70 and 60 degrees C, because Tk-propeptide is not effectively degraded by mat-Tk-subtilisin* and forms an inactive complex with mat-Tk-subtilisin* at <80 degrees C. Random mutagenesis in the entire prepro-Tk-subtilisin gene, followed by screening for mutant proteins with halo-forming activity at 70 and 60 degrees C, allowed us to identify single Gly56 --> Ser mutation in the propeptide region responsible for low-temperature adaptation of pro-Tk-subtilisin. SDS-PAGE analyses and mat-Tk-subtilisin* activity assay of pro-G56S-subtilisin indicated more rapid maturation than pro-Tk-subtilisin. The resultant active form was indistinguishable from mat-Tk-subtilisin* in activity and stability, indicating that Gly56 --> Ser mutation does not seriously affect the folding of the mature domain. However, this mutation greatly destabilized the propeptide, making it unstructured in an isolated form. As a result, Tk-propeptide with Gly56 --> Ser mutation (G56S-propeptide) was more susceptible to proteolytic degradation and less effectively inhibited mat-Tk-subtilisin* activity than Tk-propeptide. These results suggest that pro-G56S-subtilisin is more effectively matured than pro-Tk-subtilisin at lower temperatures, because autoprocessed G56S-propeptide is unstructured upon dissociation from mat-Tk-subtilisin* and is therefore effectively degraded by mat-Tk-subtilisin*.
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Affiliation(s)
- M A Pulido
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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20
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Reetz MT, Carballeira JD, Vogel A. Iterative Saturation Mutagenesis on the Basis of B Factors as a Strategy for Increasing Protein Thermostability. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200602795] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Srimathi S, Jayaraman G, Narayanan P. Improved thermodynamic stability of subtilisin Carlsberg by covalent modification. Enzyme Microb Technol 2006. [DOI: 10.1016/j.enzmictec.2005.10.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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22
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Arroyo-Reyna A, Tello-Solís SR, Rojo-Domínguez A. Stability parameters for one-step mechanism of irreversible protein denaturation: a method based on nonlinear regression of calorimetric peaks with nonzero deltaCp. Anal Biochem 2005; 328:123-30. [PMID: 15113687 DOI: 10.1016/j.ab.2004.02.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2003] [Indexed: 10/26/2022]
Abstract
Thermal transitions of many proteins have been found to be calorimetrically irreversible and scan-rate dependent. Calorimetric determinations of stability parameters of proteins which unfold irreversibly according to a first-order kinetic scheme have been reported. These methods require the approximation that the increase in heat capacity upon denaturation deltaCp is zero. A method to obtain thermodynamic parameters and activation energy for the two-state irreversible process N --> D from nonlinear fitting to calorimetric traces is proposed here. It is based on a molar excess heat capacity function which considers irreversibility and a nonzero constant deltaCp. This function has four parameters: (1) temperature at which the calorimetric profile reaches its maximal value (Tm), (2) calorimetric enthalpy at Tm (deltaHm), (3) deltaCp, and (4) activation energy (E). The thermal irreversible denaturation of subtilisin BPN' from Bacillus amyloliquefaciens was studied by differential scanning calorimetry at pH 7.5 to test our model. Transitions were found to be strongly scanning-rate dependent with a mean deltaCp value of 5.7 kcal K(-1)mol(-1), in agreement with values estimated by accessible surface area and significantly higher than a previously reported value.
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Affiliation(s)
- Alfonso Arroyo-Reyna
- Area de Biofisicoquímica, Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Apartado Postal 55-534, 09340 Iztapalapa, D.F., México.
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23
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McLeod AH, Murdoch H, Dickinson J, Dennis MJ, Hall GA, Buswell CM, Carr J, Taylor DM, Sutton JM, Raven NDH. Proteolytic inactivation of the bovine spongiform encephalopathy agent. Biochem Biophys Res Commun 2004; 317:1165-70. [PMID: 15094392 DOI: 10.1016/j.bbrc.2004.03.168] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2004] [Indexed: 11/17/2022]
Abstract
Thermostable proteases have been investigated for their ability to provide a novel biological solution to decontamination of prion agents responsible for transmissible spongiform encephalopathies (TSEs). Proteases were identified that digested total mouse brain homogenate (MBH) protein from uninfected mice. These proteases were then evaluated for digestion of BSE (301V) infectious MBH over a range of pH and temperatures, screened for loss of anti-prion antibody 6H4 immunoreactivity and protease-treated infectious MBH assessed in mouse bioassay using VM mice. Despite a number of proteases eliminating all 6H4-immunoreactive material, only the subtilisin-enzyme Properase showed a significant extension in incubation period in mouse bioassays following a 30-min incubation at 60 degrees C and pH 12. These results demonstrate the potential of the method to provide a practical solution to the problems of TSE contamination of surgical instruments and highlight the inadequacy of using Western blot for assessment of decontamination/inactivation of TSE agents.
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Affiliation(s)
- Anne H McLeod
- Health Protection Agency, Porton Down, Salisbury, Wiltshire SP4 0JG, UK
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24
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Abstract
Alkaline proteases are of considerable interest in view of their activity and stability at alkaline pH. This review describes the proteases that can resist extreme alkaline environments produced by a wide range of alkalophilic microorganisms. Different isolation methods are discussed which enable the screening and selection of promising organisms for industrial production. Further, strain improvement using mutagenesis and/or recombinant DNA technology can be applied to augment the efficiency of the producer strain to a commercial status. The various nutritional and environmental parameters affecting the production of alkaline proteases are delineated. The purification and properties of these proteases is discussed, and the use of alkaline proteases in diverse industrial applications is highlighted.
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Affiliation(s)
- C G Kumar
- Dairy Microbiology Division, National Dairy Research Institute, Karnal 132 001, India
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25
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Bakhtiar S, Andersson MM, Gessesse A, Mattiasson B, Hatti-Kaul R. Stability characteristics of a calcium-independent alkaline protease from Nesterenkonia sp. Enzyme Microb Technol 2003. [DOI: 10.1016/s0141-0229(02)00336-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Ness JE, Kim S, Gottman A, Pak R, Krebber A, Borchert TV, Govindarajan S, Mundorff EC, Minshull J. Synthetic shuffling expands functional protein diversity by allowing amino acids to recombine independently. Nat Biotechnol 2002; 20:1251-5. [PMID: 12426575 DOI: 10.1038/nbt754] [Citation(s) in RCA: 158] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2002] [Accepted: 09/24/2002] [Indexed: 11/09/2022]
Abstract
We describe synthetic shuffling, an evolutionary protein engineering technology in which every amino acid from a set of parents is allowed to recombine independently of every other amino acid. With the use of degenerate oligonucleotides, synthetic shuffling provides a direct route from database sequence information to functional libraries. Physical starting genes are unnecessary, and additional design criteria such as optimal codon usage or known beneficial mutations can also be incorporated. We performed synthetic shuffling of 15 subtilisin genes and obtained active and highly chimeric enzymes with desirable combinations of properties that we did not obtain by other directed-evolution methods.
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Affiliation(s)
- Jon E Ness
- Maxygen, 515 Galveston Drive, Redwood City, CA 94063, USA
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27
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Affiliation(s)
- Frank Bordusa
- Max-Planck Society, Research Unit Enzymology of Protein Folding, Weinbergweg 22, D-06120 Halle/Saale, Germany.
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28
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Almog O, Gallagher DT, Ladner JE, Strausberg S, Alexander P, Bryan P, Gilliland GL. Structural basis of thermostability. Analysis of stabilizing mutations in subtilisin BPN'. J Biol Chem 2002; 277:27553-8. [PMID: 12011071 DOI: 10.1074/jbc.m111777200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The crystal structures of two thermally stabilized subtilisin BPN' variants, S63 and S88, are reported here at 1.8 and 1.9 A resolution, respectively. The micromolar affinity calcium binding site (site A) has been deleted (Delta75-83) in these variants, enabling the activity and thermostability measurements in chelating conditions. Each of the variants includes mutations known previously to increase the thermostability of calcium-independent subtilisin in addition to new stabilizing mutations. S63 has eight amino acid replacements: D41A, M50F, A73L, Q206W, Y217K, N218S, S221C, and Q271E. S63 has 75-fold greater stability than wild type subtilisin in chelating conditions (10 mm EDTA). The other variant, S88, has ten site-specific changes: Q2K, S3C, P5S, K43N, M50F, A73L, Q206C, Y217K, N218S, and Q271E. The two new cysteines form a disulfide bond, and S88 has 1000 times greater stability than wild type subtilisin in chelating conditions. Comparisons of the two new crystal structures (S63 in space group P2(1) with A cell constants 41.2, 78.1, 36.7, and beta = 114.6 degrees and S88 in space group P2(1)2(1)2(1) with cell constants 54.2, 60.4, and 82.7) with previous structures of subtilisin BPN' reveal that the principal changes are in the N-terminal region. The structural bases of the stabilization effects of the new mutations Q2K, S3C, P5S, D41A, Q206C, and Q206W are generally apparent. The effects are attributed to the new disulfide cross-link and to improved hydrophobic packing, new hydrogen bonds, and other rearrangements in the N-terminal region.
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Affiliation(s)
- Orna Almog
- Department of Clinical Biochemistry, Faculty of Health Sciences, Ben-Gurion University, Beer-Sheva 84105, Israel
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29
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Affiliation(s)
- O H Kwon
- Department of Polymer Science and Engineering, Kumoh National University of Technology, 188 Shinpyung-dong, Kumi, Kyungbuk 730-701, Korea
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30
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Affiliation(s)
- A Gershenson
- Division of Chemistry & Chemical Engineering 210-41, California Institute of Technology, Pasadena, CA 91125, USA
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31
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Ness JE, Del Cardayré SB, Minshull J, Stemmer WP. Molecular breeding: the natural approach to protein design. ADVANCES IN PROTEIN CHEMISTRY 2001; 55:261-92. [PMID: 11050936 DOI: 10.1016/s0065-3233(01)55006-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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32
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Abstract
The serine protease subtilisin is an important industrial enzyme as well as a model for understanding the enormous rate enhancements affected by enzymes. For these reasons along with the timely cloning of the gene, ease of expression and purification and availability of atomic resolution structures, subtilisin became a model system for protein engineering studies in the 1980s. Fifteen years later, mutations in well over 50% of the 275 amino acids of subtilisin have been reported in the scientific literature. Most subtilisin engineering has involved catalytic amino acids, substrate binding regions and stabilizing mutations. Stability has been the property of subtilisin which has been most amenable to enhancement, yet perhaps least understood. This review will give a brief overview of the subtilisin engineering field, critically review what has been learned about subtilisin stability from protein engineering experiments and conclude with some speculation about the prospects for future subtilisin engineering.
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Affiliation(s)
- P N Bryan
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, 20850, Rockville, MD, USA.
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33
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Abstract
A remarkable thermal stable and oxidation-resistant mutant was obtained using the random mutagenesis PCR technique on the mutant M222A gene of subtilisin E. Sequencing analysis revealed an A was replaced by G at nucleotide 671 of the subtilisin E gene, converting the asparagine codon (AAT) to serine codon (AGT) at position 118. The half-life of M222A/N118S enzyme activity, when heated at 65 degrees C, was approximately 80 min while the half-life of M222A and wild-type subtilisin E were 13 min and 15 min, respectively. This suggested the stability of the M222A/N118S mutant was five times greater than that of the wild-type enzyme. The mutant was also as oxidation resistant as the mutant M222A of subtilisin E. These results indicated the M222A/N118S mutant is both an oxidation-resistant and a heat-stable variant of subtilisin E.
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Affiliation(s)
- Y Yang
- Shanghai Research Center of Biotechnology, Chinese Academy of Sciences, 200233, Shanghai, PR China.
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34
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Graycar T, Knapp M, Ganshaw G, Dauberman J, Bott R. Engineered Bacillus lentus subtilisins having altered flexibility. J Mol Biol 1999; 292:97-109. [PMID: 10493860 DOI: 10.1006/jmbi.1999.3033] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The three-dimensional structures of engineered variants of Bacillus lentus subtilisin having increased enzymatic activity, K27R/N87S/V104Y/N123S/T274A (RSYSA) and N76D/N87S/S103A/V104I (DSAI), were determined by X-ray crystallography. In addition to identifying changes in atomic position we report a method that identifies protein segments having altered flexibility. The method utilizes a statistical analysis of variance to delineate main-chain temperature factors that represent significant departures from the overall variance between equivalent regions seen throughout the structure. This method reveals changes in main-chain mobility in both variants. Residues 125-127 have increased mobility in the RSYSA variant while residues 100-104 have decreased mobility in the DSAI variant. These segments are located at the substrate-binding site and changes in their mobility are believed to relate to the observed changes in proteolytic activity. The effect of altered crystal lattice contacts on segment flexibility becomes apparent when identical variants, determined in two crystal forms, are compared with the native enzyme.
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Affiliation(s)
- T Graycar
- Genencor International, 925 Page Mill Road, Palo Alto, CA 94304, USA
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35
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Ness JE, Welch M, Giver L, Bueno M, Cherry JR, Borchert TV, Stemmer WP, Minshull J. DNA shuffling of subgenomic sequences of subtilisin. Nat Biotechnol 1999; 17:893-6. [PMID: 10471932 DOI: 10.1038/12884] [Citation(s) in RCA: 158] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA family shuffling of 26 protease genes was used to create a library of chimeric proteases that was screened for four distinct enzymatic properties. Multiple clones were identified that were significantly improved over any of the parental enzymes for each individual property. Family shuffling, also known as molecular breeding, efficiently created all of the combinations of parental properties, producing a great diversity of property combinations in the progeny enzymes. Thus, molecular breeding, like classical breeding, is a powerful tool for recombining existing diversity to tailor biological systems for multiple functional parameters.
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Affiliation(s)
- J E Ness
- Maxygen, 3410 Central Expressway, Santa Clara, CA 95051, USA
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36
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Colombo G, Merz KM. Stability and Activity of Mesophilic Subtilisin E and Its Thermophilic Homolog: Insights from Molecular Dynamics Simulations. J Am Chem Soc 1999. [DOI: 10.1021/ja990420s] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Giorgio Colombo
- Department of Chemistry, 152 Davey Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802 and Istituto di Biocatalisi e Riconoscimento Molecolare CNR, via Mario Bianco, 9 20131, Milano, Italy
| | - Kenneth M. Merz
- Department of Chemistry, 152 Davey Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802 and Istituto di Biocatalisi e Riconoscimento Molecolare CNR, via Mario Bianco, 9 20131, Milano, Italy
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37
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38
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Mikami B, Yoon HJ, Yoshigi N. The crystal structure of the sevenfold mutant of barley beta-amylase with increased thermostability at 2.5 A resolution. J Mol Biol 1999; 285:1235-43. [PMID: 9918723 DOI: 10.1006/jmbi.1998.2379] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The three-dimensional structure of the sevenfold mutant of barley beta-amylase (BBA-7s) with increased thermostability was determined by X-ray crystallography. The enzyme was purified as a single component and crystallized by a hanging drop method in the presence of 14 % PEG 6000. The crystals belong to space group P43212 with cell dimensions a=b=72.11 A, c=250.51 A. The diffraction data up to 2.5 A were collected after soaking the crystal in 100 mM maltose with Rsym of 8.6 %. The structure was determined by a molecular replacement method using soybean beta-amylase (SBA) as a search model and refined to an R-factor of 18.7 %. The final model included 500 amino acid residues, 141 water molecules and three glucose residues, which were located at subsites 1-2 and 4 in the active site. The r.m.s. distance of 485 Calpha atoms between BBA-7s and SBA was 0.62 A. Out of the seven mutated amino acids, four (Ser295Ala, Ile297Val, Ser351Pro and Ala376Ser) were substitutions from the common residues with SBA to the thermostable forms. A comparison of the structures of BBA-7s and SBA indicated that the side-chain of Ser376 makes new hydrogen bonds to the main-chain of an adjacent beta-strand, and that the side-chains of Val297 reduce an unfavorable interaction between the side-chains of Ala314. The mutation of Ser295Ala breaks the hydrogen bond between Ser295 OG and Tyr195 OH, which seems to be the reason for the unoccupied glucose residue at subsite 3. The tandem mutations at 350-352 including substitutions to two Pro residues suggested the reduction of main-chain entropy in the unfolded structure of this solvent-exposed protruded loop.
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Affiliation(s)
- B Mikami
- Kyoto University, Uji, Kyoto, 611, Japan.
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39
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Zhao H, Arnold FH. Directed evolution converts subtilisin E into a functional equivalent of thermitase. PROTEIN ENGINEERING 1999; 12:47-53. [PMID: 10065710 DOI: 10.1093/protein/12.1.47] [Citation(s) in RCA: 232] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
We used directed evolution to convert Bacillus subtilis subtilisin E into an enzyme functionally equivalent to its thermophilic homolog thermitase from Thermoactinomyces vulgaris. Five generations of random mutagenesis, recombination and screening created subtilisin E 5-3H5, whose half-life at 83 degrees C (3.5 min) and temperature optimum for activity (Topt, 76 degrees C) are identical with those of thermitase. The Topt of the evolved enzyme is 17 degrees C higher and its half-life at 65 degrees C is >200 times that of wild-type subtilisin E. In addition, 5-3H5 is more active towards the hydrolysis of succinyl-Ala-Ala-Pro-Phe-p-nitroanilide than wild-type at all temperatures from 10 to 90 degrees C. Thermitase differs from subtilisin E at 157 amino acid positions. However, only eight amino acid substitutions were sufficient to convert subtilisin E into an enzyme equally thermostable. The eight substitutions, which include known stabilizing mutations (N218S, N76D) and also several not previously reported, are distributed over the surface of the enzyme. Only two (N218S, N181D) are found in thermitase. Directed evolution provides a powerful tool to unveil mechanisms of thermal adaptation and is an effective and efficient approach to increasing thermostability without compromising enzyme activity.
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Affiliation(s)
- H Zhao
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, Pasadena 91125, USA
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40
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Jain SC, Shinde U, Li Y, Inouye M, Berman HM. The crystal structure of an autoprocessed Ser221Cys-subtilisin E-propeptide complex at 2.0 A resolution. J Mol Biol 1998; 284:137-44. [PMID: 9811547 DOI: 10.1006/jmbi.1998.2161] [Citation(s) in RCA: 122] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report here the crystallographic structure determination of an autoprocessed (Ser221Cys)-subtilisin E-propeptide complex at 2.0 A resolution. The subtilisin domain sequence has a single substitution (Ser221Cys) which has been shown to block the maturation process prior to degradation of the propeptide domain (77 residues) that acts as an intramolecular chaperon. This mutation, however, did not prevent the enzyme from cleaving its propeptide domain with a 60-80% efficiency. The current determination is the first example of a subtilisin E-propeptide complex which has been autoprocessed. A previous structure determination of a BPN'-prosegment complex has been reported in which the subtilisin domain was extensively mutated and a calcium binding loop was deleted. Further, in this earlier determination, the complex was formed by the addition of separately expressed propeptide domain. The structure determination reported here provides additional information about the nature of the interaction between the subtilisin and propeptide domains in this complex.
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Affiliation(s)
- S C Jain
- Department of Chemistry, Rutgers University, 610 Taylor Road, Piscataway, NJ, 08854-8087, USA
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41
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Almog O, Gallagher T, Tordova M, Hoskins J, Bryan P, Gilliland GL. Crystal structure of calcium-independent subtilisin BPN' with restored thermal stability folded without the prodomain. Proteins 1998; 31:21-32. [PMID: 9552156 DOI: 10.1002/(sici)1097-0134(19980401)31:1<21::aid-prot3>3.0.co;2-k] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The three-dimensional structure of a subtilisin BPN' construct that was produced and folded without its prodomain shows the tertiary structure is nearly identical to the wild-type enzyme and not a folding intermediate. The subtilisin BPN' variant, Sbt70, was cloned and expressed in Escherichia coli without the prodomain, the 77-residue N-terminal domain that catalyzes the folding of the enzyme into its native tertiary structure. Sbt70 has the high-affinity calcium-binding loop, residues 75 to 83, deleted. Such calcium-independent forms of subtilisin BPN' refold independently while retaining high levels of activity [Bryan et al., Biochemistry, 31:4937-4945, 1992]. Sbt70 has, in addition, seven stabilizing mutations, K43N, M50F, A73L, Q206V, Y217K, N218S, Q271E, and the active site serine has been replaced with alanine to prevent autolysis. The purified Sbt70 folded spontaneously without the prodomain and crystallized at room temperature. Crystals of Sbt70 belong to space group P2(1)2(1)2(1) with unit cell parameters a = 53.5 A, b = 60.3 A, and c = 83.4 A. Comparison of the refined structure with other high-resolution structures of subtilisin BPN' establishes that the conformation of Sbt70 is essentially the same as that previously determined for other calcium-independent forms and that of other wild-type subtilisin BPN' structures, all folded in the presence of the prodomain. These findings confirm the results of previous solution studies that showed subtilisin BPN' can be refolded into a native conformation without the presence of the prodomain [Bryan et al., Biochemistry 31:4937-4945, 1992]. The structure analysis also provides the first descriptions of four stabilizing mutations, K43N, A73L, Q206V, and Q271E, and provides details of the interaction between the enzyme and the Ala-Leu-Ala-Leu tetrapeptide found in the active-site cleft.
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Affiliation(s)
- O Almog
- Center for Advanced Research in Biotechnology of the University of Maryland Biotechnology Institute and the National Institute of Standards and Technology, Rockville 20850, USA
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42
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Zhu X, Muller L, Mains RE, Lindberg I. Structural elements of PC2 required for interaction with its helper protein 7B2. J Biol Chem 1998; 273:1158-64. [PMID: 9422782 DOI: 10.1074/jbc.273.2.1158] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The structures of the eukaryotic subtilisin protease family members can be divided into four distinct domains as follows: the proregion, the catalytic domain, the P domain, and the carboxyl-terminal region. Although these enzymes are evolutionarily related, only prohormone convertase 2 (PC2) requires 7B2 for activation. To examine the potential contribution of each domain of PC2 to PC2-7B2 interactions, we performed sequential deletions, site-directed mutagenesis, and domain swapping to replace individual domains or particular amino acids of pro-PC2 with the corresponding segments/amino acids of pro-PC1. These chimeras and mutant enzyme molecules were then expressed in AtT-20 cells and analyzed for 7B2 binding, maturation ability, and enzymatic activity. The results revealed that 1) the PC2 proregion is required but is not sufficient to confer 7B2 binding; 2) the P domain is required for the stabilization of PC2 structure and is not exchangeable with the P domain of PC1; and 3) the carboxyl-terminal domain is not involved in 7B2 binding. Site-directed mutagenesis of pro-PC2 further showed that a single residue replacement in the catalytic domain, Tyr-194 --> Asp, prevented pro-PC2 from binding 7B2 and blocked activation. This residue is present within a loop rich in aromatic amino acids which appears to be on the surface of the molecule as extrapolated from the crystal structure of subtilisin. This loop may represent the primary recognition site for 7B2 within the catalytic domain.
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Affiliation(s)
- X Zhu
- Department of Biochemistry and Molecular Biology, Louisiana State University Medical Center, New Orleans, Louisiana 70112, USA
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43
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Abstract
Directed enzyme evolution has emerged in the past few years as a powerful alternative to rational approaches for engineering biocatalysts. Prerequisites for successful directed evolution are functional expression in a suitable microbial host, a rapid screen for the desired feature(s) and a well-thought-out working strategy for navigating protein landscapes. The rapidly growing body of literature on enzyme evolution in vitro includes techniques for creating and searching combinatorial enzyme libraries, as well as several successful examples of different evolutionary strategies being used.
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Affiliation(s)
- O Kuchner
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, Pasadena 91125, USA
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44
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Toba S, Merz KM. The Concept of Solvent Compatibility and Its Impact on Protein Stability and Activity Enhancement in Nonaqueous Solvents. J Am Chem Soc 1997. [DOI: 10.1021/ja970629a] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Samuel Toba
- Contribution from the Department of Chemistry, The Pennsylvania State University, 152 Davey Laboratory, University Park, Pennsylvania 16802
| | - Kenneth M. Merz
- Contribution from the Department of Chemistry, The Pennsylvania State University, 152 Davey Laboratory, University Park, Pennsylvania 16802
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45
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Xiao G, Xie Y, Zhang J, Sun X, Wu X, Chen X, Wang Q. Construction and screening of a multi-point site-specific mutant library of subtilisin E with a set of oligonucleotides. SCIENCE IN CHINA. SERIES C, LIFE SCIENCES 1997; 40:337-44. [PMID: 18762871 DOI: 10.1007/bf02881725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/1996] [Indexed: 12/01/2022]
Abstract
A mutant library of subtilisin E containing random combinations of various mutagenized sites was constructed by one-round mutagenesis with 15 mutagenic oligonucleotides. Mutants were screened through dot blot hybridization and DNA sequencing. A single-point mutant (Met 222Ala) and a three-point (Asn 76Asp/Asn109Ser/ I le 205/Cys) mutant gene from the library were expressed. The mutant proteins exhibited conspicuously improved resistance to oxidation and heat treatment, as reported before. The results show that the library is reliable and very useful for protease subtilisin E engineering.
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Affiliation(s)
- G Xiao
- Institute of Genetics, Fudan University, Shanghai, China
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46
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Zhao H, Arnold FH. Functional and nonfunctional mutations distinguished by random recombination of homologous genes. Proc Natl Acad Sci U S A 1997; 94:7997-8000. [PMID: 9223302 PMCID: PMC21544 DOI: 10.1073/pnas.94.15.7997] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We describe a convenient method for distinguishing functional from nonfunctional or deleterious mutations in homologous genes. High fidelity in vitro gene recombination ("DNA shuffling") coupled with sequence analysis of a small sampling of the shuffled library exhibiting the evolved behavior allows identification of those mutations responsible for the behavior in a background of neutral and deleterious mutations. Functional mutations are expected to occur in 100% of the sequenced screened sample; neutral mutations are found in 50% on average, and deleterious mutations do not appear at all. When used to analyze 10 mutations in a laboratory-evolved gene encoding a thermostable subtilisin E, this method rapidly identified the two responsible for the observed protease thermostability; the remaining eight were neutral with respect to thermostability, within the precision of the screening assay. A similar approach, coupled with selection for growth and survival of the host organism, could be used to distinguish adaptive from neutral mutations.
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Affiliation(s)
- H Zhao
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, Pasadena, CA 91125, USA
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47
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Abstract
Evolutionary biotechnology applies the principles of molecular evolution to biotechnology, leading to novel techniques for the creation of biomolecules with a great variety of functions for technical and medical purposes. Several basic principles for the application of evolutionary strategies can be derived from a comprehensive theory of molecular evolution. Prerequisites for evolutionary biotechnology are summarized with respect to the different classes of biomolecules and a few, selected applications are described in detail. Concepts for the technical implementation of evolutionary strategies are presented which allow automatized, high throughput processes.
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Affiliation(s)
- A Koltermann
- Max-Planck-Institut für biophysikalische Chemie, Abteilung Biochemische Kinetik, Göttingen, Germany
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48
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Martin JR, Mulder FA, Karimi-Nejad Y, van der Zwan J, Mariani M, Schipper D, Boelens R. The solution structure of serine protease PB92 from Bacillus alcalophilus presents a rigid fold with a flexible substrate-binding site. Structure 1997; 5:521-32. [PMID: 9115441 DOI: 10.1016/s0969-2126(97)00208-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Research on high-alkaline proteases, such as serine protease PB92, has been largely inspired by their industrial application as protein-degrading components of washing powders. Serine protease PB92 is a member of the subtilase family of enzymes, which has been extensively studied. These studies have included exhaustive protein engineering investigations and X-ray crystallography, in order to provide insight into the mechanism and specificity of enzyme catalysis. Distortions have been observed in the substrate-binding region of subtilisin crystal structures, due to crystal contacts. In addition, the structural variability in the substrate-binding region of subtilisins is often attributed to flexibility. It was hoped that the solution structure of this enzyme would provide further details about the conformation of this key region and give new insights into the functional properties of these enzymes. RESULTS The three-dimensional solution structure of the 269-residue (27 kDa) serine protease PB92 has been determined using distance and dihedral angle constraints derived from triple-resonance NMR data. The solution structure is represented by a family of 18 conformers which overlay onto the average structure with backbone and all-heavy-atom root mean square deviations (for the main body of the molecule) of 0.88 and 1.21 A, respectively. The family of structures contains a number of regions of relatively high conformational heterogeneity, including various segments that are involved in the formation of the substrate-binding site. The presence of flexibility within these segments has been established from NMR relaxation parameters and measurements of amide proton exchange rates. CONCLUSIONS The solution structure of the serine protease PB92 presents a well defined global fold which is rigid with the exception of a restricted number of sites. Among the limited number of residues involved in significant internal mobility are those of two pockets, termed S1 and S4, within the substrate-binding site. The presence of flexibility within the binding site supports the proposed induced fit mechanism of substrate binding.
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Affiliation(s)
- J R Martin
- Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH, Utrecht, The Netherlands
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49
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Fastrez J. In vivo versus in vitro screening or selection for catalytic activity in enzymes and abzymes. Mol Biotechnol 1997; 7:37-55. [PMID: 9163721 DOI: 10.1007/bf02821543] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The recent development of catalytic antibodies and the introduction of new techniques to generate huge libraries of random mutants of existing enzymes have created the need for powerful tools for finding in large populations of cells those producing the catalytically most active proteins. Several approaches have been developed and used to reach this goal. The screening techniques aim at easily detecting the clones producing active enzymes or abzymes; the selection techniques are designed to extract these clones from mixtures. These techniques have been applied both in vivo and in vitro. This review describes the advantages and limitations of the various methods in terms of ease of use, sensitivity, and convenience for handling large libraries. Examples are analyzed and tentative rules proposed. These techniques prove to be quite powerful to study the relationship between structure and function and to alter the properties of enzymes.
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Affiliation(s)
- J Fastrez
- Laboratoire de Biochimie Physique et des Biopolymères, Louvain-la-Neuve, Belgium
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50
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Genicot S, Rentier-Delrue F, Edwards D, VanBeeumen J, Gerday C. Trypsin and trypsinogen from an Antarctic fish: molecular basis of cold adaptation. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1298:45-57. [PMID: 8948488 DOI: 10.1016/s0167-4838(96)00095-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Trypsin from Antarctic fish Paranotothenia magellanica displays molecular and kinetic properties typical of enzymes produced by psychrophilic organisms. The enzyme has a high catalytic efficiency at low and moderate temperatures and is rapidly inactivated at temperatures higher than 30 degrees C. The nucleotide sequence was determined after mRNA extraction and cDNA synthesis. The cDNA encodes a pretrypsinogen which includes a seven residue activation peptide containing only three acidic residues preceeding the 222 amino-acid mature enzyme. A three-dimensional model of the enzyme was built. Structural parameters possibly involved in the adaptation to cold have been derived from comparison with the three-dimensional structure of the bovine enzyme. Among them are the lack of Tyr-151 in the substrate binding pocket, an overall decrease in the number of salt bridges and hydrophobicity and the increase in the surface hydrophilicity.
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Affiliation(s)
- S Genicot
- Laboratory of Biochemistry, University of Liège, Belgium
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