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Han Y, Zhang H, Zeng Z, Liu Z, Lu D, Liu Z. Descriptor-augmented machine learning for enzyme-chemical interaction predictions. Synth Syst Biotechnol 2024; 9:259-268. [PMID: 38450325 PMCID: PMC10915406 DOI: 10.1016/j.synbio.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/08/2024] Open
Abstract
Descriptors play a pivotal role in enzyme design for the greener synthesis of biochemicals, as they could characterize enzymes and chemicals from the physicochemical and evolutionary perspective. This study examined the effects of various descriptors on the performance of Random Forest model used for enzyme-chemical relationships prediction. We curated activity data of seven specific enzyme families from the literature and developed the pipeline for evaluation the machine learning model performance using 10-fold cross-validation. The influence of protein and chemical descriptors was assessed in three scenarios, which were predicting the activity of unknown relations between known enzymes and known chemicals (new relationship evaluation), predicting the activity of novel enzymes on known chemicals (new enzyme evaluation), and predicting the activity of new chemicals on known enzymes (new chemical evaluation). The results showed that protein descriptors significantly enhanced the classification performance of model on new enzyme evaluation in three out of the seven datasets with the greatest number of enzymes, whereas chemical descriptors appear no effect. A variety of sequence-based and structure-based protein descriptors were constructed, among which the esm-2 descriptor achieved the best results. Using enzyme families as labels showed that descriptors could cluster proteins well, which could explain the contributions of descriptors to the machine learning model. As a counterpart, in the new chemical evaluation, chemical descriptors made significant improvement in four out of the seven datasets, while protein descriptors appear no effect. We attempted to evaluate the generalization ability of the model by correlating the statistics of the datasets with the performance of the models. The results showed that datasets with higher sequence similarity were more likely to get better results in the new enzyme evaluation and datasets with more enzymes were more likely beneficial from the protein descriptor strategy. This work provides guidance for the development of machine learning models for specific enzyme families.
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Affiliation(s)
- Yilei Han
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Haoye Zhang
- Department of Computer Science and Technology, Tsinghua University, Beijing, 100084, China
| | - Zheni Zeng
- Department of Computer Science and Technology, Tsinghua University, Beijing, 100084, China
| | - Zhiyuan Liu
- Department of Computer Science and Technology, Tsinghua University, Beijing, 100084, China
| | - Diannan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Zheng Liu
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
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2
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Foroutan Kalourazi A, Nazemi SA, Unniram Parambil AR, Muñoz-Tafalla R, Vidal P, Shahangian SS, Guallar V, Ferrer M, Shahgaldian P. Exploiting cyclodextrins as artificial chaperones to enhance enzyme protection through supramolecular engineering. NANOSCALE 2024; 16:5123-5129. [PMID: 38349359 DOI: 10.1039/d3nr06044f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
We report a method of enzyme stabilisation exploiting the artificial protein chaperone properties of β-cyclodextrin (β-CD) covalently embedded in an ultrathin organosilica layer. Putative interaction points of this artificial chaperone system with the surface of the selected enzyme were studied in silico using a protein energy landscape exploration simulation algorithm. We show that this enzyme shielding method allows for drastic enhancement of enzyme stability under thermal and chemical stress conditions, along with broadening the optimal temperature range of the biocatalyst. The presence of the β-CD macrocycle within the protective layer supports protein refolding after treatment with a surfactant.
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Affiliation(s)
- Ali Foroutan Kalourazi
- School of Life Science, University of Applied Sciences and Arts Northwestern Switzerland, Hofackerstrasse 30, Muttenz CH-4132, Switzerland.
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran.
| | - Seyed Amirabbas Nazemi
- School of Life Science, University of Applied Sciences and Arts Northwestern Switzerland, Hofackerstrasse 30, Muttenz CH-4132, Switzerland.
| | - Ajmal Roshan Unniram Parambil
- School of Life Science, University of Applied Sciences and Arts Northwestern Switzerland, Hofackerstrasse 30, Muttenz CH-4132, Switzerland.
- Swiss Nanoscience Institute, Klingelbergstrasse 82, Basel CH-4056, Switzerland
| | - Ruben Muñoz-Tafalla
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Faculty of Pharmacy and Food Science, Universitat de Barcelona (UB), 08007 Barcelona, Spain
| | - Paula Vidal
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049 Madrid, Spain
| | - S Shirin Shahangian
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran.
| | - Victor Guallar
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049 Madrid, Spain
| | - Patrick Shahgaldian
- School of Life Science, University of Applied Sciences and Arts Northwestern Switzerland, Hofackerstrasse 30, Muttenz CH-4132, Switzerland.
- Swiss Nanoscience Institute, Klingelbergstrasse 82, Basel CH-4056, Switzerland
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3
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Fernandez-Lopez L, Roda S, Gonzalez-Alfonso JL, Plou FJ, Guallar V, Ferrer M. Design and Characterization of In-One Protease-Esterase PluriZyme. Int J Mol Sci 2022; 23:13337. [PMID: 36362119 PMCID: PMC9655419 DOI: 10.3390/ijms232113337] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/25/2022] [Accepted: 10/29/2022] [Indexed: 10/14/2023] Open
Abstract
Proteases are abundant in prokaryotic genomes (~10 per genome), but their recovery encounters expression problems, as only 1% can be produced at high levels; this value differs from that of similarly abundant esterases (1-15 per genome), 50% of which can be expressed at good levels. Here, we design a catalytically efficient artificial protease that can be easily produced. The PluriZyme EH1AB1 with two active sites supporting the esterase activity was employed. A Leu24Cys mutation in EH1AB1, remodelled one of the esterase sites into a proteolytic one through the incorporation of a catalytic dyad (Cys24 and His214). The resulting artificial enzyme, EH1AB1C, efficiently hydrolysed (azo)casein at pH 6.5-8.0 and 60-70 °C. The presence of both esterase and protease activities in the same scaffold allowed the one-pot cascade synthesis (55.0 ± 0.6% conversion, 24 h) of L-histidine methyl ester from the dipeptide L-carnosine in the presence of methanol. This study demonstrates that active sites supporting proteolytic activity can be artificially introduced into an esterase scaffold to design easy-to-produce in-one protease-esterase PluriZymes for cascade reactions, namely, the synthesis of amino acid esters from dipeptides. It is also possible to design artificial proteases with good production yields, in contrast to natural proteases that are difficult to express.
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Affiliation(s)
| | - Sergi Roda
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | | | | | - Víctor Guallar
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - Manuel Ferrer
- Department of Applied Biocatalysis, ICP, CSIC, 28049 Madrid, Spain
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4
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Roda S, Fernandez-Lopez L, Benedens M, Bollinger A, Thies S, Schumacher J, Coscolín C, Kazemi M, Santiago G, Gertzen CGW, Gonzalez-Alfonso JL, Plou FJ, Jaeger KE, Smits SHJ, Ferrer M, Guallar V. A Plurizyme with Transaminase and Hydrolase Activity Catalyzes Cascade Reactions. Angew Chem Int Ed Engl 2022; 61:e202207344. [PMID: 35734849 PMCID: PMC9540564 DOI: 10.1002/anie.202207344] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Indexed: 01/01/2023]
Abstract
Engineering dual‐function single polypeptide catalysts with two abiotic or biotic catalytic entities (or combinations of both) supporting cascade reactions is becoming an important area of enzyme engineering and catalysis. Herein we present the development of a PluriZyme, TR2E2, with efficient native transaminase (kcat: 69.49±1.77 min−1) and artificial esterase (kcat: 3908–0.41 min−1) activities integrated into a single scaffold, and evaluate its utility in a cascade reaction. TR2E2 (pHopt: 8.0–9.5; Topt: 60–65 °C) efficiently converts methyl 3‐oxo‐4‐(2,4,5‐trifluorophenyl)butanoate into 3‐(R)‐amino‐4‐(2,4,5‐trifluorophenyl)butanoic acid, a crucial intermediate for the synthesis of antidiabetic drugs. The reaction proceeds through the conversion of the β‐keto ester into the β‐keto acid at the hydrolytic site and subsequently into the β‐amino acid (e.e. >99 %) at the transaminase site. The catalytic power of the TR2E2PluriZyme was proven with a set of β‐keto esters, demonstrating the potential of such designs to address bioinspired cascade reactions.
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Affiliation(s)
- Sergi Roda
- Department of Life Sciences, Barcelona Supercomputing Center, Carrer de Jordi Girona, 31, 08034, Barcelona, Spain
| | | | - Marius Benedens
- Center for Structural Studies, Heinrich-Heine-University, Building 26.44.01.62, Universitaetsstr 1, 40228, Duesseldorf, Germany
| | - Alexander Bollinger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Building 26.44.01.62, Universitaetsstr 1, 40228, Duesseldorf, Germany.,Forschungszentrum Jülich, Building 15.8, 01/303, 52428, Wilhelm Johnen Straße, Jülich, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Building 26.44.01.62, Universitaetsstr 1, 40228, Duesseldorf, Germany.,Forschungszentrum Jülich, Building 15.8, 01/303, 52428, Wilhelm Johnen Straße, Jülich, Germany
| | - Julia Schumacher
- Center for Structural Studies, Heinrich-Heine-University, Building 26.44.01.62, Universitaetsstr 1, 40228, Duesseldorf, Germany
| | - Cristina Coscolín
- Department of Applied Biocatalysis, ICP, CSIC, Marie Curie 2, 28049, Madrid, Spain
| | - Masoud Kazemi
- Department of Life Sciences, Barcelona Supercomputing Center, Carrer de Jordi Girona, 31, 08034, Barcelona, Spain
| | - Gerard Santiago
- Department of Life Sciences, Barcelona Supercomputing Center, Carrer de Jordi Girona, 31, 08034, Barcelona, Spain
| | - Christoph G W Gertzen
- Center for Structural Studies, Heinrich-Heine-University, Building 26.44.01.62, Universitaetsstr 1, 40228, Duesseldorf, Germany
| | | | - Francisco J Plou
- Department of Applied Biocatalysis, ICP, CSIC, Marie Curie 2, 28049, Madrid, Spain
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Building 26.44.01.62, Universitaetsstr 1, 40228, Duesseldorf, Germany.,Forschungszentrum Jülich, Building 15.8, 01/303, 52428, Wilhelm Johnen Straße, Jülich, Germany
| | - Sander H J Smits
- Center for Structural Studies, Heinrich-Heine-University, Building 26.44.01.62, Universitaetsstr 1, 40228, Duesseldorf, Germany
| | - Manuel Ferrer
- Department of Applied Biocatalysis, ICP, CSIC, Marie Curie 2, 28049, Madrid, Spain
| | - Víctor Guallar
- Department of Life Sciences, Barcelona Supercomputing Center, Carrer de Jordi Girona, 31, 08034, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
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5
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Roda S, Fernandez-Lopez L, Benedens M, Bollinger A, Thies S, Schumacher J, Coscolín C, Kazemi M, Santiago G, Gertzen CGW, Gonzalez-Alfonso JL, Plou FJ, Jaeger KE, Smits SHJ, Ferrer M, Guallar V. A Plurizyme with Transaminase and Hydrolase Activity Catalyzes Cascade Reactions. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sergi Roda
- Barcelona Supercomputing Center: Centro Nacional de Supercomputacion Department of Life Sciences Carrer de Jordi Girona, 31 08034 Barcelona SPAIN
| | - Laura Fernandez-Lopez
- ICP: Instituto de Catalisis y Petroleoquimica Department of Applied Biocatalysis Marie Curie 2 28049 Madrid SPAIN
| | - Marius Benedens
- Heinrich-Heine-Universität Düsseldorf: Heinrich-Heine-Universitat Dusseldorf Center for Structural Studies Wilhelm Johnen Straße, Bldg 15.8, 01/303 40228 Düsseldorf GERMANY
| | - Alexander Bollinger
- Forschungszentrum Jülich: Forschungszentrum Julich GmbH Institute of Molecular Enzyme Technology Wilhelm Johnen Straße, Bldg 15.8, 01/303 52428 Jülich GERMANY
| | - Stephan Thies
- Forschungszentrum Jülich: Forschungszentrum Julich GmbH Institute of Molecular Enzyme Technology Wilhelm Johnen Straße, Bldg 15.8, 01/303 52428 Jülich GERMANY
| | - Julia Schumacher
- Heinrich-Heine-Universitat Dusseldorf Center for Structural Studies Building 26.44.01.62, Universitaetsstr 1 40228 Düsseldorf GERMANY
| | - Cristina Coscolín
- ICP: Instituto de Catalisis y Petroleoquimica Department of Applied Biocatalysis Marie Curie 28049 Madrid SPAIN
| | - Masoud Kazemi
- Barcelona Supercomputing Center: Centro Nacional de Supercomputacion Department of Life Sciences Carrer de Jordi Girona, 31 08034 Barcelona SPAIN
| | - Gerard Santiago
- Barcelona Supercomputing Center: Centro Nacional de Supercomputacion Department of Life Sciences Carrer de Jordi Girona, 31 08034 Barcelona SPAIN
| | - Christoph G. W. Gertzen
- Heinrich Heine University Düsseldorf: Heinrich-Heine-Universitat Dusseldorf Institute for Pharmaceutical and Medicinal Chemistry 40228 Düsseldorf GERMANY
| | - Jose L. Gonzalez-Alfonso
- ICP: Instituto de Catalisis y Petroleoquimica Department of Applied Biocatalysis Marie Curie 2 28049 Madrid SPAIN
| | - Francisco J. Plou
- ICP: Instituto de Catalisis y Petroleoquimica Department of Applied Biocatalysis Marie Curie 2 28049 Madrid SPAIN
| | - Karl-Erich Jaeger
- Forschungszentrum Julich ICG: Forschungszentrum Julich GmbH Institute of Molecular Enzyme Technology Wilhelm Johnen Straße, Bldg 15.8, 01/303 52428 Jülich GERMANY
| | - Sander H. J. Smits
- Heinrich Heine University Düsseldorf: Heinrich-Heine-Universitat Dusseldorf Center for Structural Studies 40228 Düsseldorf GERMANY
| | - Manuel Ferrer
- Institute of Catalysis CSIC Department of Biocatalysis Marie Curie 2Campus Cantoblanco 28049 Madrid SPAIN
| | - Víctor Guallar
- Barcelona Supercomputing Center: Centro Nacional de Supercomputacion Department of Life Sciences Carrer de Jordi Girona, 31 08034 Barcelona SPAIN
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6
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Liu Y, Wang P, Tian J, Seidi F, Guo J, Zhu W, Xiao H, Song J. Carbohydrate-Binding Modules of Potential Resources: Occurrence in Nature, Function, and Application in Fiber Recognition and Treatment. Polymers (Basel) 2022; 14:polym14091806. [PMID: 35566977 PMCID: PMC9100146 DOI: 10.3390/polym14091806] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/21/2022] [Accepted: 04/24/2022] [Indexed: 02/04/2023] Open
Abstract
Great interests have recently been aroused in the independent associative domain of glycoside hydrolases that utilize insoluble polysaccharides-carbohydrate-binding module (CBM), which responds to binding while the catalytic domain reacts with the substrate. In this mini-review, we first provide a brief introduction on CBM and its subtypes including the classifications, potential sources, structures, and functions. Afterward, the applications of CBMs in substrate recognition based on different types of CBMs have been reviewed. Additionally, the progress of CBMs in paper industry as a new type of environmentally friendly auxiliary agent for fiber treatment is summarized. At last, other applications of CBMs and the future outlook have prospected. Due to the specificity in substrate recognition and diversity in structures, CBM can be a prosperous and promising ‘tool’ for wood and fiber processing in the future.
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Affiliation(s)
- Yena Liu
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (P.W.); (J.T.); (F.S.); (J.G.); (W.Z.)
| | - Peipei Wang
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (P.W.); (J.T.); (F.S.); (J.G.); (W.Z.)
| | - Jing Tian
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (P.W.); (J.T.); (F.S.); (J.G.); (W.Z.)
| | - Farzad Seidi
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (P.W.); (J.T.); (F.S.); (J.G.); (W.Z.)
| | - Jiaqi Guo
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (P.W.); (J.T.); (F.S.); (J.G.); (W.Z.)
| | - Wenyuan Zhu
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (P.W.); (J.T.); (F.S.); (J.G.); (W.Z.)
| | - Huining Xiao
- Department of Chemical Engineering, University of New Brunswick, Fredericton, NB E3B 5A3, Canada;
| | - Junlong Song
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (P.W.); (J.T.); (F.S.); (J.G.); (W.Z.)
- Correspondence: ; Tel.: +86-25-8542-8163; Fax: +86-25-8542-8689
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7
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Ott F, Rabe KS, Niemeyer CM, Gygli G. Toward Reproducible Enzyme Modeling with Isothermal Titration Calorimetry. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Felix Ott
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Kersten S. Rabe
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Gudrun Gygli
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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8
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Roda S, Robles-Martín A, Xiang R, Kazemi M, Guallar V. Structural-Based Modeling in Protein Engineering. A Must Do. J Phys Chem B 2021; 125:6491-6500. [PMID: 34106727 DOI: 10.1021/acs.jpcb.1c02545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Biotechnological solutions will be a key aspect in our immediate future society, where optimized enzymatic processes through enzyme engineering might be an important solution for waste transformation, clean energy production, biodegradable materials, and green chemistry, for example. Here we advocate the importance of structural-based bioinformatics and molecular modeling tools in such developments. We summarize our recent experiences indicating a great prediction/success ratio, and we suggest that an early in silico phase should be performed in enzyme engineering studies. Moreover, we demonstrate the potential of a new technique combining Rosetta and PELE, which could provide a faster and more automated procedure, an essential aspect for a broader use.
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Affiliation(s)
- Sergi Roda
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | | | - Ruite Xiang
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Masoud Kazemi
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Victor Guallar
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
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