51
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Lipsh-Sokolik R, Khersonsky O, Schröder SP, de Boer C, Hoch SY, Davies GJ, Overkleeft HS, Fleishman SJ. Combinatorial assembly and design of enzymes. Science 2023; 379:195-201. [PMID: 36634164 DOI: 10.1126/science.ade9434] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The design of structurally diverse enzymes is constrained by long-range interactions that are necessary for accurate folding. We introduce an atomistic and machine learning strategy for the combinatorial assembly and design of enzymes (CADENZ) to design fragments that combine with one another to generate diverse, low-energy structures with stable catalytic constellations. We applied CADENZ to endoxylanases and used activity-based protein profiling to recover thousands of structurally diverse enzymes. Functional designs exhibit high active-site preorganization and more stable and compact packing outside the active site. Implementing these lessons into CADENZ led to a 10-fold improved hit rate and more than 10,000 recovered enzymes. This design-test-learn loop can be applied, in principle, to any modular protein family, yielding huge diversity and general lessons on protein design principles.
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Affiliation(s)
- R Lipsh-Sokolik
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - O Khersonsky
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - S P Schröder
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, Netherlands
| | - C de Boer
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, Netherlands
| | - S-Y Hoch
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - G J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5DD, UK
| | - H S Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, Netherlands
| | - S J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
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52
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Deckers J, Anbergen T, Hokke AM, de Dreu A, Schrijver DP, de Bruin K, Toner YC, Beldman TJ, Spangler JB, de Greef TFA, Grisoni F, van der Meel R, Joosten LAB, Merkx M, Netea MG, Mulder WJM. Engineering cytokine therapeutics. NATURE REVIEWS BIOENGINEERING 2023; 1:286-303. [PMID: 37064653 PMCID: PMC9933837 DOI: 10.1038/s44222-023-00030-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Cytokines have pivotal roles in immunity, making them attractive as therapeutics for a variety of immune-related disorders. However, the widespread clinical use of cytokines has been limited by their short blood half-lives and severe side effects caused by low specificity and unfavourable biodistribution. Innovations in bioengineering have aided in advancing our knowledge of cytokine biology and yielded new technologies for cytokine engineering. In this Review, we discuss how the development of bioanalytical methods, such as sequencing and high-resolution imaging combined with genetic techniques, have facilitated a better understanding of cytokine biology. We then present an overview of therapeutics arising from cytokine re-engineering, targeting and delivery, mRNA therapeutics and cell therapy. We also highlight the application of these strategies to adjust the immunological imbalance in different immune-mediated disorders, including cancer, infection and autoimmune diseases. Finally, we look ahead to the hurdles that must be overcome before cytokine therapeutics can live up to their full potential.
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Affiliation(s)
- Jeroen Deckers
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Medical Centre, Nijmegen, Netherlands
| | - Tom Anbergen
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Medical Centre, Nijmegen, Netherlands
| | - Ayla M. Hokke
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Anne de Dreu
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - David P. Schrijver
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Koen de Bruin
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Yohana C. Toner
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Medical Centre, Nijmegen, Netherlands
| | - Thijs J. Beldman
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Medical Centre, Nijmegen, Netherlands
| | - Jamie B. Spangler
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD USA
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Tom F. A. de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
- Centre for Living Technologies, Alliance Eindhoven University of Technology, Wageningen University & Research, Utrecht University and University Medical Center Utrecht (EWUU), Utrecht, Netherlands
| | - Francesca Grisoni
- Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
- Centre for Living Technologies, Alliance Eindhoven University of Technology, Wageningen University & Research, Utrecht University and University Medical Center Utrecht (EWUU), Utrecht, Netherlands
| | - Roy van der Meel
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Present Address: Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Leo A. B. Joosten
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Medical Centre, Nijmegen, Netherlands
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Centre, Nijmegen, Netherlands
- Department of Medical Genetics, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Maarten Merkx
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Present Address: Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Medical Centre, Nijmegen, Netherlands
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Centre, Nijmegen, Netherlands
- Department for Genomics and Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Willem J. M. Mulder
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Medical Centre, Nijmegen, Netherlands
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Present Address: Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
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53
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Pang C, Liu S, Zhang G, Zhou J, Du G, Li J. Improving the catalytic efficiency of Pseudomonas aeruginosa lipoxygenase by semi-rational design. Enzyme Microb Technol 2023; 162:110120. [DOI: 10.1016/j.enzmictec.2022.110120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 10/14/2022]
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54
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Jiang Y, Stull SL, Shao Q, Yang ZJ. Convergence in determining enzyme functional descriptors across Kemp eliminase variants. ELECTRONIC STRUCTURE (BRISTOL, ENGLAND) 2022; 4:044007. [PMID: 37425623 PMCID: PMC10327861 DOI: 10.1088/2516-1075/acad51] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Molecular simulations have been extensively employed to accelerate biocatalytic discoveries. Enzyme functional descriptors derived from molecular simulations have been leveraged to guide the search for beneficial enzyme mutants. However, the ideal active-site region size for computing the descriptors over multiple enzyme variants remains untested. Here, we conducted convergence tests for dynamics-derived and electrostatic descriptors on 18 Kemp eliminase variants across six active-site regions with various boundary distances to the substrate. The tested descriptors include the root-mean-square deviation of the active-site region, the solvent accessible surface area ratio between the substrate and active site, and the projection of the electric field (EF) on the breaking C-H bond. All descriptors were evaluated using molecular mechanics methods. To understand the effects of electronic structure, the EF was also evaluated using quantum mechanics/molecular mechanics methods. The descriptor values were computed for 18 Kemp eliminase variants. Spearman correlation matrices were used to determine the region size condition under which further expansion of the region boundary does not substantially change the ranking of descriptor values. We observed that protein dynamics-derived descriptors, including RMSDactive_site and SASAratio, converge at a distance cutoff of 5 Å from the substrate. The electrostatic descriptor, EFC-H, converges at 6 Å using molecular mechanics methods with truncated enzyme models and 4 Å using quantum mechanics/molecular mechanics methods with whole enzyme model. This study serves as a future reference to determine descriptors for predictive modeling of enzyme engineering.
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Affiliation(s)
- Yaoyukun Jiang
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America
| | - Sebastian L Stull
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America
| | - Qianzhen Shao
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America
| | - Zhongyue J Yang
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, United States of America
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, United States of America
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, United States of America
- Data Science Institute, Vanderbilt University, Nashville, TN 37235, United States of America
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, United States of America
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55
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Ospina F, Schülke KH, Soler J, Klein A, Prosenc B, Garcia‐Borràs M, Hammer SC. Selective Biocatalytic N-Methylation of Unsaturated Heterocycles. Angew Chem Int Ed Engl 2022; 61:e202213056. [PMID: 36202763 PMCID: PMC9827881 DOI: 10.1002/anie.202213056] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Indexed: 11/19/2022]
Abstract
Methods for regioselective N-methylation and -alkylation of unsaturated heterocycles with "off the shelf" reagents are highly sought-after. This reaction could drastically simplify synthesis of privileged bioactive molecules. Here we report engineered and natural methyltransferases for challenging N-(m)ethylation of heterocycles, including benzimidazoles, benzotriazoles, imidazoles and indazoles. The reactions are performed through a cyclic enzyme cascade that consists of two methyltransferases using only iodoalkanes or methyl tosylate as simple reagents. This method enables the selective synthesis of important molecules that are otherwise difficult to access, proceeds with high regioselectivity (r.r. up to >99 %), yield (up to 99 %), on a preparative scale, and with nearly equimolar concentrations of simple starting materials.
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Affiliation(s)
- Felipe Ospina
- Faculty of ChemistryOrganic Chemistry and BiocatalysisBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| | - Kai H. Schülke
- Faculty of ChemistryOrganic Chemistry and BiocatalysisBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| | - Jordi Soler
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de QuímicaUniversitat de GironaCarrer Maria Aurèlia Capmany 69Girona17003CataloniaSpain
| | - Alina Klein
- Faculty of ChemistryOrganic Chemistry and BiocatalysisBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| | - Benjamin Prosenc
- Faculty of ChemistryOrganic Chemistry and BiocatalysisBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| | - Marc Garcia‐Borràs
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de QuímicaUniversitat de GironaCarrer Maria Aurèlia Capmany 69Girona17003CataloniaSpain
| | - Stephan C. Hammer
- Faculty of ChemistryOrganic Chemistry and BiocatalysisBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
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56
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Barber-Zucker S, Mateljak I, Goldsmith M, Kupervaser M, Alcalde M, Fleishman SJ. Designed High-Redox Potential Laccases Exhibit High Functional Diversity. ACS Catal 2022; 12:13164-13173. [PMID: 36366766 PMCID: PMC9638991 DOI: 10.1021/acscatal.2c03006] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/29/2022] [Indexed: 11/29/2022]
Abstract
White-rot fungi secrete an impressive repertoire of high-redox potential laccases (HRPLs) and peroxidases for efficient oxidation and utilization of lignin. Laccases are attractive enzymes for the chemical industry due to their broad substrate range and low environmental impact. Since expression of functional recombinant HRPLs is challenging, however, iterative-directed evolution protocols have been applied to improve their expression, activity, and stability. We implement a rational, stabilize-and-diversify strategy to two HRPLs that we could not functionally express. First, we use the PROSS stability-design algorithm to allow functional expression in yeast. Second, we use the stabilized enzymes as starting points for FuncLib active-site design to improve their activity and substrate diversity. Four of the FuncLib-designed HRPLs and their PROSS progenitor exhibit substantial diversity in reactivity profiles against high-redox potential substrates, including lignin monomers. Combinations of 3-4 subtle mutations that change the polarity, solvation, and sterics of the substrate-oxidation site result in orders of magnitude changes in reactivity profiles. These stable and versatile HRPLs are a step toward generating an effective lignin-degrading consortium of enzymes that can be secreted from yeast. The stabilize-and-diversify strategy can be applied to other challenging enzyme families to study and expand the utility of natural enzymes.
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Affiliation(s)
- Shiran Barber-Zucker
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot 7600001, Israel
| | - Ivan Mateljak
- Department
of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, Madrid 28049, Spain
- EvoEnzyme
S.L., Parque Científico de Madrid, C/Faraday, 7, Campus de Cantoblanco, Madrid 28049, Spain
| | - Moshe Goldsmith
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot 7600001, Israel
| | - Meital Kupervaser
- Nancy
and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7600001, Israel
| | - Miguel Alcalde
- Department
of Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, Madrid 28049, Spain
| | - Sarel J. Fleishman
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot 7600001, Israel
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57
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Wittmund M, Cadet F, Davari MD. Learning Epistasis and Residue Coevolution Patterns: Current Trends and Future Perspectives for Advancing Enzyme Engineering. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Marcel Wittmund
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Frederic Cadet
- Laboratory of Excellence LABEX GR, DSIMB, Inserm UMR S1134, University of Paris city & University of Reunion, Paris 75014, France
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
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58
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Liu Y, Khusnutdinova A, Chen J, Crisante D, Batyrova K, Raj K, Feigis M, Shirzadi E, Wang X, Dorakhan R, Wang X, Stogios PJ, Yakunin AF, Sargent EH, Mahadevan R. Systems engineering of Escherichia coli for n-butane production. Metab Eng 2022; 74:98-107. [DOI: 10.1016/j.ymben.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/05/2022] [Accepted: 10/08/2022] [Indexed: 10/31/2022]
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59
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Luo Y, Jiang Y, Chen L, Li C, Wang Y. Applications of protein engineering in the microbial synthesis of plant triterpenoids. Synth Syst Biotechnol 2022; 8:20-32. [PMID: 36381964 PMCID: PMC9634032 DOI: 10.1016/j.synbio.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/26/2022] Open
Abstract
Triterpenoids are a class of natural products widely used in fields related to medicine and health due to their biological activities such as hepatoprotection, anti-inflammation, anti-viral, and anti-tumor. With the advancement in biotechnology, microorganisms have been used as cell factories to produce diverse natural products. Despite the significant progress that has been made in the construction of microbial cell factories for the heterogeneous biosynthesis of triterpenoids, the industrial production of triterpenoids employing microorganisms has been stymied due to the shortage of efficient enzymes as well as the low expression and low catalytic activity of heterologous proteins in microbes. Protein engineering has been demonstrated as an effective way for improving the specificity, catalytic activity, and stability of the enzyme, which can be employed to overcome these challenges. This review summarizes the current progress in the studies of Oxidosqualene cyclases (OSCs), cytochrome P450s (P450s), and UDP-glycosyltransferases (UGTs), the key enzymes in the triterpenoids synthetic pathway. The main obstacles restricting the efficient catalysis of these key enzymes are analyzed, the applications of protein engineering for the three key enzymes in the microbial synthesis of triterpenoids are systematically reviewed, and the challenges and prospects of protein engineering are also discussed.
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Affiliation(s)
- Yan Luo
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Yaozhu Jiang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Linhao Chen
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China,Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Ying Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China,Corresponding author.
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60
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Kim D, Noh MH, Park M, Kim I, Ahn H, Ye DY, Jung GY, Kim S. Enzyme activity engineering based on sequence co-evolution analysis. Metab Eng 2022; 74:49-60. [PMID: 36113751 DOI: 10.1016/j.ymben.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 11/17/2022]
Abstract
The utility of engineering enzyme activity is expanding with the development of biotechnology. Conventional methods have limited applicability as they require high-throughput screening or three-dimensional structures to direct target residues of activity control. An alternative method uses sequence evolution of natural selection. A repertoire of mutations was selected for fine-tuning enzyme activities to adapt to varying environments during the evolution. Here, we devised a strategy called sequence co-evolutionary analysis to control the efficiency of enzyme reactions (SCANEER), which scans the evolution of protein sequences and direct mutation strategy to improve enzyme activity. We hypothesized that amino acid pairs for various enzyme activity were encoded in the evolutionary history of protein sequences, whereas loss-of-function mutations were avoided since those are depleted during the evolution. SCANEER successfully predicted the enzyme activities of beta-lactamase and aminoglycoside 3'-phosphotransferase. SCANEER was further experimentally validated to control the activities of three different enzymes of great interest in chemical production: cis-aconitate decarboxylase, α-ketoglutaric semialdehyde dehydrogenase, and inositol oxygenase. Activity-enhancing mutations that improve substrate-binding affinity or turnover rate were found at sites distal from known active sites or ligand-binding pockets. We provide SCANEER to control desired enzyme activity through a user-friendly webserver.
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Affiliation(s)
- Donghyo Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, South Korea
| | - Minhyuk Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Inhae Kim
- ImmunoBiome Inc., Pohang, South Korea
| | - Hyunsoo Ahn
- Graduate School of Artificial Intelligence, Pohang University of Science and Technology, Pohang, South Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, South Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, South Korea; Institute of Convergence Research and Education in Advanced Technology, Yonsei University, Seoul, South Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, South Korea.
| | - Sanguk Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea; Graduate School of Artificial Intelligence, Pohang University of Science and Technology, Pohang, South Korea; Institute of Convergence Research and Education in Advanced Technology, Yonsei University, Seoul, South Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, South Korea.
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61
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Listov D, Lipsh‐Sokolik R, Rosset S, Yang C, Correia BE, Fleishman SJ. Assessing and enhancing foldability in designed proteins. Protein Sci 2022; 31:e4400. [PMID: 36040259 PMCID: PMC9375437 DOI: 10.1002/pro.4400] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/09/2022] [Accepted: 07/11/2022] [Indexed: 11/11/2022]
Abstract
Recent advances in protein-design methodology have led to a dramatic increase in reliability and scale. With these advances, dozens and even thousands of designed proteins are automatically generated and screened. Nevertheless, the success rate, particularly in design of functional proteins, is low and fundamental goals such as reliable de novo design of efficient enzymes remain beyond reach. Experimental analyses have consistently indicated that a major reason for design failure is inaccuracy and misfolding relative to the design conception. To address this challenge, we describe complementary methods to diagnose and ameliorate suboptimal regions in designed proteins: first, we develop a Rosetta atomistic computational mutation scanning approach to detect energetically suboptimal positions in designs (available on a web server https://pSUFER.weizmann.ac.il); second, we demonstrate that AlphaFold2 ab initio structure prediction flags regions that may misfold in designed enzymes and binders; and third, we focus FuncLib design calculations on suboptimal positions in a previously designed low-efficiency enzyme, improving its catalytic efficiency by 330-fold. Furthermore, applied to a de novo designed protein that exhibited limited stability, the same approach markedly improved stability and expressibility. Thus, foldability analysis and enhancement may dramatically increase the success rate in design of functional proteins.
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Affiliation(s)
- Dina Listov
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | | | - Stéphane Rosset
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Che Yang
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Bruno E. Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
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62
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Gutierrez-Rus LI, Alcalde M, Risso VA, Sanchez-Ruiz JM. Efficient Base-Catalyzed Kemp Elimination in an Engineered Ancestral Enzyme. Int J Mol Sci 2022; 23:8934. [PMID: 36012203 PMCID: PMC9408544 DOI: 10.3390/ijms23168934] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/25/2022] Open
Abstract
The routine generation of enzymes with completely new active sites is a major unsolved problem in protein engineering. Advances in this field have thus far been modest, perhaps due, at least in part, to the widespread use of modern natural proteins as scaffolds for de novo engineering. Most modern proteins are highly evolved and specialized and, consequently, difficult to repurpose for completely new functionalities. Conceivably, resurrected ancestral proteins with the biophysical properties that promote evolvability, such as high stability and conformational diversity, could provide better scaffolds for de novo enzyme generation. Kemp elimination, a non-natural reaction that provides a simple model of proton abstraction from carbon, has been extensively used as a benchmark in de novo enzyme engineering. Here, we present an engineered ancestral β-lactamase with a new active site that is capable of efficiently catalyzing Kemp elimination. The engineering of our Kemp eliminase involved minimalist design based on a single function-generating mutation, inclusion of an extra polypeptide segment at a position close to the de novo active site, and sharply focused, low-throughput library screening. Nevertheless, its catalytic parameters (kcat/KM~2·105 M-1 s-1, kcat~635 s-1) compare favorably with the average modern natural enzyme and match the best proton-abstraction de novo Kemp eliminases that are reported in the literature. The general implications of our results for de novo enzyme engineering are discussed.
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Affiliation(s)
- Luis I. Gutierrez-Rus
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain
| | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry, CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Valeria A. Risso
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain
| | - Jose M. Sanchez-Ruiz
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain
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63
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Saez-Jimenez V, Scrima S, Lambrughi M, Papaleo E, Mapelli V, Engqvist MKM, Olsson L. Directed Evolution of ( R)-2-Hydroxyglutarate Dehydrogenase Improves 2-Oxoadipate Reduction by 2 Orders of Magnitude. ACS Synth Biol 2022; 11:2779-2790. [PMID: 35939387 PMCID: PMC9396657 DOI: 10.1021/acssynbio.2c00162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Pathway engineering is commonly employed to improve the
production
of various metabolites but may incur in bottlenecks due to the low
catalytic activity of a particular reaction step. The reduction of
2-oxoadipate to (R)-2-hydroxyadipate is a key reaction
in metabolic pathways that exploit 2-oxoadipate conversion via α-reduction
to produce adipic acid, an industrially important platform chemical.
Here, we engineered (R)-2-hydroxyglutarate dehydrogenase
from Acidaminococcus fermentans (Hgdh)
with the aim of improving 2-oxoadipate reduction. Using a combination
of computational analysis, saturation mutagenesis, and random mutagenesis,
three mutant variants with a 100-fold higher catalytic efficiency
were obtained. As revealed by rational analysis of the mutations found
in the variants, this improvement could be ascribed to a general synergistic
effect where mutation A206V played a key role since it boosted the
enzyme’s activity by 4.8-fold. The Hgdh variants with increased
activity toward 2-oxoadipate generated within this study pave the
way for the bio-based production of adipic acid.
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Affiliation(s)
- Veronica Saez-Jimenez
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Simone Scrima
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark.,Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Matteo Lambrughi
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark.,Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Valeria Mapelli
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Martin K M Engqvist
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Lisbeth Olsson
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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64
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Matsumura I, Patrick WM. Dan Tawfik's Lessons for Protein Engineers about Enzymes Adapting to New Substrates. Biochemistry 2022; 62:158-162. [PMID: 35820168 PMCID: PMC9851151 DOI: 10.1021/acs.biochem.2c00230] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Natural evolution has been creating new complex systems for billions of years. The process is spontaneous and requires neither intelligence nor moral purpose but is nevertheless difficult to understand. The late Dan Tawfik spent years studying enzymes as they adapted to recognize new substrates. Much of his work focused on gaining fundamental insights, so the practical utility of his experiments may not be obvious even to accomplished protein engineers. Here we focus on two questions fundamental to any directed evolution experiment. Which proteins are the best starting points for such experiments? Which trait(s) of the chosen parental protein should be evolved to achieve the desired outcome? We summarize Tawfik's contributions to our understanding of these problems, to honor his memory and encourage those unfamiliar with his ideas to read his publications.
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Affiliation(s)
- Ichiro Matsumura
- O.
Wayne Rollins Research Center, 1510 Clifton Road NE, Room 4001, Atlanta, Georgia 30322, United States,E-mail:
| | - Wayne M. Patrick
- Centre
for Biodiscovery, School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand,E-mail:
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65
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Zhang S, Zhang J, Luo W, Wang P, Zhu Y. A preorganization oriented computational method for de novo design of Kemp elimination enzymes. Enzyme Microb Technol 2022; 160:110093. [DOI: 10.1016/j.enzmictec.2022.110093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/13/2022] [Accepted: 06/30/2022] [Indexed: 11/26/2022]
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66
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Vos PD, Rossetti G, Mantegna JL, Siira SJ, Gandadireja AP, Bruce M, Raven SA, Khersonsky O, Fleishman SJ, Filipovska A, Rackham O. Computationally designed hyperactive Cas9 enzymes. Nat Commun 2022; 13:3023. [PMID: 35641498 PMCID: PMC9156780 DOI: 10.1038/s41467-022-30598-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 05/10/2022] [Indexed: 12/01/2022] Open
Abstract
The ability to alter the genomes of living cells is key to understanding how genes influence the functions of organisms and will be critical to modify living systems for useful purposes. However, this promise has long been limited by the technical challenges involved in genetic engineering. Recent advances in gene editing have bypassed some of these challenges but they are still far from ideal. Here we use FuncLib to computationally design Cas9 enzymes with substantially higher donor-independent editing activities. We use genetic circuits linked to cell survival in yeast to quantify Cas9 activity and discover synergistic interactions between engineered regions. These hyperactive Cas9 variants function efficiently in mammalian cells and introduce larger and more diverse pools of insertions and deletions into targeted genomic regions, providing tools to enhance and expand the possible applications of CRISPR-based gene editing. The ability to alter the genomes of living cells is key to understanding how genes influence the functions of organisms and will be critical to modify living systems for useful purposes. Here, the authors use computational design to discover Cas9 enzymes with increased activity.
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Affiliation(s)
- Pascal D Vos
- Curtin Medical School, Curtin University, Bentley, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia.,Centre for Medical Research, The University of Western Australia, Nedlands, WA, Australia.,School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Giulia Rossetti
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia.,Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia
| | - Jessica L Mantegna
- Curtin Medical School, Curtin University, Bentley, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
| | - Stefan J Siira
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
| | - Andrianto P Gandadireja
- Curtin Medical School, Curtin University, Bentley, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
| | - Mitchell Bruce
- Curtin Medical School, Curtin University, Bentley, WA, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
| | - Samuel A Raven
- Curtin Medical School, Curtin University, Bentley, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia.,Centre for Medical Research, The University of Western Australia, Nedlands, WA, Australia
| | - Olga Khersonsky
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia.,Centre for Medical Research, The University of Western Australia, Nedlands, WA, Australia.,School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia.,Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia
| | - Oliver Rackham
- Curtin Medical School, Curtin University, Bentley, WA, Australia. .,Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia. .,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia. .,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia. .,Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia.
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67
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Tee WV, Wah Tan Z, Guarnera E, Berezovsky IN. Conservation and diversity in allosteric fingerprints of proteins for evolutionary-inspired engineering and design. J Mol Biol 2022; 434:167577. [PMID: 35395233 DOI: 10.1016/j.jmb.2022.167577] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/30/2022] [Accepted: 03/30/2022] [Indexed: 11/26/2022]
Abstract
Hand-in-hand work of physics and evolution delivered protein universe with diversity of forms, sizes, and functions. Pervasiveness and advantageous traits of allostery made it an important component of the protein function regulation, calling for thorough investigation of its structural determinants and evolution. Learning directly from nature, we explored here allosteric communication in several major folds and repeat proteins, including α/β and β-barrels, β-propellers, Ig-like fold, ankyrin and α/β leucine-rich repeat proteins, which provide structural platforms for many different enzymatic and signalling functions. We obtained a picture of conserved allosteric communication characteristic in different fold types, modifications of the structure-driven signalling patterns via sequence-determined divergence to specific functions, as well as emergence and potential diversification of allosteric regulation in multi-domain proteins and oligomeric assemblies. Our observations will be instrumental in facilitating the engineering and de novo design of proteins with allosterically regulated functions, including development of therapeutic biologics. In particular, results described here may guide the identification of the optimal structural platforms (e.g. fold type, size, and oligomerization states) and the types of diversifications/perturbations, such as mutations, effector binding, and order-disorder transition. The tunable allosteric linkage across distant regions can be used as a pivotal component in the design/engineering of modular biological systems beyond the traditional scaffolding function.
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Affiliation(s)
- Wei-Ven Tee
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Zhen Wah Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Enrico Guarnera
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671; Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, Singapore 117597.
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68
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Vasina M, Velecký J, Planas-Iglesias J, Marques SM, Skarupova J, Damborsky J, Bednar D, Mazurenko S, Prokop Z. Tools for computational design and high-throughput screening of therapeutic enzymes. Adv Drug Deliv Rev 2022; 183:114143. [PMID: 35167900 DOI: 10.1016/j.addr.2022.114143] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 02/04/2022] [Accepted: 02/09/2022] [Indexed: 12/16/2022]
Abstract
Therapeutic enzymes are valuable biopharmaceuticals in various biomedical applications. They have been successfully applied for fibrinolysis, cancer treatment, enzyme replacement therapies, and the treatment of rare diseases. Still, there is a permanent demand to find new or better therapeutic enzymes, which would be sufficiently soluble, stable, and active to meet specific medical needs. Here, we highlight the benefits of coupling computational approaches with high-throughput experimental technologies, which significantly accelerate the identification and engineering of catalytic therapeutic agents. New enzymes can be identified in genomic and metagenomic databases, which grow thanks to next-generation sequencing technologies exponentially. Computational design and machine learning methods are being developed to improve catalytically potent enzymes and predict their properties to guide the selection of target enzymes. High-throughput experimental pipelines, increasingly relying on microfluidics, ensure functional screening and biochemical characterization of target enzymes to reach efficient therapeutic enzymes.
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Affiliation(s)
- Michal Vasina
- Loschmidt Laboratories, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic; Loschmidt Laboratories, RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, Pekarska 53, Brno, Czech Republic
| | - Jan Velecký
- Loschmidt Laboratories, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic; Loschmidt Laboratories, RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Joan Planas-Iglesias
- Loschmidt Laboratories, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic; Loschmidt Laboratories, RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, Pekarska 53, Brno, Czech Republic
| | - Sergio M Marques
- Loschmidt Laboratories, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic; Loschmidt Laboratories, RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, Pekarska 53, Brno, Czech Republic
| | - Jana Skarupova
- Loschmidt Laboratories, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic; Loschmidt Laboratories, RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic; Loschmidt Laboratories, RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, Pekarska 53, Brno, Czech Republic; Enantis, INBIT, Kamenice 34, Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic; Loschmidt Laboratories, RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, Pekarska 53, Brno, Czech Republic.
| | - Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic; Loschmidt Laboratories, RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, Pekarska 53, Brno, Czech Republic.
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic; Loschmidt Laboratories, RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, Pekarska 53, Brno, Czech Republic.
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69
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Khersonsky O, Fleishman SJ. What Have We Learned from Design of Function in Large Proteins? BIODESIGN RESEARCH 2022; 2022:9787581. [PMID: 37850148 PMCID: PMC10521758 DOI: 10.34133/2022/9787581] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 02/21/2022] [Indexed: 10/19/2023] Open
Abstract
The overarching goal of computational protein design is to gain complete control over protein structure and function. The majority of sophisticated binders and enzymes, however, are large and exhibit diverse and complex folds that defy atomistic design calculations. Encouragingly, recent strategies that combine evolutionary constraints from natural homologs with atomistic calculations have significantly improved design accuracy. In these approaches, evolutionary constraints mitigate the risk from misfolding and aggregation, focusing atomistic design calculations on a small but highly enriched sequence subspace. Such methods have dramatically optimized diverse proteins, including vaccine immunogens, enzymes for sustainable chemistry, and proteins with therapeutic potential. The new generation of deep learning-based ab initio structure predictors can be combined with these methods to extend the scope of protein design, in principle, to any natural protein of known sequence. We envision that protein engineering will come to rely on completely computational methods to efficiently discover and optimize biomolecular activities.
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Affiliation(s)
- Olga Khersonsky
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sarel J. Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
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70
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Computational enzyme redesign: large jumps in function. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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71
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72
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Leonard AC, Weinstein JJ, Steiner PJ, Erbse AH, Fleishman SJ, Whitehead TA. Stabilization of the SARS-CoV-2 receptor binding domain by protein core redesign and deep mutational scanning. Protein Eng Des Sel 2022; 35:gzac002. [PMID: 35325236 PMCID: PMC9077414 DOI: 10.1093/protein/gzac002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/21/2022] [Accepted: 02/16/2022] [Indexed: 11/12/2022] Open
Abstract
Stabilizing antigenic proteins as vaccine immunogens or diagnostic reagents is a stringent case of protein engineering and design as the exterior surface must maintain recognition by receptor(s) and antigen-specific antibodies at multiple distinct epitopes. This is a challenge, as stability enhancing mutations must be focused on the protein core, whereas successful computational stabilization algorithms typically select mutations at solvent-facing positions. In this study, we report the stabilization of SARS-CoV-2 Wuhan Hu-1 Spike receptor binding domain using a combination of deep mutational scanning and computational design, including the FuncLib algorithm. Our most successful design encodes I358F, Y365W, T430I, and I513L receptor binding domain mutations, maintains recognition by the receptor ACE2 and a panel of different anti-receptor binding domain monoclonal antibodies, is between 1 and 2°C more thermally stable than the original receptor binding domain using a thermal shift assay, and is less proteolytically sensitive to chymotrypsin and thermolysin than the original receptor binding domain. Our approach could be applied to the computational stabilization of a wide range of proteins without requiring detailed knowledge of active sites or binding epitopes. We envision that this strategy may be particularly powerful for cases when there are multiple or unknown binding sites.
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Affiliation(s)
- Alison C Leonard
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80303, USA
| | - Jonathan J Weinstein
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Paul J Steiner
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80303, USA
| | - Annette H Erbse
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80303, USA
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73
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Mali H, Shah C, Patel DH, Trivedi U, Subramanian RB. Bio-catalytic system of metallohydrolases for remediation of neurotoxin organophosphates and applications with a future vision. J Inorg Biochem 2022; 231:111771. [DOI: 10.1016/j.jinorgbio.2022.111771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 02/15/2022] [Accepted: 02/19/2022] [Indexed: 12/29/2022]
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74
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Cadet XF, Gelly JC, van Noord A, Cadet F, Acevedo-Rocha CG. Learning Strategies in Protein Directed Evolution. Methods Mol Biol 2022; 2461:225-275. [PMID: 35727454 DOI: 10.1007/978-1-0716-2152-3_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Synthetic biology is a fast-evolving research field that combines biology and engineering principles to develop new biological systems for medical, pharmacological, and industrial applications. Synthetic biologists use iterative "design, build, test, and learn" cycles to efficiently engineer genetic systems that are reliable, reproducible, and predictable. Protein engineering by directed evolution can benefit from such a systematic engineering approach for various reasons. Learning can be carried out before starting, throughout or after finalizing a directed evolution project. Computational tools, bioinformatics, and scanning mutagenesis methods can be excellent starting points, while molecular dynamics simulations and other strategies can guide engineering efforts. Similarly, studying protein intermediates along evolutionary pathways offers fascinating insights into the molecular mechanisms shaped by evolution. The learning step of the cycle is not only crucial for proteins or enzymes that are not suitable for high-throughput screening or selection systems, but it is also valuable for any platform that can generate a large amount of data that can be aided by machine learning algorithms. The main challenge in protein engineering is to predict the effect of a single mutation on one functional parameter-to say nothing of several mutations on multiple parameters. This is largely due to nonadditive mutational interactions, known as epistatic effects-beneficial mutations present in a genetic background may not be beneficial in another genetic background. In this work, we provide an overview of experimental and computational strategies that can guide the user to learn protein function at different stages in a directed evolution project. We also discuss how epistatic effects can influence the success of directed evolution projects. Since machine learning is gaining momentum in protein engineering and the field is becoming more interdisciplinary thanks to collaboration between mathematicians, computational scientists, engineers, molecular biologists, and chemists, we provide a general workflow that familiarizes nonexperts with the basic concepts, dataset requirements, learning approaches, model capabilities and performance metrics of this intriguing area. Finally, we also provide some practical recommendations on how machine learning can harness epistatic effects for engineering proteins in an "outside-the-box" way.
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Affiliation(s)
- Xavier F Cadet
- PEACCEL, Artificial Intelligence Department, Paris, France
| | - Jean Christophe Gelly
- Laboratoire d'Excellence GR-Ex, Paris, France
- BIGR, DSIMB, UMR_S1134, INSERM, University of Paris & University of Reunion, Paris, France
| | | | - Frédéric Cadet
- Laboratoire d'Excellence GR-Ex, Paris, France
- BIGR, DSIMB, UMR_S1134, INSERM, University of Paris & University of Reunion, Paris, France
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75
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Monza E, Gil V, Lucas MF. Computational Enzyme Design at Zymvol. Methods Mol Biol 2022; 2397:249-259. [PMID: 34813068 DOI: 10.1007/978-1-0716-1826-4_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Directed evolution is the most recognized methodology for enzyme engineering. The main drawback resides in its random nature and in the limited sequence exploration; both require screening of thousands (if not millions) of variants to achieve a target function. Computer-driven approaches can limit laboratorial screening to a few hundred candidates, enabling and accelerating the development of industrial enzymes. In this book chapter, the technology adopted at Zymvol is described. An overview of the current development and future directions in the company is also provided.
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Affiliation(s)
- Emanuele Monza
- Zymvol Biomodeling SL, Carrer Roc Boronat 117, Barcelona, Spain.
| | - Victor Gil
- Zymvol Biomodeling SL, Carrer Roc Boronat 117, Barcelona, Spain
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76
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Whitefield C, Hong N, Mitchell JA, Jackson CJ. Computational design and experimental characterisation of a stable human heparanase variant. RSC Chem Biol 2022; 3:341-349. [PMID: 35382258 PMCID: PMC8905545 DOI: 10.1039/d1cb00239b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/11/2022] [Indexed: 11/25/2022] Open
Abstract
Heparanase is the only human enzyme known to hydrolyse heparin sulfate and is involved in many important physiological processes. However, it is also unregulated in many disease states, such as cancer, diabetes and Covid-19. It is thus an important drug target, yet the heterologous production of heparanase is challenging and only possible in mammalian or insect expression systems, which limits the ability of many laboratories to study it. Here we describe the computational redesign of heparanase to allow high yield expression in Escherchia coli. This mutated form of heparanase exhibits essentially identical kinetics, inhibition, structure and protein dynamics to the wild type protein, despite the presence of 26 mutations. This variant will facilitate wider study of this important enzyme and contributes to a growing body of literature that shows evolutionarily conserved and functionally neutral mutations can have significant effects on protein folding and expression. A mutant heparanase that exhibits wild type structure and activity but can be heterologously produced in bacterial protein expression systems.![]()
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Affiliation(s)
- Cassidy Whitefield
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Nansook Hong
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Joshua A. Mitchell
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Colin J. Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 2601, Australia
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77
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Green biomanufacturing promoted by automatic retrobiosynthesis planning and computational enzyme design. Chin J Chem Eng 2022. [DOI: 10.1016/j.cjche.2021.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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78
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Fungal cellulases: protein engineering and post-translational modifications. Appl Microbiol Biotechnol 2021; 106:1-24. [PMID: 34889986 DOI: 10.1007/s00253-021-11723-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 12/18/2022]
Abstract
Enzymatic degradation of lignocelluloses into fermentable sugars to produce biofuels and other biomaterials is critical for environmentally sustainable development and energy resource supply. However, there are problems in enzymatic cellulose hydrolysis, such as the complex cellulase composition, low degradation efficiency, high production cost, and post-translational modifications (PTMs), all of which are closely related to specific characteristics of cellulases that remain unclear. These problems hinder the practical application of cellulases. Due to the rapid development of computer technology in recent years, computer-aided protein engineering is being widely used, which also brings new opportunities for the development of cellulases. Especially in recent years, a large number of studies have reported on the application of computer-aided protein engineering in the development of cellulases; however, these articles have not been systematically reviewed. This article focused on the aspect of protein engineering and PTMs of fungal cellulases. In this manuscript, the latest literatures and the distribution of potential sites of cellulases for engineering have been systematically summarized, which provide reference for further improvement of cellulase properties. KEY POINTS: •Rational design based on virtual mutagenesis can improve cellulase properties. •Modifying protein side chains and glycans helps obtain superior cellulases. •N-terminal glutamine-pyroglutamate conversion stabilizes fungal cellulases.
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79
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Liu Z, Li K, Liu X, Zhao J, Yu Y, Wang L, Kong Y, Chen M. Production of microhomogeneous glycopeptide by a mutated NGT according FuncLib with unique sugar as substrate. Enzyme Microb Technol 2021; 154:109949. [PMID: 34864335 DOI: 10.1016/j.enzmictec.2021.109949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 11/29/2022]
Abstract
N-glycosylation is one of the most important post-translational modifications of proteins. Cytoplasmic soluble N-glycosyltransferase (NGT) exists in bacteria, which is able to transfer different monosaccharide from sugar nucleotide to the NXS/T(X ≠ Pro) consensus sequence in a polypeptide. At present, the NGT enzymes reported could transfer a variety of different sugars to protein, which will lead to the heterogeneity of the sugar chain and the complexity and instability of the structure and function of glycopeptides. According to the FuncLib algorithm, we obtained mutant ApNGT-P1 from ApNGT (the NGT from Actinobacillus pleuropneumoniae) with increased substrate specificity. Compared with the wild-type ApNGT, mutant ApNGT-P1 could only utilize UDP-Glc as sugar donors. The optimum temperature of ApNGT-P1 was about 40 °C and the optimum pH was 7.5-8.0 in PBS buffer. ApNGT-P1 exhibited better tolerance for K+, Mn2+, Ca2+, and Mg2+, but was strongly inhibited by Na+, Cu2+ and Zn2+. The mutant can be applied to the efficient production of glycosylated peptides or proteins with uniform glucose at their glycosylation sites. Besides, this work provided a feasible pathway for further studies on the improving donor substrates selectivity of NGTs.
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Affiliation(s)
- Zhaoxi Liu
- The State Key Laboratory of Microbial Technology, National Glycoengineering Research Centers, Shandong University, Qingdao, Shandong 266237, China
| | - Kun Li
- The State Key Laboratory of Microbial Technology, National Glycoengineering Research Centers, Shandong University, Qingdao, Shandong 266237, China
| | - Xiaoyu Liu
- The State Key Laboratory of Microbial Technology, National Glycoengineering Research Centers, Shandong University, Qingdao, Shandong 266237, China
| | - Jiayu Zhao
- The State Key Laboratory of Microbial Technology, National Glycoengineering Research Centers, Shandong University, Qingdao, Shandong 266237, China
| | - Yue Yu
- College of Life Sciences, Shandong Normal University, Jinan, Shandong 250013, China
| | - Lushan Wang
- The State Key Laboratory of Microbial Technology, National Glycoengineering Research Centers, Shandong University, Qingdao, Shandong 266237, China
| | - Yun Kong
- The State Key Laboratory of Microbial Technology, National Glycoengineering Research Centers, Shandong University, Qingdao, Shandong 266237, China
| | - Min Chen
- The State Key Laboratory of Microbial Technology, National Glycoengineering Research Centers, Shandong University, Qingdao, Shandong 266237, China.
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80
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Leonard AC, Weinstein JJ, Steiner PJ, Erbse AH, Fleishman SJ, Whitehead TA. Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning.. [PMID: 34845448 PMCID: PMC8629191 DOI: 10.1101/2021.11.22.469552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Stabilizing antigenic proteins as vaccine immunogens or diagnostic reagents is a stringent case of protein engineering and design as the exterior surface must maintain recognition by receptor(s) and antigen—specific antibodies at multiple distinct epitopes. This is a challenge, as stability-enhancing mutations must be focused on the protein core, whereas successful computational stabilization algorithms typically select mutations at solvent-facing positions. In this study we report the stabilization of SARS-CoV-2 Wuhan Hu-1 Spike receptor binding domain (S RBD) using a combination of deep mutational scanning and computational design, including the FuncLib algorithm. Our most successful design encodes I358F, Y365W, T430I, and I513L RBD mutations, maintains recognition by the receptor ACE2 and a panel of different anti-RBD monoclonal antibodies, is between 1–2°C more thermally stable than the original RBD using a thermal shift assay, and is less proteolytically sensitive to chymotrypsin and thermolysin than the original RBD. Our approach could be applied to the computational stabilization of a wide range of proteins without requiring detailed knowledge of active sites or binding epitopes, particularly powerful for cases when there are multiple or unknown binding sites.
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81
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Ospina F, Schülke KH, Hammer SC. Biocatalytic Alkylation Chemistry: Building Molecular Complexity with High Selectivity. Chempluschem 2021; 87:e202100454. [PMID: 34821073 DOI: 10.1002/cplu.202100454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/05/2021] [Indexed: 12/28/2022]
Abstract
Biocatalysis has traditionally been viewed as a field that primarily enables access to chiral centers. This includes the synthesis of chiral alcohols, amines and carbonyl compounds, often through functional group interconversion via hydrolytic or oxidation-reduction reactions. This limitation is partly being overcome by the design and evolution of new enzymes. Here, we provide an overview of a recently thriving research field that we summarize as biocatalytic alkylation chemistry. In the past 3-4 years, numerous new enzymes have been developed that catalyze sp3 C-C/N/O/S bond formations. These enzymes utilize different mechanisms to generate molecular complexity by coupling simple fragments with high activity and selectivity. In many cases, the engineered enzymes perform reactions that are difficult or impossible to achieve with current small-molecule catalysts such as organocatalysts and transition-metal complexes. This review further highlights that the design of new enzyme function is particularly successful when off-the-shelf synthetic reagents are utilized to access non-natural reactive intermediates. This underscores how biocatalysis is gradually moving to a field that build molecules through selective bond forming reactions.
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Affiliation(s)
- Felipe Ospina
- Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Kai H Schülke
- Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Stephan C Hammer
- Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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82
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Wang J, Anderson K, Yang E, He L, Lidstrom ME. Enzyme engineering and in vivo testing of a formate reduction pathway. Synth Biol (Oxf) 2021; 6:ysab020. [PMID: 34651085 PMCID: PMC8511477 DOI: 10.1093/synbio/ysab020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 07/08/2021] [Accepted: 08/04/2021] [Indexed: 11/13/2022] Open
Abstract
Formate is an attractive feedstock for sustainable microbial production of fuels and chemicals, but its potential is limited by the lack of efficient assimilation pathways. The reduction of formate to formaldehyde would allow efficient downstream assimilation, but no efficient enzymes are known for this transformation. To develop a 2-step formate reduction pathway, we screened natural variants of acyl-CoA synthetase (ACS) and acylating aldehyde dehydrogenase (ACDH) for activity on one-carbon substrates and identified active and highly expressed homologs of both enzymes. We then performed directed evolution, increasing ACDH-specific activity by 2.5-fold and ACS lysate activity by 5-fold. To test for the in vivo activity of our pathway, we expressed it in a methylotroph which can natively assimilate formaldehyde. Although the enzymes were active in cell extracts, we could not detect formate assimilation into biomass, indicating that further improvement will be required for formatotrophy. Our work provides a foundation for further development of a versatile pathway for formate assimilation.
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Affiliation(s)
- Jue Wang
- Department of Chemical Engineering, University of Washington, Seattle, DC, USA
| | - Karl Anderson
- Department of Chemical Engineering, University of Washington, Seattle, DC, USA
| | - Ellen Yang
- Department of Chemical Engineering, University of Washington, Seattle, DC, USA
| | - Lian He
- Department of Chemical Engineering, University of Washington, Seattle, DC, USA
| | - Mary E Lidstrom
- Department of Chemical Engineering, University of Washington, Seattle, DC, USA
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83
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Bigley AN, Harvey SP, Narindoshvili T, Raushel FM. Substrate Analogues for the Enzyme-Catalyzed Detoxification of the Organophosphate Nerve Agents-Sarin, Soman, and Cyclosarin. Biochemistry 2021; 60:2875-2887. [PMID: 34494832 DOI: 10.1021/acs.biochem.1c00361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The G-type nerve agents, sarin (GB), soman (GD), and cyclosarin (GF), are among the most toxic compounds known. Much progress has been made in evolving the enzyme phosphotriesterase (PTE) from Pseudomonas diminuta for the decontamination of the G-agents; however, the extreme toxicity of the G-agents makes the use of substrate analogues necessary. Typical analogues utilize a chromogenic leaving group to facilitate high-throughput screening, and substitution of an O-methyl for the P-methyl group found in the G-agents, in an effort to reduce toxicity. Till date, there has been no systematic evaluation of the effects of these substitutions on catalytic activity, and the presumed reduction in toxicity has not been tested. A series of 21 G-agent analogues, including all combinations of O-methyl, p-nitrophenyl, and thiophosphate substitutions, have been synthesized and evaluated for their ability to unveil the stereoselectivity and catalytic activity of PTE variants against the authentic G-type nerve agents. The potential toxicity of these analogues was evaluated by measuring the rate of inactivation of acetylcholinesterase (AChE). All of the substitutions reduced inactivation of AChE by more than 100-fold, with the most effective being the thiophosphate analogues, which reduced the rate of inactivation by about 4-5 orders of magnitude. The analogues were found to reliably predict changes in catalytic activity and stereoselectivity of the PTE variants and led to the identification of the BHR-30 variant, which has no apparent stereoselectivity against GD and a kcat/Km of 1.4 × 106, making it the most efficient enzyme for GD decontamination reported till date.
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Affiliation(s)
- Andrew N Bigley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Steven P Harvey
- US Army DEVCOM-CBC, FCDD-CBR-CC E3400, 5183 Blackhawk Rd. Aberdeen Proving Ground, Aberdeen, Maryland 21010, United States
| | - Tamari Narindoshvili
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Frank M Raushel
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States.,Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 7784, United States
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84
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Pinto GP, Corbella M, Demkiv AO, Kamerlin SCL. Exploiting enzyme evolution for computational protein design. Trends Biochem Sci 2021; 47:375-389. [PMID: 34544655 DOI: 10.1016/j.tibs.2021.08.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/18/2021] [Accepted: 08/24/2021] [Indexed: 11/15/2022]
Abstract
Recent years have seen an explosion of interest in understanding the physicochemical parameters that shape enzyme evolution, as well as substantial advances in computational enzyme design. This review discusses three areas where evolutionary information can be used as part of the design process: (i) using ancestral sequence reconstruction (ASR) to generate new starting points for enzyme design efforts; (ii) learning from how nature uses conformational dynamics in enzyme evolution to mimic this process in silico; and (iii) modular design of enzymes from smaller fragments, again mimicking the process by which nature appears to create new protein folds. Using showcase examples, we highlight the importance of incorporating evolutionary information to continue to push forward the boundaries of enzyme design studies.
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Affiliation(s)
- Gaspar P Pinto
- Department of Chemistry - BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Marina Corbella
- Department of Chemistry - BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Andrey O Demkiv
- Department of Chemistry - BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
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85
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Computationally designed pyocyanin demethylase acts synergistically with tobramycin to kill recalcitrant Pseudomonas aeruginosa biofilms. Proc Natl Acad Sci U S A 2021; 118:2022012118. [PMID: 33723058 DOI: 10.1073/pnas.2022012118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that develops difficult-to-treat biofilms in immunocompromised individuals, cystic fibrosis patients, and in chronic wounds. P. aeruginosa has an arsenal of physiological attributes that enable it to evade standard antibiotic treatments, particularly in the context of biofilms where it grows slowly and becomes tolerant to many drugs. One of its survival strategies involves the production of the redox-active phenazine, pyocyanin, which promotes biofilm development. We previously identified an enzyme, PodA, that demethylated pyocyanin and disrupted P. aeruginosa biofilm development in vitro. Here, we asked if this protein could be used as a potential therapeutic for P. aeruginosa infections together with tobramycin, an antibiotic typically used in the clinic. A major roadblock to answering this question was the poor yield and stability of wild-type PodA purified from standard Escherichia coli overexpression systems. We hypothesized that the insufficient yields were due to poor packing within PodA's obligatory homotrimeric interfaces. We therefore applied the protein design algorithm, AffiLib, to optimize the symmetric core of this interface, resulting in a design that incorporated five mutations leading to a 20-fold increase in protein yield from heterologous expression and purification and a substantial increase in stability to environmental conditions. The addition of the designed PodA with tobramycin led to increased killing of P. aeruginosa cultures under oxic and hypoxic conditions in both the planktonic and biofilm states. This study highlights the potential for targeting extracellular metabolites to assist the control of P. aeruginosa biofilms that tolerate conventional antibiotic treatment.
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86
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Biorefinery Gets Hot: Thermophilic Enzymes and Microorganisms for Second-Generation Bioethanol Production. Processes (Basel) 2021. [DOI: 10.3390/pr9091583] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
To mitigate the current global energy and the environmental crisis, biofuels such as bioethanol have progressively gained attention from both scientific and industrial perspectives. However, at present, commercialized bioethanol is mainly derived from edible crops, thus raising serious concerns given its competition with feed production. For this reason, lignocellulosic biomasses (LCBs) have been recognized as important alternatives for bioethanol production. Because LCBs supply is sustainable, abundant, widespread, and cheap, LCBs-derived bioethanol currently represents one of the most viable solutions to meet the global demand for liquid fuel. However, the cost-effective conversion of LCBs into ethanol remains a challenge and its implementation has been hampered by several bottlenecks that must still be tackled. Among other factors related to the challenging and variable nature of LCBs, we highlight: (i) energy-demanding pretreatments, (ii) expensive hydrolytic enzyme blends, and (iii) the need for microorganisms that can ferment mixed sugars. In this regard, thermophiles represent valuable tools to overcome some of these limitations. Thus, the aim of this review is to provide an overview of the state-of-the-art technologies involved, such as the use of thermophilic enzymes and microorganisms in industrial-relevant conditions, and to propose possible means to implement thermophiles into second-generation ethanol biorefineries that are already in operation.
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87
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Heath RS, Ruscoe RE, Turner NJ. The beauty of biocatalysis: sustainable synthesis of ingredients in cosmetics. Nat Prod Rep 2021; 39:335-388. [PMID: 34879125 DOI: 10.1039/d1np00027f] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: 2015 up to July 2021The market for cosmetics is consumer driven and the desire for green, sustainable and natural ingredients is increasing. The use of isolated enzymes and whole-cell organisms to synthesise these products is congruent with these values, especially when combined with the use of renewable, recyclable or waste feedstocks. The literature of biocatalysis for the synthesis of ingredients in cosmetics in the past five years is herein reviewed.
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Affiliation(s)
- Rachel S Heath
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Rebecca E Ruscoe
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Nicholas J Turner
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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88
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Currin A, Parker S, Robinson CJ, Takano E, Scrutton NS, Breitling R. The evolving art of creating genetic diversity: From directed evolution to synthetic biology. Biotechnol Adv 2021; 50:107762. [PMID: 34000294 PMCID: PMC8299547 DOI: 10.1016/j.biotechadv.2021.107762] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 04/21/2021] [Accepted: 04/25/2021] [Indexed: 12/31/2022]
Abstract
The ability to engineer biological systems, whether to introduce novel functionality or improved performance, is a cornerstone of biotechnology and synthetic biology. Typically, this requires the generation of genetic diversity to explore variations in phenotype, a process that can be performed at many levels, from single molecule targets (i.e., in directed evolution of enzymes) to whole organisms (e.g., in chassis engineering). Recent advances in DNA synthesis technology and automation have enhanced our ability to create variant libraries with greater control and throughput. This review highlights the latest developments in approaches to create such a hierarchy of diversity from the enzyme level to entire pathways in vitro, with a focus on the creation of combinatorial libraries that are required to navigate a target's vast design space successfully to uncover significant improvements in function.
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Affiliation(s)
- Andrew Currin
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom.
| | - Steven Parker
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Christopher J Robinson
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Eriko Takano
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Nigel S Scrutton
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Rainer Breitling
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom.
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89
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Tang Q, Pavlidis IV, Badenhorst CPS, Bornscheuer UT. From Natural Methylation to Versatile Alkylations Using Halide Methyltransferases. Chembiochem 2021; 22:2584-2590. [PMID: 33890381 PMCID: PMC8453949 DOI: 10.1002/cbic.202100153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/22/2021] [Indexed: 11/06/2022]
Abstract
Halide methyltransferases (HMTs) enable the enzymatic synthesis of S-adenosyl-l-methionine (SAM) from S-adenosyl-l-homocysteine (SAH) and methyl iodide. Characterisation of a range of naturally occurring HMTs and subsequent protein engineering led to HMT variants capable of synthesising ethyl, propyl, and allyl analogues of SAM. Notably, HMTs do not depend on chemical synthesis of methionine analogues, as required by methionine adenosyltransferases (MATs). However, at the moment MATs have a much broader substrate scope than the HMTs. Herein we provide an overview of the discovery and engineering of promiscuous HMTs and how these strategies will pave the way towards a toolbox of HMT variants for versatile chemo- and regioselective biocatalytic alkylations.
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Affiliation(s)
- Qingyun Tang
- Institute of BiochemistryUniversity of GreifswaldFelix-Hausdorff-Str. 417489GreifswaldGermany
| | - Ioannis V. Pavlidis
- Dept. of ChemistryUniversity of CreteVoutes University Campus70013HeraklionGreece
| | | | - Uwe T. Bornscheuer
- Institute of BiochemistryUniversity of GreifswaldFelix-Hausdorff-Str. 417489GreifswaldGermany
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90
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Borenstein-Katz A, Warszawski S, Amon R, Eilon M, Cohen-Dvashi H, Leviatan Ben-Arye S, Tasnima N, Yu H, Chen X, Padler-Karavani V, Fleishman SJ, Diskin R. Biomolecular Recognition of the Glycan Neoantigen CA19-9 by Distinct Antibodies. J Mol Biol 2021; 433:167099. [PMID: 34119488 PMCID: PMC7611348 DOI: 10.1016/j.jmb.2021.167099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/11/2021] [Accepted: 06/05/2021] [Indexed: 10/21/2022]
Abstract
Glycans decorate the cell surface, secreted glycoproteins and glycolipids, and altered glycans are often found in cancers. Despite their high diagnostic and therapeutic potential, however, glycans are polar and flexible molecules that are quite challenging for the development and design of high-affinity binding antibodies. To understand the mechanisms by which glycan neoantigens are specifically recognized by antibodies, we analyze the biomolecular recognition of the tumor-associated carbohydrate antigen CA19-9 by two distinct antibodies using X-ray crystallography. Despite the potential plasticity of glycans and the very different antigen-binding surfaces presented by the antibodies, both structures reveal an essentially identical extended CA19-9 conformer, suggesting that this conformer's stability selects the antibodies. Starting from the bound structure of one of the antibodies, we use the AbLIFT computational algorithm to design a variant with seven core mutations in the variable domain's light-heavy chain interface that exhibits tenfold improved affinity for CA19-9. The results reveal strategies used by antibodies to specifically recognize glycan antigens and show how automated antibody-optimization methods may be used to enhance the clinical potential of existing antibodies.
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Affiliation(s)
- Aliza Borenstein-Katz
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Shira Warszawski
- Department of Biomolecular Sciences, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Ron Amon
- Department of Cell Research and Immunology, The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Maayan Eilon
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Hadas Cohen-Dvashi
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Shani Leviatan Ben-Arye
- Department of Cell Research and Immunology, The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nova Tasnima
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Hai Yu
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Xi Chen
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Vered Padler-Karavani
- Department of Cell Research and Immunology, The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Sarel Jacob Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Ron Diskin
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel.
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91
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Affiliation(s)
- Amir Aharoni
- Department of Life Sciences Ben‐Gurion University of the Negev Be’er Sheva Israel
| | - Sarel J. Fleishman
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot Israel
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92
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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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93
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Scherer M, Fleishman SJ, Jones PR, Dandekar T, Bencurova E. Computational Enzyme Engineering Pipelines for Optimized Production of Renewable Chemicals. Front Bioeng Biotechnol 2021; 9:673005. [PMID: 34211966 PMCID: PMC8239229 DOI: 10.3389/fbioe.2021.673005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/06/2021] [Indexed: 11/13/2022] Open
Abstract
To enable a sustainable supply of chemicals, novel biotechnological solutions are required that replace the reliance on fossil resources. One potential solution is to utilize tailored biosynthetic modules for the metabolic conversion of CO2 or organic waste to chemicals and fuel by microorganisms. Currently, it is challenging to commercialize biotechnological processes for renewable chemical biomanufacturing because of a lack of highly active and specific biocatalysts. As experimental methods to engineer biocatalysts are time- and cost-intensive, it is important to establish efficient and reliable computational tools that can speed up the identification or optimization of selective, highly active, and stable enzyme variants for utilization in the biotechnological industry. Here, we review and suggest combinations of effective state-of-the-art software and online tools available for computational enzyme engineering pipelines to optimize metabolic pathways for the biosynthesis of renewable chemicals. Using examples relevant for biotechnology, we explain the underlying principles of enzyme engineering and design and illuminate future directions for automated optimization of biocatalysts for the assembly of synthetic metabolic pathways.
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Affiliation(s)
- Marc Scherer
- Department of Bioinformatics, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Patrik R Jones
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Thomas Dandekar
- Department of Bioinformatics, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Elena Bencurova
- Department of Bioinformatics, Julius-Maximilians University of Würzburg, Würzburg, Germany
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94
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Frappier V, Keating AE. Data-driven computational protein design. Curr Opin Struct Biol 2021; 69:63-69. [PMID: 33910104 DOI: 10.1016/j.sbi.2021.03.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 01/28/2023]
Abstract
Computational protein design can generate proteins not found in nature that adopt desired structures and perform novel functions. Although proteins could, in theory, be designed with ab initio methods, practical success has come from using large amounts of data that describe the sequences, structures, and functions of existing proteins and their variants. We present recent creative uses of multiple-sequence alignments, protein structures, and high-throughput functional assays in computational protein design. Approaches range from enhancing structure-based design with experimental data to building regression models to training deep neural nets that generate novel sequences. Looking ahead, deep learning will be increasingly important for maximizing the value of data for protein design.
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Affiliation(s)
- Vincent Frappier
- Generate Biomedicines, 26 Landsdowne Street, Cambridge, MA, 02139, USA
| | - Amy E Keating
- MIT Departments of Biology and Biological Engineering, 77 Massachusetts Ave., Cambridge, MA, 02139, USA.
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95
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Meinen BA, Bahl CD. Breakthroughs in computational design methods open up new frontiers for de novo protein engineering. Protein Eng Des Sel 2021; 34:6243354. [DOI: 10.1093/protein/gzab007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/16/2021] [Accepted: 03/08/2021] [Indexed: 02/03/2023] Open
Abstract
Abstract
Proteins catalyze the majority of chemical reactions in organisms, and harnessing this power has long been the focus of the protein engineering field. Computational protein design aims to create new proteins and functions in silico, and in doing so, accelerate the process, reduce costs and enable more sophisticated engineering goals to be accomplished. Challenges that very recently seemed impossible are now within reach thanks to several landmark advances in computational protein design methods. Here, we summarize these new methods, with a particular emphasis on de novo protein design advancements occurring within the past 5 years.
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Affiliation(s)
- Ben A Meinen
- Institute for Protein Innovation, Harvard Institutes of Medicine 4 Blackfan Circle, Room 941 Boston, MA 02115-5701 Boston, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Christopher D Bahl
- Institute for Protein Innovation, Harvard Institutes of Medicine 4 Blackfan Circle, Room 941 Boston, MA 02115-5701 Boston, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
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96
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Wang L, Sun Y. Engineering organophosphate hydrolase for enhanced biocatalytic performance: A review. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.107945] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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97
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Peleg Y, Vincentelli R, Collins BM, Chen KE, Livingstone EK, Weeratunga S, Leneva N, Guo Q, Remans K, Perez K, Bjerga GEK, Larsen Ø, Vaněk O, Skořepa O, Jacquemin S, Poterszman A, Kjær S, Christodoulou E, Albeck S, Dym O, Ainbinder E, Unger T, Schuetz A, Matthes S, Bader M, de Marco A, Storici P, Semrau MS, Stolt-Bergner P, Aigner C, Suppmann S, Goldenzweig A, Fleishman SJ. Community-Wide Experimental Evaluation of the PROSS Stability-Design Method. J Mol Biol 2021; 433:166964. [PMID: 33781758 DOI: 10.1016/j.jmb.2021.166964] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/08/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
Recent years have seen a dramatic improvement in protein-design methodology. Nevertheless, most methods demand expert intervention, limiting their widespread adoption. By contrast, the PROSS algorithm for improving protein stability and heterologous expression levels has been successfully applied to a range of challenging enzymes and binding proteins. Here, we benchmark the application of PROSS as a stand-alone tool for protein scientists with no or limited experience in modeling. Twelve laboratories from the Protein Production and Purification Partnership in Europe (P4EU) challenged the PROSS algorithm with 14 unrelated protein targets without support from the PROSS developers. For each target, up to six designs were evaluated for expression levels and in some cases, for thermal stability and activity. In nine targets, designs exhibited increased heterologous expression levels either in prokaryotic and/or eukaryotic expression systems under experimental conditions that were tailored for each target protein. Furthermore, we observed increased thermal stability in nine of ten tested targets. In two prime examples, the human Stem Cell Factor (hSCF) and human Cadherin-Like Domain (CLD12) from the RET receptor, the wild type proteins were not expressible as soluble proteins in E. coli, yet the PROSS designs exhibited high expression levels in E. coli and HEK293 cells, respectively, and improved thermal stability. We conclude that PROSS may improve stability and expressibility in diverse cases, and that improvement typically requires target-specific expression conditions. This study demonstrates the strengths of community-wide efforts to probe the generality of new methods and recommends areas for future research to advance practically useful algorithms for protein science.
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Affiliation(s)
- Yoav Peleg
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Renaud Vincentelli
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Brett M Collins
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Kai-En Chen
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Emma K Livingstone
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Saroja Weeratunga
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Natalya Leneva
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Qian Guo
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Kim Remans
- European Molecular Biology Laboratory (EMBL), Protein Expression and Purification Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Kathryn Perez
- European Molecular Biology Laboratory (EMBL), Protein Expression and Purification Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gro E K Bjerga
- NORCE Norwegian Research Centre, Postboks 22 Nygårdstangen, 5038 Bergen, Norway
| | - Øivind Larsen
- NORCE Norwegian Research Centre, Postboks 22 Nygårdstangen, 5038 Bergen, Norway
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Ondřej Skořepa
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Sophie Jacquemin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, France
| | - Arnaud Poterszman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, France
| | - Svend Kjær
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Evangelos Christodoulou
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Shira Albeck
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Orly Dym
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elena Ainbinder
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tamar Unger
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anja Schuetz
- Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Susann Matthes
- Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Michael Bader
- Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany; University of Lübeck, Institute for Biology, Ratzeburger Allee 160, 23562 Lübeck, Germany; Charité University Medicine, Charitéplatz 1, 10117 Berlin, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Slovenia
| | - Paola Storici
- Elettra Sincrotrone Trieste - SS 14 - km 163, 5 in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Marta S Semrau
- Elettra Sincrotrone Trieste - SS 14 - km 163, 5 in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Peggy Stolt-Bergner
- Vienna Biocenter Core Facilities GmbH, Dr. Bohr-gasse 3, 1030 Vienna, Austria
| | - Christian Aigner
- Vienna Biocenter Core Facilities GmbH, Dr. Bohr-gasse 3, 1030 Vienna, Austria
| | - Sabine Suppmann
- Max-Planck Institute of Biochemistry, Biochemistry Core Facility, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Adi Goldenzweig
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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98
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Marques SM, Planas-Iglesias J, Damborsky J. Web-based tools for computational enzyme design. Curr Opin Struct Biol 2021; 69:19-34. [PMID: 33667757 DOI: 10.1016/j.sbi.2021.01.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 12/30/2022]
Abstract
Enzymes are in high demand for very diverse biotechnological applications. However, natural biocatalysts often need to be engineered for fine-tuning their properties towards the end applications, such as the activity, selectivity, stability to temperature or co-solvents, and solubility. Computational methods are increasingly used in this task, providing predictions that narrow down the space of possible mutations significantly and can enormously reduce the experimental burden. Many computational tools are available as web-based platforms, making them accessible to non-expert users. These platforms are typically user-friendly, contain walk-throughs, and do not require deep expertise and installations. Here we describe some of the most recent outstanding web-tools for enzyme engineering and formulate future perspectives in this field.
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Affiliation(s)
- Sérgio M Marques
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic; International Centre for Clinical Research, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Joan Planas-Iglesias
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic; International Centre for Clinical Research, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic; International Centre for Clinical Research, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic.
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99
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Sormani G, Harteveld Z, Rosset S, Correia B, Laio A. A Rosetta-based protein design protocol converging to natural sequences. J Chem Phys 2021; 154:074114. [DOI: 10.1063/5.0039240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
| | - Zander Harteveld
- Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne, Lausanne CH-1015, Switzerland and Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Stéphane Rosset
- Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne, Lausanne CH-1015, Switzerland and Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Bruno Correia
- Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne, Lausanne CH-1015, Switzerland and Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
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100
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Bengel LL, Aberle B, Egler-Kemmerer AN, Kienzle S, Hauer B, Hammer SC. Engineered Enzymes Enable Selective N-Alkylation of Pyrazoles With Simple Haloalkanes. Angew Chem Int Ed Engl 2021; 60:5554-5560. [PMID: 33300646 PMCID: PMC7986378 DOI: 10.1002/anie.202014239] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/01/2020] [Indexed: 01/06/2023]
Abstract
Selective alkylation of pyrazoles could solve a challenge in chemistry and streamline synthesis of important molecules. Here we report catalyst‐controlled pyrazole alkylation by a cyclic two‐enzyme cascade. In this enzymatic system, a promiscuous enzyme uses haloalkanes as precursors to generate non‐natural analogs of the common cosubstrate S‐adenosyl‐l‐methionine. A second engineered enzyme transfers the alkyl group in highly selective C−N bond formations to the pyrazole substrate. The cosubstrate is recycled and only used in catalytic amounts. Key is a computational enzyme‐library design tool that converted a promiscuous methyltransferase into a small enzyme family of pyrazole‐alkylating enzymes in one round of mutagenesis and screening. With this enzymatic system, pyrazole alkylation (methylation, ethylation, propylation) was achieved with unprecedented regioselectivity (>99 %), regiodivergence, and in a first example on preparative scale.
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Affiliation(s)
- Ludwig L Bengel
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Benjamin Aberle
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Alexander-N Egler-Kemmerer
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Samuel Kienzle
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Bernhard Hauer
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Stephan C Hammer
- Faculty of Chemistry, Organic Chemistry and Biocatalysis, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany.,Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
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