1
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Hilvert D. Spiers Memorial Lecture: Engineering biocatalysts. Faraday Discuss 2024. [PMID: 39046423 DOI: 10.1039/d4fd00139g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Enzymes are being engineered to catalyze chemical reactions for many practical applications in chemistry and biotechnology. The approaches used are surveyed in this short review, emphasizing methods for accessing reactivities not expressed by native protein scaffolds. The successful generation of completely de novo enzymes that rival the rates and selectivities of their natural counterparts highlights the potential role that designer enzymes may play in the coming years in research, industry, and medicine. Some challenges that need to be addressed to realize this ambitious dream are considered together with possible solutions.
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Affiliation(s)
- Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, 8093 Zürich, Switzerland.
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2
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Cristobal J, Hegazy R, Richard JP. Glycerol 3-Phosphate Dehydrogenase: Role of the Protein Conformational Change in Activation of a Readily Reversible Enzyme-Catalyzed Hydride Transfer Reaction. Biochemistry 2024; 63:1016-1025. [PMID: 38546289 PMCID: PMC11025551 DOI: 10.1021/acs.biochem.3c00702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/26/2024] [Accepted: 03/13/2024] [Indexed: 04/17/2024]
Abstract
Kinetic parameters are reported for glycerol 3-phosphate dehydrogenase (GPDH)-catalyzed hydride transfer from the whole substrate glycerol 3-phosphate (G3P) or truncated substrate ethylene glycol (EtG) to NAD, and for activation of the hydride transfer reaction of EtG by phosphite dianion. These kinetic parameters were combined with parameters for enzyme-catalyzed hydride transfer in the microscopic reverse direction to give the reaction equilibrium constants Keq. Hydride transfer from G3P is favored in comparison to EtG because the carbonyl product of the former reaction is stabilized by hyperconjugative electron donation from the -CH2R keto substituent. The kinetic data show that the phosphite dianion provides the same 7.6 ± 0.1 kcal/mol stabilization of the transition states for enzyme-catalyzed reactions in the forward [reduction of NAD by EtG] and reverse [oxidation of NADH by glycolaldehyde] directions. The experimental evidence that supports a role for phosphite dianion in stabilizing the active closed form of the GPDH (EC) relative to the ca. 6 kcal/mol more unstable open form (EO) is summarized.
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Affiliation(s)
- Judith
R. Cristobal
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Rania Hegazy
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - John P. Richard
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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3
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Rakotoharisoa RV, Seifinoferest B, Zarifi N, Miller JDM, Rodriguez JM, Thompson MC, Chica RA. Design of Efficient Artificial Enzymes Using Crystallographically Enhanced Conformational Sampling. J Am Chem Soc 2024; 146:10001-10013. [PMID: 38532610 DOI: 10.1021/jacs.4c00677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
The ability to create efficient artificial enzymes for any chemical reaction is of great interest. Here, we describe a computational design method for increasing the catalytic efficiency of de novo enzymes by several orders of magnitude without relying on directed evolution and high-throughput screening. Using structural ensembles generated from dynamics-based refinement against X-ray diffraction data collected from crystals of Kemp eliminases HG3 (kcat/KM 125 M-1 s-1) and KE70 (kcat/KM 57 M-1 s-1), we design from each enzyme ≤10 sequences predicted to catalyze this reaction more efficiently. The most active designs display kcat/KM values improved by 100-250-fold, comparable to mutants obtained after screening thousands of variants in multiple rounds of directed evolution. Crystal structures show excellent agreement with computational models, with catalytic contacts present as designed and transition-state root-mean-square deviations of ≤0.65 Å. Our work shows how ensemble-based design can generate efficient artificial enzymes by exploiting the true conformational ensemble to design improved active sites.
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Affiliation(s)
- Rojo V Rakotoharisoa
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- Center for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Behnoush Seifinoferest
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Niayesh Zarifi
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- Center for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Jack D M Miller
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- Center for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Joshua M Rodriguez
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Michael C Thompson
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Roberto A Chica
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- Center for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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4
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Bell EL, Hutton AE, Burke AJ, O'Connell A, Barry A, O'Reilly E, Green AP. Strategies for designing biocatalysts with new functions. Chem Soc Rev 2024; 53:2851-2862. [PMID: 38353665 PMCID: PMC10946311 DOI: 10.1039/d3cs00972f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Indexed: 03/19/2024]
Abstract
The engineering of natural enzymes has led to the availability of a broad range of biocatalysts that can be used for the sustainable manufacturing of a variety of chemicals and pharmaceuticals. However, for many important chemical transformations there are no known enzymes that can serve as starting templates for biocatalyst development. These limitations have fuelled efforts to build entirely new catalytic sites into proteins in order to generate enzymes with functions beyond those found in Nature. This bottom-up approach to enzyme development can also reveal new fundamental insights into the molecular origins of efficient protein catalysis. In this tutorial review, we will survey the different strategies that have been explored for designing new protein catalysts. These methods will be illustrated through key selected examples, which demonstrate how highly proficient and selective biocatalysts can be developed through experimental protein engineering and/or computational design. Given the rapid pace of development in the field, we are optimistic that designer enzymes will begin to play an increasingly prominent role as industrial biocatalysts in the coming years.
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Affiliation(s)
- Elizabeth L Bell
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Amy E Hutton
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Ashleigh J Burke
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Adam O'Connell
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Amber Barry
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Elaine O'Reilly
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Anthony P Green
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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5
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Ruiz-Pernía JJ, Świderek K, Bertran J, Moliner V, Tuñón I. Electrostatics as a Guiding Principle in Understanding and Designing Enzymes. J Chem Theory Comput 2024; 20:1783-1795. [PMID: 38410913 PMCID: PMC10938506 DOI: 10.1021/acs.jctc.3c01395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 02/28/2024]
Abstract
Enzyme design faces challenges related to the implementation of the basic principles that govern the catalytic activity in natural enzymes. In this work, we revisit basic electrostatic concepts that have been shown to explain the origin of enzymatic efficiency like preorganization and reorganization. Using magnitudes such as the electrostatic potential and the electric field generated by the protein, we explain how these concepts work in different enzymes and how they can be used to rationalize the consequences of point mutations. We also discuss examples of protein design in which electrostatic effects have been implemented. For the near future, molecular simulations, coupled with the use of machine learning methods, can be used to implement electrostatics as a guiding principle for enzyme designs.
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Affiliation(s)
| | - Katarzyna Świderek
- Biocomp
group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón Spain
| | - Joan Bertran
- Departament
de Química, Universitat Autònoma
de Barcelona, 08193 Bellaterra, Spain
| | - Vicent Moliner
- Biocomp
group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón Spain
| | - Iñaki Tuñón
- Departament
de Química Física, Universitat
de València, 46100 Burjassot, Spain
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6
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Hutton AE, Foster J, Crawshaw R, Hardy FJ, Johannissen LO, Lister TM, Gérard EF, Birch-Price Z, Obexer R, Hay S, Green AP. A non-canonical nucleophile unlocks a new mechanistic pathway in a designed enzyme. Nat Commun 2024; 15:1956. [PMID: 38438341 PMCID: PMC10912507 DOI: 10.1038/s41467-024-46123-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/09/2024] [Indexed: 03/06/2024] Open
Abstract
Directed evolution of computationally designed enzymes has provided new insights into the emergence of sophisticated catalytic sites in proteins. In this regard, we have recently shown that a histidine nucleophile and a flexible arginine can work in synergy to accelerate the Morita-Baylis-Hillman (MBH) reaction with unrivalled efficiency. Here, we show that replacing the catalytic histidine with a non-canonical Nδ-methylhistidine (MeHis23) nucleophile leads to a substantially altered evolutionary outcome in which the catalytic Arg124 has been abandoned. Instead, Glu26 has emerged, which mediates a rate-limiting proton transfer step to deliver an enzyme (BHMeHis1.8) that is more than an order of magnitude more active than our earlier MBHase. Interestingly, although MeHis23 to His substitution in BHMeHis1.8 reduces activity by 4-fold, the resulting His containing variant is still a potent MBH biocatalyst. However, analysis of the BHMeHis1.8 evolutionary trajectory reveals that the MeHis nucleophile was crucial in the early stages of engineering to unlock the new mechanistic pathway. This study demonstrates how even subtle perturbations to key catalytic elements of designed enzymes can lead to vastly different evolutionary outcomes, resulting in new mechanistic solutions to complex chemical transformations.
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Affiliation(s)
- Amy E Hutton
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Jake Foster
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Rebecca Crawshaw
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Florence J Hardy
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Linus O Johannissen
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Thomas M Lister
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Emilie F Gérard
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Zachary Birch-Price
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Richard Obexer
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Sam Hay
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Anthony P Green
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK.
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7
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Mao J, Jin X, Shi M, Heidenreich D, Brown LJ, Brown RCD, Lelli M, He X, Glaubitz C. Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins. SCIENCE ADVANCES 2024; 10:eadj0384. [PMID: 38266078 PMCID: PMC10807816 DOI: 10.1126/sciadv.adj0384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
Proteorhodopsins are widely distributed photoreceptors from marine bacteria. Their discovery revealed a high degree of evolutionary adaptation to ambient light, resulting in blue- and green-absorbing variants that correlate with a conserved glutamine/leucine at position 105. On the basis of an integrated approach combining sensitivity-enhanced solid-state nuclear magnetic resonance (ssNMR) spectroscopy and linear-scaling quantum mechanics/molecular mechanics (QM/MM) methods, this single residue is shown to be responsible for a variety of synergistically coupled structural and electrostatic changes along the retinal polyene chain, ionone ring, and within the binding pocket. They collectively explain the observed color shift. Furthermore, analysis of the differences in chemical shift between nuclei within the same residues in green and blue proteorhodopsins also reveals a correlation with the respective degree of conservation. Our data show that the highly conserved color change mainly affects other highly conserved residues, illustrating a high degree of robustness of the color phenotype to sequence variation.
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Affiliation(s)
- Jiafei Mao
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Straße 9, 60438 Frankfurt am Main, Germany
| | - Xinsheng Jin
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Man Shi
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - David Heidenreich
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Straße 9, 60438 Frankfurt am Main, Germany
| | - Lynda J. Brown
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ UK
| | - Richard C. D. Brown
- Department of Chemistry, University of Southampton, Southampton, SO17 1BJ UK
| | - Moreno Lelli
- Department of Chemistry “Ugo Schiff” and Magnetic Resonance Center (CERM), University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Italy
- Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Italy
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
- New York University–East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai, 200062, China
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Straße 9, 60438 Frankfurt am Main, Germany
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8
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Jiang Y, Ding N, Shao Q, Stull SL, Cheng Z, Yang ZJ. Substrate Positioning Dynamics Involves a Non-Electrostatic Component to Mediate Catalysis. J Phys Chem Lett 2023; 14:11480-11489. [PMID: 38085952 PMCID: PMC11211065 DOI: 10.1021/acs.jpclett.3c02444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Substrate positioning dynamics (SPD) orients the substrate in the active site, thereby influencing catalytic efficiency. However, it remains unknown whether SPD effects originate primarily from electrostatic perturbation inside the enzyme or can independently mediate catalysis with a significant non-electrostatic component. In this work, we investigated how the non-electrostatic component of SPD affects transition state (TS) stabilization. Using high-throughput enzyme modeling, we selected Kemp eliminase variants with similar electrostatics inside the enzyme but significantly different SPD. The kinetic parameters of these mutants were experimentally characterized. We observed a valley-shaped, two-segment linear correlation between the TS stabilization free energy (converted from kinetic parameters) and substrate positioning index (a metric to quantify SPD). The energy varies by approximately 2 kcal/mol. Favorable SPD was observed for the distal mutant R154W, increasing the proportion of reactive conformations and leading to the lowest activation free energy. These results indicate the substantial contribution of the non-electrostatic component of SPD to enzyme catalytic efficiency.
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Affiliation(s)
- Yaoyukun Jiang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ning Ding
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Qianzhen Shao
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Sebastian L. Stull
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Zihao Cheng
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Zhongyue J. Yang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
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9
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Yang ZJ, Shao Q, Jiang Y, Jurich C, Ran X, Juarez RJ, Yan B, Stull SL, Gollu A, Ding N. Mutexa: A Computational Ecosystem for Intelligent Protein Engineering. J Chem Theory Comput 2023; 19:7459-7477. [PMID: 37828731 PMCID: PMC10653112 DOI: 10.1021/acs.jctc.3c00602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Indexed: 10/14/2023]
Abstract
Protein engineering holds immense promise in shaping the future of biomedicine and biotechnology. This Review focuses on our ongoing development of Mutexa, a computational ecosystem designed to enable "intelligent protein engineering". In this vision, researchers will seamlessly acquire sequences of protein variants with desired functions as biocatalysts, therapeutic peptides, and diagnostic proteins through a finely-tuned computational machine, akin to Amazon Alexa's role as a versatile virtual assistant. The technical foundation of Mutexa has been established through the development of a database that combines and relates enzyme structures and their respective functions (e.g., IntEnzyDB), workflow software packages that enable high-throughput protein modeling (e.g., EnzyHTP and LassoHTP), and scoring functions that map the sequence-structure-function relationship of proteins (e.g., EnzyKR and DeepLasso). We will showcase the applications of these tools in benchmarking the convergence conditions of enzyme functional descriptors across mutants, investigating protein electrostatics and cavity distributions in SAM-dependent methyltransferases, and understanding the role of nonelectrostatic dynamic effects in enzyme catalysis. Finally, we will conclude by addressing the future steps and fundamental challenges in our endeavor to develop new Mutexa applications that assist the identification of beneficial mutants in protein engineering.
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Affiliation(s)
- Zhongyue J. Yang
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- Data
Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Qianzhen Shao
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Yaoyukun Jiang
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Christopher Jurich
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt
Institute of Chemical Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
| | - Xinchun Ran
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Reecan J. Juarez
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Chemical
and Physical Biology Program, Vanderbilt
University, Nashville, Tennessee 37235, United States
| | - Bailu Yan
- Department
of Biostatistics, Vanderbilt University, Nashville, Tennessee 37205, United States
| | - Sebastian L. Stull
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Anvita Gollu
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ning Ding
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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10
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Rakotoharisoa RV, Seifinoferest B, Zarifi N, Miller JD, Rodriguez JM, Thompson MC, Chica RA. Design of efficient artificial enzymes using crystallographically-enhanced conformational sampling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.01.564846. [PMID: 37961474 PMCID: PMC10635043 DOI: 10.1101/2023.11.01.564846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The ability to create efficient artificial enzymes for any chemical reaction is of great interest. Here, we describe a computational design method for increasing catalytic efficiency of de novo enzymes to a level comparable to their natural counterparts without relying on directed evolution. Using structural ensembles generated from dynamics-based refinement against X-ray diffraction data collected from crystals of Kemp eliminases HG3 (kcat/KM 125 M-1 s-1) and KE70 (kcat/KM 57 M-1 s-1), we design from each enzyme ≤10 sequences predicted to catalyze this reaction more efficiently. The most active designs display kcat/KM values improved by 100-250-fold, comparable to mutants obtained after screening thousands of variants in multiple rounds of directed evolution. Crystal structures show excellent agreement with computational models. Our work shows how computational design can generate efficient artificial enzymes by exploiting the true conformational ensemble to more effectively stabilize the transition state.
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Affiliation(s)
- Rojo V. Rakotoharisoa
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
- Center for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
| | - Behnoush Seifinoferest
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Niayesh Zarifi
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
- Center for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
| | - Jack D.M. Miller
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
- Center for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
| | - Joshua M. Rodriguez
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Michael C. Thompson
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Roberto A. Chica
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
- Center for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
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11
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Marshall LR, Bhattacharya S, Korendovych IV. Fishing for Catalysis: Experimental Approaches to Narrowing Search Space in Directed Evolution of Enzymes. JACS AU 2023; 3:2402-2412. [PMID: 37772192 PMCID: PMC10523367 DOI: 10.1021/jacsau.3c00315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 09/30/2023]
Abstract
Directed evolution has transformed protein engineering offering a path to rapid improvement of protein properties. Yet, in practice it is limited by the hyper-astronomic protein sequence search space, and approaches to identify mutagenic hot spots, i.e., locations where mutations are most likely to have a productive impact, are needed. In this perspective, we categorize and discuss recent progress in the experimental approaches (broadly defined as structural, bioinformatic, and dynamic) to hot spot identification. Recent successes in harnessing protein dynamics and machine learning approaches provide new opportunities for the field and will undoubtedly help directed evolution reach its full potential.
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Affiliation(s)
- Liam R. Marshall
- Department of Chemistry, Syracuse
University, 111 College Place, Syracuse, New York 13224, United States
| | - Sagar Bhattacharya
- Department of Chemistry, Syracuse
University, 111 College Place, Syracuse, New York 13224, United States
| | - Ivan V. Korendovych
- Department of Chemistry, Syracuse
University, 111 College Place, Syracuse, New York 13224, United States
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12
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Patsch D, Eichenberger M, Voss M, Bornscheuer UT, Buller RM. LibGENiE - A bioinformatic pipeline for the design of information-enriched enzyme libraries. Comput Struct Biotechnol J 2023; 21:4488-4496. [PMID: 37736300 PMCID: PMC10510078 DOI: 10.1016/j.csbj.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
Enzymes are potent catalysts with high specificity and selectivity. To leverage nature's synthetic potential for industrial applications, various protein engineering techniques have emerged which allow to tailor the catalytic, biophysical, and molecular recognition properties of enzymes. However, the many possible ways a protein can be altered forces researchers to carefully balance between the exhaustiveness of an enzyme screening campaign and the required resources. Consequently, the optimal engineering strategy is often defined on a case-by-case basis. Strikingly, while predicting mutations that lead to an improved target function is challenging, here we show that the prediction and exclusion of deleterious mutations is a much more straightforward task as analyzed for an engineered carbonic acid anhydrase, a transaminase, a squalene-hopene cyclase and a Kemp eliminase. Combining such a pre-selection of allowed residues with advanced gene synthesis methods opens a path toward an efficient and generalizable library construction approach for protein engineering. To give researchers easy access to this methodology, we provide the website LibGENiE containing the bioinformatic tools for the library design workflow.
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Affiliation(s)
- David Patsch
- Zurich University of Applied Sciences, School of Life Sciences and Facility Management, Institute of Chemistry and Biotechnology, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
| | - Michael Eichenberger
- Zurich University of Applied Sciences, School of Life Sciences and Facility Management, Institute of Chemistry and Biotechnology, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Moritz Voss
- Zurich University of Applied Sciences, School of Life Sciences and Facility Management, Institute of Chemistry and Biotechnology, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Uwe T. Bornscheuer
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
| | - Rebecca M. Buller
- Zurich University of Applied Sciences, School of Life Sciences and Facility Management, Institute of Chemistry and Biotechnology, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
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13
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Belinskaia DA, Voronina PA, Popova PI, Voitenko NG, Shmurak VI, Vovk MA, Baranova TI, Batalova AA, Korf EA, Avdonin PV, Jenkins RO, Goncharov NV. Albumin Is a Component of the Esterase Status of Human Blood Plasma. Int J Mol Sci 2023; 24:10383. [PMID: 37373530 DOI: 10.3390/ijms241210383] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/13/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
The esterase status of blood plasma can claim to be one of the universal markers of various diseases; therefore, it deserves attention when searching for markers of the severity of COVID-19 and other infectious and non-infectious pathologies. When analyzing the esterase status of blood plasma, the esterase activity of serum albumin, which is the major protein in the blood of mammals, should not be ignored. The purpose of this study is to expand understanding of the esterase status of blood plasma and to evaluate the relationship of the esterase status, which includes information on the amount and enzymatic activity of human serum albumin (HSA), with other biochemical parameters of human blood, using the example of surviving and deceased patients with confirmed COVID-19. In experiments in vitro and in silico, the activity of human plasma and pure HSA towards various substrates was studied, and the effect of various inhibitors on this activity was tested. Then, a comparative analysis of the esterase status and a number of basic biochemical parameters of the blood plasma of healthy subjects and patients with confirmed COVID-19 was performed. Statistically significant differences have been found in esterase status and biochemical indices (including albumin levels) between healthy subjects and patients with COVID-19, as well as between surviving and deceased patients. Additional evidence has been obtained for the importance of albumin as a diagnostic marker. Of particular interest is a new index, [Urea] × [MDA] × 1000/(BChEb × [ALB]), which in the group of deceased patients was 10 times higher than in the group of survivors and 26 times higher than the value in the group of apparently healthy elderly subjects.
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Affiliation(s)
- Daria A Belinskaia
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, pr. Torez 44, 194223 St. Petersburg, Russia
| | - Polina A Voronina
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, pr. Torez 44, 194223 St. Petersburg, Russia
| | - Polina I Popova
- City Polyclinic No. 112, 25 Academician Baykov Str., 195427 St. Petersburg, Russia
| | - Natalia G Voitenko
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, pr. Torez 44, 194223 St. Petersburg, Russia
| | - Vladimir I Shmurak
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, pr. Torez 44, 194223 St. Petersburg, Russia
| | - Mikhail A Vovk
- Centre for Magnetic Resonance, St. Petersburg State University, Universitetskij pr., 26, Peterhof, 198504 St. Petersburg, Russia
| | - Tatiana I Baranova
- Faculty of Biology, St. Petersburg State University, 7-9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Anastasia A Batalova
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, pr. Torez 44, 194223 St. Petersburg, Russia
| | - Ekaterina A Korf
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, pr. Torez 44, 194223 St. Petersburg, Russia
| | - Pavel V Avdonin
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilova Str., 119334 Moscow, Russia
| | - Richard O Jenkins
- Leicester School of Allied Health Sciences, De Montfort University, The Gateway, Leicester LE1 9BH, UK
| | - Nikolay V Goncharov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, pr. Torez 44, 194223 St. Petersburg, Russia
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14
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Hou Q, Rooman M, Pucci F. Enzyme Stability-Activity Trade-Off: New Insights from Protein Stability Weaknesses and Evolutionary Conservation. J Chem Theory Comput 2023. [PMID: 37276063 DOI: 10.1021/acs.jctc.3c00036] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A general limitation of the use of enzymes in biotechnological processes under sometimes nonphysiological conditions is the complex interplay between two key quantities, enzyme activity and stability, where the increase of one is often associated with the decrease of the other. A precise stability-activity trade-off is necessary for the enzymes to be fully functional, but its weight in different protein regions and its dependence on environmental conditions is not yet elucidated. To advance this issue, we used the formalism that we have recently developed to effectively identify stability strength and weakness regions in protein structures and applied it to a large set of globular enzymes with known experimental structure and catalytic sites. Our analysis showed a striking oscillatory pattern of free energy compensation centered on the catalytic region. Indeed, catalytic residues are usually nonoptimal with respect to stability, but residues in the first shell around the catalytic site are, on the average, stability strengths and thus compensate for this lack of stability; residues in the second shell are weaker again, and so on. This trend is consistent across all enzyme families. It is accompanied by a similar, but less pronounced, pattern of residue conservation across evolution. In addition, we analyzed cold- and heat-adapted enzymes separately and highlighted different patterns of stability strengths and weaknesses, which provide insight into the longstanding problem of catalytic rate enhancement in cold environments. The successful comparison of our stability and conservation results with experimental fitness data, obtained by deep mutagenesis scanning, led us to propose criteria for improving catalytic activity while maintaining enzyme stability, a key goal in enzyme design.
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Affiliation(s)
- Qingzhen Hou
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
- National Institute of Health Data Science of China, Shandong University, Jinan, Shandong 250002, China
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
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15
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Deng J, Cui Q. Second-Shell Residues Contribute to Catalysis by Predominately Preorganizing the Apo State in PafA. J Am Chem Soc 2023; 145:11333-11347. [PMID: 37172218 PMCID: PMC10810092 DOI: 10.1021/jacs.3c02423] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Residues beyond the first coordination shell are often observed to make considerable cumulative contributions in enzymes. Due to typically indirect perturbations of multiple physicochemical properties of the active site, however, their individual and specific roles in enzyme catalysis and disease-causing mutations remain difficult to predict and understand at the molecular level. Here we analyze the contributions of several second-shell residues in phosphate-irrepressible alkaline phosphatase of flavobacterium (PafA), a representative system as one of the most efficient enzymes. By adopting a multifaceted approach that integrates quantum-mechanical/molecular-mechanical free energy computations, molecular-mechanical molecular dynamics simulations, and density functional theory cluster model calculations, we probe the rate-limiting phosphoryl transfer step and structural properties of all relevant enzyme states. In combination with available experimental data, our computational results show that mutations of the studied second-shell residues impact catalytic efficiency mainly by perturbation of the apo state and therefore substrate binding, while they do not affect the ground state or alter the nature of phosphoryl transfer transition state significantly. Several second-shell mutations also modulate the active site hydration level, which in turn influences the energetics of phosphoryl transfer. These mechanistic insights also help inform strategies that may improve the efficiency of enzyme design and engineering by going beyond the current focus on the first coordination shell.
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Affiliation(s)
- Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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16
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Weinstein JY, Martí-Gómez C, Lipsh-Sokolik R, Hoch SY, Liebermann D, Nevo R, Weissman H, Petrovich-Kopitman E, Margulies D, Ivankov D, McCandlish DM, Fleishman SJ. Designed active-site library reveals thousands of functional GFP variants. Nat Commun 2023; 14:2890. [PMID: 37210560 DOI: 10.1038/s41467-023-38099-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 04/13/2023] [Indexed: 05/22/2023] Open
Abstract
Mutations in a protein active site can lead to dramatic and useful changes in protein activity. The active site, however, is sensitive to mutations due to a high density of molecular interactions, substantially reducing the likelihood of obtaining functional multipoint mutants. We introduce an atomistic and machine-learning-based approach, called high-throughput Functional Libraries (htFuncLib), that designs a sequence space in which mutations form low-energy combinations that mitigate the risk of incompatible interactions. We apply htFuncLib to the GFP chromophore-binding pocket, and, using fluorescence readout, recover >16,000 unique designs encoding as many as eight active-site mutations. Many designs exhibit substantial and useful diversity in functional thermostability (up to 96 °C), fluorescence lifetime, and quantum yield. By eliminating incompatible active-site mutations, htFuncLib generates a large diversity of functional sequences. We envision that htFuncLib will be used in one-shot optimization of activity in enzymes, binders, and other proteins.
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Affiliation(s)
| | - Carlos Martí-Gómez
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Rosalie Lipsh-Sokolik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shlomo Yakir Hoch
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Demian Liebermann
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Reinat Nevo
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Haim Weissman
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | | | - David Margulies
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Dmitry Ivankov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - David M McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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17
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Crnjar A, Griñen A, Kamerlin SCL, Ramírez-Sarmiento CA. Conformational Selection of a Tryptophan Side Chain Drives the Generalized Increase in Activity of PET Hydrolases through a Ser/Ile Double Mutation. ACS ORGANIC & INORGANIC AU 2023; 3:109-119. [PMID: 37035283 PMCID: PMC10080609 DOI: 10.1021/acsorginorgau.2c00054] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 04/12/2023]
Abstract
Poly(ethylene terephthalate) (PET) is the most common polyester plastic in the packaging industry and a major source of environmental pollution due to its single use. Several enzymes, termed PET hydrolases, have been found to hydrolyze this polymer at different temperatures, with the enzyme from Ideonella sakaiensis (IsPETase) having optimal catalytic activity at 30-35 °C. Crystal structures of IsPETase have revealed that the side chain of a conserved tryptophan residue within an active site loop (W185) shifts between three conformations to enable substrate binding and product release. This is facilitated by two residues unique to IsPETase, S214 and I218. When these residues are inserted into other PET hydrolases in place of the otherwise strictly conserved histidine and phenylalanine residues found at their respective positions, they enhance activity and decrease T opt. Herein, we combine molecular dynamics and well-tempered metadynamics simulations to investigate dynamic changes of the S214/I218 and H214/F218 variants of IsPETase, as well as three other mesophilic and thermophilic PET hydrolases, at their respective temperature and pH optima. Our simulations show that the S214/I218 insertion both increases the flexibility of active site loop regions harboring key catalytic residues and the conserved tryptophan and expands the conformational plasticity of this tryptophan side chain, enabling the conformational transitions that allow for substrate binding and product release in IsPETase. The observed catalytic enhancement caused by this substitution in other PET hydrolases appears to be due to conformational selection, by capturing the conformational ensemble observed in IsPETase.
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Affiliation(s)
- Alessandro Crnjar
- Department
of Chemistry—BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Aransa Griñen
- Institute
for Biological and Medical Engineering, Schools of Engineering, Medicine
and Biological Sciences, Pontificia Universidad
Católica de Chile, Av. Vicuña Mackenna 4860, Santiago 7820436, Chile
- ANID—Millennium
Science Initiative Program—Millennium Institute for Integrative
Biology (iBio), Av. Libertador
Bernardo O’Higgins 340, Santiago 8331150, Chile
| | - Shina C. L. Kamerlin
- Department
of Chemistry—BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic
Drive NW, Atlanta, Georgia 30332-0400, United
States
| | - César A. Ramírez-Sarmiento
- Institute
for Biological and Medical Engineering, Schools of Engineering, Medicine
and Biological Sciences, Pontificia Universidad
Católica de Chile, Av. Vicuña Mackenna 4860, Santiago 7820436, Chile
- ANID—Millennium
Science Initiative Program—Millennium Institute for Integrative
Biology (iBio), Av. Libertador
Bernardo O’Higgins 340, Santiago 8331150, Chile
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18
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Valle-Rodríguez JO, Siewers V, Nielsen J, Shi S. Directed evolution of a wax ester synthase for production of fatty acid ethyl esters in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2023; 107:2921-2932. [PMID: 36976306 DOI: 10.1007/s00253-023-12466-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 02/21/2023] [Accepted: 02/24/2023] [Indexed: 03/29/2023]
Abstract
Wax ester synthases (WSs) utilize a fatty alcohol and a fatty acyl-coenzyme A (activated fatty acid) to synthesize the corresponding wax ester. There is much interest in developing novel cell factories that can produce shorter esters, e.g., fatty acid ethyl esters (FAEEs), with properties similar to biodiesel in order to use these as transportation fuels. However, ethanol is a poor substrate for WSs, and this may limit the biosynthesis of FAEEs. Here, we implemented a random mutagenesis approach to enhance the catalytic efficiency of a WS from Marinobacter hydrocarbonoclasticus (MhWS2, encoded by the ws2 gene). Our selection system was based on FAEE formation serving as a detoxification mechanism for excessive oleate, where high WS activity was essential for a storage-lipid free yeast to survive. A random mutagenesis library of ws2 was used to transform the storage-lipid free yeast, and mutants could be selected by plating the transformants on oleate containing plates. The variants encoding WS with improved activity were sequenced, and an identified point mutation translated into the residue substitution at position A344 was discovered to substantially increase the selectivity of MhWS2 toward ethanol and other shorter alcohols. Structural modeling indicated that an A344T substitution might affect the alcohol selectivity due to change of both steric effects and polarity changes near the active site. This work not only provides a new WS variant with altered selectivity to shorter alcohols but also presents a new high-throughput selection system to isolate WSs with a desired selectivity. KEY POINTS: • The work provides WS variants with altered substrate preference for shorter alcohols • A novel method was developed for directed evolution of WS of desired selectivity.
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Affiliation(s)
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970, Hørsholm, Denmark.
| | - Shuobo Shi
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden.
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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19
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Liang Z, Sun Y, Zeng H, Qin H, Yang R, Qu L, Zhang K, Li Z. Broad-Specificity Screening of Pyrethroids Enabled by the Catalytic Function of Human Serum Albumin on Coumarin Hydrolysis. Anal Chem 2023; 95:5678-5686. [PMID: 36952638 DOI: 10.1021/acs.analchem.2c05556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Sensing systems based on cholinesterase and carboxylesterase coupled with different transduction technologies have emerged for pesticide screening owing to their simple operation, fast response, and suitability for on-site analysis. However, the broad spectrum and specificity screening of pyrethroids over organophosphates and carbamates remains an unmet challenge for current enzymatic sensors. Human serum albumin (HSA), a multifunctional protein, can promote various chemical transformations and show a high affinity for pyrethroids, which offer a route for specific and broad-spectrum pyrethroid screening. Herein, for the first time, we evaluated the catalytic hydrolysis function of human serum albumin (HSA) on the coumarin lactone bond and revealed that HSA can act as an enzyme to catalyze the hydrolysis of the coumarin lactone bond. Molecular docking and chemical modifications indicate that lysine 199 and tyrosine 411 serve as the catalytic general base and contribute to most of the catalytic activity. Utilizing this enzymatic activity, a broad specific ratiometric fluorescence pyrethroids sensing system was developed. The binding energetics and binding constants of pesticides and HSA show that pyrethroids bind to HSA more easily than organophosphates and carbamates, which is responsible for the specificity of the sensing system. This study provides a general sensor platform and strategy for screening pesticides and reveals the catalytic activity of HSA on the hydrolysis of the coumarin lactone bond, which may open innovative horizons for the chemical sensing and biomedical applications of HSA.
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Affiliation(s)
- Zengqiang Liang
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Yuanqiang Sun
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Huajin Zeng
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Haimei Qin
- Fujian Provincial Key Lab of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Ran Yang
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Lingbo Qu
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
- Key Laboratory of Food Safety Quick Testing and Smart Supervision Technology for State Market Regulation, Zhengzhou 450001, China
| | - Ke Zhang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Zhaohui Li
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
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20
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Gutierrez-Rus LI, Gamiz-Arco G, Gavira JA, Gaucher EA, Risso VA, Sanchez-Ruiz JM. Protection of catalytic cofactors by polypeptides as a driver for the emergence of primordial enzymes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532612. [PMID: 36993774 PMCID: PMC10055001 DOI: 10.1101/2023.03.14.532612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Enzymes catalyze the chemical reactions of life. For nearly half of known enzymes, catalysis requires the binding of small molecules known as cofactors. Polypeptide-cofactor complexes likely formed at a primordial stage and became starting points for the evolution of many efficient enzymes. Yet, evolution has no foresight so the driver for the primordial complex formation is unknown. Here, we use a resurrected ancestral TIM-barrel protein to identify one potential driver. Heme binding at a flexible region of the ancestral structure yields a peroxidation catalyst with enhanced efficiency when compared to free heme. This enhancement, however, does not arise from protein-mediated promotion of catalysis. Rather, it reflects protection of bound heme from common degradation processes and a resulting longer life time and higher effective concentration for the catalyst. Protection of catalytic cofactors by polypeptides emerges as a general mechanism to enhance catalysis and may have plausibly benefited primordial polypeptide-cofactor associations.
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21
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Wang P, Zhang J, Zhang S, Lu D, Zhu Y. Using High-Throughput Molecular Dynamics Simulation to Enhance the Computational Design of Kemp Elimination Enzymes. J Chem Inf Model 2023; 63:1323-1337. [PMID: 36782360 DOI: 10.1021/acs.jcim.3c00002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Computational enzyme design has been successfully applied to identify new alternatives to natural enzymes for the biosynthesis of important compounds. However, the moderate catalytic activities of de novo designed enzymes indicate that the modeling accuracy of current computational enzyme design methods should be improved. Here, high-throughput molecular dynamics simulations were used to enhance computational enzyme design, thus allowing the identification of variants with higher activities in silico. Different time schemes of high-throughput molecular dynamics simulations were tested to identify the catalytic features of evolved Kemp eliminases. The 20 × 1 ns molecular dynamics simulation scheme was sufficiently accurate and computationally viable to screen the computationally designed massive variants of Kemp elimination enzymes. The developed hybrid computational strategy was used to redesign the most active Kemp eliminase, HG3.17, and five variants were generated and experimentally confirmed to afford higher catalytic efficiencies than that of HG3.17, with one double variant (D52Q/A53S) exhibiting a 55% increase. The hybrid computational enzyme design strategy is general and computationally economical, with which we anticipate the efficient creation of practical enzymes for industrial biocatalysis.
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Affiliation(s)
- Pengyu Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.,Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Jun Zhang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Shengyu Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Diannan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yushan Zhu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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22
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Raczyńska A, Kapica P, Papaj K, Stańczak A, Shyntum D, Spychalska P, Byczek-Wyrostek A, Góra A. Transient binding sites at the surface of haloalkane dehalogenase LinB as locations for fine-tuning enzymatic activity. PLoS One 2023; 18:e0280776. [PMID: 36827335 PMCID: PMC9956002 DOI: 10.1371/journal.pone.0280776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 01/09/2023] [Indexed: 02/25/2023] Open
Abstract
The haloalkane dehalogenase LinB is a well-known enzyme that contains buried active site and is used for many modelling studies. Using classical molecular dynamics simulations of enzymes and substrates, we searched for transient binding sites on the surface of the LinB protein by calculating maps of enzyme-ligand interactions that were then transformed into sparse matrices. All residues considered as functionally important for enzyme performance (e.g., tunnel entrances) were excluded from the analysis to concentrate rather on non-obvious surface residues. From a set of 130 surface residues, twenty-six were proposed as a promising improvement of enzyme performance. Eventually, based on rational selection and filtering out the potentially unstable mutants, a small library of ten mutants was proposed to validate the possibility of fine-tuning the LinB protein. Nearly half of the predicted mutant structures showed improved activity towards the selected substrates, which demonstrates that the proposed approach could be applied to identify non-obvious yet beneficial mutations for enzyme performance especially when obvious locations have already been explored.
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Affiliation(s)
- Agata Raczyńska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Patryk Kapica
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Katarzyna Papaj
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Agnieszka Stańczak
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Divine Shyntum
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Patrycja Spychalska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | | | - Artur Góra
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
- * E-mail:
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23
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Liu Y, Wu Z, Deska J. Coding Synthetic Chemistry Strategies for Furan Valorization into Bacterial Designer Cells. CHEMSUSCHEM 2023; 16:e202201790. [PMID: 36416391 PMCID: PMC10107124 DOI: 10.1002/cssc.202201790] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 05/11/2023]
Abstract
Following a synthetic chemistry blueprint for the valorization of lignocellulosic platform chemicals, this study showcases a so far unprecedented approach to implement non-natural enzyme modules in vivo. For the design of a novel functional whole cell tool, two purely abiotic transformations, a styrene monooxygenase-catalyzed Achmatowicz rearrangement and an alcohol dehydrogenase-mediated borrowing hydrogen redox isomerization, were incorporated into a recombinant bacterial host. Introducing this type of chemistry otherwise unknown in biosynthesis, the cellular factories were enabled to produce complex lactone building blocks in good yield from bio-based furan substrates. This whole cell system streamlined the synthetic cascade, eliminated isolation and purification steps, and provided a high degree of stereoselectivity that has so far been elusive in the chemical methodology.
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Affiliation(s)
- Yu‐Chang Liu
- Department of ChemistryUniversity of HelsinkiA.I. Virtasen aukio 100560HelsinkiFinland
- Department of ChemistryAalto UniversityKemistintie 102150EspooFinland
| | - Zhong‐Liu Wu
- CAS Key Laboratory of Environmental and Applied MicrobiologyEnvironmental Microbiology Key Laboratory of Sichuan ProvinceChengdu Institute of BiologyChinese Academy of SciencesChengdu610041P. R. China
| | - Jan Deska
- Department of ChemistryUniversity of HelsinkiA.I. Virtasen aukio 100560HelsinkiFinland
- Department of ChemistryAalto UniversityKemistintie 102150EspooFinland
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24
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Schmidt S. Photoexcited Enzymes for Asymmetric Csp 3 -Csp 3 Cross-Electrophile Couplings. Angew Chem Int Ed Engl 2022; 61:e202214313. [PMID: 36239986 PMCID: PMC10100153 DOI: 10.1002/anie.202214313] [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: 09/28/2022] [Indexed: 11/07/2022]
Abstract
Enzymes have several advantages over conventional catalysts for organic synthesis. Over the last two decades, much effort has been made to further extend the scope of biocatalytic reactions available to synthetic chemists, particularly by expanding the repertoire of enzymes for abiological transformations. In this regard, exciting new developments in the area of photobiocatalysis enable now the introduction of non-natural reactivity in enzymes to solve long-standing synthetic challenges. A recently described example from the Hyster group demonstrates in an unprecedented way how the combination of photochemistry with enzyme catalysis empowers the catalytic asymmetric construction of Csp3 -Csp3 bonds with high chemo- and enantioselectivity.
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Affiliation(s)
- Sandy Schmidt
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, Antonius Deusinglaan 1, 9713 AV, Groningen (The, Netherlands
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25
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Ashworth MA, Bombino E, de Jong RM, Wijma HJ, Janssen DB, McLean KJ, Munro AW. Computation-Aided Engineering of Cytochrome P450 for the Production of Pravastatin. ACS Catal 2022; 12:15028-15044. [PMID: 36570080 PMCID: PMC9764288 DOI: 10.1021/acscatal.2c03974] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/22/2022] [Indexed: 11/29/2022]
Abstract
CYP105AS1 is a cytochrome P450 from Amycolatopsis orientalis that catalyzes monooxygenation of compactin to 6-epi-pravastatin. For fermentative production of the cholesterol-lowering drug pravastatin, the stereoselectivity of the enzyme needs to be inverted, which has been partially achieved by error-prone PCR mutagenesis and screening. In the current study, we report further optimization of the stereoselectivity by a computationally aided approach. Using the CoupledMoves protocol of Rosetta, a virtual library of mutants was designed to bind compactin in a pro-pravastatin orientation. By examining the frequency of occurrence of beneficial substitutions and rational inspection of their interactions, a small set of eight mutants was predicted to show the desired selectivity and these variants were tested experimentally. The best CYP105AS1 variant gave >99% stereoselective hydroxylation of compactin to pravastatin, with complete elimination of the unwanted 6-epi-pravastatin diastereomer. The enzyme-substrate complexes were also examined by ultrashort molecular dynamics simulations of 50 × 100 ps and 5 × 22 ns, which revealed that the frequency of occurrence of near-attack conformations agreed with the experimentally observed stereoselectivity. These results show that a combination of computational methods and rational inspection could improve CYP105AS1 stereoselectivity beyond what was obtained by directed evolution. Moreover, the work lays out a general in silico framework for specificity engineering of enzymes of known structure.
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Affiliation(s)
- Mark A. Ashworth
- Manchester
Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Elvira Bombino
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, Netherlands
| | - René M. de Jong
- DSM
Food & Beverage, Alexander Fleminglaan 1, 2613 AX Delft, the Netherlands
| | - Hein J. Wijma
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, Netherlands
| | - Dick B. Janssen
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, Netherlands,
| | - Kirsty J. McLean
- Manchester
Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom,Department
of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, United Kingdom
| | - Andrew W. Munro
- Manchester
Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom
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Bhattacharya S, Margheritis EG, Takahashi K, Kulesha A, D'Souza A, Kim I, Yoon JH, Tame JRH, Volkov AN, Makhlynets OV, Korendovych IV. NMR-guided directed evolution. Nature 2022; 610:389-393. [PMID: 36198791 PMCID: PMC10116341 DOI: 10.1038/s41586-022-05278-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 08/25/2022] [Indexed: 11/09/2022]
Abstract
Directed evolution is a powerful tool for improving existing properties and imparting completely new functionalities to proteins1-4. Nonetheless, its potential in even small proteins is inherently limited by the astronomical number of possible amino acid sequences. Sampling the complete sequence space of a 100-residue protein would require testing of 20100 combinations, which is beyond any existing experimental approach. In practice, selective modification of relatively few residues is sufficient for efficient improvement, functional enhancement and repurposing of existing proteins5. Moreover, computational methods have been developed to predict the locations and, in certain cases, identities of potentially productive mutations6-9. Importantly, all current approaches for prediction of hot spots and productive mutations rely heavily on structural information and/or bioinformatics, which is not always available for proteins of interest. Moreover, they offer a limited ability to identify beneficial mutations far from the active site, even though such changes may markedly improve the catalytic properties of an enzyme10. Machine learning methods have recently showed promise in predicting productive mutations11, but they frequently require large, high-quality training datasets, which are difficult to obtain in directed evolution experiments. Here we show that mutagenic hot spots in enzymes can be identified using NMR spectroscopy. In a proof-of-concept study, we converted myoglobin, a non-enzymatic oxygen storage protein, into a highly efficient Kemp eliminase using only three mutations. The observed levels of catalytic efficiency exceed those of proteins designed using current approaches and are similar with those of natural enzymes for the reactions that they are evolved to catalyse. Given the simplicity of this experimental approach, which requires no a priori structural or bioinformatic knowledge, we expect it to be widely applicable and to enable the full potential of directed enzyme evolution.
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Affiliation(s)
| | - Eleonora G Margheritis
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Katsuya Takahashi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Alona Kulesha
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Areetha D'Souza
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Inhye Kim
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Jennifer H Yoon
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Jeremy R H Tame
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Alexander N Volkov
- VIB Centre for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium.
- Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), Brussels, Belgium.
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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:ijms23168934. [PMID: 36012203 PMCID: PMC9408544 DOI: 10.3390/ijms23168934] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [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
- Correspondence: (V.A.R.); (J.M.S.-R.)
| | - 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
- Correspondence: (V.A.R.); (J.M.S.-R.)
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28
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Natural Evolution Provides Strong Hints about Laboratory Evolution of Designer Enzymes. Proc Natl Acad Sci U S A 2022; 119:e2207904119. [PMID: 35901204 PMCID: PMC9351539 DOI: 10.1073/pnas.2207904119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Laboratory evolution combined with computational enzyme design provides the opportunity to generate novel biocatalysts. Nevertheless, it has been challenging to understand how laboratory evolution optimizes designer enzymes by introducing seemingly random mutations. A typical enzyme optimized with laboratory evolution is the abiological Kemp eliminase, initially designed by grafting active site residues into a natural protein scaffold. Here, we relate the catalytic power of laboratory-evolved Kemp eliminases to the statistical energy ([Formula: see text]) inferred from their natural homologous sequences using the maximum entropy model. The [Formula: see text] of designs generated by directed evolution is correlated with enhanced activity and reduced stability, thus displaying a stability-activity trade-off. In contrast, the [Formula: see text] for mutants in catalytic-active remote regions (in which remote residues are important for catalysis) is strongly anticorrelated with the activity. These findings provide an insight into the role of protein scaffolds in the adaption to new enzymatic functions. It also indicates that the valley in the [Formula: see text] landscape can guide enzyme design for abiological catalysis. Overall, the connection between laboratory and natural evolution contributes to understanding what is optimized in the laboratory and how new enzymatic function emerges in nature, and provides guidance for computational enzyme design.
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29
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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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Abstract
The ability to design efficient enzymes from scratch would have a profound effect on chemistry, biotechnology and medicine. Rapid progress in protein engineering over the past decade makes us optimistic that this ambition is within reach. The development of artificial enzymes containing metal cofactors and noncanonical organocatalytic groups shows how protein structure can be optimized to harness the reactivity of nonproteinogenic elements. In parallel, computational methods have been used to design protein catalysts for diverse reactions on the basis of fundamental principles of transition state stabilization. Although the activities of designed catalysts have been quite low, extensive laboratory evolution has been used to generate efficient enzymes. Structural analysis of these systems has revealed the high degree of precision that will be needed to design catalysts with greater activity. To this end, emerging protein design methods, including deep learning, hold particular promise for improving model accuracy. Here we take stock of key developments in the field and highlight new opportunities for innovation that should allow us to transition beyond the current state of the art and enable the robust design of biocatalysts to address societal needs.
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31
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Galmés MÀ, Nödling AR, He K, Luk LYP, Świderek K, Moliner V. Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases. Chem Sci 2022; 13:4779-4787. [PMID: 35655887 PMCID: PMC9067594 DOI: 10.1039/d2sc00778a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/14/2022] [Indexed: 11/29/2022] Open
Abstract
While there has been emerging interest in designing new enzymes to solve practical challenges, computer-based options to redesign catalytically active proteins are rather limited. Here, a rational QM/MM molecular dynamics strategy based on combining the best electrostatic properties of enzymes with activity in a common reaction is presented. The computational protocol has been applied to the re-design of the protein scaffold of an existing promiscuous esterase from Bacillus subtilis Bs2 to enhance its secondary amidase activity. After the alignment of Bs2 with a non-homologous amidase Candida antarctica lipase B (CALB) within rotation quaternions, a relevant spatial aspartate residue of the latter was transferred to the former as a means to favor the electrostatics of transition state formation, where a clear separation of charges takes place. Deep computational insights, however, revealed a significant conformational change caused by the amino acid replacement, provoking a shift in the pK a of the inserted aspartate and counteracting the anticipated catalytic effect. This prediction was experimentally confirmed with a 1.3-fold increase in activity. The good agreement between theoretical and experimental results, as well as the linear correlation between the electrostatic properties and the activation energy barriers, suggest that the presented computational-based investigation can transform in an enzyme engineering approach.
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Affiliation(s)
- Miquel À Galmés
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castellón Spain +34 964728084
| | - Alexander R Nödling
- School of Chemistry, Cardiff University Main Building, Park Pl Cardiff CF10 3AT UK +44 (0)29 2251 0161
| | - Kaining He
- School of Chemistry, Cardiff University Main Building, Park Pl Cardiff CF10 3AT UK +44 (0)29 2251 0161
| | - Louis Y P Luk
- School of Chemistry, Cardiff University Main Building, Park Pl Cardiff CF10 3AT UK +44 (0)29 2251 0161
| | - Katarzyna Świderek
- Department of Physical and Analytical Chemistry, Universitat Jaume I 12071 Castellón Spain +34 964728070
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castellón Spain +34 964728084
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32
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Reetz MT. Making Enzymes Suitable for Organic Chemistry by Rational Protein Design. Chembiochem 2022; 23:e202200049. [PMID: 35389556 PMCID: PMC9401064 DOI: 10.1002/cbic.202200049] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/07/2022] [Indexed: 11/25/2022]
Abstract
This review outlines recent developments in protein engineering of stereo‐ and regioselective enzymes, which are of prime interest in organic and pharmaceutical chemistry as well as biotechnology. The widespread application of enzymes was hampered for decades due to limited enantio‐, diastereo‐ and regioselectivity, which was the reason why most organic chemists were not interested in biocatalysis. This attitude began to change with the advent of semi‐rational directed evolution methods based on focused saturation mutagenesis at sites lining the binding pocket. Screening constitutes the labor‐intensive step (bottleneck), which is the reason why various research groups are continuing to develop techniques for the generation of small and smart mutant libraries. Rational enzyme design, traditionally an alternative to directed evolution, provides small collections of mutants which require minimal screening. This approach first focused on thermostabilization, and did not enter the field of stereoselectivity until later. Computational guides such as the Rosetta algorithms, HotSpot Wizard metric, and machine learning (ML) contribute significantly to decision making. The newest advancements show that semi‐rational directed evolution such as CAST/ISM and rational enzyme design no longer develop on separate tracks, instead, they have started to merge. Indeed, researchers utilizing the two approaches have learned from each other. Today, the toolbox of organic chemists includes enzymes, primarily because the possibility of controlling stereoselectivity by protein engineering has ensured reliability when facing synthetic challenges. This review was also written with the hope that undergraduate and graduate education will include enzymes more so than in the past.
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Affiliation(s)
- Manfred T Reetz
- Max-Planck-Institut fur Kohlenforschung, Biocatalysis, Kaiser-Wilhelm-Platz 1, 45470, Muelheim an der Ruhr, GERMANY
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33
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Engineering an efficient and enantioselective enzyme for the Morita-Baylis-Hillman reaction. Nat Chem 2022; 14:313-320. [PMID: 34916595 PMCID: PMC7612480 DOI: 10.1038/s41557-021-00833-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/05/2021] [Indexed: 11/08/2022]
Abstract
The combination of computational design and directed evolution could offer a general strategy to create enzymes with new functions. So far, this approach has delivered enzymes for a handful of model reactions. Here we show that new catalytic mechanisms can be engineered into proteins to accelerate more challenging chemical transformations. Evolutionary optimization of a primitive design afforded an efficient and enantioselective enzyme (BH32.14) for the Morita-Baylis-Hillman (MBH) reaction. BH32.14 is suitable for preparative-scale transformations, accepts a broad range of aldehyde and enone coupling partners and is able to promote selective monofunctionalizations of dialdehydes. Crystallographic, biochemical and computational studies reveal that BH32.14 operates via a sophisticated catalytic mechanism comprising a His23 nucleophile paired with a judiciously positioned Arg124. This catalytic arginine shuttles between conformational states to stabilize multiple oxyanion intermediates and serves as a genetically encoded surrogate of privileged bidentate hydrogen-bonding catalysts (for example, thioureas). This study demonstrates that elaborate catalytic devices can be built from scratch to promote demanding multi-step processes not observed in nature.
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34
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Affiliation(s)
- Elaine O'Reilly
- School of Chemistry, Science Centre South, University College Dublin, Dublin, Ireland.
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35
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Åqvist J. Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05814] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Johan Åqvist
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
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36
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Miller DC, Athavale SV, Arnold FH. Combining chemistry and protein engineering for new-to-nature biocatalysis. NATURE SYNTHESIS 2022; 1:18-23. [PMID: 35415721 DOI: 10.1038/s44160-021-00008-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biocatalysis, the application of enzymes to solve synthetic problems of human import, has blossomed into a powerful technology for chemical innovation. In the past decade, a threefold partnership, where nature provides blueprints for enzymatic catalysis, chemists introduce innovative activity modes with abiological substrates, and protein engineers develop new tools and algorithms to tune and improve enzymatic function, has unveiled the frontier of new-to-nature enzyme catalysis. In this perspective, we highlight examples of interdisciplinary studies which have helped to expand the scope of biocatalysis, including concepts of enzymatic versatility explored through the lens of biomimicry, to achieve both activities and selectivities that are not currently possible with chemocatalysis. We indicate how modern tools, such as directed evolution, computational protein design and machine learning-based protein engineering methods, have already impacted and will continue to influence enzyme engineering for new abiological transformations. A sustained collaborative effort across disciplines is anticipated to spur further advances in biocatalysis in the coming years.
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Affiliation(s)
- David C Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology Pasadena, California, 91125
| | - Soumitra V Athavale
- Division of Chemistry and Chemical Engineering, California Institute of Technology Pasadena, California, 91125
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology Pasadena, California, 91125
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37
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Mokhtari DA, Appel MJ, Fordyce PM, Herschlag D. High throughput and quantitative enzymology in the genomic era. Curr Opin Struct Biol 2021; 71:259-273. [PMID: 34592682 PMCID: PMC8648990 DOI: 10.1016/j.sbi.2021.07.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/23/2021] [Indexed: 12/28/2022]
Abstract
Accurate predictions from models based on physical principles are the ultimate metric of our biophysical understanding. Although there has been stunning progress toward structure prediction, quantitative prediction of enzyme function has remained challenging. Realizing this goal will require large numbers of quantitative measurements of rate and binding constants and the use of these ground-truth data sets to guide the development and testing of these quantitative models. Ground truth data more closely linked to the underlying physical forces are also desired. Here, we describe technological advances that enable both types of ground truth measurements. These advances allow classic models to be tested, provide novel mechanistic insights, and place us on the path toward a predictive understanding of enzyme structure and function.
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Affiliation(s)
- D A Mokhtari
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | - M J Appel
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | - P M Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA, 94305, USA; Department of Genetics, Stanford University, Stanford, CA, 94305, USA; Chan Zuckerberg Biohub San Francisco, CA, 94110, USA.
| | - D Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA, 94305, USA.
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38
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Evolution of dynamical networks enhances catalysis in a designer enzyme. Nat Chem 2021; 13:1017-1022. [PMID: 34413499 DOI: 10.1038/s41557-021-00763-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 06/30/2021] [Indexed: 02/08/2023]
Abstract
Activation heat capacity is emerging as a crucial factor in enzyme thermoadaptation, as shown by the non-Arrhenius behaviour of many natural enzymes. However, its physical origin and relationship to the evolution of catalytic activity remain uncertain. Here we show that directed evolution of a computationally designed Kemp eliminase reshapes protein dynamics, which gives rise to an activation heat capacity absent in the original design. These changes buttress transition-state stabilization. Extensive molecular dynamics simulations show that evolution results in the closure of solvent-exposed loops and a better packing of the active site. Remarkably, this gives rise to a correlated dynamical network that involves the transition state and large parts of the protein. This network tightens the transition-state ensemble, which induces a negative activation heat capacity and non-linearity in the activity-temperature dependence. Our results have implications for understanding enzyme evolution and suggest that selectively targeting the conformational dynamics of the transition-state ensemble by design and evolution will expedite the creation of novel enzymes.
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39
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Ma EJ, Siirola E, Moore C, Kummer A, Stoeckli M, Faller M, Bouquet C, Eggimann F, Ligibel M, Huynh D, Cutler G, Siegrist L, Lewis RA, Acker AC, Freund E, Koch E, Vogel M, Schlingensiepen H, Oakeley EJ, Snajdrova R. Machine-Directed Evolution of an Imine Reductase for Activity and Stereoselectivity. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02786] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Eric J. Ma
- NIBR Informatics, Novartis Institutes for BioMedical Research (NIBR), 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Elina Siirola
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Charles Moore
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Arkadij Kummer
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Markus Stoeckli
- Analytical Sciences and Imaging, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Michael Faller
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Caroline Bouquet
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Fabian Eggimann
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Mathieu Ligibel
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Dan Huynh
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Geoffrey Cutler
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Luca Siegrist
- NIBR Biologics Center, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Richard A. Lewis
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Anne-Christine Acker
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Ernst Freund
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Elke Koch
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Markus Vogel
- NIBR Biologics Center, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Holger Schlingensiepen
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Edward J. Oakeley
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
| | - Radka Snajdrova
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research (NIBR), Novartis Campus, CH-4056 Basel, Switzerland
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40
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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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41
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Baiyoumy A, Vallapurackal J, Schwizer F, Heinisch T, Kardashliev T, Held M, Panke S, Ward TR. Directed Evolution of a Surface-Displayed Artificial Allylic Deallylase Relying on a GFP Reporter Protein. ACS Catal 2021; 11:10705-10712. [PMID: 34504734 PMCID: PMC8419837 DOI: 10.1021/acscatal.1c02405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/26/2021] [Indexed: 12/14/2022]
Abstract
Artificial metalloenzymes (ArMs) combine characteristics of both homogeneous catalysts and enzymes. Merging abiotic and biotic features allows for the implementation of new-to-nature reactions in living organisms. Here, we present the directed evolution of an artificial metalloenzyme based on Escherichia coli surface-displayed streptavidin (SavSD hereafter). Through the binding of a ruthenium-pianostool cofactor to SavSD, an artificial allylic deallylase (ADAse hereafter) is assembled, which displays catalytic activity toward the deprotection of alloc-protected 3-hydroxyaniline. The uncaged aminophenol acts as a gene switch and triggers the overexpression of a fluorescent green fluorescent protein (GFP) reporter protein. This straightforward readout of ADAse activity allowed the simultaneous saturation mutagenesis of two amino acid residues in Sav near the ruthenium cofactor, expediting the screening of 2762 individual clones. A 1.7-fold increase of in vivo activity was observed for SavSD S112T-K121G compared to the wild-type SavSD (wt-SavSD). Finally, the best performing Sav isoforms were purified and tested in vitro (SavPP hereafter). For SavPP S112M-K121A, a total turnover number of 372 was achieved, corresponding to a 5.9-fold increase vs wt-SavPP. To analyze the marked difference in activity observed between the surface-displayed and purified ArMs, the oligomeric state of SavSD was determined. For this purpose, crosslinking experiments of E. coli cells overexpressing SavSD were carried out, followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot. The data suggest that SavSD is most likely displayed as a monomer on the surface of E. coli. We hypothesize that the difference between the in vivo and in vitro screening results may reflect the difference in the oligomeric state of SavSD vs soluble SavPP (monomeric vs tetrameric). Accordingly, care should be applied when evolving oligomeric proteins using E. coli surface display.
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Affiliation(s)
- Alain Baiyoumy
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
- Molecular
Systems Engineering, National Competence
Center in Research (NCCR), 4058 Basel, Switzerland
| | - Jaicy Vallapurackal
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
- Molecular
Systems Engineering, National Competence
Center in Research (NCCR), 4058 Basel, Switzerland
| | - Fabian Schwizer
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Tillmann Heinisch
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
| | | | - Martin Held
- ETH
Zürich, D-BSSE, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Sven Panke
- ETH
Zürich, D-BSSE, Mattenstrasse 26, 4058 Basel, Switzerland
- Molecular
Systems Engineering, National Competence
Center in Research (NCCR), 4058 Basel, Switzerland
| | - Thomas R. Ward
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
- Molecular
Systems Engineering, National Competence
Center in Research (NCCR), 4058 Basel, Switzerland
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42
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Zhang J, Kong K, Li X, Zhang Q. Kemp-type elimination of 1-arylsulfonyl-3-iodo-1 H-indazoles. SYNTHETIC COMMUN 2021. [DOI: 10.1080/00397911.2021.1939053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Jiawei Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
| | - Kaimin Kong
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
| | - Xiangjun Li
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
| | - Qian Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
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43
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Wang Y, Xue P, Cao M, Yu T, Lane ST, Zhao H. Directed Evolution: Methodologies and Applications. Chem Rev 2021; 121:12384-12444. [PMID: 34297541 DOI: 10.1021/acs.chemrev.1c00260] [Citation(s) in RCA: 184] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Directed evolution aims to expedite the natural evolution process of biological molecules and systems in a test tube through iterative rounds of gene diversifications and library screening/selection. It has become one of the most powerful and widespread tools for engineering improved or novel functions in proteins, metabolic pathways, and even whole genomes. This review describes the commonly used gene diversification strategies, screening/selection methods, and recently developed continuous evolution strategies for directed evolution. Moreover, we highlight some representative applications of directed evolution in engineering nucleic acids, proteins, pathways, genetic circuits, viruses, and whole cells. Finally, we discuss the challenges and future perspectives in directed evolution.
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Affiliation(s)
- Yajie Wang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pu Xue
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mingfeng Cao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tianhao Yu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stephan T Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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44
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Mariz BDP, Carvalho S, Batalha IL, Pina AS. Artificial enzymes bringing together computational design and directed evolution. Org Biomol Chem 2021; 19:1915-1925. [PMID: 33443278 DOI: 10.1039/d0ob02143a] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Enzymes are proteins that catalyse chemical reactions and, as such, have been widely used to facilitate a variety of natural and industrial processes, dating back to ancient times. In fact, the global enzymes market is projected to reach $10.5 billion in 2024. The development of computational and DNA editing tools boosted the creation of artificial enzymes (de novo enzymes) - synthetic or organic molecules created to present abiological catalytic functions. These novel catalysts seek to expand the catalytic power offered by nature through new functions and properties. In this manuscript, we discuss the advantages of combining computational design with directed evolution for the development of artificial enzymes and how this strategy allows to fill in the gaps that these methods present individually by providing key insights about the sequence-function relationship. We also review examples, and respective strategies, where this approach has enabled the creation of artificial enzymes with promising catalytic activity. Such key enabling technologies are opening new windows of opportunity in a variety of industries, including pharmaceutical, chemical, biofuels, and food, contributing towards a more sustainable development.
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Affiliation(s)
- Beatriz de Pina Mariz
- UCIBIO, Chemistry Department, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal.
| | - Sara Carvalho
- UCIBIO, Chemistry Department, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal.
| | - Iris L Batalha
- Nanoscience Centre, Department of Engineering, University of Cambridge, 11 J.J. Thomson Avenue, Cambridge, CB3 0FF, UK
| | - Ana Sofia Pina
- UCIBIO, Chemistry Department, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal.
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45
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Advances in optimizing enzyme electrostatic preorganization. Curr Opin Struct Biol 2021; 72:1-8. [PMID: 34280872 DOI: 10.1016/j.sbi.2021.06.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/28/2021] [Accepted: 06/05/2021] [Indexed: 12/19/2022]
Abstract
Utilizing electric fields to catalyze chemical reactions is not a new idea, but in enzymology it undergoes a renaissance, inspired by Warhsel's concept of electrostatic preorganization. According to this concept, the source of the immense catalytic efficiency of enzymes is the intramolecular electric field that permanently favors the reaction transition state over the reactants. Within enzyme design, computational efforts have fallen short in designing enzymes with natural-like efficacy. The outcome could improve if long-range electrostatics (often omitted in current protocols) would be optimized. Here, we highlight the major developments in methods for analyzing and designing electric fields generated by the protein scaffolds, in order to both better understand how natural enzymes function, and aid artificial enzyme design.
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46
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Deng J, Cui Q. Reverse Protonation of Buried Ion-Pairs in Staphylococcal Nuclease Mutants. J Chem Theory Comput 2021; 17:4550-4563. [PMID: 34143626 DOI: 10.1021/acs.jctc.1c00355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Although buried titratable residues in protein cavities are often of major functional importance, it is generally challenging to understand their properties such as the ionization state and factors of stabilization based on experimental studies alone. A specific set of examples involve buried Glu-Lys pairs in a series of variants of Staphylococcal nuclease, for which recent structural and thermodynamic studies appeared to suggest that both the stability and the ionization state of the buried Glu-Lys pair are sensitive to its orientation (i.e., Glu23-Lys36 vs Lys23-Glu36). To further clarify the situation, especially ionization states of the buried Glu-Lys pairs, we have conducted extensive molecular dynamics simulations and free energy computations. Microsecond molecular dynamics simulations show that the hydration level of the cavity depends on the orientation of the buried ion-pair therein as well as its ionization state; free energy simulations recapitulate the relative stability of Glu23-Lys36 (EK) vs Lys23-Glu36 (KE) mutants measured experimentally, although the difference is similar in magnitude regardless of the ionization state of the Glu-Lys pair. A complementary set of free energy simulations strongly suggests that, in contrast to the original suggestion in the experimental analysis, the Glu and Lys residues prefer to adopt their charge-neutral rather than the ionized states. This result is consistent with the low dielectric constant computed for water in the cavity, which makes it difficult for the protein cavity to stabilize a pair of charged Glu-Lys residues, even with water penetration. The current study highlights the role of free energy simulations in understanding the ionization state of buried titratable residues and the relevant energetic contributions, forming the basis for the rational design of buried charge networks in proteins.
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Affiliation(s)
- Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Departments of Chemistry, Physics, and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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47
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Liang Y, Li W, Liang H, Lou X, Liu R, Zhang Q, Bartlam M. Structural characterization and Kemp eliminase activity of the Mycobacterium smegmatis Ketosteroid Isomerase. Biochem Biophys Res Commun 2021; 560:159-164. [PMID: 33992958 DOI: 10.1016/j.bbrc.2021.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 11/26/2022]
Abstract
The Kemp elimination reaction, involving the ring-opening of benzoxazole and its derivatives under the action of natural enzymes or chemical catalysts, has been of interest to researchers since its discovery. Because this reaction does not exist in all currently known metabolic pathways, the computational design of Kemp eliminases has provided valuable insights into principles of enzymatic catalysis. However, it was discovered that the naturally occurring promiscuous enzymes ydbC, xapA and ketosteroid isomerase also can catalyze Kemp elimination. Here, we report the crystal structure of ketosteroid isomerase (KSI) from Mycobacterium smegmatis MC2 155. MsKSI crystallizes in the P212121 space group with two molecules in an asymmetric unit, and ultracentrifugation data confirms that it forms a stable dimer in solution, consistent with the 1.9 Å-resolution structure. Our assays confirm that MsKSI accelerates the Kemp elimination of 5-nitrobenzoxazole (5NBI) with an optimal pH of 5.5. A 2.35 Å resolution crystal structure of the MsKSI-5NBI complex reveals that the substrate 5NBI is bound in the active pocket of the enzyme composed of hydrophobic residues. In addition, the Glu127 residue is proposed to play an important role as a general base in proton transfer and breaking weak O-N bonds to open the five-membered ring. This work provides a starting point for exploring the artificial modification of MsKSI using the natural enzyme as the backbone.
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Affiliation(s)
- Yakun Liang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Weiping Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Han Liang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xiaorui Lou
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Ruihua Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Qionglin Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
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48
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Vrancken JPM, Noguchi H, Zhang KYJ, Tame JRH, Voet ARD. The symmetric designer protein Pizza as a scaffold for metal coordination. Proteins 2021; 89:945-951. [PMID: 33713051 DOI: 10.1002/prot.26072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 12/14/2020] [Accepted: 03/04/2021] [Indexed: 01/17/2023]
Abstract
Symmetric proteins are currently of interest as they allow creation of larger assemblies and facilitate the incorporation of metal ions in the larger complexes. Recently this was demonstrated by the biomineralization of the cadmium-chloride nanocrystal via the Pizza designer protein. However, the mechanism behind this formation remained unclear. Here, we set out to investigate the mechanism driving the formation of this nanocrystal via truncation, mutation, and circular permutations. In addition, the interaction of other biologically relevant metal ions with these symmetric proteins to form larger symmetric complexes was also studied. The formation of the initial nanocrystal is shown to originate from steric strain, where His 58 induces a different rotameric conformation on His 73, thereby distorting an otherwise perfect planar ring of alternating cadmium and chlorine ions, resulting in the smallest nanocrystal. Similar highly symmetric complexes were also observed for the other biological relevant metal ions. However, the flexibility of the coordinating histidine residues allows each metal ion to adopt its preferred geometry leading to either monomeric or dimeric β-propeller units, where the metal ions are located at the interface between both propeller units. These results demonstrate that symmetric proteins are not only interesting to generate larger assemblies, but are also the perfect scaffold to create more complex metal based assemblies. Such metal protein assemblies may then find applications in bionanotechnology or biocatalysis.
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Affiliation(s)
- Jeroen P M Vrancken
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Hiroki Noguchi
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Kanagawa, Japan
| | - Jeremy R H Tame
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Arnout R D Voet
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Leuven, Belgium
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49
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Naudin EA, McEwen AG, Tan SK, Poussin-Courmontagne P, Schmitt JL, Birck C, DeGrado WF, Torbeev V. Acyl Transfer Catalytic Activity in De Novo Designed Protein with N-Terminus of α-Helix As Oxyanion-Binding Site. J Am Chem Soc 2021; 143:3330-3339. [PMID: 33635059 PMCID: PMC8012002 DOI: 10.1021/jacs.0c10053] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The design of catalytic proteins with functional sites capable of specific chemistry is gaining momentum and a number of artificial enzymes have recently been reported, including hydrolases, oxidoreductases, retro-aldolases, and others. Our goal is to develop a peptide ligase for robust catalysis of amide bond formation that possesses no stringent restrictions to the amino acid composition at the ligation junction. We report here the successful completion of the first step in this long-term project by building a completely de novo protein with predefined acyl transfer catalytic activity. We applied a minimalist approach to rationally design an oxyanion hole within a small cavity that contains an adjacent thiol nucleophile. The N-terminus of the α-helix with unpaired hydrogen-bond donors was exploited as a structural motif to stabilize negatively charged tetrahedral intermediates in nucleophilic addition-elimination reactions at the acyl group. Cysteine acting as a principal catalytic residue was introduced at the second residue position of the α-helix N-terminus in a designed three-α-helix protein based on structural informatics prediction. We showed that this minimal set of functional elements is sufficient for the emergence of catalytic activity in a de novo protein. Using peptide-αthioesters as acyl-donors, we demonstrated their catalyzed amidation concomitant with hydrolysis and proved that the environment at the catalytic site critically influences the reaction outcome. These results represent a promising starting point for the development of efficient catalysts for protein labeling, conjugation, and peptide ligation.
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Affiliation(s)
- Elise A Naudin
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006), Strasbourg 67000, France
| | - Alastair G McEwen
- Integrated Structural Biology Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), INSERM (U1258), University of Strasbourg, Illkirch 67404, France
| | - Sophia K Tan
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94158-9001, United States
| | - Pierre Poussin-Courmontagne
- Integrated Structural Biology Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), INSERM (U1258), University of Strasbourg, Illkirch 67404, France
| | - Jean-Louis Schmitt
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006), Strasbourg 67000, France
| | - Catherine Birck
- Integrated Structural Biology Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), INSERM (U1258), University of Strasbourg, Illkirch 67404, France
| | - William F DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94158-9001, United States
| | - Vladimir Torbeev
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006), Strasbourg 67000, France
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50
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Pollastrini M, Marafon G, Clayden J, Moretto A. Light-mediated control of activity in a photosensitive foldamer that mimics an esterase. Chem Commun (Camb) 2021; 57:2269-2272. [PMID: 33533349 DOI: 10.1039/d0cc08309g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a catalytic foldamer in which a fumaramide chromophore links a Ser residue to a helical domain that contains within its sequence the residues His and Asp. Photoisomerization of the fumaramide chromophore (with E geometry) to the corresponding maleamide (with Z geometry) brings together a 'catalytic triad' of Ser, His, and Asp, triggering esterase activity that is absent in the fumaramide isomer. The fumaramide/maleamide linker thus acts as a light-sensitive switchable cofactor for activation of catalytic activity in short foldamers.
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Affiliation(s)
- Matteo Pollastrini
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy.
| | - Giulia Marafon
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy.
| | - Jonathan Clayden
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Alessandro Moretto
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy.
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