1
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Bowling PE, Dasgupta S, Herbert JM. Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites. J Chem Inf Model 2024; 64:3912-3922. [PMID: 38648614 DOI: 10.1021/acs.jcim.4c00221] [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: 04/25/2024]
Abstract
In constructing finite models of enzyme active sites for quantum-chemical calculations, atoms at the periphery of the model must be constrained to prevent unphysical rearrangements during geometry relaxation. A simple fixed-atom or "coordinate-lock" approach is commonly employed but leads to undesirable artifacts in the form of small imaginary frequencies. These preclude evaluation of finite-temperature free-energy corrections, limiting thermochemical calculations to enthalpies only. Full-dimensional vibrational frequency calculations are possible by replacing the fixed-atom constraints with harmonic confining potentials. Here, we compare that approach to an alternative strategy in which fixed-atom contributions to the Hessian are simply omitted. While the latter strategy does eliminate imaginary frequencies, it tends to underestimate both the zero-point energy and the vibrational entropy while introducing artificial rigidity. Harmonic confining potentials eliminate imaginary frequencies and provide a flexible means to construct active-site models that can be used in unconstrained geometry relaxations, affording better convergence of reaction energies and barrier heights with respect to the model size, as compared to models with fixed-atom constraints.
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Affiliation(s)
- Paige E Bowling
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, California 92093, United States
| | - John M Herbert
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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2
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Vargas DA, Ren X, Sengupta A, Zhu L, Roy S, Garcia-Borràs M, Houk KN, Fasan R. Biocatalytic strategy for the construction of sp 3-rich polycyclic compounds from directed evolution and computational modelling. Nat Chem 2024; 16:817-826. [PMID: 38351380 PMCID: PMC11088497 DOI: 10.1038/s41557-023-01435-3] [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: 05/09/2022] [Accepted: 12/20/2023] [Indexed: 02/17/2024]
Abstract
Catalysis with engineered enzymes has provided more efficient routes for the production of active pharmaceutical agents. However, the potential of biocatalysis to assist in early-stage drug discovery campaigns remains largely untapped. In this study, we have developed a biocatalytic strategy for the construction of sp3-rich polycyclic compounds via the intramolecular cyclopropanation of benzothiophenes and related heterocycles. Two carbene transferases with complementary regioisomer selectivity were evolved to catalyse the stereoselective cyclization of benzothiophene substrates bearing diazo ester groups at the C2 or C3 position of the heterocycle. The detailed mechanisms of these reactions were elucidated by a combination of crystallographic and computational analyses. Leveraging these insights, the substrate scope of one of the biocatalysts could be expanded to include previously unreactive substrates, highlighting the value of integrating evolutionary and rational strategies to develop enzymes for new-to-nature transformations. The molecular scaffolds accessed here feature a combination of three-dimensional and stereochemical complexity with 'rule-of-three' properties, which should make them highly valuable for fragment-based drug discovery campaigns.
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Affiliation(s)
- David A Vargas
- Process Research and Development, Merck, Rahway, NJ, USA
| | - Xinkun Ren
- College of Engineering and Applied Sciences, Nanjing University, Nanjing, China
| | - Arkajyoti Sengupta
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Ledong Zhu
- Environment Research Institute, Shandong University, Qingdao, People's Republic of China
| | - Satyajit Roy
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, USA
| | - Marc Garcia-Borràs
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Girona, Spain
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA.
| | - Rudi Fasan
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, USA.
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3
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Abstract
ConspectusThe quantum chemical cluster approach has been used for modeling enzyme active sites and reaction mechanisms for more than two decades. In this methodology, a relatively small part of the enzyme around the active site is selected as a model, and quantum chemical methods, typically density functional theory, are used to calculate energies and other properties. The surrounding enzyme is modeled using implicit solvation and atom fixing techniques. Over the years, a large number of enzyme mechanisms have been solved using this method. The models have gradually become larger as a result of the faster computers, and new kinds of questions have been addressed. In this Account, we review how the cluster approach can be utilized in the field of biocatalysis. Examples from our recent work are chosen to illustrate various aspects of the methodology. The use of the cluster model to explore substrate binding is discussed first. It is emphasized that a comprehensive search is necessary in order to identify the lowest-energy binding mode(s). It is also argued that the best binding mode might not be the productive one, and the full reactions for a number of enzyme-substrate complexes have therefore to be considered to find the lowest-energy reaction pathway. Next, examples are given of how the cluster approach can help in the elucidation of detailed reaction mechanisms of biocatalytically interesting enzymes, and how this knowledge can be exploited to develop enzymes with new functions or to understand the reasons for lack of activity toward non-natural substrates. The enzymes discussed in this context are phenolic acid decarboxylase and metal-dependent decarboxylases from the amidohydrolase superfamily. Next, the application of the cluster approach in the investigation of enzymatic enantioselectivity is discussed. The reaction of strictosidine synthase is selected as a case study, where the cluster calculations could reproduce and rationalize the selectivities of both the natural and non-natural substrates. Finally, we discuss how the cluster approach can be used to guide the rational design of enzyme variants with improved activity and selectivity. Acyl transferase from Mycobacterium smegmatis serves as an instructive example here, for which the calculations could pinpoint the factors controlling the reaction specificity and enantioselectivity. The cases discussed in this Account highlight thus the value of the cluster approach as a tool in biocatalysis. It complements experiments and other computational techniques in this field and provides insights that can be used to understand existing enzymes and to develop new variants with tailored properties.
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Affiliation(s)
- Xiang Sheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, PR China
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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4
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Meelua W, Wanjai T, Thinkumrob N, Oláh J, Cairns JRK, Hannongbua S, Ryde U, Jitonnom J. A computational study of the reaction mechanism and stereospecificity of dihydropyrimidinase. Phys Chem Chem Phys 2023; 25:8767-8778. [PMID: 36912034 DOI: 10.1039/d2cp05262h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Dihydropyrimidinase (DHPase) is a key enzyme in the pyrimidine pathway, the catabolic route for synthesis of β-amino acids. It catalyses the reversible conversion of 5,6-dihydrouracil (DHU) or 5,6-dihydrothymine (DHT) to the corresponding N-carbamoyl-β-amino acids. This enzyme has the potential to be used as a tool in the production of β-amino acids. Here, the reaction mechanism and origin of stereospecificity of DHPases from Saccharomyces kluyveri and Sinorhizobium meliloti CECT4114 were investigated and compared using a quantum mechanical cluster approach based on density functional theory. Two models of the enzyme active site were designed from the X-ray crystal structure of the native enzyme: a small cluster to characterize the mechanism and the stationary points and a large model to probe the stereospecificity and the role of stereo-gate-loop (SGL) residues. It is shown that a hydroxide ion first performs a nucleophilic attack on the substrate, followed by the abstraction of a proton by Asp358, which occurs concertedly with protonation of the ring nitrogen by the same residue. For the DHT substrate, the enzyme displays a preference for the L-configuration, in good agreement with experimental observation. Comparison of the reaction energetics of the two models reveals the importance of SGL residues in the stereospecificity of catalysis. The role of the conserved Tyr172 residue in transition-state stabilization is confirmed as the Tyr172Phe mutation increases the activation barrier of the reaction by ∼8 kcal mol-1. A detailed understanding of the catalytic mechanism of the enzyme could offer insight for engineering in order to enhance its activity and substrate scope.
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Affiliation(s)
- Wijitra Meelua
- Demonstration School, University of Phayao, Phayao 56000, Thailand
- Unit of Excellence in Computational Molecular Science and Catalysis, and Division of Chemistry, School of Science, University of Phayao, Phayao 56000, Thailand.
| | - Tanchanok Wanjai
- Unit of Excellence in Computational Molecular Science and Catalysis, and Division of Chemistry, School of Science, University of Phayao, Phayao 56000, Thailand.
| | - Natechanok Thinkumrob
- Unit of Excellence in Computational Molecular Science and Catalysis, and Division of Chemistry, School of Science, University of Phayao, Phayao 56000, Thailand.
| | - Julianna Oláh
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Műegyetem rakpart 3, Budapest H-1111, Hungary
| | - James R Ketudat Cairns
- Center for Biomolecular Structure, Function and Application and School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, Lund SE-221 00, Sweden
| | - Jitrayut Jitonnom
- Unit of Excellence in Computational Molecular Science and Catalysis, and Division of Chemistry, School of Science, University of Phayao, Phayao 56000, Thailand.
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5
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Li JK, Qu G, Li X, Tian Y, Cui C, Zhang FG, Zhang W, Ma JA, Reetz MT, Sun Z. Rational enzyme design for enabling biocatalytic Baldwin cyclization and asymmetric synthesis of chiral heterocycles. Nat Commun 2022; 13:7813. [PMID: 36535947 PMCID: PMC9763437 DOI: 10.1038/s41467-022-35468-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Chiral heterocyclic compounds are needed for important medicinal applications. We report an in silico strategy for the biocatalytic synthesis of chiral N- and O-heterocycles via Baldwin cyclization modes of hydroxy- and amino-substituted epoxides and oxetanes using the limonene epoxide hydrolase from Rhodococcus erythropolis. This enzyme normally catalyzes hydrolysis with formation of vicinal diols. Firstly, the required shutdown of the undesired natural water-mediated ring-opening is achieved by rational mutagenesis of the active site. In silico enzyme design is then continued with generation of the improved mutants. These variants prove to be versatile catalysts for preparing chiral N- and O-heterocycles with up to 99% conversion, and enantiomeric ratios up to 99:1. Crystal structural data and computational modeling reveal that Baldwin-type cyclizations, catalyzed by the reprogrammed enzyme, are enabled by reshaping the active-site environment that directs the distal RHN and HO-substituents to be intramolecular nucleophiles.
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Affiliation(s)
- Jun-Kuan Li
- grid.33763.320000 0004 1761 2484Department of Chemistry, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072 China ,grid.9227.e0000000119573309Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Ge Qu
- grid.9227.e0000000119573309Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China ,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Xu Li
- grid.9227.e0000000119573309Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China ,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Yuchen Tian
- grid.33763.320000 0004 1761 2484Department of Chemistry, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072 China
| | - Chengsen Cui
- grid.9227.e0000000119573309Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China ,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Fa-Guang Zhang
- grid.33763.320000 0004 1761 2484Department of Chemistry, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072 China
| | - Wuyuan Zhang
- grid.9227.e0000000119573309Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China ,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
| | - Jun-An Ma
- grid.33763.320000 0004 1761 2484Department of Chemistry, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072 China
| | - Manfred T. Reetz
- grid.9227.e0000000119573309Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China ,grid.419607.d0000 0001 2096 9941Biocatalysis Section, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Zhoutong Sun
- grid.9227.e0000000119573309Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China ,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308 China
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6
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Jiang Y, Qu G, Sheng X, Tong F, Sun Z. Unraveling the mechanism of enantio-controlling switches of an alcohol dehydrogenase toward sterically small ketone. Catal Sci Technol 2022. [DOI: 10.1039/d2cy00031h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Efficient synthesis of chiral compounds under mild conditions is highly desirable in the chemical and pharmaceutical communities, but it often faces difficulties. Although various enzymes have been harnessed as biocatalysts...
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7
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Prejanò M, Sheng X, Himo F. Computational Study of Mechanism and Enantioselectivity of Imine Reductase from Amycolatopsis orientalis. ChemistryOpen 2022; 11:e202100250. [PMID: 34825518 PMCID: PMC8734122 DOI: 10.1002/open.202100250] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/04/2021] [Indexed: 11/24/2022] Open
Abstract
Imine reductases (IREDs) are NADPH-dependent enzymes (NADPH=nicotinamide adenine dinucleotide phosphate) that catalyze the reduction of imines to amines. They exhibit high enantioselectivity for a broad range of substrates, making them of interest for biocatalytic applications. In this work, we have employed density functional theory (DFT) calculations to elucidate the reaction mechanism and the origins of enantioselectivity of IRED from Amycolatopsis orientalis. Two substrates are considered, namely 1-methyl-3,4-dihydroisoquinoline and 2-propyl-piperideine. A model of the active site is built on the basis of the available crystal structure. For both substrates, different binding modes are first evaluated, followed by calculation of the hydride transfer transition states from each complex. We have also investigated the effect of mutations of certain important active site residues (Tyr179Ala and Asn241Ala) on the enantioselectivity. The calculated energies are consistent with the experimental observations and the analysis of transition states geometries provides insights into the origins of enantioselectivity of this enzyme.
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Affiliation(s)
- Mario Prejanò
- Department of Organic ChemistryArrhenius LaboratoryStockholm University10691StockholmSweden
| | - Xiang Sheng
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences and National Technology Innovation Center of Synthetic BiologyTianjin300308China
| | - Fahmi Himo
- Department of Organic ChemistryArrhenius LaboratoryStockholm University10691StockholmSweden
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8
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Modeling Catalysis in Allosteric Enzymes: Capturing Conformational Consequences. Top Catal 2021; 65:165-186. [DOI: 10.1007/s11244-021-01521-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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9
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Wu L, Qin L, Nie Y, Xu Y, Zhao YL. Computer-aided understanding and engineering of enzymatic selectivity. Biotechnol Adv 2021; 54:107793. [PMID: 34217814 DOI: 10.1016/j.biotechadv.2021.107793] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/26/2021] [Accepted: 06/28/2021] [Indexed: 12/26/2022]
Abstract
Enzymes offering chemo-, regio-, and stereoselectivity enable the asymmetric synthesis of high-value chiral molecules. Unfortunately, the drawback that naturally occurring enzymes are often inefficient or have undesired selectivity toward non-native substrates hinders the broadening of biocatalytic applications. To match the demands of specific selectivity in asymmetric synthesis, biochemists have implemented various computer-aided strategies in understanding and engineering enzymatic selectivity, diversifying the available repository of artificial enzymes. Here, given that the entire asymmetric catalytic cycle, involving precise interactions within the active pocket and substrate transport in the enzyme channel, could affect the enzymatic efficiency and selectivity, we presented a comprehensive overview of the computer-aided workflow for enzymatic selectivity. This review includes a mechanistic understanding of enzymatic selectivity based on quantum mechanical calculations, rational design of enzymatic selectivity guided by enzyme-substrate interactions, and enzymatic selectivity regulation via enzyme channel engineering. Finally, we discussed the computational paradigm for designing enzyme selectivity in silico to facilitate the advancement of asymmetric biosynthesis.
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Affiliation(s)
- Lunjie Wu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Lei Qin
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yao Nie
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Suqian Industrial Technology Research Institute of Jiangnan University, Suqian 223814, China.
| | - Yan Xu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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10
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Jiang C, He BB, Zhao RL, Xu MJ, Houk KN, Zhao YL. Computational Exploration of How Enzyme XimE Converts Natural S-Epoxide to Pyran and R-Epoxide to Furan. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01335] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Chuchu Jiang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People’s Republic of China
| | - Bei-Bei He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People’s Republic of China
| | - Rosalinda L. Zhao
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Min-Juan Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People’s Republic of China
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11
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Li G, Qin Y, Fontaine NT, Ng Fuk Chong M, Maria‐Solano MA, Feixas F, Cadet XF, Pandjaitan R, Garcia‐Borràs M, Cadet F, Reetz MT. Machine Learning Enables Selection of Epistatic Enzyme Mutants for Stability Against Unfolding and Detrimental Aggregation. Chembiochem 2021; 22:904-914. [PMID: 33094545 PMCID: PMC7984044 DOI: 10.1002/cbic.202000612] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/22/2020] [Indexed: 12/15/2022]
Abstract
Machine learning (ML) has pervaded most areas of protein engineering, including stability and stereoselectivity. Using limonene epoxide hydrolase as the model enzyme and innov'SAR as the ML platform, comprising a digital signal process, we achieved high protein robustness that can resist unfolding with concomitant detrimental aggregation. Fourier transform (FT) allows us to take into account the order of the protein sequence and the nonlinear interactions between positions, and thus to grasp epistatic phenomena. The innov'SAR approach is interpolative, extrapolative and makes outside-the-box, predictions not found in other state-of-the-art ML or deep learning approaches. Equally significant is the finding that our approach to ML in the present context, flanked by advanced molecular dynamics simulations, uncovers the connection between epistatic mutational interactions and protein robustness.
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Affiliation(s)
- Guangyue Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety Ministry of Agriculture, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100081P. R. China
| | - Youcai Qin
- State Key Laboratory for Biology of Plant Diseases and Insect Pests Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety Ministry of Agriculture, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing100081P. R. China
| | - Nicolas T. Fontaine
- PEACCELArtificial Intelligence Department6 Square Albin Cachot, Box 4275013ParisFrance) .
| | - Matthieu Ng Fuk Chong
- PEACCELArtificial Intelligence Department6 Square Albin Cachot, Box 4275013ParisFrance) .
| | - Miguel A. Maria‐Solano
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de Girona Campus Montilivi17003Girona, CataloniaSpain) .
| | - Ferran Feixas
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de Girona Campus Montilivi17003Girona, CataloniaSpain) .
| | - Xavier F. Cadet
- PEACCELArtificial Intelligence Department6 Square Albin Cachot, Box 4275013ParisFrance) .
| | - Rudy Pandjaitan
- PEACCELArtificial Intelligence Department6 Square Albin Cachot, Box 4275013ParisFrance) .
| | - Marc Garcia‐Borràs
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de Girona Campus Montilivi17003Girona, CataloniaSpain) .
| | - Frederic Cadet
- PEACCELArtificial Intelligence Department6 Square Albin Cachot, Box 4275013ParisFrance) .
| | - Manfred T. Reetz
- Department of ChemistryPhilipps-Universität35032MarburgGermany) .
- Max-Planck-Institut fuer Kohlenforschung45470MülheimGermany
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences32 West 7th Avenue, Tianjin Airport Economic Area300308TianjinP. R. China
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12
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Sheng X, Himo F. Computational Study of Pictet–Spenglerase Strictosidine Synthase: Reaction Mechanism and Origins of Enantioselectivity of Natural and Non-Natural Substrates. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03758] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xiang Sheng
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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13
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Cesario D, Fortino M, Marino T, Nunzi F, Russo N, Sicilia E. The role of the halogen bond in iodothyronine deiodinase: Dependence on chalcogen substitution in naphthyl-based mimetics. J Comput Chem 2020; 40:944-951. [PMID: 30681189 DOI: 10.1002/jcc.25775] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/07/2018] [Accepted: 12/14/2018] [Indexed: 11/06/2022]
Abstract
The effects on the activity of thyroxine (T4) due to the chalcogen replacement in a series of peri-substituted naphthalenes mimicking the catalytic function of deiodinase enzymes are computationally examined using density functional theory. In particular, T4 inner-ring deiodination pathways assisted by naphthyl-based models bearing two tellurols and a tellurol-thiol pair in peri-position are explored and compared with the analogous energy profiles for the naphthalene mimic having two selenols. The presence of a halogen bond (XB) in the intermediate formed in the first step and involved in the rate-determining step of the reaction is assumed to facilitate the process increasing the rate of the reaction. The rate-determining step calculated energy barrier heights allow rationalizing the experimentally observed superior catalytic activity of tellurium containing mimics. Charge displacement analysis is used to ascertain the presence and the role of the electron density charge transfer occurring in the rate-determining step of the reaction, suggesting the incipient formation or presence of a XB interaction. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Diego Cesario
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands.,Department of Chemistry, Biology and Biotechnology, University of Perugia, I-06123, Perugia, Italy
| | - Mariagrazia Fortino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, I-87030, Arcavacata di Rende, Italy
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, I-87030, Arcavacata di Rende, Italy
| | - Francesca Nunzi
- Department of Chemistry, Biology and Biotechnology, University of Perugia, I-06123, Perugia, Italy.,Istituto di Scienze e Tecnologie Molecolari del CNR (ISTM-CNR), I-06123, Perugia, Italy.,Consortium for Computational Molecular and Materials Sciences (CMS)2, I-06123, Perugia, Italy
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, I-87030, Arcavacata di Rende, Italy
| | - Emilia Sicilia
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, I-87030, Arcavacata di Rende, Italy
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14
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Sheng X, Kazemi M, Planas F, Himo F. Modeling Enzymatic Enantioselectivity using Quantum Chemical Methodology. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00983] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xiang Sheng
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
| | - Masoud Kazemi
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
| | - Ferran Planas
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
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15
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Arabnejad H, Bombino E, Colpa DI, Jekel PA, Trajkovic M, Wijma HJ, Janssen DB. Computational Design of Enantiocomplementary Epoxide Hydrolases for Asymmetric Synthesis of Aliphatic and Aromatic Diols. Chembiochem 2020; 21:1893-1904. [PMID: 31961471 PMCID: PMC7383614 DOI: 10.1002/cbic.201900726] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/16/2020] [Indexed: 12/13/2022]
Abstract
The use of enzymes in preparative biocatalysis often requires tailoring enzyme selectivity by protein engineering. Herein we explore the use of computational library design and molecular dynamics simulations to create variants of limonene epoxide hydrolase that produce enantiomeric diols from meso‐epoxides. Three substrates of different sizes were targeted: cis‐2,3‐butene oxide, cyclopentene oxide, and cis‐stilbene oxide. Most of the 28 designs tested were active and showed the predicted enantioselectivity. Excellent enantioselectivities were obtained for the bulky substrate cis‐stilbene oxide, and enantiocomplementary mutants produced (S,S)‐ and (R,R)‐stilbene diol with >97 % enantiomeric excess. An (R,R)‐selective mutant was used to prepare (R,R)‐stilbene diol with high enantiopurity (98 % conversion into diol, >99 % ee). Some variants displayed higher catalytic rates (kcat) than the original enzyme, but in most cases KM values increased as well. The results demonstrate the feasibility of computational design and screening to engineer enantioselective epoxide hydrolase variants with very limited laboratory screening.
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Affiliation(s)
- Hesam Arabnejad
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Elvira Bombino
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Dana I. Colpa
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Peter A. Jekel
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Milos Trajkovic
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Hein J. Wijma
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
| | - Dick B. Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747 AGGroningenThe Netherlands
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16
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Chen Q, Xiao Y, Zhang W, Mu W. Current methods and applications in computational protein design for food industry. Crit Rev Food Sci Nutr 2019; 60:3259-3270. [DOI: 10.1080/10408398.2019.1682513] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Qiuming Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yaqin Xiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
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17
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Kazemi M, Sheng X, Himo F. Origins of Enantiopreference of
Mycobacterium smegmatis
Acyl Transferase: A Computational Analysis. Chemistry 2019; 25:11945-11954. [DOI: 10.1002/chem.201902351] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Masoud Kazemi
- Department of Organic ChemistryArrhenius Laboratory Stockholm University 10691 Stockholm Sweden
| | - Xiang Sheng
- Department of Organic ChemistryArrhenius Laboratory Stockholm University 10691 Stockholm Sweden
| | - Fahmi Himo
- Department of Organic ChemistryArrhenius Laboratory Stockholm University 10691 Stockholm Sweden
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18
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Sheng X, Himo F. Enzymatic Pictet–Spengler Reaction: Computational Study of the Mechanism and Enantioselectivity of Norcoclaurine Synthase. J Am Chem Soc 2019; 141:11230-11238. [DOI: 10.1021/jacs.9b04591] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Xiang Sheng
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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19
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Planas F, McLeish MJ, Himo F. Computational Study of Enantioselective Carboligation Catalyzed by Benzoylformate Decarboxylase. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01084] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ferran Planas
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Michael J. McLeish
- Department of Chemistry and Chemical Biology, Indiana University−Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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20
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Wei WJ, Qian HX, Wang WJ, Liao RZ. Computational Understanding of the Selectivities in Metalloenzymes. Front Chem 2018; 6:638. [PMID: 30622942 PMCID: PMC6308299 DOI: 10.3389/fchem.2018.00638] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 12/07/2018] [Indexed: 01/26/2023] Open
Abstract
Metalloenzymes catalyze many different types of biological reactions with high efficiency and remarkable selectivity. The quantum chemical cluster approach and the combined quantum mechanics/molecular mechanics methods have proven very successful in the elucidation of the reaction mechanism and rationalization of selectivities in enzymes. In this review, recent progress in the computational understanding of various selectivities including chemoselectivity, regioselectivity, and stereoselectivity, in metalloenzymes, is discussed.
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Affiliation(s)
| | | | | | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, China
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21
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Voss M, Das D, Genz M, Kumar A, Kulkarni N, Kustosz J, Kumar P, Bornscheuer UT, Höhne M. In Silico Based Engineering Approach to Improve Transaminases for the Conversion of Bulky Substrates. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03900] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Moritz Voss
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Devashish Das
- Quantumzyme, LLP, No. 110/8, Krishnappa Layout, Lalbagh Road, Bangalore 560027, India
| | - Maika Genz
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Anurag Kumar
- Quantumzyme, LLP, No. 110/8, Krishnappa Layout, Lalbagh Road, Bangalore 560027, India
| | - Naveen Kulkarni
- Quantumzyme, LLP, No. 110/8, Krishnappa Layout, Lalbagh Road, Bangalore 560027, India
| | - Jakub Kustosz
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Pravin Kumar
- Quantumzyme, LLP, No. 110/8, Krishnappa Layout, Lalbagh Road, Bangalore 560027, India
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Matthias Höhne
- Protein Biochemistry, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
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22
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Rinaldi S, Van der Kamp MW, Ranaghan KE, Mulholland AJ, Colombo G. Understanding Complex Mechanisms of Enzyme Reactivity: The Case of Limonene-1,2-Epoxide Hydrolases. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00863] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Silvia Rinaldi
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Via Mario Bianco 9, 20131 Milano, Italy
| | - Marc W. Van der Kamp
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
| | - Kara E. Ranaghan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Via Mario Bianco 9, 20131 Milano, Italy
- Dipartimento di Chimica, Università degli Studi di Pavia, Via Taramelli 12, 27100 Pavia, Italy
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23
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Sun Z, Wu L, Bocola M, Chan HCS, Lonsdale R, Kong XD, Yuan S, Zhou J, Reetz MT. Structural and Computational Insight into the Catalytic Mechanism of Limonene Epoxide Hydrolase Mutants in Stereoselective Transformations. J Am Chem Soc 2017; 140:310-318. [DOI: 10.1021/jacs.7b10278] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Lian Wu
- State
Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Marco Bocola
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - H. C. Stephen Chan
- Laboratory
of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH B3 495 (Bâtiment CH) Station
6, CH-1015 Lausanne, Switzerland
| | - Richard Lonsdale
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Xu-Dong Kong
- State
Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Shuguang Yuan
- Laboratory
of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH B3 495 (Bâtiment CH) Station
6, CH-1015 Lausanne, Switzerland
| | - Jiahai Zhou
- State
Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
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24
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Moa S, Himo F. Quantum chemical study of mechanism and stereoselectivity of secondary alcohol dehydrogenase. J Inorg Biochem 2017; 175:259-266. [PMID: 28803132 DOI: 10.1016/j.jinorgbio.2017.07.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/02/2017] [Accepted: 07/18/2017] [Indexed: 11/17/2022]
Abstract
Secondary alcohol dehydrogenase from Thermoanaerobacter brockii (TbSADH) is a Zn- and NADP-dependent enzyme that catalyses the reversible transformation of secondary alcohols into ketones. It is of potential biocatalytic interest as it can be used in the synthesis of chiral alcohols by asymmetric reduction of ketones. In this paper, density functional theory calculations are employed to elucidate the origins of the enantioselectivity of TbSADH using a large model of the active site and considering two different substrates, 2-butanol and 3-hexanol. For these two substrates the enzyme has experimentally been shown to have the opposite enantioselectivity. The energy profiles for the reactions are calculated and the stationary points along the reaction path are characterised. The calculations first confirm that the general mechanism proposed for other alcohol dehydrogenases is energetically viable. In this mechanism, a proton is first transferred from the substrate to a histidine residue at the surface, followed by a hydride transfer to the NADP cofactor. The calculated overall energy barrier is consistent with the measured rate constant. Very importantly, the calculations are able to reproduce and rationalise the enantioselectivity of the enzyme for both substrates. The detailed characterisation of the energies and geometries of the involved transition states will be valuable in the rational engineering of TbSADH to expand its utility in biocatalysis.
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Affiliation(s)
- Sara Moa
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden.
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25
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Abstract
The quantum chemical cluster approach is a powerful method for investigating enzymatic reactions. Over the past two decades, a large number of highly diverse systems have been studied and a great wealth of mechanistic insight has been developed using this technique. This Perspective reviews the current status of the methodology. The latest technical developments are highlighted, and challenges are discussed. Some recent applications are presented to illustrate the capabilities and progress of this approach, and likely future directions are outlined.
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Affiliation(s)
- Fahmi Himo
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University , SE-106 91 Stockholm, Sweden
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26
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Sheng X, Himo F. Theoretical Study of Enzyme Promiscuity: Mechanisms of Hydration and Carboxylation Activities of Phenolic Acid Decarboxylase. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03249] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Xiang Sheng
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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27
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Amrein BA, Steffen-Munsberg F, Szeler I, Purg M, Kulkarni Y, Kamerlin SCL. CADEE: Computer-Aided Directed Evolution of Enzymes. IUCRJ 2017; 4:50-64. [PMID: 28250941 PMCID: PMC5331465 DOI: 10.1107/s2052252516018017] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/09/2016] [Indexed: 05/10/2023]
Abstract
The tremendous interest in enzymes as biocatalysts has led to extensive work in enzyme engineering, as well as associated methodology development. Here, a new framework for computer-aided directed evolution of enzymes (CADEE) is presented which allows a drastic reduction in the time necessary to prepare and analyze in silico semi-automated directed evolution of enzymes. A pedagogical example of the application of CADEE to a real biological system is also presented in order to illustrate the CADEE workflow.
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Affiliation(s)
- Beat Anton Amrein
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Fabian Steffen-Munsberg
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Ireneusz Szeler
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Miha Purg
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Yashraj Kulkarni
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
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28
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Romero-Rivera A, Garcia-Borràs M, Osuna S. Computational tools for the evaluation of laboratory-engineered biocatalysts. Chem Commun (Camb) 2016; 53:284-297. [PMID: 27812570 PMCID: PMC5310519 DOI: 10.1039/c6cc06055b] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/06/2016] [Indexed: 12/18/2022]
Abstract
Biocatalysis is based on the application of natural catalysts for new purposes, for which enzymes were not designed. Although the first examples of biocatalysis were reported more than a century ago, biocatalysis was revolutionized after the discovery of an in vitro version of Darwinian evolution called Directed Evolution (DE). Despite the recent advances in the field, major challenges remain to be addressed. Currently, the best experimental approach consists of creating multiple mutations simultaneously while limiting the choices using statistical methods. Still, tens of thousands of variants need to be tested experimentally, and little information is available on how these mutations lead to enhanced enzyme proficiency. This review aims to provide a brief description of the available computational techniques to unveil the molecular basis of improved catalysis achieved by DE. An overview of the strengths and weaknesses of current computational strategies is explored with some recent representative examples. The understanding of how this powerful technique is able to obtain highly active variants is important for the future development of more robust computational methods to predict amino-acid changes needed for activity.
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Affiliation(s)
- Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona, Campus Montilivi, 17071 Girona, Catalonia, Spain.
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, 607 Charles E. Young Drive, Los Angeles, California 90095, USA
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona, Campus Montilivi, 17071 Girona, Catalonia, Spain.
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29
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Zhang X, Chung LW. Alternative Mechanistic Strategy for Enzyme Catalysis in a Ni-Dependent Lactate Racemase (LarA): Intermediate Destabilization by the Cofactor. Chemistry 2016; 23:3623-3630. [DOI: 10.1002/chem.201604893] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Xiaoyong Zhang
- Department of Chemistry; South University of Science and Technology of China; Shenzhen 518055 P. R. China
| | - Lung W. Chung
- Department of Chemistry; South University of Science and Technology of China; Shenzhen 518055 P. R. China
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30
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Lind MES, Himo F. Quantum Chemical Modeling of Enantioconvergency in Soluble Epoxide Hydrolase. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01562] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Maria E. S. Lind
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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31
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Jafari S, Ryde U, Irani M. Catalytic mechanism of human glyoxalase I studied by quantum-mechanical cluster calculations. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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32
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Sousa SF, Ribeiro AJM, Neves RPP, Brás NF, Cerqueira NMFSA, Fernandes PA, Ramos MJ. Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1281] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Sérgio Filipe Sousa
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - António J. M. Ribeiro
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - Rui P. P. Neves
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - Natércia F. Brás
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - Nuno M. F. S. A. Cerqueira
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - Pedro A. Fernandes
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - Maria João Ramos
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
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33
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Bauer P, Carlsson ÅJ, Amrein BA, Dobritzsch D, Widersten M, Kamerlin SCL. Conformational diversity and enantioconvergence in potato epoxide hydrolase 1. Org Biomol Chem 2016; 14:5639-51. [PMID: 27049844 PMCID: PMC5315018 DOI: 10.1039/c6ob00060f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 03/31/2016] [Indexed: 01/11/2023]
Abstract
Potato epoxide hydrolase 1 (StEH1) is a biocatalytically important enzyme that exhibits rich enantio- and regioselectivity in the hydrolysis of chiral epoxide substrates. In particular, StEH1 has been demonstrated to enantioconvergently hydrolyze racemic mixes of styrene oxide (SO) to yield (R)-1-phenylethanediol. This work combines computational, crystallographic and biochemical analyses to understand both the origins of the enantioconvergent behavior of the wild-type enzyme, as well as shifts in activities and substrate binding preferences in an engineered StEH1 variant, R-C1B1, which contains four active site substitutions (W106L, L109Y, V141K and I155V). Our calculations are able to reproduce both the enantio- and regioselectivities of StEH1, and demonstrate a clear link between different substrate binding modes and the corresponding selectivity, with the preferred binding modes being shifted between the wild-type enzyme and the R-C1B1 variant. Additionally, we demonstrate that the observed changes in selectivity and the corresponding enantioconvergent behavior are due to a combination of steric and electrostatic effects that modulate both the accessibility of the different carbon atoms to the nucleophilic side chain of D105, as well as the interactions between the substrate and protein amino acid side chains and active site water molecules. Being able to computationally predict such subtle effects for different substrate enantiomers, as well as to understand their origin and how they are affected by mutations, is an important advance towards the computational design of improved biocatalysts for enantioselective synthesis.
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Affiliation(s)
- P. Bauer
- Science for Life Laboratory , Department of Cell and Molecular Biology , Uppsala University , BMC Box 596 , S-751 24 Uppsala , Sweden .
| | - Å. Janfalk Carlsson
- Department of Chemistry-BMC , Uppsala University , BMC Box 576 , S-751 23 Uppsala , Sweden . ;
| | - B. A. Amrein
- Science for Life Laboratory , Department of Cell and Molecular Biology , Uppsala University , BMC Box 596 , S-751 24 Uppsala , Sweden .
| | - D. Dobritzsch
- Department of Chemistry-BMC , Uppsala University , BMC Box 576 , S-751 23 Uppsala , Sweden . ;
| | - M. Widersten
- Department of Chemistry-BMC , Uppsala University , BMC Box 576 , S-751 23 Uppsala , Sweden . ;
| | - S. C. L. Kamerlin
- Science for Life Laboratory , Department of Cell and Molecular Biology , Uppsala University , BMC Box 596 , S-751 24 Uppsala , Sweden .
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34
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Seguin TJ, Wheeler SE. Electrostatic Basis for Enantioselective Brønsted-Acid-Catalyzed Asymmetric Ring Openings of meso-Epoxides. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00538] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Trevor J. Seguin
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Steven E. Wheeler
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
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35
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Sun Z, Wikmark Y, Bäckvall JE, Reetz MT. New Concepts for Increasing the Efficiency in Directed Evolution of Stereoselective Enzymes. Chemistry 2016; 22:5046-54. [DOI: 10.1002/chem.201504406] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Indexed: 01/28/2023]
Affiliation(s)
- Zhoutong Sun
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
| | - Ylva Wikmark
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University; 106 91 Stockholm Sweden
| | - Jan-E. Bäckvall
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University; 106 91 Stockholm Sweden
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Strasse 4 35032 Marburg Germany
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Sun Z, Lonsdale R, Wu L, Li G, Li A, Wang J, Zhou J, Reetz MT. Structure-Guided Triple-Code Saturation Mutagenesis: Efficient Tuning of the Stereoselectivity of an Epoxide Hydrolase. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02751] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Zhoutong Sun
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Richard Lonsdale
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Lian Wu
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guangyue Li
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Aitao Li
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Jianbo Wang
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
| | - Jiahai Zhou
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Fachbereich Chemie der Philipps-Universität, Hans-Meerwein-Strasse, 35032 Marburg, Germany
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37
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Reinscheid F, Reinscheid U. Stereochemical analysis of (+)-limonene using theoretical and experimental NMR and chiroptical data. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.10.061] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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38
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Abstract
With the advent of directed evolution of stereoselective enzymes almost 20 years ago and the rapid development of this exciting area of research, the traditional limitations of biocatalysts in organic chemistry have been eliminated.
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Affiliation(s)
- Guangyue Li
- Max-Planck-Institut für Kohlenforschung
- Kaiser-Wilhelm-Platz 1
- 45470, Mülheim an der Ruhr
- Germany
- Fachbereich Chemie
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung
- Kaiser-Wilhelm-Platz 1
- 45470, Mülheim an der Ruhr
- Germany
- Fachbereich Chemie
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39
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Amrein BA, Bauer P, Duarte F, Janfalk Carlsson Å, Naworyta A, Mowbray SL, Widersten M, Kamerlin SCL. Expanding the Catalytic Triad in Epoxide Hydrolases and Related Enzymes. ACS Catal 2015; 5:5702-5713. [PMID: 26527505 PMCID: PMC4613740 DOI: 10.1021/acscatal.5b01639] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 08/15/2015] [Indexed: 11/30/2022]
Abstract
Potato epoxide hydrolase 1 exhibits rich enantio- and regioselectivity in the hydrolysis of a broad range of substrates. The enzyme can be engineered to increase the yield of optically pure products as a result of changes in both enantio- and regioselectivity. It is thus highly attractive in biocatalysis, particularly for the generation of enantiopure fine chemicals and pharmaceuticals. The present work aims to establish the principles underlying the activity and selectivity of the enzyme through a combined computational, structural, and kinetic study using the substrate trans-stilbene oxide as a model system. Extensive empirical valence bond simulations have been performed on the wild-type enzyme together with several experimentally characterized mutants. We are able to computationally reproduce the differences between the activities of different stereoisomers of the substrate and the effects of mutations of several active-site residues. In addition, our results indicate the involvement of a previously neglected residue, H104, which is electrostatically linked to the general base H300. We find that this residue, which is highly conserved in epoxide hydrolases and related hydrolytic enzymes, needs to be in its protonated form in order to provide charge balance in an otherwise negatively charged active site. Our data show that unless the active-site charge balance is correctly treated in simulations, it is not possible to generate a physically meaningful model for the enzyme that can accurately reproduce activity and selectivity trends. We also expand our understanding of other catalytic residues, demonstrating in particular the role of a noncanonical residue, E35, as a "backup base" in the absence of H300. Our results provide a detailed view of the main factors driving catalysis and regioselectivity in this enzyme and identify targets for subsequent enzyme design efforts.
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Affiliation(s)
- Beat A. Amrein
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC
Box 596, SE-751 24 Uppsala, Sweden
| | - Paul Bauer
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC
Box 596, SE-751 24 Uppsala, Sweden
| | - Fernanda Duarte
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC
Box 596, SE-751 24 Uppsala, Sweden
| | - Åsa Janfalk Carlsson
- Department
of Chemistry-BMC, Uppsala University, BMC Box 576, SE-751 23 Uppsala, Sweden
| | - Agata Naworyta
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC
Box 596, SE-751 24 Uppsala, Sweden
| | - Sherry L. Mowbray
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC
Box 596, SE-751 24 Uppsala, Sweden
| | - Mikael Widersten
- Department
of Chemistry-BMC, Uppsala University, BMC Box 576, SE-751 23 Uppsala, Sweden
| | - Shina C. L. Kamerlin
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC
Box 596, SE-751 24 Uppsala, Sweden
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40
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Zhang HM, Chen SL. Include Dispersion in Quantum Chemical Modeling of Enzymatic Reactions: The Case of Isoaspartyl Dipeptidase. J Chem Theory Comput 2015; 11:2525-35. [DOI: 10.1021/acs.jctc.5b00246] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hai-Mei Zhang
- Key Laboratory
of Cluster
Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic
Conversion Materials, School of Chemistry, Beijing Institute of Technology, Beijing 100081, China
| | - Shi-Lu Chen
- Key Laboratory
of Cluster
Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic
Conversion Materials, School of Chemistry, Beijing Institute of Technology, Beijing 100081, China
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41
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Sun Z, Lonsdale R, Kong XD, Xu JH, Zhou J, Reetz MT. Reshaping an Enzyme Binding Pocket for Enhanced and Inverted Stereoselectivity: Use of Smallest Amino Acid Alphabets in Directed Evolution. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501809] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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42
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Sun Z, Lonsdale R, Kong XD, Xu JH, Zhou J, Reetz MT. Reshaping an Enzyme Binding Pocket for Enhanced and Inverted Stereoselectivity: Use of Smallest Amino Acid Alphabets in Directed Evolution. Angew Chem Int Ed Engl 2015; 54:12410-5. [DOI: 10.1002/anie.201501809] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Indexed: 01/06/2023]
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43
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Denard CA, Ren H, Zhao H. Improving and repurposing biocatalysts via directed evolution. Curr Opin Chem Biol 2015; 25:55-64. [DOI: 10.1016/j.cbpa.2014.12.036] [Citation(s) in RCA: 204] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/14/2014] [Accepted: 12/18/2014] [Indexed: 11/27/2022]
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44
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Wijma HJ, Floor RJ, Bjelic S, Marrink SJ, Baker D, Janssen DB. Enantioselective enzymes by computational design and in silico screening. Angew Chem Int Ed Engl 2015; 54:3726-30. [PMID: 25651000 DOI: 10.1002/anie.201411415] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Indexed: 01/08/2023]
Abstract
Computational enzyme design holds great promise for providing new biocatalysts for synthetic chemistry. A strategy to design small mutant libraries of complementary enantioselective epoxide hydrolase variants for the production of highly enantioenriched (S,S)-diols and (R,R)-diols is developed. Key features of this strategy (CASCO, catalytic selectivity by computational design) are the design of mutations that favor binding of the substrate in a predefined orientation, the introduction of steric hindrance to prevent unwanted substrate binding modes, and ranking of designs by high-throughput molecular dynamics simulations. Using this strategy we obtained highly stereoselective mutants of limonene epoxide hydrolase after experimental screening of only 37 variants. The results indicate that computational methods can replace a substantial amount of laboratory work when developing enantioselective enzymes.
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Affiliation(s)
- Hein J Wijma
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands)
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45
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Wijma HJ, Floor RJ, Bjelic S, Marrink SJ, Baker D, Janssen DB. Enantioselective Enzymes by Computational Design and In Silico Screening. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201411415] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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46
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Ortega-Carrasco E, Lledós A, Maréchal JD. Unravelling novel synergies between organometallic and biological partners: a quantum mechanics/molecular mechanics study of an artificial metalloenzyme. J R Soc Interface 2014; 11:rsif.2014.0090. [PMID: 24829279 DOI: 10.1098/rsif.2014.0090] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In recent years, the design of artificial metalloenzymes obtained by the insertion of homogeneous catalysts into biological macromolecules has become a major field of research. These hybrids, and the corresponding X-ray structures of several of them, are offering opportunities to better understand the synergy between organometallic and biological subsystems. In this work, we investigate the resting state and activation process of a hybrid inspired by an oxidative haemoenzyme but presenting an unexpected reactivity and structural features. An extensive series of quantum mechanics/molecular mechanics calculations show that the resting state and the activation processes of the novel enzyme differ from naturally occurring haemoenzymes in terms of the electronic state of the metal, participation of the first coordination sphere of the metal and the dynamic process. This study presents novel insights into the sensitivity of the association between organometallic and biological partners and illustrates the molecular challenge that represents the design of efficient enzymes based on this strategy.
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Affiliation(s)
| | - Agustí Lledós
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
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47
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Sheng X, Liu Y, Zhang R. A theoretical study of the catalytic mechanism of oxalyl-CoA decarboxylase, an enzyme for treating urolithiasis. RSC Adv 2014. [DOI: 10.1039/c4ra03611e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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48
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Wijma HJ, Marrink SJ, Janssen DB. Computationally efficient and accurate enantioselectivity modeling by clusters of molecular dynamics simulations. J Chem Inf Model 2014; 54:2079-92. [PMID: 24916632 DOI: 10.1021/ci500126x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Computational approaches could decrease the need for the laborious high-throughput experimental screening that is often required to improve enzymes by mutagenesis. Here, we report that using multiple short molecular dynamics (MD) simulations makes it possible to accurately model enantioselectivity for large numbers of enzyme-substrate combinations at low computational costs. We chose four different haloalkane dehalogenases as model systems because of the availability of a large set of experimental data on the enantioselective conversion of 45 different substrates. To model the enantioselectivity, we quantified the frequency of occurrence of catalytically productive conformations (near attack conformations) for pairs of enantiomers during MD simulations. We found that the angle of nucleophilic attack that leads to carbon-halogen bond cleavage was a critical variable that limited the occurrence of productive conformations; enantiomers for which this angle reached values close to 180° were preferentially converted. A cluster of 20-40 very short (10 ps) MD simulations allowed adequate conformational sampling and resulted in much better agreement to experimental enantioselectivities than single long MD simulations (22 ns), while the computational costs were 50-100 fold lower. With single long MD simulations, the dynamics of enzyme-substrate complexes remained confined to a conformational subspace that rarely changed significantly, whereas with multiple short MD simulations a larger diversity of conformations of enzyme-substrate complexes was observed.
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Affiliation(s)
- Hein J Wijma
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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49
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Sheng X, Liu Y. Theoretical study of the catalytic mechanism of E1 subunit of pyruvate dehydrogenase multienzyme complex from Bacillus stearothermophilus. Biochemistry 2013; 52:8079-93. [PMID: 24171427 DOI: 10.1021/bi400577f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pyruvate dehydrogenase multienzyme complex (PDHc) is a member of a family of 2-oxo acid dehydrogenase (OADH) multienzyme complexes involved in several central points of oxidative metabolism, and the E1 subunit is the most important component in the entire PDHc catalytic system, which catalyzes the reversible transfer of an acetyl group from a pyruvate to the lipoyl group of E2 subunit lipoly domain. In this article, the catalytic mechanism of the E1 subunit has been systematically studied using density functional theory (DFT). Four possible pathways with different general acid/base catalysts in decarboxylation and reductive acylation processes were explored. Our calculation results indicate that the 4'-amino pyrimidine of ThDP and residue His128 are the most likely proton donors in the decarboxylation and reductive acylation processes, respectively. During the reaction, each C-C and C-S bond formation or cleavage process, except for the liberation of CO2, is always accompanied by a proton transfer between the substrates and proton donors. The liberation of CO2 is calculated to be the rate-limiting step for the overall reaction, with an energy barrier of 13.57 kcal/mol. The decarboxylation process is endothermic by 5.32 kcal/mol, whereas the reductive acylation process is exothermic with a value of 5.74 kcal/mol. The assignment of protonation states of the surrounding residues can greatly influence the reaction. Residues His128 and His271 play roles in positioning the first substrate pyruvate and second substrate lipoyl group, respectively.
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Affiliation(s)
- Xiang Sheng
- Key Laboratory of Theoretical and Computational Chemistry in Universities of Shandong, School of Chemistry and Chemical Engineering, Shandong University , Jinan, Shandong 250100, China
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