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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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Rothkranz B, Rieb M, Unrau EL, Frindi-Wosch I, Hemmerich J, Sehl T, Rother D. High Cell Density Cultivation Combined with high Specific Enzyme Activity: Cultivation Protocol for the Production of an Amine Transaminase from Bacillus megaterium in E. coli. Chembiochem 2024; 25:e202400006. [PMID: 38457364 DOI: 10.1002/cbic.202400006] [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: 01/10/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/10/2024]
Abstract
High cell density cultivation is an established method for the production of various industrially important products such as recombinant proteins. However, these protocols are not always suitable for biocatalytic processes as the focus often lies on biomass production rather than high specific activities of the enzyme inside the cells. In contrast, a range of shake flask protocols are well known with high specific activities but rather low cell densities. To overcome this gap, we established a tailor-made fed-batch protocol combining both aspects: high cell density and high specific activities of heterologously produced enzyme. Using the example of an industrially relevant amine transaminase from Bacillus megaterium, we describe a strategy to optimize the cultivation yield based on the feed rate, IPTG concentration, and post-induction temperature. By adjusting these key parameters, we were able to increase the specific activity by 2.6-fold and the wet cell weight by even 17-fold compared to shake flasks. Finally, we were able to verify our established protocol by transferring it to another experimenter. With that, our optimization strategy can serve as a template for the production of high titers of heterologously produced, active enzymes and might enable the availability of these catalysts for upscaling biocatalytic processes.
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Affiliation(s)
- Berit Rothkranz
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geo Science 1 (IBG-1): Biotechnology, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
- RWTH Aachen University, Aachen Biology and Biotechnology (ABBt), Worringer Weg 1, 52074, Aachen, Germany
| | - Matthias Rieb
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geo Science 1 (IBG-1): Biotechnology, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
| | - Evelin Lisa Unrau
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geo Science 1 (IBG-1): Biotechnology, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
| | - Ilona Frindi-Wosch
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geo Science 1 (IBG-1): Biotechnology, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
| | - Johannes Hemmerich
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geo Science 1 (IBG-1): Biotechnology, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
- dsm-firmenich, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - Torsten Sehl
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geo Science 1 (IBG-1): Biotechnology, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
| | - Dörte Rother
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geo Science 1 (IBG-1): Biotechnology, Wilhelm-Johnen-Straße, 52425, Jülich, Germany
- RWTH Aachen University, Aachen Biology and Biotechnology (ABBt), Worringer Weg 1, 52074, Aachen, Germany
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Yi X, Yu H, Ye L. Rational design of transaminases based on comparative analysis of catalytically active and distance-free modes of the high-energy intermediate state. Biotechnol Bioeng 2024; 121:1005-1015. [PMID: 38108196 DOI: 10.1002/bit.28626] [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: 08/21/2023] [Revised: 11/14/2023] [Accepted: 12/03/2023] [Indexed: 12/19/2023]
Abstract
Bioproduction of chiral amines is limited by low transaminase (TA) activity on nonnatural substrates, leading to the need for protein engineering. To address the challenge of quickly and precisely identifying the engineering targets, a strategy was proposed based on analyzing the mode changes in the high-energy intermediate state (H-state) of the substrate-enzyme complex during catalysis. By substituting the residues with minimal structural changes in catalytically active mode (A-mode) and distance-free mode (F-mode) of the H-state complex with more conserved ones to stabilize it, a TA mutant M5(T295C/L387A/V436A) with 121.9-fold higher activity for synthesizing the (S)-Rivastigmine precursor (S)-1-(3-methoxyphenyl)ethylamine was created. The applicability of this strategy was also validated by engineering another TA for 1.52-fold higher activity and >99% selectivity toward (R)-3-amino-1-butanol biopreparation. The much higher stereoselectivity of the mutant compared with the wild type (28.3%) demonstrated that this strategy is not only advantageous in engineering enzyme activity but also applicable for modulating stereoselectivity.
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Affiliation(s)
- Xiaomin Yi
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Hongwei Yu
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Lidan Ye
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
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4
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Li X, Sun X. 1,3-Proton Transfer of Pyridoxal 5'-Phosphate Schiff Base in the Branched-Chain Aminotransferase: Concerted or Stepwise Mechanism? J Phys Chem B 2024; 128:77-85. [PMID: 38131279 DOI: 10.1021/acs.jpcb.3c05875] [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: 12/23/2023]
Abstract
The branched-chain aminotransferase from Mycobacterium tuberculosis (MtIlvE) is a pyridoxal 5'-phosphate (PLP) dependent enzyme, and it is essential for the synthesis of the branched-chain amino acids. Ketimine is an important intermediate in the catalytic process. We have investigated the mechanism of ketimine formation and the energy landscape using the multiple computational methods. It is found that the 1,3-proton transfer involved in ketimine formation occurs through a stepwise process rather than a one-step process. Lys204 is identified as a key residue for ligand binding and as a base that abstracts the Cα proton from the PLP-Glu Schiff base, yielding a carbanionic intermediate. The first proton transfer is the rate-limiting step with an energy barrier of 17.8 kcal mol-1. Our study disclosed the detailed pathway of the proton transfer from external aldimine to ketimine, providing novel insights into the catalytic mechanism of other PLP-dependent enzymes.
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Affiliation(s)
- Xue Li
- School of Life Sciences, Changchun Normal University, Changchun 130023, People's Republic of China
| | - Xiaoli Sun
- Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People's Republic of China
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Han SW, Jang Y, Kook J, Jang J, Shin JS. Reprogramming biocatalytic futile cycles through computational engineering of stereochemical promiscuity to create an amine racemase. Nat Commun 2024; 15:49. [PMID: 38169460 PMCID: PMC10761954 DOI: 10.1038/s41467-023-44218-7] [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: 05/22/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
Repurposing the intrinsic properties of natural enzymes can offer a viable solution to current synthetic challenges through the development of novel biocatalytic processes. Although amino acid racemases are ubiquitous in living organisms, an amine racemase (AR) has not yet been discovered despite its synthetic potential for producing chiral amines. Here, we report the creation of an AR based on the serendipitous discovery that amine transaminases (ATAs) can perform stereoinversion of 2-aminobutane. Kinetic modeling revealed that the unexpected off-pathway activity results from stereochemically promiscuous futile cycles due to incomplete stereoselectivity for 2-aminobutane. This finding motivated us to engineer an S-selective ATA through in silico alanine scanning and empirical combinatorial mutations, creating an AR with broad substrate specificity. The resulting AR, carrying double point mutations, enables the racemization of both enantiomers of diverse chiral amines in the presence of a cognate ketone. This strategy may be generally applicable to a wide range of transaminases, paving the way for the development of new-to-nature racemases.
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Affiliation(s)
- Sang-Woo Han
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
- Department of Biotechnology, Konkuk University, Chungju, South Korea
| | - Youngho Jang
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
| | - Jihyun Kook
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
| | - Jeesu Jang
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
| | - Jong-Shik Shin
- Department of Biotechnology, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea.
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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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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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Dong L, Liu Y. Catalytic Mechanism of Pyridoxal 5'-Phosphate-Dependent Aminodeoxychorismate Lyase: A Computational QM/MM Study. J Chem Inf Model 2023; 63:1313-1322. [PMID: 36745546 DOI: 10.1021/acs.jcim.2c01593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aminodeoxychorismate lyase (ADCL) is a kind of pyridoxal-5'-phosphate (PLP)-dependent enzyme that catalyzes the conversion of 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate (PABA), which is a key step for the biosynthesis of folate. To illuminate the reaction details at the atomistic level, an enzyme-substrate reactant model has been constructed, and QM/MM calculations have been performed. Our calculation results reveal that the overall catalytic cycle contains 11 elementary steps, which can be described by three stages, including the transamination reaction of PLP, the release of pyruvate and aromatization of ADC, and the recovery to the initial aldimine. During the reaction, a series of intramolecular proton transfer are involved, which are the key for the C-N bond formation and cleavage as well as the aromatization of the ADC ring. In addition to forming the Schiff base with the pocket residue Lys251 and substrate in the internal aldimine and the external aldimine, respectively, the coenzyme PLP also plays a critical role in the intramolecular proton transfer by employing its hydroxyl oxygen anion and phosphate group. These findings may provide useful information for further understanding the catalytic mechanism of other PLP-dependent enzymes.
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Affiliation(s)
- Lihua Dong
- School of Chemistry and Chemical Engineering, Qilu Normal University, Jinan, Shandong 250013, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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Wang H, Tao Y, Masuku MV, Cao J, Yang J, Huang K, Ge Y, Yu Y, Xiao Z, Kuang Y, Huang J, Yang S. Effects of deep eutectic solvents on the biotransformation efficiency of ω-transaminase. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Yang L, Zhang K, Xu M, Xie Y, Meng X, Wang H, Wei D. Mechanism-Guided Computational Design of ω-Transaminase by Reprograming of High-Energy-Barrier Steps. Angew Chem Int Ed Engl 2022; 61:e202212555. [PMID: 36300723 DOI: 10.1002/anie.202212555] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Indexed: 11/06/2022]
Abstract
ω-Transaminases (ω-TAs) show considerable potential for the synthesis of chiral amines. However, their low catalytic efficiency towards bulky substrates limits their application, and complicated catalytic mechanisms prevent precise enzyme design. Herein, we address this challenge using a mechanism-guided computational enzyme design strategy by reprograming the transition and ground states in key reaction steps. The common features among the three high-energy-barrier steps responsible for the low catalytic efficiency were revealed using quantum mechanics (QM). Five key residues were simultaneously tailored to stabilize the rate-limiting transition state with the aid of the Rosetta design. The 14 top-ranked variants showed 16.9-143-fold improved catalytic activity. The catalytic efficiency of the best variant, M9 (Q25F/M60W/W64F/I266A), was significantly increased, with a 1660-fold increase in kcat /Km and a 1.5-26.8-fold increase in turnover number (TON) towards various indanone derivatives.
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Affiliation(s)
- Lin Yang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology East China University of Science and Technology, Shanghai, P. R. China
| | - Kaiyue Zhang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology East China University of Science and Technology, Shanghai, P. R. China
| | - Meng Xu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology East China University of Science and Technology, Shanghai, P. R. China
| | - Youyu Xie
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology East China University of Science and Technology, Shanghai, P. R. China
| | - Xiangqi Meng
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology East China University of Science and Technology, Shanghai, P. R. China
| | - Hualei Wang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology East China University of Science and Technology, Shanghai, P. R. China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology East China University of Science and Technology, Shanghai, P. R. China
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Wang Q, Ma L, Wang Z, Chen Q, Wang Q, Qi Q. Construction and yield optimization of a cinnamylamine biosynthesis route in Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:100. [PMID: 36175923 PMCID: PMC9524069 DOI: 10.1186/s13068-022-02199-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/22/2022] [Indexed: 11/10/2022]
Abstract
Background With the development of metabolic engineering and synthetic biology, the biosynthesis of aromatic compounds has attracted much attention. Cinnamylamine is an aromatic compound derived from l-phenylalanine, which is used in the synthesis of biologically active molecules, including drugs, and energetic materials. Cinnamylamine has been mainly synthesized by chemical methods to date, and few reports have focused on the biosynthesis of cinnamylamine. Therefore, it is desirable to establish an efficient biosynthesis method for cinnamylamine. Results The ω-aminotransferase Cv-ωTA from Chromobacterium violaceum has been demonstrated to have high enzyme activity in the conversion of cinnamaldehyde to cinnamylamine. To prevent the preferable conversion of cinnamaldehyde to cinnamyl alcohol in wild-type Escherichia coli, the E. coli MG1655 strain with reduced aromatic aldehyde reduction (RARE) in which six aldehyde ketone reductase and alcohol dehydrogenase genes have been knocked out was employed. Then, the carboxylic acid reductase from Neurospora crassa (NcCAR) and phosphopantetheinyl transferase (PPTase) from E. coli were screened for a high conversion rate of cinnamic acid to cinnamaldehyde. To shift the equilibrium of the reaction toward cinnamylamine, saturation mutagenesis of Cv-ωTA at key amino acid residues was performed, and Cv-ωTA Y168G had the highest conversion rate with 88.56 mg/L cinnamylamine obtained after 4 h of fermentation. Finally, by optimizing the substrates and the supply of the cofactors, PLP and NADPH, in the fermentation, the yield of cinnamylamine in engineered E. coli reached 523.15 mg/L. Conclusion We achieved the first biosynthesis of cinnamylamine using cinnamic acid as the precursor in E. coli using a combinatorial metabolic engineering strategy. This study provides a reference for the biosynthesis of other amine compounds and lays a foundation for the de novo synthesis of cinnamylamine. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02199-7.
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Kollipara M, Matzel P, Bornscheuer U, Höhne M. Activity Levels of Amine Transaminases Correlate with Active Site Hydrophobicity. CHEM-ING-TECH 2022. [DOI: 10.1002/cite.202200062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Manideep Kollipara
- University of Greifswald Institute of Biochemistry, Protein Biochemistry Felix-Hausdorff-Straße 4 17489 Greifswald Germany
| | - Philipp Matzel
- University of Greifswald Institute of Biochemistry, Protein Biochemistry Felix-Hausdorff-Straße 4 17489 Greifswald Germany
| | - Uwe Bornscheuer
- University of Greifswald Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis Felix-Hausdorff-Straße 4 17489 Greifswald Germany
| | - Matthias Höhne
- University of Greifswald Institute of Biochemistry, Protein Biochemistry Felix-Hausdorff-Straße 4 17489 Greifswald Germany
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Yamabe S, Tsuchida N, Yamazaki S. A DFT study of the active role of the phosphate group of an internal aldimine in a transamination reaction. Org Biomol Chem 2022; 20:5334-5341. [PMID: 35748359 DOI: 10.1039/d2ob00913g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A transamination reaction from an internal aldimine ([PLP]) and (S)-alanine to pyridoxamine phosphate (PMP) and pyruvic acid was investigated by DFT calculations. As [PLP], a model where the lysine (-Lys) part was approximated by -CH[-NH-C(O)-CH3]-C(O)-NH-CH3 was adopted. (H2O)4 was also included to trace reaction paths involving proton transfers. 13 elementary processes were obtained. For (the external aldimine → quinoid), (quinoid → ketimine) and (ketimine → carbinol amine) processes, the water dimer was found to connect a phosphate-group oxygen with the moving proton. The connection promoted the Grotthuss-type proton transfer in transition states. It was revealed that the phosphate group is not a mere substituent but has the central role in the transfer.
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Affiliation(s)
- Shinichi Yamabe
- Department of Chemistry, Nara University of Education, Takabatake-cho, Nara 630-8528, Japan.
| | - Noriko Tsuchida
- Department of Liberal Arts, Faculty of Medicine, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Shoko Yamazaki
- Department of Chemistry, Nara University of Education, Takabatake-cho, Nara 630-8528, Japan.
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14
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Bím D, Navrátil M, Gutten O, Konvalinka J, Kutil Z, Culka M, Navrátil V, Alexandrova AN, Bařinka C, Rulíšek L. Predicting Effects of Site-Directed Mutagenesis on Enzyme Kinetics by QM/MM and QM Calculations: A Case of Glutamate Carboxypeptidase II. J Phys Chem B 2022; 126:132-143. [PMID: 34978450 DOI: 10.1021/acs.jpcb.1c09240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Quantum and molecular mechanics (QM/MM) and QM-only (cluster model) modeling techniques represent the two workhorses in mechanistic understanding of enzyme catalysis. One of the stringent tests for QM/MM and/or QM approaches is to provide quantitative answers to real-world biochemical questions, such as the effect of single-point mutations on enzyme kinetics. This translates into predicting the relative activation energies to 1-2 kcal·mol-1 accuracy; such predictions can be used for the rational design of novel enzyme variants with desired/improved characteristics. Herein, we employ glutamate carboxypeptidase II (GCPII), a dizinc metallopeptidase, also known as the prostate specific membrane antigen, as a model system. The structure and activity of this major cancer antigen have been thoroughly studied, both experimentally and computationally, which makes it an ideal model system for method development. Its reaction mechanism is quite well understood: the reaction coordinate comprises a "tetrahedral intermediate" and two transition states and experimental activation Gibbs free energy of ∼17.5 kcal·mol-1 can be inferred for the known kcat ≈ 1 s-1. We correlate experimental kinetic data (including the E424H variant, newly characterized in this work) for various GCPII mutants (kcat = 8.6 × 10-5 s-1 to 2.7 s-1) with the energy profiles calculated by QM/MM and QM-only (cluster model) approaches. We show that the near-quantitative agreement between the experimental values and the calculated activation energies (ΔH⧧) can be obtained and recommend the combination of the two protocols: QM/MM optimized structures and cluster model (QM) energetics. The trend in relative activation energies is mostly independent of the QM method (DFT functional) used. Last but not least, a satisfactory correlation between experimental and theoretical data allows us to provide qualitative and fairly simple explanations of the observed kinetic effects which are thus based on a rigorous footing.
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Affiliation(s)
- Daniel Bím
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic.,Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Michal Navrátil
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Ondrej Gutten
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 2120 00 Prague, Czech Republic
| | - Zsófia Kutil
- Institute of Biotechnology of the Czech Academy of Sciences, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Václav Navrátil
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Cyril Bařinka
- Institute of Biotechnology of the Czech Academy of Sciences, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
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15
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Ramírez-Palacios C, Wijma HJ, Thallmair S, Marrink SJ, Janssen DB. Computational Prediction of ω-Transaminase Specificity by a Combination of Docking and Molecular Dynamics Simulations. J Chem Inf Model 2021; 61:5569-5580. [PMID: 34653331 PMCID: PMC8611723 DOI: 10.1021/acs.jcim.1c00617] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
ω-Transaminases (ω-TAs) catalyze the conversion of ketones to chiral amines, often with high enantioselectivity and specificity, which makes them attractive for industrial production of chiral amines. Tailoring ω-TAs to accept non-natural substrates is necessary because of their limited substrate range. We present a computational protocol for predicting the enantioselectivity and catalytic selectivity of an ω-TA from Vibrio fluvialis with different substrates and benchmark it against 62 compounds gathered from the literature. Rosetta-generated complexes containing an external aldimine intermediate of the transamination reaction are used as starting conformations for multiple short independent molecular dynamics (MD) simulations. The combination of molecular docking and MD simulations ensures sufficient and accurate sampling of the relevant conformational space. Based on the frequency of near-attack conformations observed during the MD trajectories, enantioselectivities can be quantitatively predicted. The predicted enantioselectivities are in agreement with a benchmark dataset of experimentally determined ee% values. The substrate-range predictions can be based on the docking score of the external aldimine intermediate. The low computational cost required to run the presented framework makes it feasible for use in enzyme design to screen thousands of enzyme variants.
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Affiliation(s)
- Carlos Ramírez-Palacios
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Hein J Wijma
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sebastian Thallmair
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.,Frankfurt Institute for Advanced Studies, Ruth-Moufang-Str. 1, 60438 Frankfurt am Main, Germany
| | - Siewert J Marrink
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Dick B Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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16
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Yu J, Zong W, Ding Y, Liu J, Chen L, Zhang H, Jiao Q. Fabrication of ω‐Transaminase@Metal‐Organic Framework Biocomposites for Efficiently Synthesizing Benzylamines and Pyridylmethylamines. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jinhai Yu
- State Key Laboratory of Pharmaceutical Biotechnology School of Life Science Nanjing University Nanjing 210093 People's Republic of China
| | - Weilu Zong
- State Key Laboratory of Pharmaceutical Biotechnology School of Life Science Nanjing University Nanjing 210093 People's Republic of China
| | - Yingying Ding
- School of Pharmacy Nanjing Medical University Nanjing 211166 People's Republic of China
| | - Junzhong Liu
- State Key Laboratory of Pharmaceutical Biotechnology School of Life Science Nanjing University Nanjing 210093 People's Republic of China
| | - Lina Chen
- School of Pharmacy Nanjing Medical University Nanjing 211166 People's Republic of China
| | - Hongjuan Zhang
- School of Pharmacy Nanjing Medical University Nanjing 211166 People's Republic of China
| | - Qingcai Jiao
- State Key Laboratory of Pharmaceutical Biotechnology School of Life Science Nanjing University Nanjing 210093 People's Republic of China
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17
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Reetz MT, Garcia-Borràs M. The Unexplored Importance of Fleeting Chiral Intermediates in Enzyme-Catalyzed Reactions. J Am Chem Soc 2021; 143:14939-14950. [PMID: 34491742 PMCID: PMC8461649 DOI: 10.1021/jacs.1c04551] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Indexed: 02/07/2023]
Abstract
Decades of extensive research efforts by biochemists, organic chemists, and protein engineers have led to an understanding of the basic mechanisms of essentially all known types of enzymes, but in a formidable number of cases an essential aspect has been overlooked. The occurrence of short-lived chiral intermediates formed by symmetry-breaking of prochiral precursors in enzyme catalyzed reactions has been systematically neglected. We designate these elusive species as fleeting chiral intermediates and analyze such crucial questions as "Do such intermediates occur in homochiral form?" If so, what is the absolute configuration, and why did Nature choose that particular stereoisomeric form, even when the isolable final product may be achiral? Does the absolute configuration of a chiral product depend in any way on the absolute configuration of the fleeting chiral precursor? How does this affect the catalytic proficiency of the enzyme? If these issues continue to be unexplored, then an understanding of the mechanisms of many enzyme types remains incomplete. We have systematized the occurrence of these chiral intermediates according to their structures and enzyme types. This is followed by critical analyses of selected case studies and by final conclusions and perspectives. We hope that the fascinating concept of fleeting chiral intermediates will attract the attention of scientists, thereby opening an exciting new research field.
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Affiliation(s)
- Manfred T. Reetz
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport
Economic Area, Tianjin 300308, China
| | - Marc Garcia-Borràs
- Institute
of Computational Chemistry and Catalysis (IQCC) and Departament de
Química, Universitat de Girona, Carrer Maria Aurèlia Capmany
69, 17003 Girona, Spain
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18
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Meng Q, Ramírez-Palacios C, Capra N, Hooghwinkel ME, Thallmair S, Rozeboom HJ, Thunnissen AMWH, Wijma HJ, Marrink SJ, Janssen DB. Computational Redesign of an ω-Transaminase from Pseudomonas jessenii for Asymmetric Synthesis of Enantiopure Bulky Amines. ACS Catal 2021; 11:10733-10747. [PMID: 34504735 PMCID: PMC8419838 DOI: 10.1021/acscatal.1c02053] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/26/2021] [Indexed: 01/19/2023]
Abstract
![]()
ω-Transaminases
(ω-TA) are attractive biocatalysts
for the production of chiral amines from prochiral ketones via asymmetric synthesis. However, the substrate scope of
ω-TAs is usually limited due to steric hindrance at the active
site pockets. We explored a protein engineering strategy using computational
design to expand the substrate scope of an (S)-selective
ω-TA from Pseudomonas jessenii (PjTA-R6) toward the production of bulky amines. PjTA-R6 is attractive for use in applied biocatalysis due
to its thermostability, tolerance to organic solvents, and acceptance
of high concentrations of isopropylamine as amino donor. PjTA-R6 showed no detectable activity for the synthesis of six bicyclic
or bulky amines targeted in this study. Six small libraries composed
of 7–18 variants each were separately designed via computational methods and tested in the laboratory for ketone to
amine conversion. In each library, the vast majority of the variants
displayed the desired activity, and of the 40 different designs, 38
produced the target amine in good yield with >99% enantiomeric
excess.
This shows that the substrate scope and enantioselectivity of PjTA mutants could be predicted in silico with high accuracy. The single mutant W58G showed the best performance
in the synthesis of five structurally similar bulky amines containing
the indan and tetralin moieties. The best variant for the other bulky
amine, 1-phenylbutylamine, was the triple mutant W58M + F86L + R417L,
indicating that Trp58 is a key residue in the large binding pocket
for PjTA-R6 redesign. Crystal structures of the two
best variants confirmed the computationally predicted structures.
The results show that computational design can be an efficient approach
to rapidly expand the substrate scope of ω-TAs to produce enantiopure
bulky amines.
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Affiliation(s)
- Qinglong Meng
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
| | - Carlos Ramírez-Palacios
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, AG Groningen 9747, Groningen, The Netherlands
| | - Nikolas Capra
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
| | - Mattijs E. Hooghwinkel
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
| | - Sebastian Thallmair
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, AG Groningen 9747, Groningen, The Netherlands
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Str. 1, Frankfurt am Main 60438, Germany
| | - Henriëtte J. Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
| | - Andy-Mark W. H. Thunnissen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
| | - Hein J. Wijma
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
| | - Siewert J. Marrink
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, AG Groningen 9747, Groningen, The Netherlands
| | - Dick B. Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, AG Groningen 9747, Groningen, The Netherlands
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19
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Bujacz A, Rum J, Rutkiewicz M, Pietrzyk-Brzezinska AJ, Bujacz G. Structural Evidence of Active Site Adaptability towards Different Sized Substrates of Aromatic Amino Acid Aminotransferase from Psychrobacter Sp. B6. MATERIALS 2021; 14:ma14123351. [PMID: 34204354 PMCID: PMC8235216 DOI: 10.3390/ma14123351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/27/2021] [Accepted: 06/09/2021] [Indexed: 01/07/2023]
Abstract
Aromatic amino acid aminotransferases present a special potential in the production of drugs and synthons, thanks to their ability to accommodate a wider range of substrates in their active site, in contrast to aliphatic amino acid aminotransferases. The mechanism of active site adjustment toward substrates of psychrophilic aromatic amino acid aminotransferase (PsyArAT) from Psychrobacter sp. B6 is discussed based on crystal structures of complexes with four hydroxy-analogs of substrates: phenylalanine, tyrosine, tryptophan and aspartic acid. These competitive inhibitors are bound in the active center of PsyArAT but do not undergo transamination reaction, which makes them an outstanding tool for examination of the enzyme catalytic center. The use of hydroxy-acids enabled insight into substrate binding by native PsyArAT, without mutating the catalytic lysine and modifying cofactor interactions. Thus, the binding mode of substrates and the resulting analysis of the volume of the catalytic site is close to a native condition. Observation of these inhibitors' binding allows for explanation of the enzyme's adaptability to process various sizes of substrates and to gain knowledge about its potential biotechnological application. Depending on the character and size of the used inhibitors, the enzyme crystallized in different space groups and showed conformational changes of the active site upon ligand binding.
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Affiliation(s)
- Anna Bujacz
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland; (J.R.); (A.J.P.-B.); (G.B.)
- Correspondence:
| | - Jedrzej Rum
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland; (J.R.); (A.J.P.-B.); (G.B.)
| | - Maria Rutkiewicz
- Macromolecular Structure and Interaction, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany;
| | - Agnieszka J. Pietrzyk-Brzezinska
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland; (J.R.); (A.J.P.-B.); (G.B.)
| | - Grzegorz Bujacz
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland; (J.R.); (A.J.P.-B.); (G.B.)
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20
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Wei WM, Xu YL, Zheng RH, Zhao T, Fang W, Qin YD. Theoretical Study on the Mechanism of the Acylate Reaction of β-Lactamase. ACS OMEGA 2021; 6:12598-12604. [PMID: 34056410 PMCID: PMC8154126 DOI: 10.1021/acsomega.1c00592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/26/2021] [Indexed: 05/25/2023]
Abstract
Using density functional theory and a cluster approach, we study the reaction potential surface and compute Gibbs free energies for the acylate reaction of β-lactamase with penicillin G, where the solvent effect is important and taken into consideration. Two reaction paths are investigated: one is a multi-step process with a rate-limit energy barrier of 19.1 kcal/mol, which is relatively small, and the reaction can easily occur; the other is a one-step process with a barrier of 45.0 kcal/mol, which is large and thus makes the reaction hard to occur. The reason why the two paths have different barriers is explained.
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Affiliation(s)
- Wen-Mei Wei
- School
of Basic Medical Sciences, Anhui Medical
University, Hefei, Anhui 230032, P.
R. China
| | - Yan-Li Xu
- School
of Basic Medical Sciences, Anhui Medical
University, Hefei, Anhui 230032, P.
R. China
| | - Ren-Hui Zheng
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory for
Structural Chemistry of Unstable and Stable Species, Institute of
Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, P. R. China
| | - Tingting Zhao
- School
of Basic Medical Sciences, Anhui Medical
University, Hefei, Anhui 230032, P.
R. China
| | - Weijun Fang
- School
of Basic Medical Sciences, Anhui Medical
University, Hefei, Anhui 230032, P.
R. China
| | - Yi-De Qin
- School
of Basic Medical Sciences, Anhui Medical
University, Hefei, Anhui 230032, P.
R. China
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21
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Efficient Amino Donor Recycling in Amination Reactions: Development of a New Alanine Dehydrogenase in Continuous Flow and Dialysis Membrane Reactors. Catalysts 2021. [DOI: 10.3390/catal11040520] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Transaminases have arisen as one of the main biocatalysts for amine production but despite their many advantages, their stability is still a concern for widespread application. One of the reasons for their instability is the need to use an excess of the amino donor when trying to synthesise amines with unfavourable equilibria. To circumvent this, recycling systems for the amino donor, such as amino acid dehydrogenases or aldolases, have proved useful to push the equilibria while avoiding high amino donor concentrations. In this work, we report the use of a new alanine dehydrogenase from the halotolerant bacteria Halomonas elongata which exhibits excellent stability to different cosolvents, combined with the well characterised CbFDH as a recycling system of L-alanine for the amination of three model substrates with unfavourable equilibria. In a step forward, the amino donor recycling system has been co-immobilised and used in flow with success as well as re-used as a dialysis enclosed system for the amination of an aromatic aldehyde.
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22
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Xie Y, Xu F, Yang L, Liu H, Xu X, Wang H, Wei D. Engineering the large pocket of an ( S)-selective transaminase for asymmetric synthesis of ( S)-1-amino-1-phenylpropane. Catal Sci Technol 2021. [DOI: 10.1039/d0cy02426k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Amine transaminases offer an environmentally benign chiral amine asymmetric synthesis route.
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Affiliation(s)
- Youyu Xie
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- People's Republic of China
| | - Feng Xu
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- People's Republic of China
| | - Lin Yang
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- People's Republic of China
| | - He Liu
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- People's Republic of China
| | | | - Hualei Wang
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- People's Republic of China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- People's Republic of China
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23
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Dutta Banik S, Bankura A, Chandra A. A QM/MM simulation study of transamination reaction at the active site of aspartate aminotransferase: Free energy landscape and proton transfer pathways. J Comput Chem 2020; 41:2684-2694. [PMID: 32932551 DOI: 10.1002/jcc.26422] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/08/2020] [Accepted: 09/03/2020] [Indexed: 11/10/2022]
Abstract
Transaminase is a key enzyme for amino acid metabolism, which reversibly catalyzes the transamination reaction with the help of PLP (pyridoxal 5' -phosphate) as its cofactor. Here we have investigated the mechanism and free energy landscape of the transamination reaction involving the aspartate transaminase (AspTase) enzyme and aspartate-PLP (Asp-PLP) complex using QM/MM simulation and metadynamics methods. The reaction is found to follow a stepwise mechanism where the active site residue Lys258 acts as a base to shuttle a proton from α-carbon (CA) to imine carbon (C4A) of the PLP-Asp Schiff base. In the first step, the Lys258 abstracts the CA proton of the substrate leading to the formation of a carbanionic intermediate which is followed by the reprotonation of the Asp-PLP Schiff base at C4A atom by Lys258. It is found that the free energy barrier for the proton abstraction by Lys258 and that for the reprotonation are 17.85 and 3.57 kcal/mol, respectively. The carbanionic intermediate is 7.14 kcal/mol higher in energy than the reactant. Hence, the first step acts as the rate limiting step. The present calculations also show that the Lys258 residue undergoes a conformational change after the first step of transamination reaction and becomes proximal to C4A atom of the Asp-PLP Schiff base to favor the second step. The active site residues Tyr70* and Gly38 anchor the Lys258 in proper position and orientation during the first step of the reaction and stabilize the positive charge over Lys258 generated at the intermediate step.
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Affiliation(s)
- Sindrila Dutta Banik
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
| | - Arindam Bankura
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
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24
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Asymmetric Synthesis of Optically Pure Aliphatic Amines with an Engineered Robust ω-Transaminase. Catalysts 2020. [DOI: 10.3390/catal10111310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The production of chiral amines by transaminase-catalyzed amination of ketones is an important application of biocatalysis in synthetic chemistry. It requires transaminases that show high enantioselectivity in asymmetric conversion of the ketone precursors. A robust derivative of ω-transaminase from Pseudomonasjessenii (PjTA-R6) that naturally acts on aliphatic substrates was constructed previously by our group. Here, we explore the catalytic potential of this thermostable enzyme for the synthesis of optically pure aliphatic amines and compare it to the well-studied transaminases from Vibrio fluvialis (VfTA) and Chromobacterium violaceum (CvTA). The product yields indicated improved performance of PjTA-R6 over the other transaminases, and in most cases, the optical purity of the produced amine was above 99% enantiomeric excess (e.e.). Structural analysis revealed that the substrate binding poses were influenced and restricted by the switching arginine and that this accounted for differences in substrate specificities. Rosetta docking calculations with external aldimine structures showed a correlation between docking scores and synthetic yields. The results show that PjTA-R6 is a promising biocatalyst for the asymmetric synthesis of aliphatic amines with a product spectrum that can be explained by its structural features.
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25
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Structural studies reveal flexible roof of active site responsible for ω-transaminase CrmG overcoming by-product inhibition. Commun Biol 2020; 3:455. [PMID: 32814814 PMCID: PMC7438487 DOI: 10.1038/s42003-020-01184-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/29/2020] [Indexed: 12/16/2022] Open
Abstract
Amine compounds biosynthesis using ω-transaminases has received considerable attention in the pharmaceutical industry. However, the application of ω-transaminases was hampered by the fundamental challenge of severe by-product inhibition. Here, we report that ω-transaminase CrmG from Actinoalloteichus cyanogriseus WH1-2216-6 is insensitive to inhibition from by-product α-ketoglutarate or pyruvate. Combined with structural and QM/MM studies, we establish the detailed catalytic mechanism for CrmG. Our structural and biochemical studies reveal that the roof of the active site in PMP-bound CrmG is flexible, which will facilitate the PMP or by-product to dissociate from PMP-bound CrmG. Our results also show that amino acceptor caerulomycin M (CRM M), but not α-ketoglutarate or pyruvate, can form strong interactions with the roof of the active site in PMP-bound CrmG. Based on our results, we propose that the flexible roof of the active site in PMP-bound CrmG may facilitate CrmG to overcome inhibition from the by-product.
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26
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Mrugała B, Miłaczewska A, Porebski PJ, Niedzialkowska E, Guzik M, Minor W, Borowski T. A study on the structure, mechanism, and biochemistry of kanamycin B dioxygenase (KanJ)-an enzyme with a broad range of substrates. FEBS J 2020; 288:1366-1386. [PMID: 32592631 DOI: 10.1111/febs.15462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/09/2020] [Accepted: 06/09/2020] [Indexed: 02/06/2023]
Abstract
Kanamycin A is an aminoglycoside antibiotic isolated from Streptomyces kanamyceticus and used against a wide spectrum of bacteria, including Mycobacterium tuberculosis. Biosynthesis of kanamycin involves an oxidative deamination step catalyzed by kanamycin B dioxygenase (KanJ), thereby the C2' position of kanamycin B is transformed into a keto group upon release of ammonia. Here, we present for the first time, structural models of KanJ with several ligands, which along with the results of ITC binding assays and HPLC activity tests explain substrate specificity of the enzyme. The large size of the binding pocket suggests that KanJ can accept a broad range of substrates, which was confirmed by activity tests. Specificity of the enzyme with respect to its substrate is determined by the hydrogen bond interactions between the methylamino group of the antibiotic and highly conserved Asp134 and Cys150 as well as between hydroxyl groups of the substrate and Asn120 and Gln80. Upon antibiotic binding, the C terminus loop is significantly rearranged and Gln80 and Asn120, which are directly involved in substrate recognition, change their conformations. Based on reaction energy profiles obtained by density functional theory (DFT) simulations, we propose a mechanism of ketone formation involving the reactive FeIV = O and proceeding either via OH rebound, which yields a hemiaminal intermediate or by abstraction of two hydrogen atoms, which leads to an imine species. At acidic pH, the latter involves a lower barrier than the OH rebound, whereas at basic pH, the barrier leading to an imine vanishes completely. DATABASES: Structural data are available in PDB database under the accession numbers: 6S0R, 6S0T, 6S0U, 6S0W, 6S0V, 6S0S. Diffraction images are available at the Integrated Resource for Reproducibility in Macromolecular Crystallography at http://proteindiffraction.org under DOIs: 10.18430/m36s0t, 10.18430/m36s0u, 10.18430/m36s0r, 10.18430/m36s0s, 10.18430/m36s0v, 10.18430/m36s0w. A data set collection of computational results is available in the Mendeley Data database under DOI: 10.17632/sbyzssjmp3.1 and in the ioChem-BD database under DOI: 10.19061/iochem-bd-4-18.
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Affiliation(s)
- Beata Mrugała
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Anna Miłaczewska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Przemyslaw Jerzy Porebski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Ewa Niedzialkowska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Maciej Guzik
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
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27
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Protein-ligand binding with the coarse-grained Martini model. Nat Commun 2020; 11:3714. [PMID: 32709852 PMCID: PMC7382508 DOI: 10.1038/s41467-020-17437-5] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 06/29/2020] [Indexed: 02/06/2023] Open
Abstract
The detailed understanding of the binding of small molecules to proteins is the key for the development of novel drugs or to increase the acceptance of substrates by enzymes. Nowadays, computer-aided design of protein–ligand binding is an important tool to accomplish this task. Current approaches typically rely on high-throughput docking essays or computationally expensive atomistic molecular dynamics simulations. Here, we present an approach to use the recently re-parametrized coarse-grained Martini model to perform unbiased millisecond sampling of protein–ligand interactions of small drug-like molecules. Remarkably, we achieve high accuracy without the need of any a priori knowledge of binding pockets or pathways. Our approach is applied to a range of systems from the well-characterized T4 lysozyme over members of the GPCR family and nuclear receptors to a variety of enzymes. The presented results open the way to high-throughput screening of ligand libraries or protein mutations using the coarse-grained Martini model. Computer-aided design of protein-ligand binding is important for the development of novel drugs. Here authors present an approach to use the recently re-parametrized coarse-grained Martini model to perform unbiased millisecond sampling of protein-ligand binding interactions of small drug-like molecules.
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28
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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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29
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Dasgupta S, Herbert JM. Using Atomic Confining Potentials for Geometry Optimization and Vibrational Frequency Calculations in Quantum-Chemical Models of Enzyme Active Sites. J Phys Chem B 2020; 124:1137-1147. [PMID: 31986049 DOI: 10.1021/acs.jpcb.9b11060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Quantum-chemical studies of enzymatic reaction mechanisms sometimes use truncated active-site models as simplified alternatives to mixed quantum mechanics molecular mechanics (QM/MM) procedures. Eliminating the MM degrees of freedom reduces the complexity of the sampling problem, but the trade-off is the need to introduce geometric constraints in order to prevent structural collapse of the model system during geometry optimizations that do not contain a full protein backbone. These constraints may impair the efficiency of the optimization, and care must be taken to avoid artifacts such as imaginary vibrational frequencies. We introduce a simple alternative in which terminal atoms of the model system are placed in soft harmonic confining potentials rather than being rigidly constrained. This modification is simple to implement and straightforward to use in vibrational frequency calculations, unlike iterative constraint-satisfaction algorithms, and allows the optimization to proceed without constraint even though the practical result is to fix the anchor atoms in space. The new approach is more efficient for optimizing minima and transition states, as compared to the use of fixed-atom constraints, and also more robust against unwanted imaginary frequencies. We illustrate the method by application to several enzymatic reaction pathways where entropy makes a significant contribution to the relevant reaction barriers. The use of confining potentials correctly describes reaction paths and facilitates calculation of both vibrational zero-point and finite-temperature entropic corrections to barrier heights.
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Affiliation(s)
- Saswata Dasgupta
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - John M Herbert
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
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30
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Miłaczewska A, Borowski T. On the reaction mechanism of an endoperoxide ring formation by fumitremorgin B endoperoxidase. The right arrangement makes a difference. Dalton Trans 2019; 48:16211-16221. [PMID: 31580360 DOI: 10.1039/c9dt02581b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Fumitremorgin B endoperoxidase (FtmF) belongs to 2-oxoglutarate dependent dioxygenases and catalyzes an unusual oxidative reaction of endoperoxide formation at the final stage of biosynthesis of verruculogen - a mycotoxin produced by Aspergillus and Penicillinum strains. The published crystal structure of FtmF (PDB: ), which is of overall good quality, contains a model of the substrate bound in the active site, which, however, has very low occupancy and its conformation does not comply with the small molecule crystal structure. Moreover, a previous computational study that employed a model based on this crystal structure revealed a substantial reaction barrier, which might indicate that the model of FtmF/substrate complex can have serious errors. The purpose of this work was to model with computational methods the structure of the enzyme-substrate complex and to investigate the mechanisms of the enzymatic reaction. Docking, molecular dynamics simulation and DFT results, all indicate the substrate most likely binds in the active site in a configuration very different from that originally suggested. Moreover, for this newly proposed structure of the enzyme-substrate complex, the reaction energy profile is characterised exclusively by low barriers and it successfully explains the observed regiospecificity of the enzymatic process. Finally, a plausible binding site for ascorbate was found and it is suggested that ascorbate is involved in the final step of the FtmF reaction.
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Affiliation(s)
- Anna Miłaczewska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Kraków, Poland.
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Kraków, Poland.
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31
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Teixeira CSS, Ramos MJ, Sousa SF, Cerqueira NMFSA. Solving the Catalytic Mechanism of Tryptophan Synthase: an Emergent Drug Target in the Treatment of Tuberculosis. ChemCatChem 2019. [DOI: 10.1002/cctc.201901505] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Carla S. Silva Teixeira
- UCIBIO@REQUIMTEBioSIMDepartamento de BiomedicinaFaculdade de MedicinaUniversidade do Porto Porto 4200-319 Portugal
| | - Maria J. Ramos
- UCIBIO@REQUIMTEDepartamento de Química e BioquímicaFaculdade de CiênciasUniversidade do Porto Porto 4169-007 Portugal
| | - Sérgio F. Sousa
- UCIBIO@REQUIMTEBioSIMDepartamento de BiomedicinaFaculdade de MedicinaUniversidade do Porto Porto 4200-319 Portugal
| | - Nuno M. F. S. A. Cerqueira
- UCIBIO@REQUIMTEBioSIMDepartamento de BiomedicinaFaculdade de MedicinaUniversidade do Porto Porto 4200-319 Portugal
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32
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Kim H, Han S, Shin J. Combinatorial Mutation Analysis of ω‐Transaminase to Create an Engineered Variant Capable of Asymmetric Amination of Isobutyrophenone. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Hong‐Gon Kim
- Department of BiotechnologyYonsei University Yonsei-Ro 50, Seodaemun-Gu Seoul 03722 South Korea
| | - Sang‐Woo Han
- Department of BiotechnologyYonsei University Yonsei-Ro 50, Seodaemun-Gu Seoul 03722 South Korea
| | - Jong‐Shik Shin
- Department of BiotechnologyYonsei University Yonsei-Ro 50, Seodaemun-Gu Seoul 03722 South Korea
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33
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Rocha JF, Pina AF, Sousa SF, Cerqueira NMFSA. PLP-dependent enzymes as important biocatalysts for the pharmaceutical, chemical and food industries: a structural and mechanistic perspective. Catal Sci Technol 2019. [DOI: 10.1039/c9cy01210a] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PLP-dependent enzymes described on this review are attractive targets for enzyme engineering towards their application in an industrial biotechnology framework.
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Affiliation(s)
- Juliana F. Rocha
- UCIBIO/REQUIMTE
- BioSIM
- Departamento de Biomedicina
- Faculdade de Medicina
- Universidade do Porto
| | - André F. Pina
- UCIBIO/REQUIMTE
- BioSIM
- Departamento de Biomedicina
- Faculdade de Medicina
- Universidade do Porto
| | - Sérgio F. Sousa
- UCIBIO/REQUIMTE
- BioSIM
- Departamento de Biomedicina
- Faculdade de Medicina
- Universidade do Porto
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34
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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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35
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Fernandes HS, Ramos MJ, Cerqueira NMFSA. Catalytic Mechanism of the Serine Hydroxymethyltransferase: A Computational ONIOM QM/MM Study. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02321] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Henrique S. Fernandes
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria João Ramos
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Nuno M. F. S. A. Cerqueira
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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36
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Wilding M, Scott C, Warden AC. Computer-Guided Surface Engineering for Enzyme Improvement. Sci Rep 2018; 8:11998. [PMID: 30097591 PMCID: PMC6086876 DOI: 10.1038/s41598-018-30434-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 07/30/2018] [Indexed: 11/12/2022] Open
Abstract
Protein engineering strategies are often guided by our understanding of how the structure of a protein determines its function. However, our understanding is generally restricted to small regions of a protein, namely the active site and its immediate vicinity, while the remainder of the protein is something of an enigma. Studying highly homologous transaminases with strictly conserved active sites, but different substrate preferences and activities, we predict and experimentally validate that the surface of the protein far from the active site carries out a decisive role in substrate selectivity and catalytic efficiency. Using a unique molecular dynamics approach and novel trajectory analysis, we demonstrate the phenomenon of surface-directed ligand diffusion in this well-known protein family for the first time. Further, we identify the residues involved in directing substrate, design surface channel variants endowed for improved kinetic properties and establish a broadly applicable new approach for protein engineering.
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Affiliation(s)
- Matthew Wilding
- CSIRO Land & Water, Black Mountain Laboratories, Canberra, ACT 2601, Australia
- Research School of Chemistry, Australian National University, Building 137 Sullivan's Creek Road, Canberra, ACT 2601, Australia
| | - Colin Scott
- CSIRO Land & Water, Black Mountain Laboratories, Canberra, ACT 2601, Australia
| | - Andrew C Warden
- CSIRO Land & Water, Black Mountain Laboratories, Canberra, ACT 2601, Australia.
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37
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Planas F, Sheng X, McLeish MJ, Himo F. A Theoretical Study of the Benzoylformate Decarboxylase Reaction Mechanism. Front Chem 2018; 6:205. [PMID: 29998094 PMCID: PMC6028569 DOI: 10.3389/fchem.2018.00205] [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: 03/13/2018] [Accepted: 05/18/2018] [Indexed: 01/27/2023] Open
Abstract
Density functional theory calculations are used to investigate the detailed reaction mechanism of benzoylformate decarboxylase, a thiamin diphosphate (ThDP)-dependent enzyme that catalyzes the nonoxidative decarboxylation of benzoylformate yielding benzaldehyde and carbon dioxide. A large model of the active site is constructed on the basis of the X-ray structure, and it is used to characterize the involved intermediates and transition states and evaluate their energies. There is generally good agreement between the calculations and available experimental data. The roles of the various active site residues are discussed and the results are compared to mutagenesis experiments. Importantly, the calculations identify off-cycle intermediate species of the ThDP cofactor that can have implications on the kinetics of the reaction.
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Affiliation(s)
- Ferran Planas
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Stockholm, Sweden
| | - Xiang Sheng
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Stockholm, Sweden
| | - Michael J McLeish
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Fahmi Himo
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Stockholm, Sweden
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38
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Contente ML, Planchestainer M, Molinari F, Paradisi F. Stereoelectronic effects in the reaction of aromatic substrates catalysed by Halomonas elongata transaminase and its mutants. Org Biomol Chem 2018; 14:9306-9311. [PMID: 27722400 DOI: 10.1039/c6ob01629d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A transaminase from Halomonas elongata and four mutants generated by an in silico-based design were recombinantly produced in E. coli, purified and applied to the amination of mono-substituted aromatic carbonyl-derivatives. While benzaldehyde derivatives were excellent substrates, only NO2-acetophenones were transformed into the (S)-amine with a high enantioselectivity. The different behaviour of wild-type and mutated transaminases was assessed by in silico substrate binding mode studies.
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Affiliation(s)
- Martina Letizia Contente
- UCD School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland and Department of Food Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milan, Italy.
| | | | - Francesco Molinari
- Department of Food Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Via Mangiagalli 25, 20133, Milan, Italy.
| | - Francesca Paradisi
- UCD School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland and School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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39
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Chen S, Berglund P, Humble MS. The effect of phosphate group binding cup coordination on the stability of the amine transaminase from Chromobacterium violaceum. MOLECULAR CATALYSIS 2018. [DOI: 10.1016/j.mcat.2017.12.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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40
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Kelly SA, Pohle S, Wharry S, Mix S, Allen CCR, Moody TS, Gilmore BF. Application of ω-Transaminases in the Pharmaceutical Industry. Chem Rev 2017; 118:349-367. [PMID: 29251912 DOI: 10.1021/acs.chemrev.7b00437] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chiral amines are valuable building blocks for the pharmaceutical industry. ω-TAms have emerged as an exciting option for their synthesis, offering a potential "green alternative" to overcome the drawbacks associated with conventional chemical methods. In this review, we explore the application of ω-TAms for pharmaceutical production. We discuss the diverse array of reactions available involving ω-TAms and process considerations of their use in both kinetic resolution and asymmetric synthesis. With the aid of specific drug intermediates and APIs, we chart the development of ω-TAms using protein engineering and their contribution to elegant one-pot cascades with other enzymes, including carbonyl reductases (CREDs), hydrolases and monoamine oxidases (MAOs), providing a comprehensive overview of their uses, beginning with initial applications through to the present day.
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Affiliation(s)
- Stephen A Kelly
- School of Pharmacy, Queen's University Belfast , Belfast BT9 7BL, N. Ireland, U.K
| | - Stefan Pohle
- Almac , Department of Biocatalysis & Isotope Chemistry, 20 Seagoe Industrial Estate, Craigavon BT63 5QD, N. Ireland, U.K
| | - Scott Wharry
- Almac , Department of Biocatalysis & Isotope Chemistry, 20 Seagoe Industrial Estate, Craigavon BT63 5QD, N. Ireland, U.K
| | - Stefan Mix
- Almac , Department of Biocatalysis & Isotope Chemistry, 20 Seagoe Industrial Estate, Craigavon BT63 5QD, N. Ireland, U.K
| | - Christopher C R Allen
- School of Biological Sciences, Queen's University Belfast , Belfast BT9 7BL, N. Ireland, U.K
| | - Thomas S Moody
- Almac , Department of Biocatalysis & Isotope Chemistry, 20 Seagoe Industrial Estate, Craigavon BT63 5QD, N. Ireland, U.K.,Arran Chemical Company Limited , Unit 1 Monksland Industrial Estate, Athlone, Co. Roscommon, Ireland
| | - Brendan F Gilmore
- School of Pharmacy, Queen's University Belfast , Belfast BT9 7BL, N. Ireland, U.K
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41
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Lin B, Tian G, Liu Y. Mechanistic insights into the γ-elimination reaction of l-methionine catalyzed by methionine γ-lyase (MGL). Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2140-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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42
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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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43
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Han SW, Kim J, Cho HS, Shin JS. Active Site Engineering of ω-Transaminase Guided by Docking Orientation Analysis and Virtual Activity Screening. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03242] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sang-Woo Han
- Department
of Biotechnology and ‡Department of Systems Biology, Yonsei University, Yonsei-Ro 50, Seodaemun-Gu, Seoul 03722, South Korea
| | - Juyeon Kim
- Department
of Biotechnology and ‡Department of Systems Biology, Yonsei University, Yonsei-Ro 50, Seodaemun-Gu, Seoul 03722, South Korea
| | - Hyun-Soo Cho
- Department
of Biotechnology and ‡Department of Systems Biology, Yonsei University, Yonsei-Ro 50, Seodaemun-Gu, Seoul 03722, South Korea
| | - Jong-Shik Shin
- Department
of Biotechnology and ‡Department of Systems Biology, Yonsei University, Yonsei-Ro 50, Seodaemun-Gu, Seoul 03722, South Korea
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44
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Manta B, Cassimjee KE, Himo F. Quantum Chemical Study of Dual-Substrate Recognition in ω-Transaminase. ACS OMEGA 2017; 2:890-898. [PMID: 30023618 PMCID: PMC6044752 DOI: 10.1021/acsomega.6b00376] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/20/2017] [Indexed: 05/14/2023]
Abstract
ω-Transaminases are attractive biocatalysts for the production of chiral amines. These enzymes usually have a broad substrate range. Their substrates include hydrophobic amines as well as amino acids, a feature referred to as dual-substrate recognition. In the present study, the reaction mechanism for the half-transamination of l-alanine to pyruvate in (S)-selective Chromobacterium violaceum ω-transaminase is investigated using density functional theory calculations. The role of a flexible arginine residue, Arg416, in the dual-substrate recognition is investigated by employing two active-site models, one including this residue and one lacking it. The results of this study are compared to those of the mechanism of the conversion of (S)-1-phenylethylamine to acetophenone. The calculations suggest that the deaminations of amino acids and hydrophobic amines follow essentially the same mechanism, but the energetics of the reactions differ significantly. It is shown that the amine is kinetically favored in the half-transamination of l-alanine/pyruvate, whereas the ketone is kinetically favored in the half-transamination of (S)-1-phenylethylamine/acetophenone. The calculations further support the proposal that the arginine residue facilitates the dual-substrate recognition by functioning as an arginine switch, where the side chain is positioned inside or outside of the active site depending on the substrate. Arg416 participates in the binding of l-alanine by forming a salt bridge to the carboxylate moiety, whereas the conversion of (S)-1-phenylethylamine is feasible in the absence of Arg416, which here represents the case in which the side chain of Arg416 is positioned outside of the active site.
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Affiliation(s)
- Bianca Manta
- 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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López-Iglesias M, González-Martínez D, Rodríguez-Mata M, Gotor V, Busto E, Kroutil W, Gotor-Fernández V. Asymmetric Biocatalytic Synthesis of Fluorinated Pyridines through Transesterification or Transamination: Computational Insights into the Reactivity of Transaminases. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201600835] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- María López-Iglesias
- Departamento de Química Orgánica e Inorgánica, Instituto Universitario de Biotecnología de Asturias; Universidad de Oviedo; 33006 Oviedo Spain
- Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, NAWI Graz; BioTechMed Graz; Heinrichstraβe 28 8010 Graz Austria
| | - Daniel González-Martínez
- Departamento de Química Orgánica e Inorgánica, Instituto Universitario de Biotecnología de Asturias; Universidad de Oviedo; 33006 Oviedo Spain
| | - María Rodríguez-Mata
- Departamento de Química Orgánica e Inorgánica, Instituto Universitario de Biotecnología de Asturias; Universidad de Oviedo; 33006 Oviedo Spain
| | - Vicente Gotor
- Departamento de Química Orgánica e Inorgánica, Instituto Universitario de Biotecnología de Asturias; Universidad de Oviedo; 33006 Oviedo Spain
| | - Eduardo Busto
- Departamento de Química Orgánica I, Facultad de Química; Universidad Complutense de Madrid; 28040 Madrid Spain
| | - Wolfgang Kroutil
- Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, NAWI Graz; BioTechMed Graz; Heinrichstraβe 28 8010 Graz Austria
| | - Vicente Gotor-Fernández
- Departamento de Química Orgánica e Inorgánica, Instituto Universitario de Biotecnología de Asturias; Universidad de Oviedo; 33006 Oviedo Spain
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Dourado DFAR, Pohle S, Carvalho ATP, Dheeman DS, Caswell JM, Skvortsov T, Miskelly I, Brown RT, Quinn DJ, Allen CCR, Kulakov L, Huang M, Moody TS. Rational Design of a (S)-Selective-Transaminase for Asymmetric Synthesis of (1S)-1-(1,1′-biphenyl-2-yl)ethanamine. ACS Catal 2016. [DOI: 10.1021/acscatal.6b02380] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daniel F. A. R. Dourado
- School
of Chemistry and Chemical Engineering, Queen’s University Belfast, David
Keir Building, Stranmillis Road, Belfast BT9 5AG, Northern Ireland, United Kingdom
- Department
of Biocatalysis and Isotope Chemistry, Almac Sciences, 20 Seagoe Industrial
Estate, Craigavon BT63
5QD, Northern Ireland, United Kingdom
| | - Stefan Pohle
- Department
of Biocatalysis and Isotope Chemistry, Almac Sciences, 20 Seagoe Industrial
Estate, Craigavon BT63
5QD, Northern Ireland, United Kingdom
| | - Alexandra T. P. Carvalho
- School
of Chemistry and Chemical Engineering, Queen’s University Belfast, David
Keir Building, Stranmillis Road, Belfast BT9 5AG, Northern Ireland, United Kingdom
- Department
of Biocatalysis and Isotope Chemistry, Almac Sciences, 20 Seagoe Industrial
Estate, Craigavon BT63
5QD, Northern Ireland, United Kingdom
| | - Dharmendra S. Dheeman
- Department
of Biocatalysis and Isotope Chemistry, Almac Sciences, 20 Seagoe Industrial
Estate, Craigavon BT63
5QD, Northern Ireland, United Kingdom
| | - Jill M. Caswell
- Department
of Biocatalysis and Isotope Chemistry, Almac Sciences, 20 Seagoe Industrial
Estate, Craigavon BT63
5QD, Northern Ireland, United Kingdom
| | - Timofey Skvortsov
- Department
of Biocatalysis and Isotope Chemistry, Almac Sciences, 20 Seagoe Industrial
Estate, Craigavon BT63
5QD, Northern Ireland, United Kingdom
- School
of Biological Sciences, Queen’s University Belfast, Medical Biology
Centre, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, United Kingdom
| | - Iain Miskelly
- Department
of Biocatalysis and Isotope Chemistry, Almac Sciences, 20 Seagoe Industrial
Estate, Craigavon BT63
5QD, Northern Ireland, United Kingdom
| | - Rodney T. Brown
- Department
of Biocatalysis and Isotope Chemistry, Almac Sciences, 20 Seagoe Industrial
Estate, Craigavon BT63
5QD, Northern Ireland, United Kingdom
| | - Derek J. Quinn
- Department
of Biocatalysis and Isotope Chemistry, Almac Sciences, 20 Seagoe Industrial
Estate, Craigavon BT63
5QD, Northern Ireland, United Kingdom
| | - Christopher C. R. Allen
- School
of Biological Sciences, Queen’s University Belfast, Medical Biology
Centre, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, United Kingdom
| | - Leonid Kulakov
- School
of Biological Sciences, Queen’s University Belfast, Medical Biology
Centre, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, United Kingdom
| | - Meilan Huang
- School
of Chemistry and Chemical Engineering, Queen’s University Belfast, David
Keir Building, Stranmillis Road, Belfast BT9 5AG, Northern Ireland, United Kingdom
| | - Thomas S. Moody
- Department
of Biocatalysis and Isotope Chemistry, Almac Sciences, 20 Seagoe Industrial
Estate, Craigavon BT63
5QD, Northern Ireland, United Kingdom
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Heintz S, Börner T, Ringborg RH, Rehn G, Grey C, Nordblad M, Krühne U, Gernaey KV, Adlercreutz P, Woodley JM. Development of in situ product removal strategies in biocatalysis applying scaled-down unit operations. Biotechnol Bioeng 2016; 114:600-609. [PMID: 27668843 DOI: 10.1002/bit.26191] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 09/11/2016] [Accepted: 09/19/2016] [Indexed: 01/25/2023]
Abstract
An experimental platform based on scaled-down unit operations combined in a plug-and-play manner enables easy and highly flexible testing of advanced biocatalytic process options such as in situ product removal (ISPR) process strategies. In such a platform, it is possible to compartmentalize different process steps while operating it as a combined system, giving the possibility to test and characterize the performance of novel process concepts and biocatalysts with minimal influence of inhibitory products. Here the capabilities of performing process development by applying scaled-down unit operations are highlighted through a case study investigating the asymmetric synthesis of 1-methyl-3-phenylpropylamine (MPPA) using ω-transaminase, an enzyme in the sub-family of amino transferases (ATAs). An on-line HPLC system was applied to avoid manual sample handling and to semi-automatically characterize ω-transaminases in a scaled-down packed-bed reactor (PBR) module, showing MPPA as a strong inhibitor. To overcome the inhibition, a two-step liquid-liquid extraction (LLE) ISPR concept was tested using scaled-down unit operations combined in a plug-and-play manner. Through the tested ISPR concept, it was possible to continuously feed the main substrate benzylacetone (BA) and extract the main product MPPA throughout the reaction, thereby overcoming the challenges of low substrate solubility and product inhibition. The tested ISPR concept achieved a product concentration of 26.5 gMPPA · L-1 , a purity up to 70% gMPPA · gtot-1 and a recovery in the range of 80% mol · mol-1 of MPPA in 20 h, with the possibility to increase the concentration, purity, and recovery further. Biotechnol. Bioeng. 2017;114: 600-609. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Søren Heintz
- Department of Chemical and Biochemical Engineering, CAPEC-PROCESS Research Center, The Technical University of Denmark (DTU), Building 229, Lyngby 2800 Kgs., Denmark
| | - Tim Börner
- Department of Biotechnology, Lund University, Lund, Sweden
| | - Rolf H Ringborg
- Department of Chemical and Biochemical Engineering, CAPEC-PROCESS Research Center, The Technical University of Denmark (DTU), Building 229, Lyngby 2800 Kgs., Denmark
| | - Gustav Rehn
- Department of Chemical and Biochemical Engineering, CAPEC-PROCESS Research Center, The Technical University of Denmark (DTU), Building 229, Lyngby 2800 Kgs., Denmark
| | - Carl Grey
- Department of Biotechnology, Lund University, Lund, Sweden
| | - Mathias Nordblad
- Department of Chemical and Biochemical Engineering, CAPEC-PROCESS Research Center, The Technical University of Denmark (DTU), Building 229, Lyngby 2800 Kgs., Denmark
| | - Ulrich Krühne
- Department of Chemical and Biochemical Engineering, CAPEC-PROCESS Research Center, The Technical University of Denmark (DTU), Building 229, Lyngby 2800 Kgs., Denmark
| | - Krist V Gernaey
- Department of Chemical and Biochemical Engineering, CAPEC-PROCESS Research Center, The Technical University of Denmark (DTU), Building 229, Lyngby 2800 Kgs., Denmark
| | | | - John M Woodley
- Department of Chemical and Biochemical Engineering, CAPEC-PROCESS Research Center, The Technical University of Denmark (DTU), Building 229, Lyngby 2800 Kgs., Denmark
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48
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Pavlidis IV, Weiß MS, Genz M, Spurr P, Hanlon SP, Wirz B, Iding H, Bornscheuer UT. Identification of (S)-selective transaminases for the asymmetric synthesis of bulky chiral amines. Nat Chem 2016; 8:1076-1082. [PMID: 27768108 DOI: 10.1038/nchem.2578] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/16/2016] [Indexed: 11/09/2022]
Abstract
The use of transaminases to access pharmaceutically relevant chiral amines is an attractive alternative to transition-metal-catalysed asymmetric chemical synthesis. However, one major challenge is their limited substrate scope. Here we report the creation of highly active and stereoselective transaminases starting from fold class I. The transaminases were developed by extensive protein engineering followed by optimization of the identified motif. The resulting enzymes exhibited up to 8,900-fold higher activity than the starting scaffold and are highly stereoselective (up to >99.9% enantiomeric excess) in the asymmetric synthesis of a set of chiral amines bearing bulky substituents. These enzymes should therefore be suitable for use in the synthesis of a wide array of potential intermediates for pharmaceuticals. We also show that the motif can be engineered into other protein scaffolds with sequence identities as low as 70%, and as such should have a broad impact in the field of biocatalytic synthesis and enzyme engineering.
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Affiliation(s)
- Ioannis V Pavlidis
- Department of Biotechnology, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany.,Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, D-34132 Kassel, Germany
| | - Martin S Weiß
- Department of Biotechnology, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany
| | - Maika Genz
- Department of Biotechnology, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany
| | - Paul Spurr
- Process Research and Development, Biocatalysis, F. Hoffmann-LaRoche Ltd, Grenzacher Str. 124, 4070 Basel, Switzerland
| | - Steven P Hanlon
- Process Research and Development, Biocatalysis, F. Hoffmann-LaRoche Ltd, Grenzacher Str. 124, 4070 Basel, Switzerland
| | - Beat Wirz
- Process Research and Development, Biocatalysis, F. Hoffmann-LaRoche Ltd, Grenzacher Str. 124, 4070 Basel, Switzerland
| | - Hans Iding
- Process Research and Development, Biocatalysis, F. Hoffmann-LaRoche Ltd, Grenzacher Str. 124, 4070 Basel, Switzerland
| | - Uwe T Bornscheuer
- Department of Biotechnology, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany
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49
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Steffen-Munsberg F, Matzel P, Sowa MA, Berglund P, Bornscheuer UT, Höhne M. Bacillus anthracis ω-amino acid:pyruvate transaminase employs a different mechanism for dual substrate recognition than other amine transaminases. Appl Microbiol Biotechnol 2016; 100:4511-21. [DOI: 10.1007/s00253-015-7275-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/17/2015] [Accepted: 12/23/2015] [Indexed: 11/25/2022]
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50
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Fuchs M, Farnberger JE, Kroutil W. The Industrial Age of Biocatalytic Transamination. European J Org Chem 2015; 2015:6965-6982. [PMID: 26726292 PMCID: PMC4690199 DOI: 10.1002/ejoc.201500852] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Indexed: 12/25/2022]
Abstract
During the last decade the use of ω-transaminases has been identified as a very powerful method for the preparation of optically pure amines from the corresponding ketones. Their immense potential for the preparation of chiral amines, together with their ease of use in combination with existing biocatalytic methods, have made these biocatalysts a competitor to any chemical methodology for (asymmetric) amination. An increasing number of examples, especially from industry, shows that this biocatalytic technology outmaneuvers existing chemical processes by its simple and flexible nature. In the last few years numerous publications and patents on synthetic routes, mainly to pharmaceuticals, involving ω-transaminases have been published. The review gives an overview of the application of ω-transaminases in organic synthesis with a focus on active pharmaceutical ingredients (APIs) and the developments during the last few years.
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Affiliation(s)
- Michael Fuchs
- Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz NAWI Graz Heinrichstrasse 28, 8010 Graz, Austria E-mail: http://biocatalysis.uni-graz.at
| | - Judith E Farnberger
- Austrian Centre of Industrial Biotechnology (acib), c/o University of Graz Heinrichstrasse 28, 8010 Graz, Austria
| | - Wolfgang Kroutil
- Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz NAWI Graz Heinrichstrasse 28, 8010 Graz, Austria E-mail: http://biocatalysis.uni-graz.at
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