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Slanska M, Stackova L, Marques SM, Stacko P, Martínek M, Jílek L, Toul M, Damborsky J, Bednar D, Klán P, Prokop Z. Azobenzene-Based Photoswitchable Substrates for Advanced Mechanistic Studies of Model Haloalkane Dehalogenase Enzyme Family. ACS Catal 2024; 14:11635-11645. [PMID: 39114093 PMCID: PMC11301625 DOI: 10.1021/acscatal.4c03503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024]
Abstract
The engineering of efficient enzymes for large-scale production of industrially relevant compounds is a challenging task. Utilizing rational protein design, which relies on a comprehensive understanding of mechanistic information, holds significant promise for achieving success in this endeavor. Pre-steady-state kinetic measurements, obtained either through fast-mixing techniques or photoswitchable substrates, provide crucial mechanistic insights. The latter approach not only furnishes mechanistic clarity but also affords real-time structural elucidation of reaction intermediates via time-resolved femtosecond crystallography. Unfortunately, only a limited number of such valuable mechanistic probes are available. To address this gap, we applied a multidisciplinary approach, including computational analysis, chemical synthesis, physicochemical property screening, and enzyme kinetics to identify promising candidates for photoswitchable probes. We demonstrate the approach by designing an azobenzene-based photoswitchable substrate tailored for haloalkane dehalogenases, a prototypic class of enzymes pivotal in developing computational tools for rational protein design. The probe was subjected to steady-state and pre-steady-state kinetic analysis, which revealed new insights about the catalytic behavior of the model biocatalysts. We employed laser-triggered Z-to-E azobenzene photoswitching to generate the productive isomer in situ, opening avenues for advanced mechanistic studies using time-resolved femtosecond crystallography. Our results not only pave the way for the mechanistic understanding of this model enzyme family, incorporating both kinetic and structural dimensions, but also propose a systematic approach to the rational design of photoswitchable enzymatic substrates.
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Affiliation(s)
- Michaela Slanska
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Lenka Stackova
- RECETOX,
Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk
University, Brno 625 00, Czech Republic
| | - Sergio M. Marques
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Brno 625 00, Czech Republic
- International
Clinical Research Centre, St. Ann’s Hospital, Brno 625 00, Czech Republic
| | - Peter Stacko
- RECETOX,
Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk
University, Brno 625 00, Czech Republic
| | - Marek Martínek
- RECETOX,
Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk
University, Brno 625 00, Czech Republic
| | - Luboš Jílek
- RECETOX,
Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk
University, Brno 625 00, Czech Republic
| | - Martin Toul
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Brno 625 00, Czech Republic
- International
Clinical Research Centre, St. Ann’s Hospital, Brno 625 00, Czech Republic
| | - Jiri Damborsky
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Brno 625 00, Czech Republic
- International
Clinical Research Centre, St. Ann’s Hospital, Brno 625 00, Czech Republic
| | - David Bednar
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Brno 625 00, Czech Republic
- International
Clinical Research Centre, St. Ann’s Hospital, Brno 625 00, Czech Republic
| | - Petr Klán
- RECETOX,
Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk
University, Brno 625 00, Czech Republic
| | - Zbynek Prokop
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Brno 625 00, Czech Republic
- International
Clinical Research Centre, St. Ann’s Hospital, Brno 625 00, Czech Republic
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2
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Wu Y, Sun Y. Cationic Polymers Remarkably Boost Haloalkane Dehalogenase Activity in Organic Solvent Solutions and the Molecular Implications. Molecules 2023; 28:6795. [PMID: 37836637 PMCID: PMC10574148 DOI: 10.3390/molecules28196795] [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: 08/17/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Applications of haloalkane dehalogenase DhaA in biocatalysis are limited by its unfavorable performance in organic solvents. Our previous work proved that mutations of surface positive-charged residues enhanced the organic solvent resistance of DhaA, which inspired us to explore the effect of cationic polymers on DhaA in organic solvents. Remarkably boosted performance was achieved in different organic solvent solutions by introducing cationic polymers, for example, there was a 6.1-fold activity increase with poly(allylamine hydrochloride) and a 5.5-fold activity increase with poly(ethylene imine) in 40 vol.% dimethylsulfoxide. The presence of cationic polymers protected DhaA from damage by organic solvents and increased the substrate concentration around the enzyme-polymer complex. Fluorescence spectroscopy and molecular dynamics simulations revealed that the binding of cationic polymers onto DhaA weakened the interactions between organic solvents and DhaA, decreased the organic solvent solvation level around DhaA, and enhanced the structural stability of DhaA in organic solvents. This comprehensive understanding of the effect of cationic polymers on DhaA can help to broaden the applications of DhaA in organic solvent-involved biocatalysis.
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Affiliation(s)
- Yin Wu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China;
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China;
- Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
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3
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Sowińska A, Rostkowski M, Krzemińska A, Englman T, Gelman F, Dybala-Defratyka A. Insights into generalization of the rate-limiting steps of the dehalogenation by LinB and DhaA: A computational approach. Arch Biochem Biophys 2023:109675. [PMID: 37343813 DOI: 10.1016/j.abb.2023.109675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 06/23/2023]
Abstract
LinB and DhaA are well-known haloalkane dehalogenases (HLDs) capable of converting a plethora of halogenated alkanes, also those considered persistent pollutants. The dehalogenation reaction that these two enzymes catalyze has been studied to determine its rate-limiting step (rls) for the last two decades now. As a result, it has been determined that HLDs can show different rate-limiting steps for individual substrates, and at this point we do not have a basis for any generalization in this matter. Therefore, in this work we aimed at gaining insights into the enzymatic dehalogenation of selected dibromo- and bromochloro-ethanes and propanes by LinB and DhaA using computational approach to determine whether defined structural similarities of the substrates result in a unified mechanism and the same rls. By predicting halogen binding isotope effects (BIEs) as well as computing interaction energy for each HLD-ligand complex the nature of the protein-ligand interactions has been characterized. Furthermore, C and Br kinetic isotope effects (KIEs) as well as the minimum free energy paths (MFEPs) were computed to investigate the chemical reaction for the selected systems. Accuracy of the approach and robustness of the computational predictions were validated by measuring KIEs on the selected reactions. Overall results strongly indicate that any generalization with respect to the enzymatic process involving various ligands in the case of DhaA is impossible, even if the considered ligands are structurally very similar as those analyzed in the present study. Moreover, even small structural differences such as changing of one of the (non-leaving) halogen substituents may lead to significant changes in the enzymatic process and result in a different rls in the case of LinB. It has also been demonstrated that KIEs themselves cannot be used as rls indicators in the reactions catalyzed by the studied HLDs.
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Affiliation(s)
- Agata Sowińska
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Michał Rostkowski
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Agnieszka Krzemińska
- Institute of Physics, Lodz University of Technology, Wolczanska 217/221, 93-005, Lodz, Poland
| | - Tzofia Englman
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Faina Gelman
- Geological Survey of Israel, Yeshayahu Leibowitz 32, Jerusalem, 9692100, Israel
| | - Agnieszka Dybala-Defratyka
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland.
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4
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Zhou D, Zhuang Y, Sheng Z. Study on effective synthesis of 7-hydroxy-4-substituted coumarins. HETEROCYCL COMMUN 2022. [DOI: 10.1515/hc-2022-0154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Abstract
Many coumarin derivatives have good biological activity and application value in fluorescent probes. Therefore, synthetic routes to coumarin derivatives have also attracted the attention of many research groups. In this work, based on the Pechmann coumarin synthesis method, the influence of various Lewis acids on the reaction was discussed, and the optimal synthesis conditions of 7-hydroxy-4-substituted coumarins were explored. Based on the experimental results, a possible mechanism was proposed, which provides a reference for future industrialized production of coumarins.
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Affiliation(s)
- Dejun Zhou
- Department of Traditional Chinese Medicine, Chengde Medical University , Chengde , 067000 , China
- Shandong Daguan Pharmaceutical Technology Co Ltd , Jinan , Shandong, 250100 , China
| | - Youchao Zhuang
- Shandong Daguan Pharmaceutical Technology Co Ltd , Jinan , Shandong, 250100 , China
| | - Zuntian Sheng
- Shandong Daguan Pharmaceutical Technology Co Ltd , Jinan , Shandong, 250100 , China
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5
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Shrestha P, Mukhopadhyay A, Dissanayake KC, Winter AH. Efficiency of Functional Group Caging with Second-Generation Green- and Red-Light-Labile BODIPY Photoremovable Protecting Groups. J Org Chem 2022; 87:14334-14341. [PMID: 36255274 DOI: 10.1021/acs.joc.2c01781] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BODIPY-based photocages release substrates by excitation with wavelengths in the visible to near-IR regions. The recent development of more efficient BODIPY photocages spurred us to evaluate the scope and efficiency of these second-generation boron-methylated green-light and red-light-absorbing BODIPY photocages. Here, we show that these more photosensitive photocages release amine, alcohol, phenol, phosphate, halides, and carboxylic acid derivatives with much higher quantum yields than first-generation BODIPY photocages and excellent chemical yields. Chemical yields are near-quantitative for the release of all functional groups except the photorelease of amines, which react with concomitantly photogenerated singlet oxygen. In these cases, high chemical yields for photoreleased amines are restored by irradiation under an inert atmosphere. The photorelease quantum yield has a weak relationship with the leaving group pKa of the green-absorbing BODIPY photocages but little relationship with the red-absorbing derivatives, suggesting that factors other than leaving group quality impact the quantum yield. For the photorelease of alcohols, in all cases a carbonate linker (that loses CO2 upon photorelease) significantly increases both the quantum yield and the chemical yield compared to those for direct photorelease via the ether.
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Affiliation(s)
- Pradeep Shrestha
- Department of Chemistry, Iowa State University, 1608 Gilman Hall, Ames, Iowa50010, United States
| | - Atreyee Mukhopadhyay
- Department of Chemistry, Iowa State University, 1608 Gilman Hall, Ames, Iowa50010, United States
| | - Komadhie C Dissanayake
- Department of Chemistry, Iowa State University, 1608 Gilman Hall, Ames, Iowa50010, United States
| | - Arthur H Winter
- Department of Chemistry, Iowa State University, 1608 Gilman Hall, Ames, Iowa50010, United States
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6
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Marques S, Slanska M, Chmelova K, Chaloupkova R, Marek M, Clark S, Damborsky J, Kool ET, Bednar D, Prokop Z. Mechanism-Based Strategy for Optimizing HaloTag Protein Labeling. JACS AU 2022; 2:1324-1337. [PMID: 35783171 PMCID: PMC9241015 DOI: 10.1021/jacsau.2c00002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/08/2022] [Accepted: 04/08/2022] [Indexed: 06/15/2023]
Abstract
HaloTag labeling technology has introduced unrivaled potential in protein chemistry and molecular and cellular biology. A wide variety of ligands have been developed to meet the specific needs of diverse applications, but only a single protein tag, DhaAHT, is routinely used for their incorporation. Following a systematic kinetic and computational analysis of different reporters, a tetramethylrhodamine- and three 4-stilbazolium-based fluorescent ligands, we showed that the mechanism of incorporating different ligands depends both on the binding step and the efficiency of the chemical reaction. By studying the different haloalkane dehalogenases DhaA, LinB, and DmmA, we found that the architecture of the access tunnels is critical for the kinetics of both steps and the ligand specificity. We showed that highly efficient labeling with specific ligands is achievable with natural dehalogenases. We propose a simple protocol for selecting the optimal protein tag for a specific ligand from the wide pool of available enzymes with diverse access tunnel architectures. The application of this protocol eliminates the need for expensive and laborious protein engineering.
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Affiliation(s)
- Sérgio
M. Marques
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital, 656
91 Brno, Czech Republic
| | - Michaela Slanska
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Klaudia Chmelova
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital, 656
91 Brno, Czech Republic
| | - Radka Chaloupkova
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, 625 00 Brno, Czech Republic
- Enantis
Ltd., Biotechnology Incubator INBIT, 625 00 Brno, Czech Republic
| | - Martin Marek
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital, 656
91 Brno, Czech Republic
| | - Spencer Clark
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jiri Damborsky
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital, 656
91 Brno, Czech Republic
| | - Eric T. Kool
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - David Bednar
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital, 656
91 Brno, Czech Republic
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7
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Hess D, Dockalova V, Kokkonen P, Bednar D, Damborsky J, deMello A, Prokop Z, Stavrakis S. Exploring mechanism of enzyme catalysis by on-chip transient kinetics coupled with global data analysis and molecular modeling. Chem 2021. [DOI: 10.1016/j.chempr.2021.02.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Kokkonen P, Slanska M, Dockalova V, Pinto GP, Sánchez-Carnerero EM, Damborsky J, Klán P, Prokop Z, Bednar D. The impact of tunnel mutations on enzymatic catalysis depends on the tunnel-substrate complementarity and the rate-limiting step. Comput Struct Biotechnol J 2020; 18:805-813. [PMID: 32308927 PMCID: PMC7152659 DOI: 10.1016/j.csbj.2020.03.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 01/18/2023] Open
Abstract
Transport of ligands between bulk solvent and the buried active sites is a critical event in the catalytic cycle of many enzymes. The rational design of transport pathways is far from trivial due to the lack of knowledge about the effect of mutations on ligand transport. The main and an auxiliary tunnel of haloalkane dehalogenase LinB have been previously engineered for improved dehalogenation of 1,2-dibromoethane (DBE). The first chemical step of DBE conversion was enhanced by L177W mutation in the main tunnel, but the rate-limiting product release was slowed down because the mutation blocked the main access tunnel and hindered protein dynamics. Three additional mutations W140A + F143L + I211L opened-up the auxiliary tunnel and enhanced the product release, making this four-point variant the most efficient catalyst with DBE. Here we study the impact of these mutations on the catalysis of bulky aromatic substrates, 4-(bromomethyl)-6,7-dimethoxycoumarin (COU) and 8-chloromethyl-4,4'-difluoro-3,5-dimethyl-4-bora-3a,4a-diaza-s-indacene (BDP). The rate-limiting step of DBE conversion is the product release, whereas the catalysis of COU and BDP is limited by the chemical step. The catalysis of COU is mainly impaired by the mutation L177W, whereas the conversion of BDP is affected primarily by the mutations W140A + F143L + I211L. The combined computational and kinetic analyses explain the differences in activities between the enzyme-substrate pairs. The effect of tunnel mutations on catalysis depends on the rate-limiting step, the complementarity of the tunnels with the substrates and is clearly specific for each enzyme-substrate pair.
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Affiliation(s)
- Piia Kokkonen
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michaela Slanska
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Veronika Dockalova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Gaspar P. Pinto
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Centre, St. Ann’s Hospital, Brno, Czech Republic
| | | | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Centre, St. Ann’s Hospital, Brno, Czech Republic
| | - Petr Klán
- Department of Chemistry and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Centre, St. Ann’s Hospital, Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Centre, St. Ann’s Hospital, Brno, Czech Republic
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