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Zhao P, Jiang Y, Wang Q, Chen J, Yao F, Cong Z. Crucial gating residues govern the enhancement of peroxygenase activity in an engineered cytochrome P450 O-demethylase. Chem Sci 2024; 15:8062-8070. [PMID: 38817576 PMCID: PMC11134341 DOI: 10.1039/d4sc02418d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024] Open
Abstract
P450-catalyzed O-demethylation reactions have recently attracted particular attention because of their potential applications in lignin bioconversion. We recently enabled the peroxygenase activity of CYP199A4, a NADH-dependent cytochrome P450 monooxygenase from Rhodopseudomonas palustris, by engineering a hydrogen peroxide (H2O2) tunnel. In this report, we reveal by crystallography and molecule dynamics simulations that key residues located at one of the water tunnels in CYP199A4 play a crucial gating role, which enhances the peroxygenase activity by regulating the inflow of H2O2. These results provide a more complete understanding of the mechanism by which monooxygenase is converted into peroxygenase activity through the H2O2 tunnel engineering (HTE) strategy. Furthermore, a library of engineered CYP199A4 peroxygenases was constructed to explore their application potentials for O-demethylation of various methoxy-substituted benzoic acid derivatives. The engineered CYP199A4 peroxygenases showed good functional group tolerance and preferential O-demethylation at the meta- or para-position, indicating potential O-demethylation of H- and G-type lignin monomers. This work reveals the feasibility of the HTE strategy in creating P450 peroxygenase from a mechanistic perspective, laying the foundation for developing an effective P450 O-demethylase applicable in lignin bioconversion.
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Affiliation(s)
- Panxia Zhao
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences Qingdao Shandong P. R. China
- University of Chinese Academy of Sciences (UCAS) Beijing 100049 P. R. China
| | - Yiping Jiang
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences Qingdao Shandong P. R. China
- Shandong Energy Institute Qingdao Shandong 266101 China
- Qingdao New Energy Shandong Laboratory Qingdao Shandong P. R. China
| | - Qian Wang
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences Qingdao Shandong P. R. China
| | - Jie Chen
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences Qingdao Shandong P. R. China
- Shandong Energy Institute Qingdao Shandong 266101 China
- Qingdao New Energy Shandong Laboratory Qingdao Shandong P. R. China
| | - Fuquan Yao
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences Qingdao Shandong P. R. China
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences Qingdao Shandong P. R. China
- Shandong Energy Institute Qingdao Shandong 266101 China
- University of Chinese Academy of Sciences (UCAS) Beijing 100049 P. R. China
- Qingdao New Energy Shandong Laboratory Qingdao Shandong P. R. China
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2
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Kim SM, Kang SH, Jeon BW, Kim YH. Tunnel engineering of gas-converting enzymes for inhibitor retardation and substrate acceleration. BIORESOURCE TECHNOLOGY 2024; 394:130248. [PMID: 38158090 DOI: 10.1016/j.biortech.2023.130248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Carbon monoxide dehydrogenase (CODH), formate dehydrogenase (FDH), hydrogenase (H2ase), and nitrogenase (N2ase) are crucial enzymatic catalysts that facilitate the conversion of industrially significant gases such as CO, CO2, H2, and N2. The tunnels in the gas-converting enzymes serve as conduits for these low molecular weight gases to access deeply buried catalytic sites. The identification of the substrate tunnels is imperative for comprehending the substrate selectivity mechanism underlying these gas-converting enzymes. This knowledge also holds substantial value for industrial applications, particularly in addressing the challenges associated with separation and utilization of byproduct gases. In this comprehensive review, we delve into the emerging field of tunnel engineering, presenting a range of approaches and analyses. Additionally, we propose methodologies for the systematic design of enzymes, with the ultimate goal of advancing protein engineering strategies.
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Affiliation(s)
- Suk Min Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
| | - Sung Heuck Kang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Byoung Wook Jeon
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea; Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
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3
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Schneider A, Ruppert J, Lystbæk TB, Bastian S, Hauer B. Expanding the Cation Cage: Squalene-Hopene Cyclase-Mediated Enantioselective Semipinacol Rearrangement. ACS Catal 2023. [DOI: 10.1021/acscatal.2c03835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Andreas Schneider
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart-Vaihingen, Germany
| | - Jacqueline Ruppert
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart-Vaihingen, Germany
| | - Thomas B. Lystbæk
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart-Vaihingen, Germany
| | - Silke Bastian
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart-Vaihingen, Germany
| | - Bernhard Hauer
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart-Vaihingen, Germany
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4
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Liu Z, Zhang Y, Sun J, Huang WC, Xue C, Mao X. A Novel Soluble Squalene-Hopene Cyclase and Its Application in Efficient Synthesis of Hopene. Front Bioeng Biotechnol 2020; 8:426. [PMID: 32478051 PMCID: PMC7232578 DOI: 10.3389/fbioe.2020.00426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/14/2020] [Indexed: 11/13/2022] Open
Abstract
Hopene is an important precursor for synthesizing bioactive hopanoids with great commercial value. However, the chemical methods for synthesizing hopene are not efficient to date. Hopene is commonly obtained by extracting from plants or bacteria like other terpenoids, but the complicated extraction process is inefficient and unfriendly to the environment. Hopene can be biological synthesized by squalene-hopene cyclase (SHC) from squalene. However, hopene production by SHC remained at a low level until now. In this work, we found a novel SHC named OUC-SaSHC from Streptomyces albolongus ATCC 27414. An easy procedure for expression and purification of OUC-SaSHC was established. The conditions for OUC-SaSHC to convert squalene into hopene are optimized as in 100 mM sodium phosphate buffer (pH 7.0) containing 0.5% Tween 80, 20 mM squalene and 0.14 mg/mL OUC-SaSHC at 30°C. In the scale-up reaction with the final volume of 100 mL, the yield of squalene could be up to 99% at 36 h, and 8.07 mg/mL hopene was produced. Our work showed a great potential of OUC-SaSHC as biocatalyst on scale-up production of hopene, hence improves the SHC-catalyzing enzyme synthesis of hopene from laboratory level to application level.
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Affiliation(s)
- Zhen Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Yinan Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Jianan Sun
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Wen-Can Huang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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5
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Mitusińska K, Raczyńska A, Bzówka M, Bagrowska W, Góra A. Applications of water molecules for analysis of macromolecule properties. Comput Struct Biotechnol J 2020; 18:355-365. [PMID: 32123557 PMCID: PMC7036622 DOI: 10.1016/j.csbj.2020.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/26/2020] [Accepted: 02/01/2020] [Indexed: 01/12/2023] Open
Abstract
Water molecules maintain proteins' structures, functions, stabilities and dynamics. They can occupy certain positions or pass quickly via a protein's interior. Regardless of their behaviour, water molecules can be used for the analysis of proteins' structural features and biochemical properties. Here, we present a list of several software programs that use the information provided by water molecules to: i) analyse protein structures and provide the optimal positions of water molecules for protein hydration, ii) identify high-occupancy water sites in order to analyse ligand binding modes, and iii) detect and describe tunnels and cavities. The analysis of water molecules' distribution and trajectories sheds a light on proteins' interactions with small molecules, on the dynamics of tunnels and cavities, on protein composition and also on the functionality, transportation network and location of functionally relevant residues. Finally, the correct placement of water molecules in protein crystal structures can significantly improve the reliability of molecular dynamics simulations.
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Affiliation(s)
| | | | | | | | - Artur Góra
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, Gliwice, Poland
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6
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Kokkonen P, Bednar D, Pinto G, Prokop Z, Damborsky J. Engineering enzyme access tunnels. Biotechnol Adv 2019; 37:107386. [PMID: 31026496 DOI: 10.1016/j.biotechadv.2019.04.008] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 12/14/2022]
Abstract
Enzymes are efficient and specific catalysts for many essential reactions in biotechnological and pharmaceutical industries. Many times, the natural enzymes do not display the catalytic efficiency, stability or specificity required for these industrial processes. The current enzyme engineering methods offer solutions to this problem, but they mainly target the buried active site where the chemical reaction takes place. Despite being many times ignored, the tunnels and channels connecting the environment with the active site are equally important for the catalytic properties of enzymes. Changes in the enzymatic tunnels and channels affect enzyme activity, specificity, promiscuity, enantioselectivity and stability. This review provides an overview of the emerging field of enzyme access tunnel engineering with case studies describing design of all the aforementioned properties. The software tools for the analysis of geometry and function of the enzymatic tunnels and channels and for the rational design of tunnel modifications will also be discussed. The combination of new software tools and enzyme engineering strategies will provide enzymes with access tunnels and channels specifically tailored for individual industrial processes.
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Affiliation(s)
- Piia Kokkonen
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Gaspar Pinto
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic.
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7
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
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Biological
membranes are tricky to investigate. They are complex
in terms of molecular composition and structure, functional
over a wide range of time scales, and characterized
by nonequilibrium conditions. Because of all of these
features, simulations are a great technique to study biomembrane
behavior. A significant part of the functional processes
in biological membranes takes place at the molecular
level; thus computer simulations are the method of
choice to explore how their properties emerge from specific
molecular features and how the interplay among the numerous
molecules gives rise to function over spatial and
time scales larger than the molecular ones. In this
review, we focus on this broad theme. We discuss the current
state-of-the-art of biomembrane simulations that, until
now, have largely focused on a rather narrow picture
of the complexity of the membranes. Given this, we
also discuss the challenges that we should unravel in the
foreseeable future. Numerous features such as the actin-cytoskeleton
network, the glycocalyx network, and nonequilibrium
transport under ATP-driven conditions have so far
received very little attention; however, the potential
of simulations to solve them would be exceptionally high. A
major milestone for this research would be that one day
we could say that computer simulations genuinely research
biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Matti Javanainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo naḿesti 542/2 , 16610 Prague , Czech Republic.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Waldemar Kulig
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Tomasz Róg
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Ilpo Vattulainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland.,MEMPHYS-Center for Biomembrane Physics
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