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Boonkumkrong R, Chunthaboon P, Munkajohnpong P, Watthaisong P, Pimviriyakul P, Maenpuen S, Chaiyen P, Tinikul R. A high catalytic efficiency and chemotolerant formate dehydrogenase from Bacillus simplex. Biotechnol J 2024; 19:e2300330. [PMID: 38180313 DOI: 10.1002/biot.202300330] [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: 07/08/2023] [Revised: 12/02/2023] [Accepted: 12/02/2023] [Indexed: 01/06/2024]
Abstract
NAD+ -dependent formate dehydrogenase (FDH) catalyzes the conversion of formate and NAD+ to produce carbon dioxide and NADH. The reaction is biotechnologically important because FDH is widely used for NADH regeneration in various enzymatic syntheses. However, major drawbacks of this versatile enzyme in industrial applications are its low activity, requiring its utilization in large amounts to achieve optimal process conditions. Here, FDH from Bacillus simplex (BsFDH) was characterized for its biochemical and catalytic properties in comparison to FDH from Pseudomonas sp. 101 (PsFDH), a commonly used FDH in various biocatalytic reactions. The data revealed that BsFDH possesses high formate oxidizing activity with a kcat value of 15.3 ± 1.9 s-1 at 25°C compared to 7.7 ± 1.0 s-1 for PsFDH. At the optimum temperature (60°C), BsFDH exhibited 6-fold greater activity than PsFDH. The BsFDH displayed higher pH stability and a superior tolerance toward sodium azide and H2 O2 inactivation, showing a 200-fold higher Ki value for azide inhibition and remaining stable in the presence of 0.5% H2 O2 compared to PsFDH. The application of BsFDH as a cofactor regeneration system for the detoxification of 4-nitrophenol by the reaction of HadA, which produced a H2 O2 byproduct was demonstrated. The biocatalytic cascades using BsFDH demonstrated a distinct superior conversion activity because the system tolerated H2 O2 well. Altogether, the data showed that BsFDH is a robust enzyme suitable for future application in industrial biotechnology.
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Affiliation(s)
- Rattima Boonkumkrong
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Paweenapon Chunthaboon
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Pobthum Munkajohnpong
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand
| | - Pratchaya Watthaisong
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand
| | - Panu Pimviriyakul
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, Thailand
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
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Antoniou D, Zoi I, Schwartz SD. Atomistic description of the relationship between protein dynamics and catalysis with transition path sampling. Methods Enzymol 2023; 685:319-340. [PMID: 37245906 PMCID: PMC10228753 DOI: 10.1016/bs.mie.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Despite initial resistance, it has been increasingly accepted that protein dynamics plays a role in enzymatic catalysis. There have been two lines of research. Some works study slow conformational motions that are not coupled to the reaction coordinate, but guide the system towards catalytically competent conformations. Understanding at the atomistic level how this is accomplished has remained elusive except for a few systems. In this review we focus on fast sub-picosecond motions that are coupled to the reaction coordinate. The use of Transition Path Sampling has allowed us an atomistic description of how these rate-promoting vibrational motions are incorporated in the reaction mechanism. We will also show how we used insights from rate-promoting motions in protein design.
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Affiliation(s)
- Dimitri Antoniou
- Department of Biochemistry, University of Arizona, Tucson, AZ, United States
| | - Ioanna Zoi
- Department of Biochemistry, University of Arizona, Tucson, AZ, United States
| | - Steven D Schwartz
- Department of Biochemistry, University of Arizona, Tucson, AZ, United States.
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Abstract
This Perspective reviews the use of Transition Path Sampling methods to study enzymatically catalyzed chemical reactions. First applied by our group to an enzymatic reaction over 15 years ago, the method has uncovered basic principles in enzymatic catalysis such as the protein promoting vibration, and it has also helped harmonize such ideas as electrostatic preorganization with dynamic views of enzyme function. It is now being used to help uncover principles of protein design necessary to artificial enzyme creation.
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Affiliation(s)
- Steven D Schwartz
- Department of Chemistry and Biochemistry University of Arizona Tucson, Arizona 85721, United States
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Rapp C, Nidetzky B. Hydride Transfer Mechanism of Enzymatic Sugar Nucleotide C2 Epimerization Probed with a Loose-Fit CDP-Glucose Substrate. ACS Catal 2022; 12:6816-6830. [PMID: 35747200 PMCID: PMC9207888 DOI: 10.1021/acscatal.2c00257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/12/2022] [Indexed: 11/29/2022]
Abstract
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Transient oxidation–reduction
through hydride transfer with
tightly bound NAD coenzyme is used by a large class of sugar nucleotide
epimerases to promote configurational inversion of carbon stereocenters
in carbohydrate substrates. A requirement for the epimerases to coordinate
hydride abstraction and re-addition with substrate rotation in the
binding pocket poses a challenge for dynamical protein conformational
selection linked to enzyme catalysis. Here, we studied the thermophilic
C2 epimerase from Thermodesulfatator atlanticus (TaCPa2E) in combination with a slow CDP-glucose
substrate (kcat ≈ 1.0 min–1; 60 °C) to explore the sensitivity of the enzymatic hydride
transfer toward environmental fluctuations affected by temperature
(20–80 °C). We determined noncompetitive primary kinetic
isotope effects (KIE) due to 2H at the glucose C2 and showed
that a normal KIE on the kcat (Dkcat) reflects isotope sensitivity of
the hydrogen abstraction to enzyme-NAD+ in a rate-limiting
transient oxidation. The Dkcat peaked at 40 °C was 6.1 and decreased to 2.1 at low (20 °C)
and 3.3 at high temperature (80 °C). The temperature profiles
for kcat with the 1H and 2H substrate showed a decrease in the rate below a dynamically
important breakpoint (∼40 °C), suggesting an equilibrium
shift to an impaired conformational landscape relevant for catalysis
in the low-temperature region. Full Marcus-like model fits of the
rate and KIE profiles provided evidence for a high-temperature reaction
via low-frequency conformational sampling associated with a broad
distribution of hydride donor–acceptor distances (long-distance
population centered at 3.31 ± 0.02 Å), only poorly suitable
for quantum mechanical tunneling. Collectively, dynamical characteristics
of TaCPa2E-catalyzed hydride transfer during transient
oxidation of CDP-glucose reveal important analogies to mechanistically
simpler enzymes such as alcohol dehydrogenase and dihydrofolate reductase.
A loose-fit substrate (in TaCPa2E) resembles structural
variants of these enzymes by extensive dynamical sampling to balance
conformational flexibility and catalytic efficiency.
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Affiliation(s)
- Christian Rapp
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Petersgasse 14, 8010 Graz, Austria
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Antoniou D, Schwartz SD. Method for Identifying Common Features in Reactive Trajectories of a Transition Path Sampling Ensemble. J Chem Theory Comput 2022; 18:3997-4004. [PMID: 35536190 DOI: 10.1021/acs.jctc.2c00186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Simulation methods like transition path sampling (TPS) generate an abundance of information buried in the collection of reactive trajectories that they generate. However, only limited use has been made of this information, mainly for the identification of the reaction coordinate. The standard TPS tools have been designed for monitoring the progress of the system from reactants to products. However, the reaction coordinate does not contain all the information regarding the mechanism. In our earlier work, we have used TPS on enzymatic systems and have identified important motions in the reactant well that prepares the system for the reaction. Since these events take place in the reactant well, they are beyond the reach of standard TPS postprocessing methods. We present a simple scheme for identifying the common trends in enzymatic trajectories. This scheme was designed for a specific class of enzymatic reactions: it can be used for identifying motions that guide the system to reaction-ready conformations. We have applied it to two enzymatic systems that we have studied in the past, formate dehydrogenase and purine nucleoside phosphorylase, and we were able to identify interactions, far from the transition state, that are important for preparing the system for the reaction but that had been overlooked in earlier work.
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Affiliation(s)
- Dimitri Antoniou
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Blvd., Tucson, Arizona 85721, United States
| | - Steven D Schwartz
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Blvd., Tucson, Arizona 85721, United States
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Guo W, Zou X, Jiang H, Koebke KJ, Hoarau M, Crisci R, Lu T, Wei T, Marsh ENG, Chen Z. Molecular Structure of the Surface-Immobilized Super Uranyl Binding Protein. J Phys Chem B 2021; 125:7706-7716. [PMID: 34254804 DOI: 10.1021/acs.jpcb.1c03849] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recently, a super uranyl binding protein (SUP) was developed, which exhibits excellent sensitivity/selectivity to bind uranyl ions. It can be immobilized onto a surface in sensing devices to detect uranyl ions. Here, sum frequency generation (SFG) vibrational spectroscopy was applied to probe the interfacial structures of surface-immobilized SUP. The collected SFG spectra were compared to the calculated orientation-dependent SUP SFG spectra using a one-excitonic Hamiltonian approach based on the SUP crystal structures to deduce the most likely surface-immobilized SUP orientation(s). Furthermore, discrete molecular dynamics (DMD) simulation was applied to refine the surface-immobilized SUP conformations and orientations. The immobilized SUP structures calculated from DMD simulations confirmed the SUP orientations obtained from SFG data analyzed based on the crystal structures and were then used for a new round of SFG orientation analysis to more accurately determine the interfacial orientations and conformations of immobilized SUP before and after uranyl ion binding, providing an in-depth understanding of molecular interactions between SUP and the surface and the effect of uranyl ion binding on the SUP interfacial structures. We believe that the developed method of combining SFG measurements, DMD simulation, and Hamiltonian data analysis approach is widely applicable to study biomolecules at solid/liquid interfaces.
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Affiliation(s)
- Wen Guo
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Xingquan Zou
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Hanjie Jiang
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Karl J Koebke
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Marie Hoarau
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Ralph Crisci
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Tieyi Lu
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Tao Wei
- Department of Chemical Engineering, Howard University, 2366 Sixth Street, NW, Washington, D.C. 20059, United States
| | - E Neil G Marsh
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Zhan Chen
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
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