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Dutra M, McElhenney S, Manley O, Makris T, Rassolov V, Garashchuk S. Modeling the Ligand Effect on the Structure of CYP 450 Within the Density Functional Theory. J Phys Chem A 2022; 126:2818-2824. [PMID: 35500128 DOI: 10.1021/acs.jpca.2c01783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An improved understanding of the P450 structure is relevant to the development of biomimetic catalysts and inhibitors for controlled CH-bond activation, an outstanding challenge of synthetic chemistry. Motivated by the experimental findings of an unusually short Fe-S bond of 2.18 Å for the wild-type (WT) OleT P450 decarboxylase relative to a cysteine pocket mutant form (A369P), a computational model that captures the effect of the thiolate axial ligand on the iron-sulfur distance is presented. With the computational efficiency and streamlined analysis in mind, this model combines a cluster representation of the enzyme─40-110 atoms, depending on the heme and ligand truncation level─with a density functional theory (DFT) description of the electronic structure (ES) and is calibrated against the experimental data. The optimized Fe-S distances show a difference of 0.25 Å between the low and high spin states, in agreement with the crystallographic structures of the OleT WT and mutant forms. We speculate that this difference is attributable to the packing of the ligand; the mutant is bulkier due to an alanine-to-proline replacement, meaning that it is excluded from the energetically favored low-spin minimum because of steric constraints. The presence of pure spin-state pairs and the intersection of the low/high spin states for the enzyme model is indicative of the limitations of single-reference ES methods in such systems and emphasizes the significance of using the proper state when modeling the hydrogen atom transfer (HAT) reaction catalyzed by OleT. At the same time, the correct characterization of both the short and long Fe-S bonds within a small DFT-based model of 42 atoms paves the way for quantum dynamics modeling of the HAT step, which initiates the OleT decarboxylation reaction.
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Affiliation(s)
- Matthew Dutra
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Shannon McElhenney
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Olivia Manley
- Department of Molecular & Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27607, United States
| | - Tom Makris
- Department of Molecular & Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27607, United States
| | - Vitaly Rassolov
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Sophya Garashchuk
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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Dutra M, Amaya JA, McElhenney S, Manley OM, Makris TM, Rassolov V, Garashchuk S. Experimental and Theoretical Examination of the Kinetic Isotope Effect in Cytochrome P450 Decarboxylase OleT. J Phys Chem B 2022; 126:3493-3504. [PMID: 35508080 DOI: 10.1021/acs.jpcb.1c10280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using a combination of experimental studies, theory, simulation, and modeling, we investigate the hydrogen atom transfer (HAT) reaction by the high-valent ferryl cytochrome P450 (CYP) intermediate known as Compound I, a species that is central to innumerable and important detoxification and biosynthetic reactions. The P450 decarboxylase known as OleT converts fatty acids, a sustainable biological feedstock, into terminal alkenes and thus is of high interest as a potential means to produce fungible biofuels. Previous experimental work has established the intermediacy of Compound I in the C─C scission reaction catalyzed by OleT and an unprecedented ability to monitor the HAT process in the presence of bound fatty acid substrates. Here, we leverage the kinetic simplicity of the OleT system to measure the activation barriers for CYP HAT and the temperature dependence of the substrate 2H kinetic isotope effect. Notably, neither measurement has been previously accessible for a CYP to date. Theoretical analysis alludes to the significance of substrate fatty acid coordination for generating the hydrogen donor/acceptor configurations that are most conducive for HAT to occur. The analysis of the two-dimensional potential energy surface, based on multireference electronic wave functions, illustrates the uncoupled character of the hydrogen motion. Quantum dynamics calculations along the hydrogen reaction path demonstrate that hydrogen tunneling is essential to qualitatively capture the experimental isotope effect, its temperature dependence, and appropriate activation energies. Overall, a more fundamental understanding of the OleT reaction coordinate contributes to the development of biomimetic catalysts for controlled C─H bond activation, an outstanding current challenge for (bio)synthetic chemistry.
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Affiliation(s)
- Matthew Dutra
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Jose A Amaya
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Shannon McElhenney
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Olivia M Manley
- Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Thomas M Makris
- Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Vitaly Rassolov
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Sophya Garashchuk
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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Fischer EW, Anders J, Saalfrank P. Cavity-altered thermal isomerization rates and dynamical resonant localization in vibro-polaritonic chemistry. J Chem Phys 2022; 156:154305. [PMID: 35459316 DOI: 10.1063/5.0076434] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It has been experimentally demonstrated that reaction rates for molecules embedded in microfluidic optical cavities are altered when compared to rates observed under "ordinary" reaction conditions. However, precise mechanisms of how strong coupling of an optical cavity mode to molecular vibrations affects the reactivity and how resonance behavior emerges are still under dispute. In the present work, we approach these mechanistic issues from the perspective of a thermal model reaction, the inversion of ammonia along the umbrella mode, in the presence of a single-cavity mode of varying frequency and coupling strength. A topological analysis of the related cavity Born-Oppenheimer potential energy surface in combination with quantum mechanical and transition state theory rate calculations reveals two quantum effects, leading to decelerated reaction rates in qualitative agreement with experiments: the stiffening of quantized modes perpendicular to the reaction path at the transition state, which reduces the number of thermally accessible reaction channels, and the broadening of the barrier region, which attenuates tunneling. We find these two effects to be very robust in a fluctuating environment, causing statistical variations of potential parameters, such as the barrier height. Furthermore, by solving the time-dependent Schrödinger equation in the vibrational strong coupling regime, we identify a resonance behavior, in qualitative agreement with experimental and earlier theoretical work. The latter manifests as reduced reaction probability when the cavity frequency ωc is tuned resonant to a molecular reactant frequency. We find this effect to be based on the dynamical localization of the vibro-polaritonic wavepacket in the reactant well.
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Affiliation(s)
- Eric W Fischer
- Theoretische Chemie, Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, D-14476 Potsdam-Golm, Germany
| | - Janet Anders
- Institut für Physik und Astronomie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, D-14476 Potsdam, Germany and CEMPS, Physics and Astronomy, University of Exeter, Exeter EX4 4QL, United Kingdom
| | - Peter Saalfrank
- Theoretische Chemie, Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, D-14476 Potsdam-Golm, Germany
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McDonald AG, Tipton KF. Parameter Reliability and Understanding Enzyme Function. Molecules 2022; 27:263. [PMID: 35011495 PMCID: PMC8746786 DOI: 10.3390/molecules27010263] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 11/16/2022] Open
Abstract
Knowledge of the Michaelis-Menten parameters and their meaning in different circumstances is an essential prerequisite to understanding enzyme function and behaviour. The published literature contains an abundance of values reported for many enzymes. The problem concerns assessing the appropriateness and validity of such material for the purpose to which it is to be applied. This review considers the evaluation of such data with particular emphasis on the assessment of its fitness for purpose.
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Affiliation(s)
- Andrew G. McDonald
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40 Dublin, Ireland;
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Gehring T, Heydeck D, Niewienda A, Janek K, Kuhn H. Do lipoxygenases occur in viruses?: Expression and characterization of a viral lipoxygenase-like protein did not provide evidence for the existence of functional viral lipoxygenases. Prostaglandins Leukot Essent Fatty Acids 2018; 138:14-23. [PMID: 30392576 DOI: 10.1016/j.plefa.2018.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/24/2018] [Accepted: 10/03/2018] [Indexed: 01/13/2023]
Abstract
Lipoxygenases are lipid peroxidizing enzymes, which frequently occur in higher plants and animals. In bacteria, these enzymes are rare and have been introduced via horizontal gene transfer. Since viruses function as horizontal gene transfer vectors and since lipoxygenases may be helpful for releasing assembled virus particles from host cells we explored whether these enzymes may actually occur in viruses. For this purpose we developed a four-step in silico screening strategy and searching the publically available viral genomes for lipoxygenase-like sequences we detected a single functional gene in the genome of a mimivirus infecting Acantamoeba polyphaga. The primary structure of this protein involved two putative metal ligand clusters but the recombinant enzyme did neither contain iron nor manganese. Most importantly, it did not exhibit lipoxygenase activity. These data suggests that this viral lipoxygenase-like sequence does not encode a functional lipoxygenase and that these enzymes do not occur in viruses.
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Affiliation(s)
- Tatjana Gehring
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Chariteplatz 1, D-10117 Berlin, Germany
| | - Dagmar Heydeck
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Chariteplatz 1, D-10117 Berlin, Germany
| | - Agathe Niewienda
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Core facility for Mass Spectrometry, Chariteplatz 1, D-10117 Berlin, Germany
| | - Katharina Janek
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Core facility for Mass Spectrometry, Chariteplatz 1, D-10117 Berlin, Germany
| | - Hartmut Kuhn
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Chariteplatz 1, D-10117 Berlin, Germany.
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Pusuluk O, Farrow T, Deliduman C, Burnett K, Vedral V. Proton tunnelling in hydrogen bonds and its implications in an induced-fit model of enzyme catalysis. Proc Math Phys Eng Sci 2018. [DOI: 10.1098/rspa.2018.0037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The role of proton tunnelling in biological catalysis is investigated here within the frameworks of quantum information theory and thermodynamics. We consider the quantum correlations generated through two hydrogen bonds between a substrate and a prototypical enzyme that first catalyses the tautomerization of the substrate to move on to a subsequent catalysis, and discuss how the enzyme can derive its catalytic potency from these correlations. In particular, we show that classical changes induced in the binding site of the enzyme spreads the quantum correlations among all of the four hydrogen-bonded atoms thanks to the directionality of hydrogen bonds. If the enzyme rapidly returns to its initial state after the binding stage, the substrate ends in a new transition state corresponding to a quantum superposition. Open quantum system dynamics can then naturally drive the reaction in the forward direction from the major tautomeric form to the minor tautomeric form without needing any additional catalytic activity. We find that in this scenario the enzyme lowers the activation energy so much that there is no energy barrier left in the tautomerization, even if the quantum correlations quickly decay.
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Affiliation(s)
- Onur Pusuluk
- Department of Physics, İstanbul Technical University, Maslak, Istanbul 34469, Turkey
| | - Tristan Farrow
- Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
- Centre for Quantum Technologies, National University of Singapore, 3 Science Drive 2, Singapore 117543, Singapore
| | - Cemsinan Deliduman
- Department of Physics, Mimar Sinan Fine Arts University, Bomonti, Istanbul 34380, Turkey
| | - Keith Burnett
- University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Vlatko Vedral
- Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
- Centre for Quantum Technologies, National University of Singapore, 3 Science Drive 2, Singapore 117543, Singapore
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