1
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Birch-Price Z, Hardy FJ, Lister TM, Kohn AR, Green AP. Noncanonical Amino Acids in Biocatalysis. Chem Rev 2024; 124:8740-8786. [PMID: 38959423 PMCID: PMC11273360 DOI: 10.1021/acs.chemrev.4c00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.
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Affiliation(s)
| | | | | | | | - Anthony P. Green
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
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2
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Čivić J, McFarlane NR, Masschelein J, Harvey JN. Exploring the selectivity of cytochrome P450 for enhanced novel anticancer agent synthesis. Faraday Discuss 2024. [PMID: 38855920 DOI: 10.1039/d4fd00004h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Cytochrome P450 monooxygenases are an extensive and unique class of enzymes, which can regio- and stereo-selectively functionalise hydrocarbons by way of oxidation reactions. These enzymes are naturally occurring but have also been extensively applied in a synthesis context, where they are used as efficient biocatalysts. Recently, a biosynthetic pathway where a cytochrome P450 monooxygenase catalyses a critical step of the pathway was uncovered, leading to the production of a number of products that display high antitumour potency. In this work, we use computational techniques to gain insight into the factors that determine the relative yields of the different products. We use conformational search algorithms to understand the substrate stereochemistry. On a machine-learned 3D protein structure, we use molecular docking to obtain a library of favourable poses for substrate-protein interaction. With molecular dynamics, we investigate the most favourable poses for reactivity on a molecular level, allowing us to investigate which protein-substrate interactions favour a given product and thus gain insight into the product selectivity.
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Affiliation(s)
- Janko Čivić
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
| | - Neil R McFarlane
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
| | - Joleen Masschelein
- Department of Biology, Vlaams Instituut voor Biotechnologie VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
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3
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Famulari A, Correddu D, Di Nardo G, Gilardi G, Mitrikas G, Chiesa M, García-Rubio I. Heme Spin Distribution in the Substrate-Free and Inhibited Novel CYP116B5hd: A Multifrequency Hyperfine Sublevel Correlation (HYSCORE) Study. Molecules 2024; 29:518. [PMID: 38276601 PMCID: PMC10819608 DOI: 10.3390/molecules29020518] [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: 12/05/2023] [Revised: 12/29/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
The cytochrome P450 family consists of ubiquitous monooxygenases with the potential to perform a wide variety of catalytic applications. Among the members of this family, CYP116B5hd shows a very prominent resistance to peracid damage, a property that makes it a promising tool for fine chemical synthesis using the peroxide shunt. In this meticulous study, we use hyperfine spectroscopy with a multifrequency approach (X- and Q-band) to characterize in detail the electronic structure of the heme iron of CYP116B5hd in the resting state, which provides structural details about its active site. The hyperfine dipole-dipole interaction between the electron and proton nuclear spins allows for the locating of two different protons from the coordinated water and a beta proton from the cysteine axial ligand of heme iron with respect to the magnetic axes centered on the iron. Additionally, since new anti-cancer therapies target the inhibition of P450s, here we use the CYP116B5hd system-imidazole as a model for studying cytochrome P450 inhibition by an azo compound. The effects of the inhibition of protein by imidazole in the active-site geometry and electron spin distribution are presented. The binding of imidazole to CYP116B5hd results in an imidazole-nitrogen axial coordination and a low-spin heme FeIII. HYSCORE experiments were used to detect the hyperfine interactions. The combined interpretation of the gyromagnetic tensor and the hyperfine and quadrupole tensors of magnetic nuclei coupled to the iron electron spin allowed us to obtain a precise picture of the active-site geometry, including the orientation of the semi-occupied orbitals and magnetic axes, which coincide with the porphyrin N-Fe-N axes. The electronic structure of the iron does not seem to be affected by imidazole binding. Two different possible coordination geometries of the axial imidazole were observed. The angles between gx (coinciding with one of the N-Fe-N axes) and the projection of the imidazole plane on the heme were determined to be -60° and -25° for each of the two possibilities via measurement of the hyperfine structure of the axially coordinated 14N.
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Affiliation(s)
- Antonino Famulari
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain;
- Department of Chemistry, University of Turin, Via Giuria 9, 10125 Torino, Italy;
| | - Danilo Correddu
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Torino, Italy (G.D.N.); (G.G.)
| | - Giovanna Di Nardo
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Torino, Italy (G.D.N.); (G.G.)
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Torino, Italy (G.D.N.); (G.G.)
| | - George Mitrikas
- Institute of Nanoscience and Nanotechnology, NCSR Demokritos, 15341 Athens, Greece;
| | - Mario Chiesa
- Department of Chemistry, University of Turin, Via Giuria 9, 10125 Torino, Italy;
| | - Inés García-Rubio
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain;
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain
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4
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Müller VVL, Simpson PV, Peng K, Basu U, Moreth D, Nagel C, Türck S, Oehninger L, Ott I, Schatzschneider U. Taming the Biological Activity of Pd(II) and Pt(II) Complexes with Triazolato "Protective" Groups: 1H, 77Se Nuclear Magnetic Resonance and X-ray Crystallographic Model Studies with Selenocysteine to Elucidate Differential Thioredoxin Reductase Inhibition. Inorg Chem 2023; 62:16203-16214. [PMID: 37713601 DOI: 10.1021/acs.inorgchem.3c02701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
Abstract
The biological activity of Pd(II) and Pt(II) complexes toward three different cancer cell lines as well as inhibition of selenoenzyme thioredoxin reductase (TrxR) was modulated in an unexpected way by the introduction of triazolate as a "protective group" to the inner metal coordination sphere using the iClick reaction of [M(N3)(terpy)]PF6 [M = Pd(II) or Pt(II) and terpy = 2,2':6',2″-terpyridine] with an electron-poor alkyne. In a cell proliferation assay using A549, HT-29, and MDA-MB-231 human cancer cell lines, the palladium compound was significantly more potent than the isostructural platinum analogue and exhibited submicromolar activity on the most responsive cell line. This difference was also reflected in the inhibitory efficiency toward TrxR with IC50 values of 0.1 versus 5.4 μM for the Pd(II) and Pt(II) complexes, respectively. UV/Vis kinetic studies revealed that the Pt compound binds to selenocysteine faster than to cysteine [k = (22.9 ± 0.2)·10-3 vs (7.1 ± 0.2)·10-3 s-1]. Selective triazolato ligand exchange of the title compounds with cysteine (Hcys) and selenocysteine (Hsec)─but not histidine (His) and 9-ethylguanine (9EtG)─was confirmed by 1H, 77Se, and 195Pt NMR spectroscopy. Crystal structures of three of the four ligand exchange products were obtained, including [Pt(sec)(terpy)]PF6 as the first metal complex of selenocysteine to be structurally characterized.
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Affiliation(s)
- Victoria V L Müller
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Peter V Simpson
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Kun Peng
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Uttara Basu
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstr. 55, D-38106 Braunschweig, Germany
| | - Dominik Moreth
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Christoph Nagel
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Sebastian Türck
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstr. 55, D-38106 Braunschweig, Germany
| | - Luciano Oehninger
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstr. 55, D-38106 Braunschweig, Germany
| | - Ingo Ott
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstr. 55, D-38106 Braunschweig, Germany
| | - Ulrich Schatzschneider
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
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5
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Follmer AH, Borovik AS. The role of basicity in selective C-H bond activation by transition metal-oxidos. Dalton Trans 2023; 52:11005-11016. [PMID: 37497779 PMCID: PMC10619463 DOI: 10.1039/d3dt01781h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
The development of (bio)catalysts capable of selectively activating strong C-H bonds is a continuing challenge in modern chemistry. In both metalloenzymes and synthetic systems capable of activating C-H bonds, transition metal-oxido intermediates serve as the active species for reactivity whose thermodynamic properties influence the bond strengths they are capable of activating. In this Frontier article, we present current ideas of how the basicity of transition metal-oxidos impacts their reactivity with C-H bonds and present new opportunities within this field. We highlight recent insights into the role basicity plays in the activation process and its influence on mechanism, as well as the important role that secondary coordination sphere effects, such as hydrogen bonds, in tuning the basicity of the metal-oxido species is discussed.
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Affiliation(s)
- Alec H Follmer
- Department of Chemistry, University of California-Irvine, Irvine, CA 92697-3900, USA.
| | - A S Borovik
- Department of Chemistry, University of California-Irvine, Irvine, CA 92697-3900, USA.
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6
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Sankari S, Babu VM, Bian K, Alhhazmi A, Andorfer MC, Avalos DM, Smith TA, Yoon K, Drennan CL, Yaffe MB, Lourido S, Walker GC. A haem-sequestering plant peptide promotes iron uptake in symbiotic bacteria. Nat Microbiol 2022; 7:1453-1465. [PMID: 35953657 PMCID: PMC9420810 DOI: 10.1038/s41564-022-01192-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/29/2022] [Indexed: 11/09/2022]
Abstract
Symbiotic partnerships with rhizobial bacteria enable legumes to grow without nitrogen fertilizer because rhizobia convert atmospheric nitrogen gas into ammonia via nitrogenase. After Sinorhizobium meliloti penetrate the root nodules that they have elicited in Medicago truncatula, the plant produces a family of about 700 nodule cysteine-rich (NCR) peptides that guide the differentiation of endocytosed bacteria into nitrogen-fixing bacteroids. The sequences of the NCR peptides are related to the defensin class of antimicrobial peptides, but have been adapted to play symbiotic roles. Using a variety of spectroscopic, biophysical and biochemical techniques, we show here that the most extensively characterized NCR peptide, 24 amino acid NCR247, binds haem with nanomolar affinity. Bound haem molecules and their iron are initially made biologically inaccessible through the formation of hexamers (6 haem/6 NCR247) and then higher-order complexes. We present evidence that NCR247 is crucial for effective nitrogen-fixing symbiosis. We propose that by sequestering haem and its bound iron, NCR247 creates a physiological state of haem deprivation. This in turn induces an iron-starvation response in rhizobia that results in iron import, which itself is required for nitrogenase activity. Using the same methods as for L-NCR247, we show that the D-enantiomer of NCR247 can bind and sequester haem in an equivalent manner. The special abilities of NCR247 and its D-enantiomer to sequester haem suggest a broad range of potential applications related to human health.
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Affiliation(s)
- Siva Sankari
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Vignesh M.P. Babu
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Ke Bian
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Areej Alhhazmi
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Mary C. Andorfer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Dante M. Avalos
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA
| | - Tyler A. Smith
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Kwan Yoon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Catherine L. Drennan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Michael B. Yaffe
- Departments of Biology and Biological Engineering, and Center for Precision Cancer Medicine, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute for Technology, Cambridge, MA 02139, USA.,Divisions of Acute Care Surgery, Trauma, and Surgical Critical Care, and Surgical Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215 USA
| | - Sebastian Lourido
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Graham C. Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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7
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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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8
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EPR characterization of the heme domain of a self-sufficient cytochrome P450 (CYP116B5). J Inorg Biochem 2022; 231:111785. [DOI: 10.1016/j.jinorgbio.2022.111785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 02/25/2022] [Accepted: 02/26/2022] [Indexed: 11/19/2022]
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9
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Ortmayer M, Hardy FJ, Quesne MG, Fisher K, Levy C, Heyes DJ, Catlow CRA, de Visser SP, Rigby SEJ, Hay S, Green AP. A Noncanonical Tryptophan Analogue Reveals an Active Site Hydrogen Bond Controlling Ferryl Reactivity in a Heme Peroxidase. JACS AU 2021; 1:913-918. [PMID: 34337604 PMCID: PMC8317151 DOI: 10.1021/jacsau.1c00145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nature employs high-energy metal-oxo intermediates embedded within enzyme active sites to perform challenging oxidative transformations with remarkable selectivity. Understanding how different local metal-oxo coordination environments control intermediate reactivity and catalytic function is a long-standing objective. However, conducting structure-activity relationships directly in active sites has proven challenging due to the limited range of amino acid substitutions achievable within the constraints of the genetic code. Here, we use an expanded genetic code to examine the impact of hydrogen bonding interactions on ferryl heme structure and reactivity, by replacing the N-H group of the active site Trp51 of cytochrome c peroxidase by an S atom. Removal of a single hydrogen bond stabilizes the porphyrin π-cation radical state of CcP W191F compound I. In contrast, this modification leads to more basic and reactive neutral ferryl heme states, as found in CcP W191F compound II and the wild-type ferryl heme-Trp191 radical pair of compound I. This increased reactivity manifests in a >60-fold activity increase toward phenolic substrates but remarkably has negligible effects on oxidation of the biological redox partner cytc. Our data highlight how Trp51 tunes the lifetimes of key ferryl intermediates and works in synergy with the redox active Trp191 and a well-defined substrate binding site to regulate catalytic function. More broadly, this work shows how noncanonical substitutions can advance our understanding of active site features governing metal-oxo structure and reactivity.
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Affiliation(s)
- Mary Ortmayer
- Department
of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Florence J. Hardy
- Department
of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Matthew G. Quesne
- Research
Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxon OX11 0FA, United
Kingdom
- Cardiff
University, School of Chemistry, Main Building, Park Place, Cardiff CF10
3AT, United Kingdom
| | - Karl Fisher
- Department
of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Colin Levy
- Department
of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Derren J. Heyes
- Department
of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - C. Richard A. Catlow
- Research
Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxon OX11 0FA, United
Kingdom
- Cardiff
University, School of Chemistry, Main Building, Park Place, Cardiff CF10
3AT, United Kingdom
- Kathleen
Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, Western Central 1H 0AJ, United Kingdom
| | - Sam P. de Visser
- Department
of Chemical Engineering and Analytical Science & Manchester Institute
of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Stephen E. J. Rigby
- Department
of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Sam Hay
- Department
of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Anthony P. Green
- Department
of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
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10
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Wang Y, Liu P, Chang J, Xu Y, Wang J. Site-Specific Selenocysteine Incorporation into Proteins by Genetic Engineering. Chembiochem 2021; 22:2918-2924. [PMID: 33949764 DOI: 10.1002/cbic.202100124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/03/2021] [Indexed: 01/23/2023]
Abstract
Selenocysteine (Sec), a rare naturally proteinogenic amino acid, is the major form of essential trace element selenium in living organisms. Selenoproteins, with one or several Sec residues, are found in all three domains of life. Many selenoproteins play a role in critical cellular functions such as maintaining cell redox homeostasis. Sec is usually encoded by an in-frame stop codon UGA in the selenoprotein mRNA, and its incorporation in vivo is highly species-dependent and requires the reprogramming of translation. This mechanistic complexity of selenoprotein synthesis poses a big challenge to produce synthetic selenoproteins. To understand the functions of natural as well as engineered selenoproteins, many strategies have recently been developed to overcome the inherent barrier for recombinant selenoprotein production. In this review, we will describe the progress in selenoprotein production methodology.
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Affiliation(s)
- Yuchuan Wang
- Shenzhen Institute of Transfusion Medicine Shenzhen Blood Center, Shenzhen, Futian District, 518052, P. R. China.,Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen, Nanshan District, 518055, P. R. China
| | - Pengcheng Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, Chaoyang District, 100101, P. R. China
| | - Jiao Chang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, Chaoyang District, 100101, P. R. China
| | - Yunping Xu
- Shenzhen Institute of Transfusion Medicine Shenzhen Blood Center, Shenzhen, Futian District, 518052, P. R. China
| | - Jiangyun Wang
- Shenzhen Institute of Transfusion Medicine Shenzhen Blood Center, Shenzhen, Futian District, 518052, P. R. China.,Institute of Biophysics, Chinese Academy of Sciences, Beijing, Chaoyang District, 100101, P. R. China.,Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen, Nanshan District, 518055, P. R. China
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11
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Takei T, Ando T, Takao T, Ohnishi Y, Kurisu G, Iwaoka M, Hojo H. Chemical synthesis of ferredoxin with 4 selenocysteine residues using a segment condensation method. Chem Commun (Camb) 2020; 56:14239-14242. [PMID: 33118552 DOI: 10.1039/d0cc06252a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ferredoxin (Fd) is an electron carrier protein containing a [2Fe-2S] cluster. In this paper, we synthesized Se-Fd, in which four Cys residues coordinated to the cluster are substituted to selenocysteine. After the one-pot segment coupling by the thioester method, followed by deprotection and cluster loading, the desired Se-Fd was successfully obtained.
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Affiliation(s)
- Toshiki Takei
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
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12
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Tinzl M, Hilvert D. Trapping Transient Protein Species by Genetic Code Expansion. Chembiochem 2020; 22:92-99. [PMID: 32810341 DOI: 10.1002/cbic.202000523] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/18/2020] [Indexed: 12/24/2022]
Abstract
Nature employs a limited number of genetically encoded amino acids for the construction of functional proteins. By engineering components of the cellular translation machinery, however, it is now possible to genetically encode noncanonical building blocks with tailored electronic and structural properties. The ability to incorporate unique chemical functionality into proteins provides a powerful tool to probe mechanism and create novel function. In this minireview, we highlight several recent studies that illustrate how noncanonical amino acids have been used to capture and characterize reactive intermediates, fine-tune the catalytic properties of enzymes, and stabilize short-lived protein-protein complexes.
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Affiliation(s)
- Matthias Tinzl
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
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13
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Ortmayer M, Fisher K, Basran J, Wolde-Michael EM, Heyes DJ, Levy C, Lovelock SL, Anderson JLR, Raven EL, Hay S, Rigby SEJ, Green AP. Rewiring the "Push-Pull" Catalytic Machinery of a Heme Enzyme Using an Expanded Genetic Code. ACS Catal 2020; 10:2735-2746. [PMID: 32550044 PMCID: PMC7273622 DOI: 10.1021/acscatal.9b05129] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/22/2020] [Indexed: 01/14/2023]
Abstract
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Nature
employs a limited number of genetically encoded axial ligands
to control diverse heme enzyme activities. Deciphering the functional
significance of these ligands requires a quantitative understanding of how their electron-donating
capabilities modulate the structures and reactivities of the iconic
ferryl intermediates compounds I and II. However, probing these relationships
experimentally has proven to be challenging as ligand substitutions
accessible via conventional mutagenesis do not allow fine tuning of
electron donation and typically abolish catalytic function. Here,
we exploit engineered translation components to replace the histidine
ligand of cytochrome c peroxidase (CcP) by a less electron-donating Nδ-methyl histidine (Me-His) with little effect on the enzyme structure.
The rate of formation (k1) and the reactivity
(k2) of compound I are unaffected by ligand
substitution. In contrast, proton-coupled electron transfer to compound
II (k3) is 10-fold slower in CcP Me-His, providing a direct link between electron donation
and compound II reactivity, which can be explained by weaker electron
donation from the Me-His ligand (“the push”) affording
an electron-deficient ferryl oxygen with reduced proton affinity (“the
pull”). The deleterious effects of the Me-His ligand can be
fully compensated by introducing a W51F mutation designed to increase
“the pull” by removing a hydrogen bond to the ferryl
oxygen. Analogous substitutions in ascorbate peroxidase lead to similar
activity trends to those observed in CcP, suggesting
that a common mechanistic strategy is employed by enzymes using distinct
electron transfer pathways. Our study highlights how noncanonical
active site substitutions can be used to directly probe and deconstruct
highly evolved bioinorganic mechanisms.
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Affiliation(s)
- Mary Ortmayer
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Karl Fisher
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Jaswir Basran
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, U.K
| | - Emmanuel M. Wolde-Michael
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Derren J. Heyes
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Colin Levy
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Sarah L. Lovelock
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - J. L. Ross Anderson
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - Emma L. Raven
- School of Chemistry, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Sam Hay
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Stephen E. J. Rigby
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Anthony P. Green
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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14
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Erdogan H. One small step for cytochrome P450 in its catalytic cycle, one giant leap for enzymology. J PORPHYR PHTHALOCYA 2019. [DOI: 10.1142/s1088424619300040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The intermediates operating in the cytochrome P450 catalytic cycle have been investigated for more than half a century, fascinating many enzymologists. Each intermediate has its unique role to carry out diverse oxidations. Natural time course of the catalytic cycle is quite fast, hence, not all of the reactive intermediates could be isolated during physiological catalysis. Different high-valent iron intermediates have been proposed as primary oxidants: the candidates are compound 0 (Cpd 0, [FeOOH][Formula: see text]P450) and compound I (Cpd I, Fe(IV)[Formula: see text]O por[Formula: see text]P450). Among them, the role of Cpd I in hydroxylation is fairly well understood due the discovery of the peroxide shunt. This review endeavors to put the outstanding research efforts conducted to isolate and characterize the intermediates together. In addition to spectral features of each intermediate in the catalytic cycle, the oxidizing powers of Cpd 0 and Cpd I will be discussed along with most recent scientific findings.
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Affiliation(s)
- Huriye Erdogan
- Department of Chemistry, Gebze Technical University, Gebze, 41400, Kocaeli, Turkey
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15
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Kolbert Z, Molnár Á, Feigl G, Van Hoewyk D. Plant selenium toxicity: Proteome in the crosshairs. JOURNAL OF PLANT PHYSIOLOGY 2019; 232:291-300. [PMID: 30544054 DOI: 10.1016/j.jplph.2018.11.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/02/2018] [Accepted: 11/02/2018] [Indexed: 05/23/2023]
Abstract
The metalloid element, selenium (Se) is in many ways special and perhaps because of this its research in human and plant systems is of great interest. Despite its non-essentiality, higher plants take it up and metabolize it via sulfur pathways, but higher amounts of Se cause toxic symptoms in plants. However, the molecular mechanisms of selenium phytotoxicity have been only partly revealed; the data obtained so far point out that Se toxicity targets the plant proteome. Besides seleno- and oxyproteins, nitroproteins are also formed due to Se stress. In order to minimize proteomic damages induced by Se, certain plants are able to redirect selenocysteine away from protein synthesis thus preventing Se-protein formation. Additionally, the damaged or malformed selenoproteins, oxyproteins and nitroproteins may be removed by proteasomes. Based on the literature this review sets Se toxicity mechanisms into a new concept and it draws attention to the importance of Se-induced protein-level changes.
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Affiliation(s)
- Z Kolbert
- Department of Plant Biology, University of Szeged, 6726 Szeged Közép fasor 52, Hungary.
| | - Á Molnár
- Department of Plant Biology, University of Szeged, 6726 Szeged Közép fasor 52, Hungary.
| | - G Feigl
- Department of Plant Biology, University of Szeged, 6726 Szeged Közép fasor 52, Hungary.
| | - D Van Hoewyk
- Department of Biology, Coastal Carolina University, Conway, SC 29526, USA.
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16
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Satheesh V, Srivastava HK, Kumar SV, Sengoden M, Punniyamurthy T. Stereospecific Al‐Catalysed Tandem
C−N
/
C−Se
Bond Formation of Isoselenocyanates with Aziridines: Synthesis and DFT Study. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201801116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Vanaparthi Satheesh
- Department of ChemistryIndian Institute of Technology Guwahati Guwahati 781039 India
| | | | | | - Mani Sengoden
- Department of ChemistryIndian Institute of Technology Guwahati Guwahati 781039 India
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17
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Hayashi T, Hilvert D, Green AP. Engineered Metalloenzymes with Non-Canonical Coordination Environments. Chemistry 2018; 24:11821-11830. [PMID: 29786902 DOI: 10.1002/chem.201800975] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Indexed: 11/09/2022]
Abstract
Nature employs a limited number of genetically encoded, metal-coordinating residues to create metalloenzymes with diverse structures and functions. Engineered components of the cellular translation machinery can now be exploited to encode non-canonical ligands with user-defined electronic and structural properties. This ability to install "chemically programmed" ligands into proteins can provide powerful chemical probes of metalloenzyme mechanism and presents excellent opportunities to create metalloprotein catalysts with augmented properties and novel activities. In this Concept article, we provide an overview of several recent studies describing the creation of engineered metalloenzymes with interesting catalytic properties, and reveal how characterization of these systems has advanced our understanding of nature's bioinorganic mechanisms. We also highlight how powerful laboratory evolution protocols can be readily adapted to allow optimization of metalloenzymes with non-canonical ligands. This approach combines beneficial features of small molecule and protein catalysis by allowing the installation of a greater variety of local metal coordination environments into evolvable protein scaffolds, and holds great promise for the future creation of powerful metalloprotein catalysts for a host of synthetically valuable transformations.
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Affiliation(s)
- Takahiro Hayashi
- Laboratory of Organic Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Anthony P Green
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
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18
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Ferentinos E, Chatziefthimiou S, Boudalis AK, Pissas M, Mathies G, Gast P, Groenen EJJ, Sanakis Y, Kyritsis P. The [Fe{(SePPh2
)2
N}2
] Complex Revisited: X-ray Crystallography, Magnetometry, High-Frequency EPR, and Mössbauer Studies Reveal Its Tetrahedral FeII
Se4
Coordination Sphere. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201701459] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Eleftherios Ferentinos
- Inorganic Chemistry Laboratory; Department of Chemistry; National and Kapodistrian University of Athens; Panepistimiopolis 15771 Athens Greece
| | - Spyros Chatziefthimiou
- Institute of Nanoscience and Nanotechnology; N.C.S.R. “Demokritos”; Aghia Paraskevi 15310 Attiki Greece
| | - Athanassios K. Boudalis
- Institute of Nanoscience and Nanotechnology; N.C.S.R. “Demokritos”; Aghia Paraskevi 15310 Attiki Greece
| | - Michael Pissas
- Institute of Nanoscience and Nanotechnology; N.C.S.R. “Demokritos”; Aghia Paraskevi 15310 Attiki Greece
| | - Guinevere Mathies
- Huygens-Kamerlingh Onnes Laboratory; Department of Physics; Leiden University; Niels Bohrweg 2 2333 CA Leiden The Netherlands
| | - Peter Gast
- Huygens-Kamerlingh Onnes Laboratory; Department of Physics; Leiden University; Niels Bohrweg 2 2333 CA Leiden The Netherlands
| | - Edgar J. J. Groenen
- Huygens-Kamerlingh Onnes Laboratory; Department of Physics; Leiden University; Niels Bohrweg 2 2333 CA Leiden The Netherlands
| | - Yiannis Sanakis
- Institute of Nanoscience and Nanotechnology; N.C.S.R. “Demokritos”; Aghia Paraskevi 15310 Attiki Greece
| | - Panayotis Kyritsis
- Inorganic Chemistry Laboratory; Department of Chemistry; National and Kapodistrian University of Athens; Panepistimiopolis 15771 Athens Greece
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19
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Pott M, Hayashi T, Mori T, Mittl PRE, Green AP, Hilvert D. A Noncanonical Proximal Heme Ligand Affords an Efficient Peroxidase in a Globin Fold. J Am Chem Soc 2018; 140:1535-1543. [DOI: 10.1021/jacs.7b12621] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Moritz Pott
- Laboratory of Organic Chemistry, ETH Zurich, Zurich 8093, Switzerland
| | - Takahiro Hayashi
- Laboratory of Organic Chemistry, ETH Zurich, Zurich 8093, Switzerland
| | - Takahiro Mori
- Laboratory of Organic Chemistry, ETH Zurich, Zurich 8093, Switzerland
| | - Peer R. E. Mittl
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - Anthony P. Green
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, Zurich 8093, Switzerland
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20
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Klein JEMN, Mandal D, Ching WM, Mallick D, Que L, Shaik S. Privileged Role of Thiolate as the Axial Ligand in Hydrogen Atom Transfer Reactions by Oxoiron(IV) Complexes in Shaping the Potential Energy Surface and Inducing Significant H-Atom Tunneling. J Am Chem Soc 2017; 139:18705-18713. [PMID: 29179544 DOI: 10.1021/jacs.7b11300] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An H/D kinetic isotope effect (KIE) of 80 is found at -20 °C for the oxidation of 9,10-dihydroanthracene by [FeIV(O)(TMCS)]+, a complex supported by the tetramethylcyclam (TMC) macrocycle with a tethered thiolate. This KIE value approaches that previously predicted by DFT calculations. Other [FeIV(O)(TMC)(anion)] complexes exhibit values of 20, suggesting that the thiolate ligand of [FeIV(O)(TMCS)]+ plays a unique role in facilitating tunneling. Calculations show that tunneling is most enhanced (a) when the bond asymmetry between C-H bond breaking and O-H bond formation in the transition state is minimized, and (b) when the electrostatic interactions in the O---H---C moiety are maximal. These two factors-which peak for the best electron donor, the thiolate ligand-afford a slim and narrow barrier through which the H-atom can tunnel most effectively.
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Affiliation(s)
- Johannes E M N Klein
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Debasish Mandal
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem , 91904 Jerusalem, Israel
| | - Wei-Min Ching
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Dibyendu Mallick
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem , 91904 Jerusalem, Israel
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem , 91904 Jerusalem, Israel
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21
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Mousa R, Notis Dardashti R, Metanis N. Selen und Selenocystein in der Proteinchemie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706876] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Reem Mousa
- The Institute of Chemistry; The Hebrew University of Jerusalem; Edmond J. Safra, Givat Ram Jerusalem 91904 Israel
| | - Rebecca Notis Dardashti
- The Institute of Chemistry; The Hebrew University of Jerusalem; Edmond J. Safra, Givat Ram Jerusalem 91904 Israel
| | - Norman Metanis
- The Institute of Chemistry; The Hebrew University of Jerusalem; Edmond J. Safra, Givat Ram Jerusalem 91904 Israel
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22
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Mousa R, Notis Dardashti R, Metanis N. Selenium and Selenocysteine in Protein Chemistry. Angew Chem Int Ed Engl 2017; 56:15818-15827. [PMID: 28857389 DOI: 10.1002/anie.201706876] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Indexed: 01/22/2023]
Abstract
Selenocysteine, the selenium-containing analogue of cysteine, is the twenty-first proteinogenic amino acid. Since its discovery almost fifty years ago, it has been exploited in unnatural systems even more often than in natural systems. Selenocysteine chemistry has attracted the attention of many chemists in the field of chemical biology owing to its high reactivity and resulting potential for various applications such as chemical modification, chemical protein (semi)synthesis, and protein folding, to name a few. In this Minireview, we will focus on the chemistry of selenium and selenocysteine and their utility in protein chemistry.
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Affiliation(s)
- Reem Mousa
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem, 91904, Israel
| | - Rebecca Notis Dardashti
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem, 91904, Israel
| | - Norman Metanis
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem, 91904, Israel
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23
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Carbon-Based Oxamate Cobalt(III) Complexes as Bioenzyme Mimics for Contaminant Elimination in High Backgrounds of Complicated Constituents. MATERIALS 2017; 10:ma10101169. [PMID: 29023394 PMCID: PMC5666975 DOI: 10.3390/ma10101169] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/20/2017] [Accepted: 09/30/2017] [Indexed: 11/16/2022]
Abstract
Complex wastewater with massive components is now a serious environmental issue facing humanity. Selective removal of low-concentration contaminants in mixed constituents holds great promise for increasing water supplies. Bioenzymes like horseradish peroxidase exhibit oxidizing power and selectivity. Here, we manufactured its mimic through immobilizing non-heme oxamate anionic cobalt(III) complex ([CoIII(opba)]−, opba = o-phenylenebis(oxamate)) onto pyridine (Py) modified multiwalled carbon nanotubes ([CoIII(opba)]−-Py-MWCNTs, MWCNTs = multiwalled carbon nanotubes), where MWCNTs captured substrates and Py functioned as the fifth ligand. We chose typical azo dye (C.I. Acid Red 1) and antibiotic (ciprofloxacin) as model substrates. Without •OH, this catalyst could detoxify target micropollutants efficiently at pH from 8 to 11. It also remained efficient in repetitive tests, and the final products were non-poisonous OH-containing acids. Combined with radical scavenger tests and electron paramagnetic resonance result, we speculated that high-valent cobalt-oxo active species and oxygen atom transfer reaction dominated in the reaction pathway. According to density functional theory calculations, the electron spin density distribution order showed that electron-withdrawing ligand was beneficial for inward pulling the excess electron and lowering the corresponding energy levels, achieving an electrophilic-attack enhancement of the catalyst. With target removal property and recyclability, this catalyst is prospective in water detoxication.
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24
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25
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Onderko EL, Silakov A, Yosca TH, Green MT. Characterization of a selenocysteine-ligated P450 compound I reveals direct link between electron donation and reactivity. Nat Chem 2017. [DOI: 10.1038/nchem.2781] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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26
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Green AP, Hayashi T, Mittl PRE, Hilvert D. A Chemically Programmed Proximal Ligand Enhances the Catalytic Properties of a Heme Enzyme. J Am Chem Soc 2016; 138:11344-52. [DOI: 10.1021/jacs.6b07029] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anthony P. Green
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Takahiro Hayashi
- Laboratory
of Organic Chemistry, ETH Zurich, 8093 Zürich, Switzerland
| | - Peer R. E. Mittl
- Department
of Biochemistry, University of Zürich, 8057 Zürich, Switzerland
| | - Donald Hilvert
- Laboratory
of Organic Chemistry, ETH Zurich, 8093 Zürich, Switzerland
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27
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28
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Morozov AN, Pardillo AD, Chatfield DC. Chloroperoxidase-Catalyzed Epoxidation of Cis-β-Methylstyrene: NH-S Hydrogen Bonds and Proximal Helix Dipole Change the Catalytic Mechanism and Significantly Lower the Reaction Barrier. J Phys Chem B 2015; 119:14350-63. [PMID: 26452587 DOI: 10.1021/acs.jpcb.5b06731] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proximal hydrogen bonding of the axial sulfur with the backbone amides (NH-S) is a conserved feature of heme-thiolate enzymes such as chloroperoxidase (CPO) and cytochrome P450 (P450). In CPO, the effect of NH-S bonds is amplified by the dipole moment of the proximal helix. Our gas-phase DFT studies show that the proximal pocket effect significantly enhances CPO's reactivity toward the epoxidation of olefinic substrates. Comparison of models with and without proximal pocket residues shows that with them, the barrier for Cβ-O bond formation is lowered by about ∼4.6 kcal/mol, while Cα-O-Cβ ring closure becomes barrierless. The dipole moment of the proximal helix was estimated to contribute 1/3 of the decrease, while the rest is attributed to the effect of NH-S bonds. The decrease of the reaction barrier correlates with increased electron density transfer to residues of the proximal pocket. The effect is most pronounced on the doublet spin surface and involves a change in the electron-transfer mechanism. A full enzyme QMMM study on the doublet spin surface gives about the same barrier as the gas-phase DFT study. The free-energy barrier was estimated to be in agreement with the experimental results for the CPO-catalyzed epoxidation of styrene.
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Affiliation(s)
- Alexander N Morozov
- Department of Chemistry and Biochemistry, Florida International University , 11200 Southwest Eighth Street, Miami, Florida 33199, United States
| | - Armando D Pardillo
- Department of Chemistry and Biochemistry, Florida International University , 11200 Southwest Eighth Street, Miami, Florida 33199, United States
| | - David C Chatfield
- Department of Chemistry and Biochemistry, Florida International University , 11200 Southwest Eighth Street, Miami, Florida 33199, United States
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29
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Vandemeulebroucke A, Aldag C, Stiebritz MT, Reiher M, Hilvert D. Kinetic Consequences of Introducing a Proximal Selenocysteine Ligand into Cytochrome P450cam. Biochemistry 2015; 54:6692-703. [DOI: 10.1021/acs.biochem.5b00939] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- An Vandemeulebroucke
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Caroline Aldag
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Martin T. Stiebritz
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Markus Reiher
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
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30
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Lin YW. The broad diversity of heme-protein cross-links: An overview. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:844-59. [DOI: 10.1016/j.bbapap.2015.04.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 03/26/2015] [Accepted: 04/17/2015] [Indexed: 12/30/2022]
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31
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Miller C, Bröcker MJ, Prat L, Ip K, Chirathivat N, Feiock A, Veszprémi M, Söll D. A synthetic tRNA for EF-Tu mediated selenocysteine incorporation in vivo and in vitro. FEBS Lett 2015; 589:2194-9. [PMID: 26160755 DOI: 10.1016/j.febslet.2015.06.039] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/24/2015] [Accepted: 06/24/2015] [Indexed: 10/23/2022]
Abstract
Incorporation of selenocysteine (Sec) in bacteria requires a UGA codon that is reassigned to Sec by the Sec-specific elongation factor SelB and a conserved mRNA motif (SECIS element). These requirements severely restrict the engineering of selenoproteins. Earlier, a synthetic tRNASec was reported that allowed canonical Sec incorporation by EF-Tu; however, serine misincorporation limited its scope. We report a superior tRNASec variant (tRNAUTuX) that facilitates EF-Tu dependent stoichiometric Sec insertion in response to UAG both in vivo in Escherichia coli and in vitro in a cellfree protein synthesis system. We also demonstrate recoding of several sense codons in a SelB supplemented cell-free system. These advances in Sec incorporation will aid rational design and directed evolution of selenoproteins.
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Affiliation(s)
- Corwin Miller
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
| | - Markus J Bröcker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Laure Prat
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Kevan Ip
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Napon Chirathivat
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Alexander Feiock
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Miklós Veszprémi
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Chemistry, Yale University, New Haven, CT 06520, USA.
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32
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Schmohl L, Wagner FR, Schümann M, Krause E, Schwarzer D. Semisynthesis and initial characterization of sortase A mutants containing selenocysteine and homocysteine. Bioorg Med Chem 2015; 23:2883-9. [PMID: 25900629 DOI: 10.1016/j.bmc.2015.03.057] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/19/2015] [Accepted: 03/21/2015] [Indexed: 12/14/2022]
Abstract
The bacterial transpeptidase sortase A is a well-established tool in protein chemistry and catalyzes the chemoselective ligation of peptides and proteins. During catalysis sortase A cleaves the conserved Leu-Pro-X-Thr-Gly sorting motif at the Thr residue under concomitant thioester formation at active site Cys184. We have used expressed protein ligation (EPL) to generate sortase mutants with Cys184 replaced by selenocysteine (Sec) and homocysteine (Hcy). Sec-sortase showed a moderate 2-3-fold reduction in catalytic activity in contrast to Hcy-sortase which is a poor catalyst with less than 1% of wild-type activity. The sensitivity of the active site nucleophiles towards an alkylation reagent correlated with the pKa values of the mutated residues. Furthermore, the pH-profile of Sec-sortase was shifted to more acidic conditions when compared to the wild-type enzyme. These observations provide information on sortase catalysis and the semisynthetic enzymes might represent useful tools for further biochemical investigations and engineering approaches of sortases A.
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Affiliation(s)
- Lena Schmohl
- Interfaculty Institute of Biochemistry, University of Tuebingen, Hoppe-Seyler-Str. 4, D-72076 Tuebingen, Germany
| | - Felix Roman Wagner
- Interfaculty Institute of Biochemistry, University of Tuebingen, Hoppe-Seyler-Str. 4, D-72076 Tuebingen, Germany
| | - Michael Schümann
- Laboratory of Mass Spectrometry, Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, D-13125 Berlin, Germany
| | - Eberhard Krause
- Laboratory of Mass Spectrometry, Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, D-13125 Berlin, Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry, University of Tuebingen, Hoppe-Seyler-Str. 4, D-72076 Tuebingen, Germany.
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Chang WJ, Kulkarni MV, Sun CM. Regioselective one-pot three component synthesis of chiral 2-iminoselenazolines under sonication. RSC Adv 2015. [DOI: 10.1039/c5ra18763j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
A one-pot multi component reaction of selenoureas, which are in situ generated from l-amino esters and isoselenocyanates, with α-bromoketone under ultrasonication.
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Affiliation(s)
- Wong-Jin Chang
- Department of Applied Chemistry
- National Chiao-Tung University
- Hsinchu 300-10
- Taiwan
| | - Manohar V. Kulkarni
- Department of Applied Chemistry
- National Chiao-Tung University
- Hsinchu 300-10
- Taiwan
| | - Chung-Ming Sun
- Department of Applied Chemistry
- National Chiao-Tung University
- Hsinchu 300-10
- Taiwan
- Department of Medicinal and Applied Chemistry
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34
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Metanis N, Hilvert D. Natural and synthetic selenoproteins. Curr Opin Chem Biol 2014; 22:27-34. [DOI: 10.1016/j.cbpa.2014.09.010] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 09/07/2014] [Accepted: 09/08/2014] [Indexed: 12/11/2022]
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Metanis N, Hilvert D. Harnessing selenocysteine reactivity for oxidative protein folding. Chem Sci 2014; 6:322-325. [PMID: 28757941 PMCID: PMC5514408 DOI: 10.1039/c4sc02379j] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 09/22/2014] [Indexed: 01/06/2023] Open
Abstract
Turbo-charged folding with selenium: targeted replacement of cysteines in proteins with selenocysteines is a valuable strategy for increasing the rates of oxidative protein folding, altering folding mechanisms, and rescuing kinetically trapped intermediates.
Although oxidative folding of disulfide-rich proteins is often sluggish, this process can be significantly enhanced by targeted replacement of cysteines with selenocysteines. In this study, we examined the effects of a selenosulfide and native versus nonnative diselenides on the folding rates and mechanism of bovine pancreatic trypsin inhibitor. Our results show that such sulfur-to-selenium substitutions alter the distribution of key folding intermediates and enhance their rates of interconversion in a context-dependent manner.
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Affiliation(s)
- Norman Metanis
- Laboratory of Organic Chemistry , ETH Zürich , 8093 Zürich , Switzerland .
| | - Donald Hilvert
- Laboratory of Organic Chemistry , ETH Zürich , 8093 Zürich , Switzerland .
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Yang Y, Zhang H, Usharani D, Bu W, Im S, Tarasev M, Rwere F, Pearl NM, Meagher J, Sun C, Stuckey J, Shaik S, Waskell L. Structural and functional characterization of a cytochrome P450 2B4 F429H mutant with an axial thiolate-histidine hydrogen bond. Biochemistry 2014; 53:5080-91. [PMID: 25029089 PMCID: PMC4131899 DOI: 10.1021/bi5003794] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 07/15/2014] [Indexed: 02/02/2023]
Abstract
The structural basis of the regulation of microsomal cytochrome P450 (P450) activity was investigated by mutating the highly conserved heme binding motif residue, Phe429, on the proximal side of cytochrome P450 2B4 to a histidine. Spectroscopic, pre-steady-state and steady-state kinetic, thermodynamic, theoretical, and structural studies of the mutant demonstrate that formation of an H-bond between His429 and the unbonded electron pair of the Cys436 axial thiolate significantly alters the properties of the enzyme. The mutant lost >90% of its activity; its redox potential was increased by 87 mV, and the half-life of the oxyferrous mutant was increased ∼37-fold. Single-crystal electronic absorption and resonance Raman spectroscopy demonstrated that the mutant was reduced by a small dose of X-ray photons. The structure revealed that the δN atom of His429 forms an H-bond with the axial Cys436 thiolate whereas the εN atom forms an H-bond with the solvent and the side chain of Gln357. The amide of Gly438 forms the only other H-bond to the tetrahedral thiolate. Theoretical quantification of the histidine-thiolate interaction demonstrates a significant electron withdrawing effect on the heme iron. Comparisons of structures of class I-IV P450s demonstrate that either a phenylalanine or tryptophan is often found at the location corresponding to Phe429. Depending on the structure of the distal pocket heme, the residue at this location may or may not regulate the thermodynamic properties of the P450. Regardless, this residue appears to protect the thiolate from solvent, oxidation, protonations, and other deleterious reactions.
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Affiliation(s)
- Yuting Yang
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Haoming Zhang
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Dandamudi Usharani
- Institute
of Chemistry and Lise Meitner-Minerva Center for Computational Quantum
Chemistry, Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Weishu Bu
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Sangchoul Im
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Michael Tarasev
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Freeborn Rwere
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Naw May Pearl
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Jennifer Meagher
- Life
Science Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Cuthbert Sun
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
| | - Jeanne Stuckey
- Life
Science Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Sason Shaik
- Institute
of Chemistry and Lise Meitner-Minerva Center for Computational Quantum
Chemistry, Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Lucy Waskell
- Department
of Anesthesiology, University of Michigan
and VA Medical Center, 2215 Fuller Road, Building 31, Room 225, Ann
Arbor, Michigan 48105, United States
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Schaefer-Ramadan S, Thorpe C, Rozovsky S. Site-specific insertion of selenium into the redox-active disulfide of the flavoprotein augmenter of liver regeneration. Arch Biochem Biophys 2014; 548:60-5. [PMID: 24582598 PMCID: PMC4009370 DOI: 10.1016/j.abb.2014.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 01/29/2014] [Accepted: 02/03/2014] [Indexed: 11/23/2022]
Abstract
Augmenter of liver regeneration (sfALR) is a small disulfide-bridged homodimeric flavoprotein with sulfhydryl oxidase activity. Here, we investigate the catalytic and spectroscopic consequences of selectively replacing C145 by a selenocysteine to complement earlier studies in which random substitution of ∼90% of the 6 cysteine residues per sfALR monomer was achieved growing Escherichia coli on selenite. A selenocysteine insertion sequence (SECIS) element was installed within the gene for human sfALR. SecALR2 showed a spectrum comparable to that of wild-type sfALR. The catalytic efficiency of SecALR2 towards dithiothreitol was 6.8-fold lower than a corresponding construct in which position 145 was returned to a cysteine residue while retaining the additional mutations introduced with the SECIS element. This all-cysteine control enzyme formed a mixed disulfide between C142 and β-mercaptoethanol releasing C145 to form a thiolate-flavin charge transfer absorbance band at ∼530nm. In contrast, SecALR2 showed a prominent long-wavelength absorbance at 585 nm consistent with the expectation that a selenolate would be a better charge-transfer donor to the isoalloxazine ring. These data show the robustness of the ALR protein fold towards the multiple mutations required to insert the SECIS element and provide the first example of a selenolate to flavin charge-transfer complex.
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Affiliation(s)
| | - Colin Thorpe
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States.
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Kolev JN, Zaengle JM, Ravikumar R, Fasan R. Enhancing the efficiency and regioselectivity of P450 oxidation catalysts by unnatural amino acid mutagenesis. Chembiochem 2014; 15:1001-10. [PMID: 24692265 DOI: 10.1002/cbic.201400060] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Indexed: 01/28/2023]
Abstract
The development of effective strategies for modulating the reactivity and selectivity of cytochrome P450 enzymes represents a key step toward expediting the use of these biocatalysts for synthetic applications. We have investigated the potential of unnatural amino acid mutagenesis to aid efforts in this direction. Four unnatural amino acids with diverse aromatic side chains were incorporated at 11 active-site positions of a substrate-promiscuous CYP102A1 variant. The resulting "uP450s" were then tested for their catalytic activity and regioselectivity in the oxidation of two representative substrates: a small-molecule drug and a natural product. Large shifts in regioselectivity resulted from these single mutations, and in particular, for para-acetyl-Phe substitutions at positions close to the heme cofactor. Screening this mini library of uP450s enabled us to identify P450 catalysts for the selective hydroxylation of four aliphatic positions in the target substrates, including a C(sp(3))-H site not oxidized by the parent enzyme. Furthermore, we discovered a general activity-enhancing effect of active-site substitutions involving the unnatural amino acid para-amino-Phe, which resulted in P450 catalysts capable of supporting the highest total turnover number reported to date on a complex molecule (34,650). The functional changes induced by the unnatural amino acids could not be reproduced by any of the 20 natural amino acids. This study thus demonstrates that unnatural amino acid mutagenesis constitutes a promising new strategy for improving the catalytic activity and regioselectivity of P450 oxidation catalysts.
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Affiliation(s)
- Joshua N Kolev
- Department of Chemistry, University of Rochester, Hutchison Hall, Rochester, NY 14620 (USA)
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Affiliation(s)
- Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Edward Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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40
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Van Hoewyk D. A tale of two toxicities: malformed selenoproteins and oxidative stress both contribute to selenium stress in plants. ANNALS OF BOTANY 2013; 112:965-72. [PMID: 23904445 PMCID: PMC3783228 DOI: 10.1093/aob/mct163] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/28/2013] [Indexed: 05/06/2023]
Abstract
BACKGROUND Despite selenium's toxicity in plants at higher levels, crops supply most of the essential dietary selenium in humans. In plants, inorganic selenium can be assimilated into selenocysteine, which can replace cysteine in proteins. Selenium toxicity in plants has been attributed to the formation of non-specific selenoproteins. However, this paradigm can be challenged now that there is increasingly abundant evidence suggesting that selenium-induced oxidative stress also contributes to toxicity in plants. SCOPE This Botanical Briefing summarizes the evidence indicating that selenium toxicity in plants is attributable to both the accumulation of non-specific selenoproteins and selenium-induced oxidative stress. Evidence is also presented to substantiate the claim that inadvertent selenocysteine replacement probably impairs or misfolds proteins, which supports the malformed selenoprotein hypothesis. The possible physiological ramifications of selenoproteins and selenium-induced oxidative stress are discussed. CONCLUSIONS Malformed selenoproteins and oxidative stress are two distinct types of stress that drive selenium toxicity in plants and could impact cellular processes in plants that have yet to be thoroughly explored. Although challenging, deciphering whether the extent of selenium toxicity in plants is imparted by selenoproteins or oxidative stress could be helpful in the development of crops with fortified levels of selenium.
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Affiliation(s)
- Doug Van Hoewyk
- Coastal Carolina University, Biology Department, Conway, SC 29526, USA
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41
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Lin YW, Sawyer EB, Wang J. Rational heme protein design: all roads lead to Rome. Chem Asian J 2013; 8:2534-44. [PMID: 23704071 DOI: 10.1002/asia.201300291] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Indexed: 01/03/2023]
Abstract
Heme proteins are among the most abundant and important metalloproteins, exerting diverse biological functions including oxygen transport, small molecule sensing, selective C-H bond activation, nitrite reduction, and electron transfer. Rational heme protein designs focus on the modification of the heme-binding active site and the heme group, protein hybridization and domain swapping, and de novo design. These strategies not only provide us with unique advantages for illustrating the structure-property-reactivity-function (SPRF) relationship of heme proteins in nature but also endow us with the ability to create novel biocatalysts and biosensors.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001 (China)
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42
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[NiFe] hydrogenases: a common active site for hydrogen metabolism under diverse conditions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:986-1002. [PMID: 23399489 DOI: 10.1016/j.bbabio.2013.01.015] [Citation(s) in RCA: 160] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 12/06/2012] [Accepted: 01/26/2013] [Indexed: 01/05/2023]
Abstract
Hydrogenase proteins catalyze the reversible conversion of molecular hydrogen to protons and electrons. The most abundant hydrogenases contain a [NiFe] active site; these proteins are generally biased towards hydrogen oxidation activity and are reversibly inhibited by oxygen. However, there are [NiFe] hydrogenase that exhibit unique properties, including aerobic hydrogen oxidation and preferential hydrogen production activity; these proteins are highly relevant in the context of biotechnological devices. This review describes four classes of these "nonstandard" [NiFe] hydrogenases and discusses the electrochemical, spectroscopic, and structural studies that have been used to understand the mechanisms behind this exceptional behavior. A revised classification protocol is suggested in the conclusions, particularly with respect to the term "oxygen-tolerance". This article is part of a special issue entitled: metals in bioenergetics and biomimetics systems.
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43
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Aldag C, Bröcker MJ, Hohn MJ, Prat L, Hammond G, Plummer A, Söll D. Rewiring translation for elongation factor Tu-dependent selenocysteine incorporation. Angew Chem Int Ed Engl 2013; 52:1441-5. [PMID: 23193031 PMCID: PMC3776052 DOI: 10.1002/anie.201207567] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Indexed: 02/01/2023]
Affiliation(s)
| | | | | | | | - Gifty Hammond
- Department of Molecular Biophysics and Biochemistry, and Chemistry, Yale University, New Haven, CT 06520, USA
| | - Abigail Plummer
- Department of Molecular Biophysics and Biochemistry, and Chemistry, Yale University, New Haven, CT 06520, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, and Chemistry, Yale University, New Haven, CT 06520, USA
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44
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Aldag C, Bröcker MJ, Hohn MJ, Prat L, Hammond G, Plummer A, Söll D. Rewiring Translation for Elongation Factor Tu-Dependent Selenocysteine Incorporation. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201207567] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Li H, O'Connor PB. Electron capture dissociation of disulfide, sulfur-selenium, and diselenide bound peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:2001-2010. [PMID: 22993041 DOI: 10.1007/s13361-012-0473-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/10/2012] [Accepted: 08/10/2012] [Indexed: 06/01/2023]
Abstract
To examine the electron capture dissociation (ECD) behavior of disulfide (S-S), sulfur-selenium (S-Se), and diselenide (Se-Se) bonds-containing peptides, a series of free cysteine (Cys) and selenocysteine (Sec) containing peptides were reacted to form interchain S-S, S-Se, and Se-Se bonds, and then studied using ECD with Fourier transform ion cyclotron mass spectrometry (FTICR MS). These results demonstrate that the radical has higher tendency to stay at selenium rather than sulfur after the cleavage of Se-S bonds by ECD. In addition, -SH (-33), -S (-32), and -S + H (-31) small neutral losses were all observed from the cleavage of C-S bonds of a disulfide bound peptide. Similar, but minor, fragments were also detected in S-Se bound peptides. In contrast, the cleavage of C-Se bonds of the Se-Se species mainly forms fragments with neutral loss of -Se + H (-78.90868), and the radical tends to stay on the selenium of its corresponding complementary pair. Although the electron affinities of S atom (2.07 eV) and Se atom (2.02 eV) are very close; they have very different reactivity towards electrons. The replacement of sulfur with selenium greatly increases the electron affinities of S-Se and Se-Se bonds comparing to S-S bonds (with an increase of electron affinity by about 0.20 eV by replacing a sulfur with a selenium) (Int J Quantum Chem 110:513-523, 2010), which in turn leads to different ECD fragmentation behavior and mechanisms. Our results are in good agreement with previously published ab initio calculations on Se-Se compounds by other groups.
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Affiliation(s)
- Huilin Li
- Department of Chemistry, University of Warwick, Coventry, UK
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46
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Boeglin WE, Brash AR. Cytochrome P450-type hydroxylation and epoxidation in a tyrosine-liganded hemoprotein, catalase-related allene oxide synthase. J Biol Chem 2012; 287:24139-47. [PMID: 22628547 DOI: 10.1074/jbc.m112.364216] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ability of hemoproteins to catalyze epoxidation or hydroxylation reactions is usually associated with a cysteine as the proximal ligand to the heme, as in cytochrome P450 or nitric oxide synthase. Catalase-related allene oxide synthase (cAOS) from the coral Plexaura homomalla, like catalase itself, has tyrosine as the proximal heme ligand. Its natural reaction is to convert 8R-hydroperoxy-eicosatetraenoic acid (8R-HPETE) to an allene epoxide, a reaction activated by the ferric heme, forming product via the Fe(IV)-OH intermediate, Compound II. Here we oxidized cAOS to Compound I (Fe(V)=O) using the oxygen donor iodosylbenzene and investigated the catalytic competence of the enzyme. 8R-hydroxyeicosatetraenoic acid (8R-HETE), the hydroxy analog of the natural substrate, normally unreactive with cAOS, was thereby epoxidized stereospecifically on the 9,10 double bond to form 8R-hydroxy-9R,10R-trans-epoxy-eicosa-5Z,11Z,14Z-trienoic acid as the predominant product; the turnover was 1/s using 100 μm iodosylbenzene. The enantiomer, 8S-HETE, was epoxidized stereospecifically, although with less regiospecificity, and was hydroxylated on the 13- and 16-carbons. Arachidonic acid was converted to two major products, 8R-HETE and 8R,9S-eicosatrienoic acid (8R,9S-EET), plus other chiral monoepoxides and bis-allylic 10S-HETE. Linoleic acid was epoxidized, whereas stearic acid was not metabolized. We conclude that when cAOS is charged with an oxygen donor, it can act as a stereospecific monooxygenase. Our results indicate that in the tyrosine-liganded cAOS, a catalase-related hemoprotein in which a polyunsaturated fatty acid can enter the active site, the enzyme has the potential to mimic the activities of typical P450 epoxygenases and some capabilities of P450 hydroxylases.
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Affiliation(s)
- William E Boeglin
- Department of Pharmacology and the Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
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47
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Du J, Sono M, Dawson JH. Ferric His93Gly myoglobin cavity mutant and its complexes with thioether and selenolate as heme protein models. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424610002872] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The composition of ferric exogenous ligand-free His93Gly sperm whale myoglobin (H93G Mb) at neutral pH has been determined by examination of the spectral properties of the protein over the pH range from 3.0 to 10.5. An apparent pKa value of ~6.6 has been observed for the conversion of a postulated six-coordinate bis-water-bound coordination structure at pH 5.0 to a five-coordinate hydroxide-bound form at pH 10.5. Starting from the exogenous ligand-free ferric H93G protein, ferric mono- and bis-thioether (tetrahydrothiophene, THT)-ligated adducts have been prepared and characterized by UV-visible (UV-vis) absorption and magnetic circular dichroism (MCD) spectroscopy. The mon-THT ferric H93G Mb species has hydroxide as the sixth ligand. The bis-THT derivative is a model for the low-spin ferric heme binding site of native bis-Met-ligated bacterioferritin or streptococcal heme-associated protein (Shp). A novel THT-bound ferryl H93G Mb moiety has been partially formed. The high-spin five-coordinate ferric H93G(selenolate) Mb complex has been prepared using benzeneselenol and characterized by UV-vis and MCD spectroscopy as a model for Se-Cys-ligated ferric cytochrome P450. The results described herein further demonstrate the versatility of the H93G cavity mutant for modeling the coordination structures of novel heme iron protein active sites.
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Affiliation(s)
- Jing Du
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter St., Columbia, SC 29208, USA
| | - Masanori Sono
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter St., Columbia, SC 29208, USA
| | - John H. Dawson
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter St., Columbia, SC 29208, USA
- School of Medicine, University of South Carolina, 631 Sumter St., Columbia, SC 29208, USA
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Sivaramakrishnan S, Ouellet H, Matsumura H, Guan S, Moënne-Loccoz P, Burlingame AL, Ortiz de Montellano PR. Proximal ligand electron donation and reactivity of the cytochrome P450 ferric-peroxo anion. J Am Chem Soc 2012; 134:6673-84. [PMID: 22444582 DOI: 10.1021/ja211499q] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
CYP125 from Mycobacterium tuberculosis catalyzes sequential oxidation of the cholesterol side-chain terminal methyl group to the alcohol, aldehyde, and finally acid. Here, we demonstrate that CYP125 simultaneously catalyzes the formation of five other products, all of which result from deformylation of the sterol side chain. The aldehyde intermediate is shown to be the precursor of both the conventional acid metabolite and the five deformylation products. The acid arises by protonation of the ferric-peroxo anion species and formation of the ferryl-oxene species, also known as Compound I, followed by hydrogen abstraction and oxygen transfer. The deformylation products arise by addition of the same ferric-peroxo anion to the aldehyde intermediate to give a peroxyhemiacetal that leads to C-C bond cleavage. This bifurcation of the catalytic sequence has allowed us to examine the effect of electron donation by the proximal ligand on the properties of the ferric-peroxo anion. Replacement of the cysteine thiolate iron ligand by a selenocysteine results in UV-vis, EPR, and resonance Raman spectral changes indicative of an increased electron donation from the proximal selenolate ligand to the iron. Analysis of the product distribution in the reaction of the selenocysteine substituted enzyme reveals a gain in the formation of the acid (Compound I pathway) at the expense of deformylation products. These observations are consistent with an increase in the pK(a) of the ferric-peroxo anion, which favors its protonation and, therefore, Compound I formation.
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Affiliation(s)
- Santhosh Sivaramakrishnan
- Department of Pharmaceutical Chemistry, University of California, 600 16th Street, San Francisco, California 94158-2517, USA
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Metanis N, Hilvert D. Strategic Use of Non-Native Diselenide Bridges to Steer Oxidative Protein Folding. Angew Chem Int Ed Engl 2012; 51:5585-8. [DOI: 10.1002/anie.201109129] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Indexed: 11/07/2022]
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Metanis N, Hilvert D. Strategic Use of Non-Native Diselenide Bridges to Steer Oxidative Protein Folding. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201109129] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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