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Lehene M, Plesa D, Ionescu-Zinca S, Iancu SD, Leopold N, Makarov SV, Brânzanic AMV, Silaghi-Dumitrescu R. Adduct of Aquacobalamin with Hydrogen Peroxide. Inorg Chem 2021; 60:12681-12684. [PMID: 34382784 DOI: 10.1021/acs.inorgchem.1c01483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aquacobalamin binds hydrogen peroxide reversibly to form a cobalt(III) hydroperoxo adduct with a 0.25 mM dissociation constant, as evidenced by UV-vis absorption spectroscopy and corroborated by NMR, Raman spectroscopy, stopped-flow UV-vis measurements, and density functional theory calculations.
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Affiliation(s)
- Maria Lehene
- Department of Chemistry, Babes-Bolyai University (BBU), Str. Arany Janos Nr. 11, RO-400028 Cluj-Napoca, Romania
| | - Diana Plesa
- Department of Chemistry, Babes-Bolyai University (BBU), Str. Arany Janos Nr. 11, RO-400028 Cluj-Napoca, Romania
| | - Stefania Ionescu-Zinca
- Department of Chemistry, Babes-Bolyai University (BBU), Str. Arany Janos Nr. 11, RO-400028 Cluj-Napoca, Romania
| | - Stefania D Iancu
- Faculty of Physics, Babes-Bolyai University (BBU), Str. Kogalniceanu 1, RO-400084 Cluj-Napoca, Romania
| | - Nicolae Leopold
- Faculty of Physics, Babes-Bolyai University (BBU), Str. Kogalniceanu 1, RO-400084 Cluj-Napoca, Romania
| | - Sergei V Makarov
- Ivanovo State University of Chemistry and Technology, Sheremetevskiy Str. 7, 153000 Ivanovo, Russia
| | - Adrian M V Brânzanic
- Department of Chemistry, Babes-Bolyai University (BBU), Str. Arany Janos Nr. 11, RO-400028 Cluj-Napoca, Romania
| | - Radu Silaghi-Dumitrescu
- Department of Chemistry, Babes-Bolyai University (BBU), Str. Arany Janos Nr. 11, RO-400028 Cluj-Napoca, Romania
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2
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Sciortino G, Maréchal JD, Garribba E. Integrated experimental/computational approaches to characterize the systems formed by vanadium with proteins and enzymes. Inorg Chem Front 2021. [DOI: 10.1039/d0qi01507e] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An integrated instrumental/computational approach to characterize metallodrug–protein adducts at the molecular level is reviewed. A series of applications are described, focusing on potential vanadium drugs with a generalization to other metals.
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Affiliation(s)
- Giuseppe Sciortino
- Departament de Química
- Universitat Autònoma de Barcelona
- Cerdanyola del Vallès
- Barcelona 08193
- Spain
| | - Jean-Didier Maréchal
- Departament de Química
- Universitat Autònoma de Barcelona
- Cerdanyola del Vallès
- Barcelona 08193
- Spain
| | - Eugenio Garribba
- Dipartimento di Chimica e Farmacia
- Università di Sassari
- 07100 Sassari
- Italy
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3
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Menon BRK, Richmond D, Menon N. Halogenases for biosynthetic pathway engineering: Toward new routes to naturals and non-naturals. CATALYSIS REVIEWS-SCIENCE AND ENGINEERING 2020. [DOI: 10.1080/01614940.2020.1823788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Binuraj R. K. Menon
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, UK
| | - Daniel Richmond
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, UK
| | - Navya Menon
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, UK
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4
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Anderson GA, Behera RN, Gomatam R. Calculation of higher protonation states and of a new resting state for vanadium chloroperoxidase using QM/MM, with an Atom-in-Molecules analysis. J Mol Graph Model 2020; 99:107624. [PMID: 32388271 DOI: 10.1016/j.jmgm.2020.107624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/12/2020] [Accepted: 04/16/2020] [Indexed: 12/18/2022]
Abstract
Earlier QM/MM studies of the resting state of vanadium chloroperoxidase (VCPO) focused on the diprotonated states of the vanadate cofactor. Herein, we report a new extensive QM/MM study that includes the tri- and quadprotonated states of VCPO at neutral pH. We identify certain di- and triprotonated states as being candidates for the resting state based on a comparison of relative energies. The quadprotonated states as well as some of the triprotonated states are ruled out as the resting state. An Atoms-in-Molecules (AIM) analysis of the complex hydrogen bonding around the vanadate cofactor helps to explain the relative energies of the protonation states considered herein, and it also indicates new hydrogen bonding which has not been recognized previously. A Natural Bond Orbital (NBO) study is presented to give a better understanding of the electronic structure of the vanadate co-factor.
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Affiliation(s)
| | - Raghu Nath Behera
- Department of Chemistry, Birla Institute of Technology and Science, Pilani - Goa Campus, Zuarinagar, Goa, 403726, India.
| | - Ravi Gomatam
- Bhaktivedanta Institute and Institute of Semantic Information Sciences and Technology, Juhu Road, Juhu, Mumbai, 400049, India
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5
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Morzan UN, Alonso de Armiño DJ, Foglia NO, Ramírez F, González Lebrero MC, Scherlis DA, Estrin DA. Spectroscopy in Complex Environments from QM–MM Simulations. Chem Rev 2018; 118:4071-4113. [DOI: 10.1021/acs.chemrev.8b00026] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Uriel N. Morzan
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Diego J. Alonso de Armiño
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Nicolás O. Foglia
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Francisco Ramírez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Mariano C. González Lebrero
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Damián A. Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
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6
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Leblanc C, Vilter H, Fournier JB, Delage L, Potin P, Rebuffet E, Michel G, Solari P, Feiters M, Czjzek M. Vanadium haloperoxidases: From the discovery 30 years ago to X-ray crystallographic and V K-edge absorption spectroscopic studies. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2015.02.013] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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7
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Gupta R, Hou G, Renirie R, Wever R, Polenova T. 51V NMR Crystallography of Vanadium Chloroperoxidase and Its Directed Evolution P395D/L241V/T343A Mutant: Protonation Environments of the Active Site. J Am Chem Soc 2015; 137:5618-28. [DOI: 10.1021/jacs.5b02635] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Rupal Gupta
- Department
of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Guangjin Hou
- Department
of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Rokus Renirie
- Van’t
Hoff Institute for Molecular Science, University of Amsterdam, POSTBUS
94157, 1090 GD, Amsterdam, The Netherlands
| | - Ron Wever
- Van’t
Hoff Institute for Molecular Science, University of Amsterdam, POSTBUS
94157, 1090 GD, Amsterdam, The Netherlands
| | - Tatyana Polenova
- Department
of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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8
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Senn HM. Insights into enzymatic halogenation from computational studies. Front Chem 2014; 2:98. [PMID: 25426489 PMCID: PMC4227530 DOI: 10.3389/fchem.2014.00098] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/20/2014] [Indexed: 12/15/2022] Open
Abstract
The halogenases are a group of enzymes that have only come to the fore over the last 10 years thanks to the discovery and characterization of several novel representatives. They have revealed the fascinating variety of distinct chemical mechanisms that nature utilizes to activate halogens and introduce them into organic substrates. Computational studies using a range of approaches have already elucidated many details of the mechanisms of these enzymes, often in synergistic combination with experiment. This Review summarizes the main insights gained from these studies. It also seeks to identify open questions that are amenable to computational investigations. The studies discussed herein serve to illustrate some of the limitations of the current computational approaches and the challenges encountered in computational mechanistic enzymology.
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Affiliation(s)
- Hans M. Senn
- WestCHEM School of Chemistry, University of GlasgowGlasgow, UK
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10
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Chatterjee PB, Goncharov-Zapata O, Quinn LL, Hou G, Hamaed H, Schurko RW, Polenova T, Crans DC. Characterization of noninnocent metal complexes using solid-state NMR spectroscopy: o-dioxolene vanadium complexes. Inorg Chem 2011; 50:9794-803. [PMID: 21842875 DOI: 10.1021/ic200046k] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
(51)V solid-state NMR (SSNMR) studies of a series of noninnocent vanadium(V) catechol complexes have been conducted to evaluate the possibility that (51)V NMR observables, quadrupolar and chemical shift anisotropies, and electronic structures of such compounds can be used to characterize these compounds. The vanadium(V) catechol complexes described in these studies have relatively small quadrupolar coupling constants, which cover a surprisingly small range from 3.4 to 4.2 MHz. On the other hand, isotropic (51)V NMR chemical shifts cover a wide range from -200 to 400 ppm in solution and from -219 to 530 ppm in the solid state. A linear correlation of (51)V NMR isotropic solution and solid-state chemical shifts of complexes containing noninnocent ligands is observed. These experimental results provide the information needed for the application of (51)V SSNMR spectroscopy in characterizing the electronic properties of a wide variety of vanadium-containing systems and, in particular, those containing noninnocent ligands and that have chemical shifts outside the populated range of -300 to -700 ppm. The studies presented in this report demonstrate that the small quadrupolar couplings covering a narrow range of values reflect the symmetric electronic charge distribution, which is also similar across these complexes. These quadrupolar interaction parameters alone are not sufficient to capture the rich electronic structure of these complexes. In contrast, the chemical shift anisotropy tensor elements accessible from (51)V SSNMR experiments are a highly sensitive probe of subtle differences in electronic distribution and orbital occupancy in these compounds. Quantum chemical (density functional theory) calculations of NMR parameters for [VO(hshed)(Cat)] yield a (51)V chemical shift anisotropy tensor in reasonable agreement with the experimental results, but surprisingly the calculated quadrupolar coupling constant is significantly greater than the experimental value. The studies demonstrate that substitution of the catechol ligand with electron-donating groups results in an increase in the HOMO-LUMO gap and can be directly followed by an upfield shift for the vanadium catechol complex. In contrast, substitution of the catechol ligand with electron-withdrawing groups results in a decrease in the HOMO-LUMO gap and can directly be followed by a downfield shift for the complex. The vanadium catechol complexes were used in this work because (51)V is a half-integer quadrupolar nucleus whose NMR observables are highly sensitive to the local environment. However, the results are general and could be extended to other redox-active complexes that exhibit coordination chemistry similar to that of the vanadium catechol complexes.
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Affiliation(s)
- Pabitra B Chatterjee
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872, USA
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11
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Pacios LF, Gálvez O. Active Site, Catalytic Cycle, and Iodination Reactions of Vanadium Iodoperoxidase: A Computational Study. J Chem Theory Comput 2010; 6:1738-52. [DOI: 10.1021/ct100041x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Luis F. Pacios
- Departamento de Biotecnología, Unidad de Química y Bioquímica, E.TSI Montes, Universidad Politécnica de Madrid, 28040 Madrid, Spain, and Departamento de Física Molecular, Instituto de Estructura de la Materia, C.S.I.C., Serrano 121, 28006 Madrid, Spain
| | - Oscar Gálvez
- Departamento de Biotecnología, Unidad de Química y Bioquímica, E.TSI Montes, Universidad Politécnica de Madrid, 28040 Madrid, Spain, and Departamento de Física Molecular, Instituto de Estructura de la Materia, C.S.I.C., Serrano 121, 28006 Madrid, Spain
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12
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Zeng B, Shen T, Wu A, Cai S, Yu X, Xu X, Chen Z. Spectroscopic and DFT Study on the Interaction System of Vanadium with l-Proline in Aqueous Solution. J Phys Chem A 2010; 114:5211-6. [DOI: 10.1021/jp1010378] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Birong Zeng
- Department of Materials Science and Engineering, and Department of Physics, Fujian Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen 361005, China and Department of Chemistry, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Tonghao Shen
- Department of Materials Science and Engineering, and Department of Physics, Fujian Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen 361005, China and Department of Chemistry, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Anan Wu
- Department of Materials Science and Engineering, and Department of Physics, Fujian Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen 361005, China and Department of Chemistry, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Shuhui Cai
- Department of Materials Science and Engineering, and Department of Physics, Fujian Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen 361005, China and Department of Chemistry, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Xianyong Yu
- Department of Materials Science and Engineering, and Department of Physics, Fujian Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen 361005, China and Department of Chemistry, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Xin Xu
- Department of Materials Science and Engineering, and Department of Physics, Fujian Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen 361005, China and Department of Chemistry, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Zhong Chen
- Department of Materials Science and Engineering, and Department of Physics, Fujian Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen 361005, China and Department of Chemistry, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
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13
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Zhao HY, Xing YH, Cao YZ, Li ZP, Wei DM, Zeng XQ, Ge MF. Synthesis, structure and properties of three new oxidovanadium complexes containing a tridentate salicylaldehydeglycine. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2009.09.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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14
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Zhao HY, Zhang YH, Xing YH, Li ZP, Cao YZ, Ge MF, Zeng XQ, Niu SY. A series of oxo-vanadium(IV) complexes containing mixed ligands of poly(pyrazolyl)borate and organic carboxylic acid: Synthesis, structural characterization and primary study of bromination reaction activities. Inorganica Chim Acta 2009. [DOI: 10.1016/j.ica.2009.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Winter JM, Moore BS. Exploring the chemistry and biology of vanadium-dependent haloperoxidases. J Biol Chem 2009; 284:18577-81. [PMID: 19363038 DOI: 10.1074/jbc.r109.001602] [Citation(s) in RCA: 164] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nature has developed an exquisite array of methods to introduce halogen atoms into organic compounds. Most of these enzymes are oxidative and require either hydrogen peroxide or molecular oxygen as a cosubstrate to generate a reactive halogen atom for catalysis. Vanadium-dependent haloperoxidases contain a vanadate prosthetic group and utilize hydrogen peroxide to oxidize a halide ion into a reactive electrophilic intermediate. These metalloenzymes have a large distribution in nature, where they are present in macroalgae, fungi, and bacteria, but have been exclusively characterized in eukaryotes. In this minireview, we highlight the chemistry and biology of vanadium-dependent haloperoxidases from fungi and marine algae and the emergence of new bacterial members that extend the biological function of these poorly understood halogenating enzymes.
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Affiliation(s)
- Jaclyn M Winter
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093, USA
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16
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Geethalakshmi KR, Waller MP, Thiel W, Bühl M. 51V NMR Chemical Shifts Calculated from QM/MM Models of Peroxo Forms of Vanadium Haloperoxidases. J Phys Chem B 2009; 113:4456-65. [DOI: 10.1021/jp8109308] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- K. R. Geethalakshmi
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany, and School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, U.K
| | - Mark P. Waller
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany, and School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, U.K
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany, and School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, U.K
| | - Michael Bühl
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany, and School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, U.K
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