1
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Simonenko SY, Bogdanova DA, Kuldyushev NA. Emerging Roles of Vitamin B 12 in Aging and Inflammation. Int J Mol Sci 2024; 25:5044. [PMID: 38732262 PMCID: PMC11084641 DOI: 10.3390/ijms25095044] [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: 04/09/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Vitamin B12 (cobalamin) is an essential nutrient for humans and animals. Metabolically active forms of B12-methylcobalamin and 5-deoxyadenosylcobalamin are cofactors for the enzymes methionine synthase and mitochondrial methylmalonyl-CoA mutase. Malfunction of these enzymes due to a scarcity of vitamin B12 leads to disturbance of one-carbon metabolism and impaired mitochondrial function. A significant fraction of the population (up to 20%) is deficient in vitamin B12, with a higher rate of deficiency among elderly people. B12 deficiency is associated with numerous hallmarks of aging at the cellular and organismal levels. Cellular senescence is characterized by high levels of DNA damage by metabolic abnormalities, increased mitochondrial dysfunction, and disturbance of epigenetic regulation. B12 deficiency could be responsible for or play a crucial part in these disorders. In this review, we focus on a comprehensive analysis of molecular mechanisms through which vitamin B12 influences aging. We review new data about how deficiency in vitamin B12 may accelerate cellular aging. Despite indications that vitamin B12 has an important role in health and healthy aging, knowledge of the influence of vitamin B12 on aging is still limited and requires further research.
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Affiliation(s)
- Sergey Yu. Simonenko
- Research Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia;
| | - Daria A. Bogdanova
- Division of Immunobiology and Biomedicine, Center for Genetics and Life Sciences, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Nikita A. Kuldyushev
- Research Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia;
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2
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Marques HM. The inorganic chemistry of the cobalt corrinoids - an update. J Inorg Biochem 2023; 242:112154. [PMID: 36871417 DOI: 10.1016/j.jinorgbio.2023.112154] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023]
Abstract
The inorganic chemistry of the cobalt corrinoids, derivatives of vitamin B12, is reviewed, with particular emphasis on equilibrium constants for, and kinetics of, their axial ligand substitution reactions. The role the corrin ligand plays in controlling and modifying the properties of the metal ion is emphasised. Other aspects of the chemistry of these compounds, including their structure, corrinoid complexes with metals other than cobalt, the redox chemistry of the cobalt corrinoids and their chemical redox reactions, and their photochemistry are discussed. Their role as catalysts in non-biological reactions and aspects of their organometallic chemistry are briefly mentioned. Particular mention is made of the role that computational methods - and especially DFT calculations - have played in developing our understanding of the inorganic chemistry of these compounds. A brief overview of the biological chemistry of the B12-dependent enzymes is also given for the reader's convenience.
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Affiliation(s)
- Helder M Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa.
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3
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Ji L, Zhang H, Ding W, Song R, Han Y, Yu H, Paneth P. Theoretical Kinetic Isotope Effects in Establishing the Precise Biodegradation Mechanisms of Organic Pollutants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4915-4929. [PMID: 36926881 DOI: 10.1021/acs.est.2c04755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Compound-specific isotope analysis (CSIA) for natural isotope ratios has been recognized as a promising tool to elucidate biodegradation pathways of organic pollutants by microbial enzymes by relating reported kinetic isotope effects (KIEs) to apparent KIEs (AKIEs) derived from bulk isotope fractionations (εbulk). However, for many environmental reactions, neither are the reference KIE ranges sufficiently narrow nor are the mechanisms elucidated to the point that rate-determining steps have been identified unequivocally. In this work, besides providing reference KIEs and rationalizing AKIEs, good relationships have been explained by DFT computations for diverse biodegradation pathways with known enzymatic models between the theoretical isotope fractionations (εbulk') from intrinsic KIEs on the rate-determining steps and the observed εbulk. (1) To confirm the mechanistic details of previously reported pathway-dependent CSIA, it includes isotope changes in MTBE biodegradation between hydroxylation by CYP450 and SN2 reaction by cobalamin-dependent methyltransferase, the regioselectivity of toluene biodegradation by CYP450, and the rate-determining step in toluene biodegradation by benzylsuccinate synthase. (2) To yield new fundamental insights into some unclear biodegradation pathways, it consists of the oxidative function of toluene dioxygenase in biodegradation of TCE, the epoxidation mode in biodegradation of TCE by toluene 4-monooxygenase, and the weighted average mechanism in biodegradation of cDCE by CYP450.
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Affiliation(s)
- Li Ji
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
| | - Huanni Zhang
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Wen Ding
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
| | - Runqian Song
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Ye Han
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Daxue Road 1, Xuzhou 221116, China
| | - Haiying Yu
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Piotr Paneth
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Lodz 90-924, Poland
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4
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Joshi RP, Schultz KJ, Wilson JW, Kruel A, Varikoti RA, Kombala CJ, Kneller DW, Galanie S, Phillips G, Zhang Q, Coates L, Parvathareddy J, Surendranathan S, Kong Y, Clyde A, Ramanathan A, Jonsson CB, Brandvold KR, Zhou M, Head MS, Kovalevsky A, Kumar N. AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2. J Chem Inf Model 2023; 63:1438-1453. [PMID: 36808989 PMCID: PMC9969887 DOI: 10.1021/acs.jcim.2c01377] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/23/2023]
Abstract
Direct-acting antivirals for the treatment of the COVID-19 pandemic caused by the SARS-CoV-2 virus are needed to complement vaccination efforts. Given the ongoing emergence of new variants, automated experimentation, and active learning based fast workflows for antiviral lead discovery remain critical to our ability to address the pandemic's evolution in a timely manner. While several such pipelines have been introduced to discover candidates with noncovalent interactions with the main protease (Mpro), here we developed a closed-loop artificial intelligence pipeline to design electrophilic warhead-based covalent candidates. This work introduces a deep learning-assisted automated computational workflow to introduce linkers and an electrophilic "warhead" to design covalent candidates and incorporates cutting-edge experimental techniques for validation. Using this process, promising candidates in the library were screened, and several potential hits were identified and tested experimentally using native mass spectrometry and fluorescence resonance energy transfer (FRET)-based screening assays. We identified four chloroacetamide-based covalent inhibitors of Mpro with micromolar affinities (KI of 5.27 μM) using our pipeline. Experimentally resolved binding modes for each compound were determined using room-temperature X-ray crystallography, which is consistent with the predicted poses. The induced conformational changes based on molecular dynamics simulations further suggest that the dynamics may be an important factor to further improve selectivity, thereby effectively lowering KI and reducing toxicity. These results demonstrate the utility of our modular and data-driven approach for potent and selective covalent inhibitor discovery and provide a platform to apply it to other emerging targets.
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Affiliation(s)
- Rajendra P. Joshi
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Katherine J. Schultz
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Jesse William Wilson
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Agustin Kruel
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Rohith Anand Varikoti
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Chathuri J. Kombala
- Elson S. Floyd College of Medicine, Department of
Nutrition and Exercise Physiology, Washington State University,
Spokane, Washington 99202, United States
| | - Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Stephanie Galanie
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Biosciences Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United
States
- Department of Process Research and Development,
Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New
Jersey 07065, United States
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Leighton Coates
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Second Target Station, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United
States
| | - Jyothi Parvathareddy
- Regional Biocontainment Laboratory, The
University of Tennessee Health Science Center, Memphis, Tennessee 38105,
United States
| | - Surekha Surendranathan
- Regional Biocontainment Laboratory, The
University of Tennessee Health Science Center, Memphis, Tennessee 38105,
United States
| | - Ying Kong
- Regional Biocontainment Laboratory, The
University of Tennessee Health Science Center, Memphis, Tennessee 38105,
United States
| | - Austin Clyde
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
| | - Arvind Ramanathan
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
| | - Colleen B. Jonsson
- Regional Biocontainment Laboratory, The
University of Tennessee Health Science Center, Memphis, Tennessee 38105,
United States
- Institute for the Study of Host-Pathogen Systems,
University of Tennessee Health Science Center, Memphis,
Tennessee 38103, United States
- Department of Microbiology, Immunology and
Biochemistry, University of Tennessee Health Science Center,
Memphis, Tennessee 38103, United States
| | - Kristoffer R. Brandvold
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- Elson S. Floyd College of Medicine, Department of
Nutrition and Exercise Physiology, Washington State University,
Spokane, Washington 99202, United States
| | - Mowei Zhou
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Martha S. Head
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Joint Institute for Biological Sciences,
Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831,
United States
- Center for Research Acceleration by Digital
Innovation, Amgen Research, Thousand Oaks, California 91320,
United States
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Neeraj Kumar
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
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5
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Ghosh AP, Toda MJ, Kozlowski PM. What Triggers the Cleavage of the Co–C 5′ Bond in Coenzyme B 12-Dependent Itaconyl-CoA Methylmalonyl-CoA Mutase? ACS Catal 2021. [DOI: 10.1021/acscatal.1c00291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Arghya Pratim Ghosh
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
| | - Megan J. Toda
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
| | - Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
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6
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Spataru T. The complete electronic structure and mechanism of the methionine synthase process as determined by the MCSCF method. J Organomet Chem 2021. [DOI: 10.1016/j.jorganchem.2021.121811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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7
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Methyl transfer reactions catalyzed by cobalamin-dependent enzymes: Insight from molecular docking. J Mol Graph Model 2020; 104:107831. [PMID: 33529932 DOI: 10.1016/j.jmgm.2020.107831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 11/22/2022]
Abstract
Methyl transfer reactions, mediated by methyltransferases (MeTrs), such as methionine synthase (MetH) or monomethylamine: CoM (MtmBC), constitute one of the most important classes of vitamin B12-dependent reactions. The challenge in exploring the catalytic function of MeTrs is related to their modular structure. From the crystallographic point of view, the structure of each subunit has been determined, but there is a lack of understanding of how each subunit interacts with each other. So far, theoretical studies of methyl group transfer were carried out for the structural models of the active site of each subunit. However, those studies do not include the effect of the enzymatic environment, which is crucial for a comprehensive understanding of enzyme-mediated methyl transfer reactions. Herein, to explore how two subunits interact with each other and how the methyl transfer reaction is catalyzed by MeTrs, molecular docking of the functional units of MetH and MtmBC was carried out. Along with the interactions of the functional units, the reaction coordinates, including the Co-C bond distance for methylation of cob(I)alamin (CoICbl) and the C-S bond distance in demethylation reaction of cob(III)alamin (CoIIICbl), were considered. The functional groups should be arranged so that there is an appropriate distance to transfer a methyl group and present results indicate that steric interactions can limit the number of potential arrangements. This calls into question the possibility of SN2-type mechanism previously proposed for MeTrs. Further, it leads to the conclusion that the methyl transfer reaction involves some spatial changes of modules suggesting an alternate radical-based pathway for MeTrs-mediated methyl transfer reactions. The calculations also showed that changes in torsion angles induce a change in reaction coordinates, namely Co-C and C-S bond distances, for the methylation and demethylation reactions catalyzed both by MetH and MtmBC.
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8
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Elucidating the mechanism of cob(I)alamin mediated methylation reactions by alkyl halides: SN2 or radical mechanism? J Catal 2019. [DOI: 10.1016/j.jcat.2019.06.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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9
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Fernandes HS, Teixeira CSS, Sousa SF, Cerqueira NMFSA. Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview. Molecules 2019; 24:E2462. [PMID: 31277490 PMCID: PMC6651669 DOI: 10.3390/molecules24132462] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 11/16/2022] Open
Abstract
Nature has tailored a wide range of metalloenzymes that play a vast array of functions in all living organisms and from which their survival and evolution depends on. These enzymes catalyze some of the most important biological processes in nature, such as photosynthesis, respiration, water oxidation, molecular oxygen reduction, and nitrogen fixation. They are also among the most proficient catalysts in terms of their activity, selectivity, and ability to operate at mild conditions of temperature, pH, and pressure. In the absence of these enzymes, these reactions would proceed very slowly, if at all, suggesting that these enzymes made the way for the emergence of life as we know today. In this review, the structure and catalytic mechanism of a selection of diverse metalloenzymes that are involved in the production of highly reactive and unstable species, such as hydroxide anions, hydrides, radical species, and superoxide molecules are analyzed. The formation of such reaction intermediates is very difficult to occur under biological conditions and only a rationalized selection of a particular metal ion, coordinated to a very specific group of ligands, and immersed in specific proteins allows these reactions to proceed. Interestingly, different metal coordination spheres can be used to produce the same reactive and unstable species, although through a different chemistry. A selection of hand-picked examples of different metalloenzymes illustrating this diversity is provided and the participation of different metal ions in similar reactions (but involving different mechanism) is discussed.
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Affiliation(s)
- Henrique S Fernandes
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Carla S Silva Teixeira
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Sérgio F Sousa
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Nuno M F S A Cerqueira
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal.
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10
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Kumar N, Bucher D, Kozlowski PM. Mechanistic Implications of Reductive Co–C Bond Cleavage in B12-Dependent Methylmalonyl CoA Mutase. J Phys Chem B 2019; 123:2210-2216. [DOI: 10.1021/acs.jpcb.8b10820] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Neeraj Kumar
- Computational Biology and Bioinformatics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Denis Bucher
- Molecular Modeling & Design at leadXpro Villigen, Canton of Aargau, Switzerland
| | - Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
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11
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Ji L, Wang C, Ji S, Kepp KP, Paneth P. Mechanism of Cobalamin-Mediated Reductive Dehalogenation of Chloroethylenes. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00540] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Li Ji
- College
of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Chenchen Wang
- College
of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Shujing Ji
- College
of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
| | - Kasper P. Kepp
- DTU
Chemistry, Technical University of Denmark, Building 206, Kgs. Lyngby DK-2800, Denmark
| | - Piotr Paneth
- Institute
of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
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12
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Electronic and structural properties of Cob(I)alamin: Ramifications for B 12 -dependent processes. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.11.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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13
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Demissie TB, Garabato BD, Ruud K, Kozlowski PM. Mercury Methylation by Cobalt Corrinoids: Relativistic Effects Dictate the Reaction Mechanism. Angew Chem Int Ed Engl 2016; 55:11503-6. [DOI: 10.1002/anie.201606001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Taye B. Demissie
- Centre for Theoretical and Computational Chemistry; Department of Chemistry; UiT The Arctic University of Norway; 9037 Tromsø Norway
| | - Brady D. Garabato
- Department of Chemistry; University of Louisville; 2320 South Brook Street Louisville KY 40292 USA
| | - Kenneth Ruud
- Centre for Theoretical and Computational Chemistry; Department of Chemistry; UiT The Arctic University of Norway; 9037 Tromsø Norway
| | - Pawel M. Kozlowski
- Department of Chemistry; University of Louisville; 2320 South Brook Street Louisville KY 40292 USA
- Department of Food Sciences; Medical University of Gdansk; Al. Gen. J. Hallera 107 80-416 Gdansk Poland
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14
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Demissie TB, Garabato BD, Ruud K, Kozlowski PM. Mercury Methylation by Cobalt Corrinoids: Relativistic Effects Dictate the Reaction Mechanism. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Taye B. Demissie
- Centre for Theoretical and Computational Chemistry; Department of Chemistry; UiT The Arctic University of Norway; 9037 Tromsø Norway
| | - Brady D. Garabato
- Department of Chemistry; University of Louisville; 2320 South Brook Street Louisville KY 40292 USA
| | - Kenneth Ruud
- Centre for Theoretical and Computational Chemistry; Department of Chemistry; UiT The Arctic University of Norway; 9037 Tromsø Norway
| | - Pawel M. Kozlowski
- Department of Chemistry; University of Louisville; 2320 South Brook Street Louisville KY 40292 USA
- Department of Food Sciences; Medical University of Gdansk; Al. Gen. J. Hallera 107 80-416 Gdansk Poland
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15
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Spataru T, Fernandez F. The Nature of the Co-C Bond Cleavage Processes in Methylcob(II)Alamin and Adenosylcob(III)Alamin. CHEMISTRY JOURNAL OF MOLDOVA 2016. [DOI: 10.19261/cjm.2016.11(1).01] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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16
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17
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Garabato BD, Kumar N, Lodowski P, Jaworska M, Kozlowski PM. Electronically excited states of cob(ii)alamin: insights from CASSCF/XMCQDPT2 and TD-DFT calculations. Phys Chem Chem Phys 2016; 18:4513-26. [DOI: 10.1039/c5cp06439b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The low-lying excited states of cob(ii)alamin were investigated using time-dependent density functional theory (TD-DFT), and multiconfigurational CASSCF/XMCQDPT2 methodology, to help understand their role in B12-mediated reactions.
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Affiliation(s)
| | - Neeraj Kumar
- Department of Chemistry
- University of Louisville
- Louisville
- USA
- Pacific Northwest National Laboratory
| | - Piotr Lodowski
- Department of Theoretical Chemistry
- Institute of Chemistry
- University of Silesia
- PL-40 006 Katowice
- Poland
| | - Maria Jaworska
- Department of Theoretical Chemistry
- Institute of Chemistry
- University of Silesia
- PL-40 006 Katowice
- Poland
| | - Pawel M. Kozlowski
- Department of Chemistry
- University of Louisville
- Louisville
- USA
- Visiting Professor at the Department of Food Sciences
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18
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Morita Y, Oohora K, Sawada A, Doitomi K, Ohbayashi J, Kamachi T, Yoshizawa K, Hisaeda Y, Hayashi T. Intraprotein transmethylation via a CH3–Co(iii) species in myoglobin reconstituted with a cobalt corrinoid complex. Dalton Trans 2016; 45:3277-84. [DOI: 10.1039/c5dt04109k] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A cobalt corrinoid complex bound in the myoglobin heme pocket demonstrates the formation of a CH3–Co(iii) bond and subsequent transmethylation.
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Affiliation(s)
- Yoshitsugu Morita
- Department of Applied Chemistry
- Graduate School of Engineering
- Osaka University
- Suita 565-0871
- Japan
| | - Koji Oohora
- Department of Applied Chemistry
- Graduate School of Engineering
- Osaka University
- Suita 565-0871
- Japan
| | - Akiyoshi Sawada
- Institute for Materials Chemistry and Engineering and International Research Centre for Molecular Systems
- Kyushu University
- Fukuoka 819-0395
- Japan
| | - Kazuki Doitomi
- Institute for Materials Chemistry and Engineering and International Research Centre for Molecular Systems
- Kyushu University
- Fukuoka 819-0395
- Japan
| | - Jun Ohbayashi
- Department of Applied Chemistry
- Graduate School of Engineering
- Osaka University
- Suita 565-0871
- Japan
| | - Takashi Kamachi
- Institute for Materials Chemistry and Engineering and International Research Centre for Molecular Systems
- Kyushu University
- Fukuoka 819-0395
- Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering and International Research Centre for Molecular Systems
- Kyushu University
- Fukuoka 819-0395
- Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB)
| | - Yoshio Hisaeda
- Department of Chemistry and Biochemistry
- Graduate School of Engineering
- Kyushu University
- Fukuoka 819-0395
- Japan
| | - Takashi Hayashi
- Department of Applied Chemistry
- Graduate School of Engineering
- Osaka University
- Suita 565-0871
- Japan
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19
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 743] [Impact Index Per Article: 82.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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20
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Surducan M, Makarov SV, Silaghi-Dumitrescu R. Redox and linkage isomerism with ligands relevant to oxidative and nitrosative stress in cobalamin. Polyhedron 2014. [DOI: 10.1016/j.poly.2014.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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21
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Liu H, Kornobis K, Lodowski P, Jaworska M, Kozlowski PM. TD-DFT insight into photodissociation of the Co-C bond in coenzyme B12. Front Chem 2014; 1:41. [PMID: 24790969 PMCID: PMC3982521 DOI: 10.3389/fchem.2013.00041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 12/24/2013] [Indexed: 11/30/2022] Open
Abstract
Coenzyme B12 (AdoCbl) is one of the most biologically active forms of vitamin B12, and continues to be a topic of active research interest. The mechanism of Co-C bond cleavage in AdoCbl, and the corresponding enzymatic reactions are however, not well understood at the molecular level. In this work, time-dependent density functional theory (TD-DFT) has been applied to investigate the photodissociation of coenzyme B12. To reduce computational cost, while retaining the major spectroscopic features of AdoCbl, a truncated model based on ribosylcobalamin (RibCbl) was used to simulate Co-C photodissociation. Equilibrium geometries of RibCbl were obtained by optimization at the DFT/BP86/TZVP level of theory, and low-lying excited states were calculated by TD-DFT using the same functional and basis set. The calculated singlet states, and absorption spectra were simulated in both the gas phase, and water, using the polarizable continuum model (PCM). Both spectra were in reasonable agreement with experimental data, and potential energy curves based on vertical excitations were plotted to explore the nature of Co-C bond dissociation. It was found that a repulsive 3(σCo−C → σ*Co−C) triplet state became dissociative at large Co-C bond distance, similar to a previous observation for methylcobalamin (MeCbl). Furthermore, potential energy surfaces (PESs) obtained as a function of both Co-CRib and Co-NIm distances, identify the S1 state as a key intermediate generated during photoexcitation of RibCbl, attributed to a mixture of a metal-to-ligand charge transfer (MLCT) and a σ bonding-ligand charge transfer (SBLCT) states.
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Affiliation(s)
- Hui Liu
- Department of Chemistry, University of Louisville Louisville, KY, USA
| | - Karina Kornobis
- Department of Chemistry, University of Louisville Louisville, KY, USA
| | - Piotr Lodowski
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia Katowice, Poland
| | - Maria Jaworska
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia Katowice, Poland
| | - Pawel M Kozlowski
- Department of Chemistry, University of Louisville Louisville, KY, USA
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22
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Kumar N, Camaioni DM, Dupuis M, Raugei S, Appel AM. Mechanistic insights into hydride transfer for catalytic hydrogenation of CO2 with cobalt complexes. Dalton Trans 2014; 43:11803-6. [DOI: 10.1039/c4dt01551g] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The catalytic hydrogenation of CO2 to formate by Co(dmpe)2H can proceed via direct hydride transfer or via CO2 coordination to Co followed by reductive elimination of formate.
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Affiliation(s)
- N. Kumar
- Pacific Northwest National Laboratory
- Richland, USA
| | | | - M. Dupuis
- Pacific Northwest National Laboratory
- Richland, USA
| | - S. Raugei
- Pacific Northwest National Laboratory
- Richland, USA
| | - A. M. Appel
- Pacific Northwest National Laboratory
- Richland, USA
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