1
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Elmendorf LD, Brunold TC. Vibronic Coupling in Vitamin B 12: A Combined Spectroscopic and Computational Study. Inorg Chem 2023; 62:12762-12772. [PMID: 37463115 DOI: 10.1021/acs.inorgchem.3c01305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Understanding the diverse reactivities of vitamin B12 and its derivatives, collectively called cobalamins, requires detailed knowledge of their geometric and electronic structures. Electronic absorption (Abs) and resonance Raman (rR) spectroscopies have proven invaluable in this area, particularly when used in concert with computational techniques such as density functional theory (DFT). There remain, however, lingering uncertainties in the computational description of electronic excited states of cobalamins, particularly surrounding the vibronic coupling that impacts the Abs bandshapes and gives rise to rR enhancement of vibrational modes. Past computational analyses of the vibrational spectra of cobalamins have either neglected rR enhancement or calculated rR enhancement for only a small number of modes. In the present study, we used the recently developed ORCA_ASA computational tool in conjunction with the popular B3LYP and BP86 functionals to predict Abs bandshapes and rR spectra for vitamin B12. The ORCA_ASA/B3LYP-computed Abs envelope in the visible spectral region and rR spectra of vitamin B12 agree remarkably well with our experimental data, while BP86 fails to reproduce both. This finding represents a significant advance in our understanding of how these two commonly used density functionals differently model the electronic properties of cobalamins. Guided by the computed frequencies for the Co-C stretching and Co-C-N bending modes, we identified, for the first time, isotope-sensitive features in our rR spectra of 12CNCbl and 13CNCbl that can be assigned to these modes. A normal coordinate analysis of the experimentally determined Co-C stretching and Co-C-N bending frequencies indicates that the Co-C force constant for vitamin B12 is 2.67 mdyn/Å, considerably larger than the Co-C force constants reported for alkylcobalamins.
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Affiliation(s)
- Laura D Elmendorf
- Department of Chemistry, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
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2
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Clyde A, Galanie S, Kneller DW, Ma H, Babuji Y, Blaiszik B, Brace A, Brettin T, Chard K, Chard R, Coates L, Foster I, Hauner D, Kertesz V, Kumar N, Lee H, Li Z, Merzky A, Schmidt JG, Tan L, Titov M, Trifan A, Turilli M, Van Dam H, Chennubhotla SC, Jha S, Kovalevsky A, Ramanathan A, Head MS, Stevens R. High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor. J Chem Inf Model 2022; 62:116-128. [PMID: 34793155 PMCID: PMC8610012 DOI: 10.1021/acs.jcim.1c00851] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Indexed: 12/27/2022]
Abstract
Despite the recent availability of vaccines against the acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the search for inhibitory therapeutic agents has assumed importance especially in the context of emerging new viral variants. In this paper, we describe the discovery of a novel noncovalent small-molecule inhibitor, MCULE-5948770040, that binds to and inhibits the SARS-Cov-2 main protease (Mpro) by employing a scalable high-throughput virtual screening (HTVS) framework and a targeted compound library of over 6.5 million molecules that could be readily ordered and purchased. Our HTVS framework leverages the U.S. supercomputing infrastructure achieving nearly 91% resource utilization and nearly 126 million docking calculations per hour. Downstream biochemical assays validate this Mpro inhibitor with an inhibition constant (Ki) of 2.9 μM (95% CI 2.2, 4.0). Furthermore, using room-temperature X-ray crystallography, we show that MCULE-5948770040 binds to a cleft in the primary binding site of Mpro forming stable hydrogen bond and hydrophobic interactions. We then used multiple μs-time scale molecular dynamics (MD) simulations and machine learning (ML) techniques to elucidate how the bound ligand alters the conformational states accessed by Mpro, involving motions both proximal and distal to the binding site. Together, our results demonstrate how MCULE-5948770040 inhibits Mpro and offers a springboard for further therapeutic design.
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Affiliation(s)
- Austin Clyde
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Stephanie Galanie
- Biosciences Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Heng Ma
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Yadu Babuji
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Ben Blaiszik
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Alexander Brace
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Thomas Brettin
- Computing Environment and Life Sciences Directorate,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Kyle Chard
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Ryan Chard
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Ian Foster
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Darin Hauner
- Computational Biology Group, Biological Science Division,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Vlimos Kertesz
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Neeraj Kumar
- Computational Biology Group, Biological Science Division,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Hyungro Lee
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Zhuozhao Li
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Andre Merzky
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Jurgen G. Schmidt
- Bioscience Division, Los Alamos National
Laboratory, Los Alamos, New Mexico 87545, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Li Tan
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Mikhail Titov
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Anda Trifan
- University of Illinois at
Urbana-Champaign, Champaign, Illinois 61820, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Matteo Turilli
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- Computational Science Initiative,
Brookhaven National Laboratory, Upton, New York 11973,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Hubertus Van Dam
- Computational Science Initiative,
Brookhaven National Laboratory, Upton, New York 11973,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Srinivas C. Chennubhotla
- Department of Computational and Systems
Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
15260, United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Shantenu Jha
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- Computational Science Initiative,
Brookhaven National Laboratory, Upton, New York 11973,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Andrey Kovalevsky
- Second Target Station, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Arvind Ramanathan
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Martha S. Head
- Joint Institute for Biological Sciences,
Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Rick Stevens
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- Computing Environment and Life Sciences Directorate,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
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3
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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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4
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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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5
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Bellows SM, Cundari TR, Jones WD. Methane Is the Best Substrate for C(sp3)–H Activation with Cp*(PMe3)Co(Me)(OTf): A Density Functional Theory Study. Organometallics 2015. [DOI: 10.1021/acs.organomet.5b00452] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sarina M. Bellows
- Department
of Chemistry, University of Rochester, New York 14627, United States
- Center for Enabling
New Technologies through Catalysis (CENTC), Department
of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - Thomas R. Cundari
- Department
of Chemistry and CASCaM, University of North Texas, Denton, Texas 76203, United States
- Center for Enabling
New Technologies through Catalysis (CENTC), Department
of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - William D. Jones
- Department
of Chemistry, University of Rochester, New York 14627, United States
- Center for Enabling
New Technologies through Catalysis (CENTC), Department
of Chemistry, University of Washington, Seattle, Washington 98195-1700
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6
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Kepp KP. Co-C dissociation of adenosylcobalamin (coenzyme B12): role of dispersion, induction effects, solvent polarity, and relativistic and thermal corrections. J Phys Chem A 2014; 118:7104-17. [PMID: 25116644 DOI: 10.1021/jp503607k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantum-chemical cluster modeling is challenged in the limit of large, soft systems by the effects of dispersion and solvent, and well as other physical interactions. Adenosylcobalamin (AdoCbl, coenzyme B12), as one of the most complex cofactors in life, constitutes such a challenge. The cleavage of its unique organometallic Co-C bond has inspired multiple studies of this cofactor. This paper reports the fully relaxed potential energy surface of Co-C cleavage of AdoCbl, including for the first time all side-chain interactions with the dissociating Ado group. Various methods and corrections for dispersion, relativistic effects, solvent polarity, basis set superposition error, and thermal and vibrational effects were investigated, totaling more than 550 single-point energies for the large model. The results show immense variability depending on method, including solvation, functional type, and dispersion, challenging the conceived accuracy of methods used for such systems. In particular, B3LYP-D3 seems to severely underestimate the Co-C bond strength, consistent with previous results, and BP86 remains accurate for cobalamins when dispersion interactions are accounted for.
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Affiliation(s)
- Kasper P Kepp
- DTU Chemistry, Technical University of Denmark , Building 206, Kgs. Lyngby, DK-2800, Denmark
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7
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Recent Developments in Computational Bioinorganic Chemistry. STRUCTURE AND BONDING 2012. [DOI: 10.1007/b97941] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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8
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Rommel JB, Kästner J. The fragmentation-recombination mechanism of the enzyme glutamate mutase studied by QM/MM simulations. J Am Chem Soc 2011; 133:10195-203. [PMID: 21612278 DOI: 10.1021/ja202312d] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The radical mechanism of the conversion of glutamate to methylaspartate catalyzed by glutamate mutase is studied with quantum mechanical/molecular mechanical (QM/MM) simulations based on density functional theory (DFT/MM). The hydrogen transfer between the substrate and the cofactor is found to be rate limiting with a barrier of 101.1 kJ mol(-1). A careful comparison to the uncatalyzed reaction in water is performed. The protein influences the reaction predominantly electrostatically and to a lesser degree sterically. Our calculations shed light on the atomistic details of the reaction mechanism. The well-known arginine claw and Glu 171 ( Clostridium cochlearium notation) are found to have the strongest influence on the reaction. However, a catalytic role of Glu 214, Lys 322, Gln 147, Glu 330, Lys 326, and Met 294 is found as well. The arginine claw keeps the intermediates in place and is probably responsible for the enantioselectivity. Glu 171 temporarily accepts a proton from the glutamyl radical intermediate and donates it back at the end of the reaction. We relate our results to experimental data when available. Our simulations lead to further understanding of how glutamate mutase catalyzes the carbon skeleton rearrangement of glutamate.
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Affiliation(s)
- Judith B Rommel
- Computational Biochemistry Group, Institute of Theoretical Chemistry, University of Stuttgart, Stuttgart, Germany
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9
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Fernández I, Cossío FP, Sierra MA. Dyotropic Reactions: Mechanisms and Synthetic Applications. Chem Rev 2009; 109:6687-711. [DOI: 10.1021/cr900209c] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Israel Fernández
- Departamento de Química Orgánica, Facultad de Química, Universidad Complutense, 28040-Madrid, Spain, and Kimika Organikoa I Saila—Departamento de Química Orgánica I, DIPC, Universidad del País Vasco—Euskal Herriko Unibertsitatea, P.K. 1072, 28080-San Sebastián Donostia, Spain
| | - Fernando P. Cossío
- Departamento de Química Orgánica, Facultad de Química, Universidad Complutense, 28040-Madrid, Spain, and Kimika Organikoa I Saila—Departamento de Química Orgánica I, DIPC, Universidad del País Vasco—Euskal Herriko Unibertsitatea, P.K. 1072, 28080-San Sebastián Donostia, Spain
| | - Miguel A. Sierra
- Departamento de Química Orgánica, Facultad de Química, Universidad Complutense, 28040-Madrid, Spain, and Kimika Organikoa I Saila—Departamento de Química Orgánica I, DIPC, Universidad del País Vasco—Euskal Herriko Unibertsitatea, P.K. 1072, 28080-San Sebastián Donostia, Spain
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10
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Mebs S, Henn J, Dittrich B, Paulmann C, Luger P. Electron Densities of Three B12 Vitamins. J Phys Chem A 2009; 113:8366-78. [DOI: 10.1021/jp902433x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stefan Mebs
- Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Fabeckstrasse 36a, 14195 Berlin, Germany, Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany, Mineralogisch-Petrographisches Institut, Universität Hamburg, Grindelallee 48, 20146 Hamburg, Germany
| | - Julian Henn
- Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Fabeckstrasse 36a, 14195 Berlin, Germany, Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany, Mineralogisch-Petrographisches Institut, Universität Hamburg, Grindelallee 48, 20146 Hamburg, Germany
| | - Birger Dittrich
- Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Fabeckstrasse 36a, 14195 Berlin, Germany, Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany, Mineralogisch-Petrographisches Institut, Universität Hamburg, Grindelallee 48, 20146 Hamburg, Germany
| | - Carsten Paulmann
- Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Fabeckstrasse 36a, 14195 Berlin, Germany, Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany, Mineralogisch-Petrographisches Institut, Universität Hamburg, Grindelallee 48, 20146 Hamburg, Germany
| | - Peter Luger
- Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Fabeckstrasse 36a, 14195 Berlin, Germany, Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany, Mineralogisch-Petrographisches Institut, Universität Hamburg, Grindelallee 48, 20146 Hamburg, Germany
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11
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Liptak MD, Van Heuvelen KM, Brunold* TC. Computational Studies of Bioorganometallic Enzymes and Cofactors. METAL-CARBON BONDS IN ENZYMES AND COFACTORS 2009. [DOI: 10.1039/9781847559333-00417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Because of their complex geometric and electronic structures, the active sites and cofactors of bioorganometallic enzymes, which are characterized by their metal–carbon bonds, pose a major challenge for computational chemists. However, recent progress in computer technology and theoretical chemistry, along with insights gained from mechanistic, spectroscopic, and X-ray crystallographic studies, have established an excellent foundation for the successful completion of computational studies aimed at elucidating the electronic structures and catalytic cycles of these species. This chapter briefly reviews the most popular computational approaches employed in theoretical studies of bioorganometallic species and summarizes important information obtained from computational studies of (i) the enzymatic formation and cleavage of the Co–C bond of coenzyme B12; (ii) the catalytic cycle of methyl-coenzyme M reductase and its nickel-containing cofactor F430; (iii) the polynuclear active-site clusters of the bifunctional enzyme carbon monoxide dehydrogenase/acetyl-coenzyme A synthase; and (iv) the magnetic properties of the active-site cluster of Fe-only hydrogenases.
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Affiliation(s)
- Matthew D. Liptak
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
| | | | - Thomas C. Brunold*
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
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12
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Andruniów T, Jaworska M, Lodowski P, Zgierski MZ, Dreos R, Randaccio L, Kozlowski PM. Time-dependent density functional theory study of cobalt corrinoids: Electronically excited states of methylcobalamin. J Chem Phys 2008; 129:085101. [DOI: 10.1063/1.2956836] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Qi XJ, Li Z, Fu Y, Guo QX, Liu L. anti-Spin-Delocalization Effect in Co−C Bond Dissociation Enthalpies. Organometallics 2008. [DOI: 10.1021/om701135c] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Xiu-Juan Qi
- Joint Laboratory of Green Synthetic Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China, and Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Zhe Li
- Joint Laboratory of Green Synthetic Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China, and Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yao Fu
- Joint Laboratory of Green Synthetic Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China, and Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Qing-Xiang Guo
- Joint Laboratory of Green Synthetic Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China, and Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Lei Liu
- Joint Laboratory of Green Synthetic Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei 230026, China, and Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
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14
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Kamachi T, Toraya T, Yoshizawa K. Computational Mutation Analysis of Hydrogen Abstraction and Radical Rearrangement Steps in the Catalysis of Coenzyme B12-Dependent Diol Dehydratase. Chemistry 2007; 13:7864-73. [PMID: 17614304 DOI: 10.1002/chem.200601466] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A mutation analysis of the catalytic functions of active-site residues of coenzyme B(12)-dependent diol dehydratase in the conversion of 1,2-propanediol to 1,1-propanediol has been carried out by using QM/MM computations. Mutants His143Ala, Glu170Gln, Glu170Ala, and Glu170Ala/Glu221Ala were considered to estimate the impact of the mutations of His143 and Glu170. In the His143Ala mutant the activation energy for OH migration increased to 16.4 from 11.5 kcal mol(-1) in the wild-type enzyme. The highest activation energy, 19.6 kcal mol(-1), was measured for hydrogen back-abstraction in this reaction. The transition state for OH migration is not sufficiently stabilized by the hydrogen-bonding interaction formed between the spectator OH group and Gln170 in the Glu170Gln mutant, which demonstrates that a strong proton acceptor is required to promote OH migration. In the Glu170Ala mutant, a new strong hydrogen bond is formed between the spectator OH group and Glu221. A computed activation energy of 13.6 kcal mol(-1) for OH migration in the Glu170Ala mutant is only 2.1 kcal mol(-1) higher than the corresponding barrier in the wild-type enzyme. Despite the low activation barrier, the Glu170Ala mutant is inactive because the subsequent hydrogen back-abstraction is energetically demanding in this mutant. OH migration is not feasible in the Glu170Ala/Glu221Ala mutant because the activation barrier for OH migration is greatly increased by the loss of COO(-) groups near the spectator OH group. This result indicates that the effect of partial deprotonation of the spectator OH group is the most important factor in reducing the activation barrier for OH migration in the conversion of 1,2-propanediol to 1,1-propanediol catalyzed by diol dehydratase.
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Affiliation(s)
- Takashi Kamachi
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
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15
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Kuta J, Patchkovskii S, Zgierski MZ, Kozlowski PM. Performance of DFT in modeling electronic and structural properties of cobalamins. J Comput Chem 2007; 27:1429-37. [PMID: 16807975 DOI: 10.1002/jcc.20454] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Computational modeling of the enzymatic activity of B12-dependent enzymes requires a detailed understanding of the factors that influence the strength of the Co--C bond and the limits associated with a particular level of theory. To address this issue, a systematic analysis of the electronic and structural properties of coenzyme B12 models has been performed to establish the performance of three different functionals including B3LYP, BP86, and revPBE. In particular the cobalt-carbon bond dissociation energies, axial bond lengths, and selected stretching frequencies have been analyzed in detail. Current analysis shows that widely used B3LYP functional significantly underestimates the strength of the Co--C bond while the nonhybrid BP86 functional produces very consistent results in comparison to experimental data. To explain such different performance of these functionals molecular orbital analysis associated with axial bonds has been performed to show differences in axial bonding provided by hybrid and nonhybrid functionals.
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Affiliation(s)
- Jadwiga Kuta
- Department of Chemistry, University of Louisville, 2320 S. Brook Street, Louisville, Kentucky 40292, USA
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16
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Kozlowski PM, Andruniow T, Jarzecki AA, Zgierski MZ, Spiro TG. DFT analysis of co-alkyl and co-adenosyl vibrational modes in B12-cofactors. Inorg Chem 2007; 45:5585-90. [PMID: 16813422 PMCID: PMC2773831 DOI: 10.1021/ic052069j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Density functional theory (DFT)-based normal mode calculations have been carried out on models for B12-cofactors to assign reported isotope-edited resonance Raman spectra, which isolate vibrations of the organo-Co group. Interpretation is straightforward for alkyl-Co derivatives, which display prominent Co-C stretching vibrational bands. DFT correctly reproduces Co-C distances and frequencies for the methyl and ethyl derivatives. However, spectra are complex for adenosyl derivatives, due to mixing of Co-C stretching with a ribose deformation coordinate and to activation of modes involving Co-C-C bending and Co-adenosyl torsion. Despite this complexity, the computed spectra provide a satisfactory re-assignment of the experimental data. Reported trends in adenosyl-cobalamin spectra upon binding to the methylmalonyl CoA mutase enzyme, as well as on subsequent binding of substrates and inhibitors, provide support for an activation mechanism involving substrate-induced deformation of the adenosyl ligand.
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Affiliation(s)
- Pawel M Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA.
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17
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Rovira C, Kozlowski PM. First Principles Study of Coenzyme B12. Crystal Packing Forces Effect on Axial Bond Lengths. J Phys Chem B 2007; 111:3251-7. [PMID: 17388442 DOI: 10.1021/jp0660029] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work we analyze the structure of coenzyme B12 (AdoCbl) by means of periodic density functional theory (DFT) in order to elucidate the influence of the corrin side chains and the crystalline environment on the properties of axial bonds. The Co-Nax axial bond is very weak and its strength of less than 8 kcal/mol is four times smaller than Co-C which in solution is approximately 31 kcal/mol. The proper description of the Co-Nax distance has been problematic in previous DFT calculations and the source of disagreement between experiment and theory remained unexplained. To resolve this discrepancy, periodic DFT calculations within the Car-Parrinello molecular dynamics (CPMD) framework were carried out on three different structural models of increased complexity. The simplest model (DBI-Ado+) contains the naked corrin ring with a total of 96 atoms. The second model is the full coenzyme B12 (AdoCbl) with 209 atoms which has been taken from crystallographic analysis. To understand the extent to which the crystal packing forces influence the structural properties of AdoCbl the complete crystal consisting of four AdoCbl molecules plus 48 water molecules periodically repeated in space was analyzed (1008 atoms). The results show that the properties associated with the Co-C bond can be well reproduced using truncated models. This does not apply to the Co-Nax axial bond and the presence of the local environment appears to be essential for the correct prediction of its bond length. The most interesting outcome of the present analysis is the finding that the actual length of the Co-Nax bond (2.262 A) is largely influenced by crystal packing forces.
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Affiliation(s)
- Carme Rovira
- Centre de Recerca en Química Teorica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain.
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18
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Noodleman L, Han WG. Structure, redox, pK a, spin. A golden tetrad for understanding metalloenzyme energetics and reaction pathways. J Biol Inorg Chem 2006; 11:674-94. [PMID: 16830148 DOI: 10.1007/s00775-006-0136-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Accepted: 06/14/2006] [Indexed: 10/24/2022]
Abstract
After a review of the current status of density functional theory (DFT) for spin-polarized and spin-coupled systems, we focus on the resting states and intermediates of redox-active metalloenzymes and electron transfer proteins, showing how comparisons of DFT-calculated spectroscopic parameters with experiment and evaluation of related energies and geometries provide important information. The topics we examine include (1) models for the active-site structure of methane monooxygenase intermediate Q and ribonucleotide reductase intermediate X; (2) the coupling of electron transfer to proton transfer in manganese superoxide dismutase, with implications for reaction kinetics; (3) redox, pK(a), and electronic structure issues in the Rieske iron-sulfur protein, including their connection to coupled electron/proton transfer, and an analysis of how partial electron delocalization strongly alters the electron paramagnetic resonance spectrum; (4) the connection between protein-induced structural distortion and the electronic structure of oxidized high-potential 4Fe4S proteins with implications for cluster reactivity; (5) an analysis of cluster assembly and central-atom insertion into the FeMo cofactor center of nitrogenase based on DFT structural and redox potential calculations.
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Affiliation(s)
- Louis Noodleman
- Department of Molecular Biology, TPC15, The Scripps Research Institute, La Jolla, CA 92037, USA.
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19
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Spataru T, Birke RL. Carbon−Cobalt Bond Distance and Bond Cleavage in One-Electron Reduced Methylcobalamin: A Failure of the Conventional DFT Method. J Phys Chem A 2006; 110:8599-604. [PMID: 16836419 DOI: 10.1021/jp062741d] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Geometry optimizations at the HF, B3LYP, and CASSCF levels of electronic structure theory have been performed for methylcobalamin (MeCbl) model compounds in both the Co(III) (MeCbl(III)) and Co(II) (MeCbl(II)) formal oxidation states. Since the HOMO-LUMO and C-Co sigma-sigma MO gaps are significantly smaller in the MeCbl(II) compounds compared with MeCbl(III), a pseudo-Jahn Teller effect is possible. CASSCF calculations show that there is strong coupling between C-Co sigma-sigma MOs for the MeCbl(II) models leading to strong state mixing with significant total charge density transfer (approximately 0.4 e-), mainly from the C-Co sigma MO to C-Co sigma MO (approximately 0.3 e-). CASSCF(9:7) calculations show that the strong state mixing leads to an increase in the C-Co bond length for MeCbl(II) model compounds from 1.969 A (DFT and HF calculations) to 2.164 A in the base-on MeCbl(II) model and from 1.938 A to 2.144 A in the base-off MeCbl(II) model. Concomitantly, the Co-N axial bond length increases from 2.121 A (DFT) to 2.344 A in the CASSCF calculation. This coupling interaction between states can be used to explain the much lower Co-C bond dissociation enthalpy and much faster bond cleavage rate for the one-electron reduced methylcobalamin radical anion compared to MeCbl(III). It may also be important for axial bond distances in other Co(II) compounds.
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20
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Kwiecien RA, Khavrutskii IV, Musaev DG, Morokuma K, Banerjee R, Paneth P. Computational insights into the mechanism of radical generation in B12-dependent methylmalonyl-CoA mutase. J Am Chem Soc 2006; 128:1287-92. [PMID: 16433547 DOI: 10.1021/ja056333j] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
ONIOM calculations have provided novel insights into the mechanism of homolytic Co-C5' bond cleavage in the 5'-deoxyadenosylcobalamin cofactor catalyzed by methylmalonyl-CoA mutase. We have shown that it is a stepwise process in which conformational changes in the 5'-deoxyadenosine moiety precede the actual homolysis step. In the transition state structure for homolysis, the Co-C5' bond elongates by approximately 0.5 Angstroms from the value found in the substrate-bound reactant complex. The overall barrier to homolysis is approximately 10 kcal/mol, and the radical products are approximately 2.5 kcal/mol less stable than the initial ternary complex of enzyme, substrate, and cofactor. The movement of the deoxyadenosine moiety during the homolysis step positions the resulting 5'-deoxyadenosyl radical for the subsequent hydrogen atom transfer from the substrate, methylmalonyl-CoA.
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Affiliation(s)
- Renata A Kwiecien
- Institute of Applied Radiation Chemistry, Technical University of Lodz, Poland
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21
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Freindorf M, Shao Y, Furlani TR, Kong J. Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31G*/AMBER potential. J Comput Chem 2005; 26:1270-8. [PMID: 15965971 DOI: 10.1002/jcc.20264] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A combined DFT quantum mechanical and AMBER molecular mechanical potential (QM/MM) is presented for use in molecular modeling and molecular simulations of large biological systems. In our approach we evaluate Lennard-Jones parameters describing the interaction between the quantum mechanical (QM) part of a system, which is described at the B3LYP/6-31+G* level of theory, and the molecular mechanical (MM) part of the system, described by the AMBER force field. The Lennard-Jones parameters for this potential are obtained by calculating hydrogen bond energies and hydrogen bond geometries for a large set of bimolecular systems, in which one hydrogen bond monomer is described quantum mechanically and the other is treated molecular mechanically. We have investigated more than 100 different bimolecular systems, finding very good agreement between hydrogen bond energies and geometries obtained from the combined QM/MM calculations and results obtained at the QM level of theory, especially with respect to geometry. Therefore, based on the Lennard-Jones parameters obtained in our study, we anticipate that the B3LYP/6-31+G*/AMBER potential will be a precise tool to explore intermolecular interactions inside a protein environment.
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Affiliation(s)
- Marek Freindorf
- Center for Computational Research, The State University of New York at Buffalo, Buffalo, NY 14260, USA.
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22
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Dölker N, Morreale A, Maseras F. Computational study on the difference between the Co–C bond dissociation energy in methylcobalamin and adenosylcobalamin. J Biol Inorg Chem 2005; 10:509-17. [PMID: 15986217 DOI: 10.1007/s00775-005-0662-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2004] [Accepted: 05/16/2005] [Indexed: 10/25/2022]
Abstract
The bond dissociation energies of the Co-C bonds in the cobalamin cofactors methylcobalamin and adenosylcobalamin were calculated using the hybrid quantum mechanics/molecular mechanics method IMOMM (integrated molecular orbital and molecular mechanics). Calculations were performed on models of differing complexities as well as on the full systems. We investigated the origin of the different experimental values for the Co-C bond dissociation energies in methylcobalamin and adenosylcobalamin, and have provided an explanation for the difficulties encountered when we attempt to reproduce this difference in quantum chemistry. Additional calculations have been performed using the Miertus-Scrocco-Tomasi method in order to estimate the influence of solvent effects on the homolytic Co-C bond cleavage. Introduction of these solvation effects is shown to be necessary for the correct reproduction of experimental trends in bond dissociation energies in solution, which consequently have no direct correlation with dissociation processes in the enzyme.
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Affiliation(s)
- Nicole Dölker
- Unitat de Química Física, Edifici C.n, Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia, Spain.
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23
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Kamachi T, Toraya T, Yoshizawa K. Catalytic Roles of Active-Site Amino Acid Residues of Coenzyme B12-Dependent Diol Dehydratase: Protonation State of Histidine and Pull Effect of Glutamate. J Am Chem Soc 2004; 126:16207-16. [PMID: 15584757 DOI: 10.1021/ja045572o] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hydrogen abstraction and the OH migration processes catalyzed by diol dehydratase are discussed by means of a quantum mechanical/molecular mechanical method. To evaluate the push effect of His143 and the pull effect of Glu170, we considered three kinds of whole-enzyme model, the protonated and two unprotonated His143 models. A calculated activation energy for the hydrogen abstraction by the adenosyl radical is 15.6 (13.6) kcal/mol in the protonated (unprotonated) His143 model. QM/MM calculational results show that the mechanism of the OH migration is significantly changed by the protonation of His143. In the protonated His143 model, the OH group migration triggered by the full proton donation from the imidazolium to the migrating OH group occurs by a stepwise OH abstraction/re-addition process in which the water production reduces the barrier for the C-O bond cleavage. On the other hand, the OH migration in the unprotonated His143 model proceeds in a concerted manner, as we previously proposed using a simple model including only K+ ion and substrate. The latter mechanism seems to be kinetically more favorable from the calculated energy profiles and is consistent with experimental results. The activation barrier of the OH group migration step is only 1.6 kcal/mol reduced by the hydrogen-bonding interaction between the O2 of the substrate and unprotonated His143. Thus, it is predicted that His143 is not protonated, and therefore the main active-site amino acid residue that lowers the energy of the transition state for the OH group migration is determined to be Glu170.
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Affiliation(s)
- Takashi Kamachi
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 812-8581, Japan
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24
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Brooks AJ, Vlasie M, Banerjee R, Brunold TC. Spectroscopic and computational studies on the adenosylcobalamin-dependent methylmalonyl-CoA mutase: evaluation of enzymatic contributions to Co-C bond activation in the Co3+ ground state. J Am Chem Soc 2004; 126:8167-80. [PMID: 15225058 DOI: 10.1021/ja039114b] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methylmalonyl-CoA mutase (MMCM) is an enzyme that utilizes the adenosylcobalamin (AdoCbl) cofactor to catalyze the rearrangement of methylmalonyl-CoA to succinyl-CoA. Despite many years of dedicated research, the mechanism by which MMCM and related AdoCbl-dependent enzymes accelerate the rate for homolytic cleavage of the cofactor's Co-C bond by approximately 12 orders of magnitude while avoiding potentially harmful side reactions remains one of the greatest subjects of debate among B(12) researchers. In this study, we have employed electronic absorption (Abs) and magnetic circular dichroism (MCD) spectroscopic techniques to probe cofactor/enzyme active site interactions in the Co(3+)Cbl "ground" state for MMCM reconstituted with both the native cofactor AdoCbl and its derivative methylcobalamin (MeCbl). In both cases, Abs and MCD spectra of the free and enzyme-bound cofactor are very similar, indicating that replacement of the intramolecular base 5,6-dimethylbenzimidazole (DMB) by a histidine residue from the enzyme active site has insignificant effects on the cofactor's electronic properties. Likewise, spectral perturbations associated with substrate (analogue) binding to holo-MMCM are minor, arguing against substrate-induced enzymatic Co-C bond activation. As compared to the AdoCbl data, however, Abs and MCD spectral changes for the sterically less constrained MeCbl cofactor upon binding to MMCM and treatment of holoenzyme with substrate (analogues) are much more substantial. Analysis of these changes within the framework of time-dependent density functional theory calculations provides uniquely detailed insight into the structural distortions imposed on the cofactor as the enzyme progresses through the reaction cycle. Together, our results indicate that, although the enzyme may serve to activate the cofactor in its Co(3+)Cbl ground state to a small degree, the dominant contribution to the enzymatic Co-C bond activation presumably comes through stabilization of the Co(2+)Cbl/Ado. post-homolysis products.
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Affiliation(s)
- Amanda J Brooks
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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25
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Kozlowski PM, Zgierski MZ. Electronic and Steric Influence of Trans Axial Base on the Stereoelectronic Properties of Cobalamins. J Phys Chem B 2004. [DOI: 10.1021/jp040373c] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Steacie Institute for Molecular Science, National Research Council of Canada, Ottawa, Ontario, Canada K1A OR6
| | - Marek Z. Zgierski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Steacie Institute for Molecular Science, National Research Council of Canada, Ottawa, Ontario, Canada K1A OR6
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26
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Stich TA, Buan NR, Brunold TC. Spectroscopic and Computational Studies of Co2+Corrinoids: Spectral and Electronic Properties of the Biologically Relevant Base-On and Base-Off Forms of Co2+Cobalamin. J Am Chem Soc 2004; 126:9735-49. [PMID: 15291577 DOI: 10.1021/ja0481631] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Co(2+)cobalmain (Co(2+)Cbl) is implicated in the catalytic cycles of all adenosylcobalamin (AdoCbl)-dependent enzymes, as in each case catalysis is initiated through homolytic cleavage of the cofactor's Co-C bond. The rate of Co-C bond homolysis, while slow for the free cofactor, is accelerated by 12 orders of magnitude when AdoCbl is bound to the protein active site, possibly through enzyme-mediated stabilization of the post-homolysis products. As an essential step toward the elucidation of the mechanism of enzymatic Co-C bond activation, we employed electronic absorption (Abs), magnetic circular dichroism (MCD), and resonance Raman spectroscopies to characterize the electronic excited states of Co(2+)Cbl and Co(2+)cobinamide (Co(2+)Cbi(+), a cobalamin derivative that lacks the nucleotide loop and 5,6-dimethylbenzimazole (DMB) base and instead binds a water molecule in the lower axial position). Although relatively modest differences exist between the Abs spectra of these two Co(2+)corrinoid species, MCD data reveal that substitution of the lower axial ligand gives rise to dramatic changes in the low-energy region where Co(2+)-centered ligand field transitions are expected to occur. Our quantitative analysis of these spectral changes within the framework of time-dependent density functional theory (TD-DFT) calculations indicates that corrin-based pi --> pi transitions, which dominate the Co(2+)corrinoid Abs spectra, are essentially insulated from perturbations of the lower ligand environment. Contrastingly, the Co(2+)-centered ligand field transitions, which are observed here for the first time using MCD spectroscopy, are extremely sensitive to alterations in the Co(2+) ligand environment and thus may serve as excellent reporters of enzyme-induced perturbations of the Co(2+) state. The power of this combined spectroscopic/computational methodology for studying Co(2+)corrinoid/enzyme active site interactions is demonstrated by the dramatic changes in the MCD spectrum as Co(2+)Cbi(+) binds to the adenosyltransferase CobA.
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Affiliation(s)
- Troy A Stich
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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27
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Selçuki C, van Eldik R, Clark T. NO Binding to Cobalamin: Influence of the Metal Oxidation State. Inorg Chem 2004; 43:2828-33. [PMID: 15106969 DOI: 10.1021/ic0347945] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Density functional and molecular orbital theory calculations on models for cobalamin suggest that NO binds similarly to the Co(II) and Co(III) oxidation states. However, Co(III) can bind water far more strongly than Co(II) as a sixth ligand, so that the competition between water and NO complexation strongly favors water for Co(III) in the gas phase. Although the Co(II) oxidation state is found to bind water slightly more strongly than NO in the gas phase, the inclusion of solvation effects via the polarizeable continuum model makes NO binding more favorable. Thus, the experimentally observed ability of cob(II)alamin to bind NO in aqueous solution is the result of its weak complexation with water and the relatively poor solvation of NO. Calculated vibrational frequencies support the interpretation of the cob(II)alamin-NO complex as being cob(III)alamin-NO-, although the DFT calculations underestimate the degree of charge transfer in comparison to Hartree-Fock calculations.
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Affiliation(s)
- Cenk Selçuki
- Computer-Chemie-Centrum der Universität Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany
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28
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Doll KM, Finke RG. Adenosylcobinamide Plus Exogenous, Sterically Hindered, Putative Axial Bases: A Reinvestigation into the Cause of Record Levels of Co−C Heterolysis. Inorg Chem 2004; 43:2611-23. [PMID: 15074980 DOI: 10.1021/ic030141c] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A reinvestigation of an earlier Ph.D. thesis (Sirovatka, J. M. Ph.D. Thesis, Colorado State University, Fort Collins, CO, 1999) is reported herein. That thesis examined the thermolysis reaction of AdoCbi(+)BF(4)(-) in ethylene glycol solution with exogenous bases, N-methylimidazole (N-Me-Im) and the sterically hindered 1,2-dimethylimidazole, (1,2-Me(2)-Im), 2-methylpyridine (2-Me-py), and 2,6-dimethylpyridine (2,6-Me(2)-py). In the present work, multiple purities of each base have been utilized as a check to see if impurities in the nitrogenous bases are causing the observed homolysis and heterolysis product distributions as others have implied (Trommel, J. S.; Warncke, K.; Marzilli, L. G. J. Am. Chem. Soc. 2001, 123, 3358). The "impurity hypothesis" is disproven by a series of results, including the following: N-Me-Im displays an invariant 52 +/- 10% heterolysis and the 1,2-Me(2)-Im system displays an invariant 83 +/- 7% heterolysis as a function of different base purification methods. Moreover, 2-Me-py and 2,6-Me(2)-py also display an invariant approximately 16 +/- 5% heterolysis as a function of different purification methods. What is responsible for the high levels of Co-C heterolysis in the AdoCbi(+) plus sterically bulky base thermolyses was uncovered via a revisitation of our four, earlier alternative hypotheses for the enhanced Co-C heterolysis (Sirovatka, J. M.; Finke, R. G. Inorg. Chem. 1999, 38, 1697). Our prior number one alternative hypothesis is shown to be correct: the added bases simply deprotonate the ethylene glycol solvent, forming ethylene glycolate anion and base-H(+)() as the key agents behind the previously ill-understood Co-C heterolyses. Also reported are Co(II)Cbi(+) titrations with five bases (1,2-Me(2)-Im, N-Me-Im, pyridine, 2-MePy, and 2,6-Me(2)-py). These experiments confirm Marzilli and co-workers' (op. cit.) results by showing that sterically hindered bases do not bind to Co(II)Cbi(+); therefore, Co(II)Cbi(+) EPR literature showing binding of bulky pyridines is erroneous as is the previously reported binding of bulky pyridine bases to Co(II)Cbi(+) by UV-vis spectroscopy (Sirovatka, J. Ph.D. Thesis, op. cit.). Also reported is our current best synthesis and purification of AdoCbi(+)BF(4)(-), work that builds off our 1987 synthesis of AdoCbi(+)BF(4)(-) (Hay, B. P.; Finke, R. G. J. Am. Chem. Soc. 1987, 109, 8012). Finally, the multiple, compounding errors which have caused problems in this project are listed, notably errors in the protein X-ray crystallography literature, the EXAFS literature, the Co(II)Cbi(+) plus bulky-bases EPR literature, the misleading B(12)-model literature, the erroneous experimental work (Sirovatka, op. cit.) and thus incorrect conclusions in one of our prior papers, as well as the erroneous implications in parts of the Marzilli and co-workers paper (op. cit.). It is hoped that a forthright reporting of these errors will help others avoid similar mistakes in the future when studying complex, bioinorganic systems.
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Affiliation(s)
- Kenneth M Doll
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
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30
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Freindorf M, Kozlowski PM. A Combined Density Functional Theory and Molecular Mechanics Study of the Relationship between the Structure of Coenzyme B12 and Its Binding to Methylmalonyl-CoA Mutase. J Am Chem Soc 2004; 126:1928-9. [PMID: 14971913 DOI: 10.1021/ja028473o] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A combined density functional theory (DFT) and molecular mechanics (MM) approach was applied to investigate the relationship between the structure of a free coenzyme B12, and bound to methylmalonyl-CoA mutase. It was found that, upon coenzyme binding to apoenzyme, the Co-C bond remains intact, while the C-Naxial bond becomes slightly elongated and labilized. The labilization of the Co-Naxial bond that takes place in coenzyme B12-dependent enzymes is most likely necessary for fine-tuning of the cobalt-nitrogen (axial base) distance. The controlling of this distance is important to inhibit abiological site reaction involving heterolysis of the Co-C bond but is not important for biologically relevant Co-C bond homolysis.
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Affiliation(s)
- Marek Freindorf
- Department of Chemistry, University of Louisville, Louisvile, Kentucky 40292, USA
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31
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Affiliation(s)
- Fahmi Himo
- Theoretical Chemistry, Department of Biotechnology, Royal Institute of Technology, SCFAB, SE-106 91 Stockholm, Sweden
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32
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Stich TA, Brooks AJ, Buan NR, Brunold TC. Spectroscopic and computational studies of Co3+-corrinoids: spectral and electronic properties of the B12 cofactors and biologically relevant precursors. J Am Chem Soc 2003; 125:5897-914. [PMID: 12733931 DOI: 10.1021/ja029328d] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The B(12) cofactors methylcobalamin (MeCbl) and 5'-deoxyadenosylcobalamin (AdoCbl) have long fascinated chemists because of their complex structures and unusual reactivities in biological systems; however, their electronic absorption (Abs) spectra have remained largely unassigned. In this study, we have used Abs, circular dichroism (CD), magnetic CD (MCD), and resonance Raman spectroscopic techniques to probe the electronic excited states of Co(3+)Cbl species that differ with respect to their upper axial ligand, including MeCbl, AdoCbl, aquacobalamin (H(2)OCbl(+)), and vitamin B(12) (cyanocobalamin, CNCbl). Also included to probe the effect of the lower axial ligand on the electronic properties of Cbls is Ado-cobinamide (AdoCbi(+)), an AdoCbl derivative that lacks the tethered base 5,6-dimethylbenzimidazole (DMB) and instead binds a water molecule in the lower axial position. Spectroscopic data for each species are analyzed within the framework of time-dependent density functional theory (TD-DFT) to assign the major spectral features (the so-called alpha/beta, D/E, and gamma bands) and to generate experimentally validated electronic-structure descriptions. These studies reveal that the "unique" Abs spectra of MeCbl and AdoCbl, which differ considerably from the "typical" Abs spectra of H(2)OCbl(+) and CNCbl, reflect the high degree of sigma-donation from the alkyl ligand to the Co center and the consequent destabilization of all Co 3d orbitals. They reveal further that with increasing sigma-donor strength of the upper axial ligand, the contribution from the formally unoccupied Co 3d(z(2)) orbital to the HOMO increases, which induces a strong Co[bond]N(DMB) sigma-antibonding interaction, consistent with the experimentally observed lengthening of this bond from H(2)OCbl(+) to CNCbl and MeCbl. Alternatively, our spectroscopic and computational data for MeCbl and MeCbi(+) reveal that substitution of the DMB by a water molecule in the lower axial position has negligible effects on the Co[bond]C. A simple model is presented that explains why the identity of the upper axial ligand has a major effect on the Co[bond]N(ax) strength, whereas the lower axial ligand does not appreciably modulate the nature of the Co[bond]C. Implications of these results with respect to enzymatic Co[bond]C activation are discussed.
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Affiliation(s)
- Troy A Stich
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Loferer MJ, Webb BM, Grant GH, Liedl KR. Energetic and stereochemical effects of the protein environment on substrate: a theoretical study of methylmalonyl-CoA mutase. J Am Chem Soc 2003; 125:1072-8. [PMID: 12537507 DOI: 10.1021/ja028906n] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
QM/MM methods were used to study the isomerization step from (2R)-methylmalonyl-CoA to succinyl-CoA. A pathway via a "fragmentation-recombination" mechanism is ruled out on energetic grounds. For the other radicalic pathway, involving an addition recombination step, geometries and vibrational contributions have been determined, and a barrier height of 11.70 kcal/mol was found. The effect of adjacent hydrogen-donating groups was found to reduce the energy barrier by 1-2 kcal/mol each and thus to provide a significant catalytic effect for this reaction. By means of molecular dynamics studies, the stereochemistry of the methylmalonyl-CoA mutase catalyzed reaction was examined. It is shown that TYR89 is essential for maintaining stereoselectivity of the abstraction of a hydrogen in the backreaction. The subsequent selective formation of one isomer of methylmalonyl-CoA is probably due to the presence of a bulky side chain.
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Affiliation(s)
- Markus J Loferer
- Institute of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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Khoroshun DV, Warncke K, Ke SC, Musaev DG, Morokuma K. Internal degrees of freedom, structural motifs, and conformational energetics of the 5'-deoxyadenosyl radical: implications for function in adenosylcobalamin-dependent enzymes. A computational study. J Am Chem Soc 2003; 125:570-9. [PMID: 12517173 DOI: 10.1021/ja028393k] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The potential energy surface of the free 5'-deoxyadenosyl radical in the gas phase is explored using density functional and second-order Møller-Plesset perturbation theories with 6-31G(d) and 6-31++G(d,p) basis sets and interpreted in terms of attractive and repulsive interactions. The 5',8-cyclization is found to be exothermic by approximately 20 kcal/mol but kinetically unfavorable; the lowest cyclization transition state (TS) lies about 7 kcal/mol higher than the highest TS for conversion between most of the open isomers. In open isomers, the two energetically most important attractive interactions are the hydrogen bonds (a) between the 2'-OH group and the N3 adenine center and (b) between the 2'-OH and 3'-OH groups. The relative ribose-adenine rotation about the C1'-N9 glycosyl bond in a certain range changes the energy by as much as 10-15 kcal/mol, the origin being (i) the repulsive 2'-H.H-C8 and O1'.N3 and (ii) the attractive 2'-OH.N3 ribose-adenine interactions. The hypothetical synergy between the glycosyl rotation and the Co-C bond scission may contribute to the experimentally established labilization of the Co-C bond in enzyme-bound adenosylcobalamin. The computational results are not inconsistent with the rotation about the C1'-N9 glycosyl bond being the principal coordinate for long-range radical migration in coenzyme B(12)-dependent enzymes. The effect of the protein environment on the model system results reported here remains an open question.
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Affiliation(s)
- Dmitry V Khoroshun
- Cherry L. Emerson Center for Scientific Computation, Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
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Abstract
The crystal structure of glutamate mutase with bound coenzyme B(12) suggests a radical shuttling mechanism within the active site of the enzyme. Quantum chemical calculations of the rearrangement in combination with kinetic and mutational studies suggest the catalytic mechanism of this enzyme to proceed via a fragmentation/recombination sequence with intermediates stabilized by partial protonation/deprotonation. Crucial residues in the active site have been identified. Solution structure studies indicate the mechanism of B(12) binding to the apoenzyme.
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Affiliation(s)
- Karl Gruber
- Institut für Chemie, Universität Graz, Heinrichstrasse 28, Austria.
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