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Toda MJ, Ghosh AP, Parmar S, Kozlowski PM. Computational investigations of B 12-dependent enzymatic reactions. Methods Enzymol 2022; 669:119-150. [PMID: 35644169 DOI: 10.1016/bs.mie.2022.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Nature employs two biologically active forms of vitamin B12, adenosylcobalamin (or coenzyme B12) and methylcobalamin, as cofactors in molecular transformations both in bacteria and mammals. Computational chemistry, guided by experimental data, has been used to explore fundamental characteristics of these enzymatic reactions. In particular, the quantum mechanics/molecular mechanics (QM/MM) method has proven to be a powerful tool in elucidating important characteristics of B12-dependent enzymatic reactions. Herein, we will present a brief tutorial in conducting QM/MM calculations for B12 enzymatic reactions. We will summarize recent contributions that target the use of QM/MM calculations in both photochemical and enzymatic reactions including AdoCbl-dependent ethanolamine ammonia lyase, glutamate mutase, and photoreceptor CarH.
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Affiliation(s)
- Megan J Toda
- Department of Chemistry, University of Louisville, Louisville, KY, United States
| | - Arghya P Ghosh
- Department of Chemistry, University of Louisville, Louisville, KY, United States
| | - Saurav Parmar
- Department of Chemistry, University of Louisville, Louisville, KY, United States
| | - Pawel M Kozlowski
- Department of Chemistry, University of Louisville, Louisville, KY, United States.
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2
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Elmendorf LD, Brunold TC. Electronic structure studies of free and enzyme-bound B 12 species by magnetic circular dichroism and complementary spectroscopic techniques. Methods Enzymol 2022; 669:333-365. [PMID: 35644179 DOI: 10.1016/bs.mie.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Electronic absorption (Abs) and circular dichroism (CD) spectroscopic techniques have been used successfully for over half a century in studies of free and enzyme-bound B12 species. More recently, magnetic circular dichroism (MCD) spectroscopy and other complementary techniques have provided an increasingly detailed understanding of the electronic structure of cobalamins. While CD spectroscopy measures the difference in the absorption of left- and right-circularly polarized light, MCD spectroscopy adds the application of a magnetic field parallel to the direction of light propagation. Transitions that are formally forbidden according to the Abs and CD selection rules, such as ligand field (or d→d) transitions, can gain MCD intensity through spin-orbit coupling. As such, MCD spectroscopy provides a uniquely sensitive probe of the different binding modes, Co oxidation states, and axial ligand environments of B12 species in enzyme active sites, and thus the distinct reactivities displayed by these species. This chapter summarizes representative MCD studies of free and enzyme-bound B12 species, including those present in adenosyltransferases, isomerases, and reductive dehalogenases. Complementary spectroscopic and computational data are also presented and discussed where appropriate.
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Affiliation(s)
- Laura D Elmendorf
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States.
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3
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Xue SW, Tian YX, Pan JC, Liu YN, Ma YL. Binding interaction of a ring-hydroxylating dioxygenase with fluoranthene in Pseudomonas aeruginosa DN1. Sci Rep 2021; 11:21317. [PMID: 34716364 PMCID: PMC8556375 DOI: 10.1038/s41598-021-00783-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/18/2021] [Indexed: 11/11/2022] Open
Abstract
Pseudomonas aeruginosa DN1 can efficiently utilize fluoranthene as its sole carbon source, and the initial reaction in the biodegradation process is catalyzed by a ring-hydroxylating dioxygenase (RHD). To clarify the binding interaction of RHD with fluoranthene in the strain DN1, the genes encoding alpha subunit (RS30940) and beta subunit (RS05115) of RHD were functionally characterized through multi-technique combination such as gene knockout and homology modeling as well as molecular docking analysis. The results showed that the mutants lacking the characteristic alpha subunit and/or beta subunit failed to degrade fluoranthene effectively. Based on the translated protein sequence and Ramachandran plot, 96.5% of the primary amino-acid sequences of the alpha subunit in the modeled structure of the RHD were in the permitted region, 2.3% in the allowed region, but 1.2% in the disallowed area. The catalytic mechanism mediated by key residues was proposed by the simulations of molecular docking, wherein the active site of alpha subunit constituted a triangle structure of the mononuclear iron atom and the two oxygen atoms coupled with the predicted catalytic ternary of His217-His222-Asp372 for the dihydroxylation reaction with fluoranthene. Those amino acid residues adjacent to fluoranthene were nonpolar groups, and the C7-C8 positions on the fluoranthene ring were estimated to be the best oxidation sites. The distance of C7-O and C8-O was 3.77 Å and 3.04 Å respectively, and both of them were parallel. The results of synchronous fluorescence and site-directed mutagenesis confirmed the roles of the predicted residues during catalysis. This binding interaction could enhance our understanding of the catalytic mechanism of RHDs and provide a solid foundation for further enzymatic modification.
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Affiliation(s)
- Shu-Wen Xue
- grid.412262.10000 0004 1761 5538Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi’an, 710069 Shaanxi China ,grid.412262.10000 0004 1761 5538College of Life Science, Northwest University, 229 Taibai North Rd, Xi’an, 710069 Shaanxi China
| | - Yue-Xin Tian
- grid.412262.10000 0004 1761 5538Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi’an, 710069 Shaanxi China ,grid.412262.10000 0004 1761 5538College of Life Science, Northwest University, 229 Taibai North Rd, Xi’an, 710069 Shaanxi China
| | - Jin-Cheng Pan
- grid.412262.10000 0004 1761 5538Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi’an, 710069 Shaanxi China ,grid.412262.10000 0004 1761 5538College of Life Science, Northwest University, 229 Taibai North Rd, Xi’an, 710069 Shaanxi China
| | - Ya-Ni Liu
- grid.412262.10000 0004 1761 5538Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi’an, 710069 Shaanxi China ,grid.412262.10000 0004 1761 5538College of Life Science, Northwest University, 229 Taibai North Rd, Xi’an, 710069 Shaanxi China
| | - Yan-Ling Ma
- grid.412262.10000 0004 1761 5538Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi’an, 710069 Shaanxi China ,grid.412262.10000 0004 1761 5538College of Life Science, Northwest University, 229 Taibai North Rd, Xi’an, 710069 Shaanxi China
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4
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Tsybizova A, Brenig C, Kieninger C, Kräutler B, Chen P. Surprising Homolytic Gas Phase Co-C Bond Dissociation Energies of Organometallic Aryl-Cobinamides Reveal Notable Non-Bonded Intramolecular Interactions. Chemistry 2021; 27:7252-7264. [PMID: 33560580 PMCID: PMC8251903 DOI: 10.1002/chem.202004589] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Indexed: 01/12/2023]
Abstract
Aryl-cobalamins are a new class of organometallic structural mimics of vitamin B12 designed as potential 'antivitamins B12 '. Here, the first cationic aryl-cobinamides are described, which were synthesized using the newly developed diaryl-iodonium method. The aryl-cobinamides were obtained as pairs of organometallic coordination isomers, the stereo-structure of which was unambiguously assigned based on homo- and heteronuclear NMR spectra. The availability of isomers with axial attachment of the aryl group, either at the 'beta' or at the 'alpha' face of the cobalt-center allowed for an unprecedented comparison of the organometallic reactivity of such pairs. The homolytic gas-phase bond dissociation energies (BDEs) of the coordination-isomeric phenyl- and 4-ethylphenyl-cobinamides were determined by ESI-MS threshold CID experiments, furnishing (Co-Csp 2 )-BDEs of 38.4 and 40.6 kcal mol-1 , respectively, for the two β-isomers, and the larger BDEs of 46.6 and 43.8 kcal mol-1 for the corresponding α-isomers. Surprisingly, the observed (Co-Csp 2 )-BDEs of the Coβ -aryl-cobinamides were smaller than the (Co-Csp 3 )-BDE of Coβ -methyl-cobinamide. DFT studies and the magnitudes of the experimental (Co-Csp 2 )-BDEs revealed relevant contributions of non-bonded interactions in aryl-cobinamides, notably steric strain between the aryl and the cobalt-corrin moieties and non-bonded interactions with and among the peripheral sidechains.
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Affiliation(s)
- Alexandra Tsybizova
- Laboratorium für Organische ChemieDepartment of Chemistry and Applied BiosciencesETH ZürichZürichSwitzerland
| | - Christopher Brenig
- Institute of Organic Chemistry & Center of Molecular BiosciencesUniversity of InnsbruckInnsbruckAustria
| | - Christoph Kieninger
- Institute of Organic Chemistry & Center of Molecular BiosciencesUniversity of InnsbruckInnsbruckAustria
| | - Bernhard Kräutler
- Institute of Organic Chemistry & Center of Molecular BiosciencesUniversity of InnsbruckInnsbruckAustria
| | - Peter Chen
- Laboratorium für Organische ChemieDepartment of Chemistry and Applied BiosciencesETH ZürichZürichSwitzerland
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5
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Handali JD, Sunden KF, Thompson BJ, Neff-Mallon NA, Kaufman EM, Brunold TC, Wright JC. Three Dimensional Triply Resonant Sum Frequency Spectroscopy Revealing Vibronic Coupling in Cobalamins: Toward a Probe of Reaction Coordinates. J Phys Chem A 2018; 122:9031-9042. [PMID: 30365322 DOI: 10.1021/acs.jpca.8b07678] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Triply resonant sum frequency (TRSF) spectroscopy is a fully coherent mixed vibrational-electronic spectroscopic technique that is ideally suited for probing the vibrational-electronic couplings that become important in driving reactions. We have used cyanocobalamin (CNCbl) and deuterated aquacobalamin (D2OCbl+) as model systems for demonstrating the feasibility of using the selectivity of coherent multidimensional spectroscopy to resolve electronic states within the broad absorption spectra of transition metal complexes and identify the nature of the vibrational and electronic state couplings. We resolve three short and long axis vibrational modes in the vibrationally congested 1400-1750 cm-1 region that are individually coupled to different electronic states in the 18 000-21 000 cm-1 region but have minimal coupling to each other. Double resonance with the individual vibrational fundamentals and their overtones selectively enhances the corresponding electronic resonances and resolves features within the broad absorption spectrum. This work demonstrates the feasibility of identifying coupling between different pairs of vibrational states with different electronic states that together form the reaction coordinate surface of transition metal enzymes.
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Affiliation(s)
- Jonathan D Handali
- Department of Chemistry , University of Wisconsin-Madison , Madison Wisconsin 53706 , United States
| | - Kyle F Sunden
- Department of Chemistry , University of Wisconsin-Madison , Madison Wisconsin 53706 , United States
| | - Blaise J Thompson
- Department of Chemistry , University of Wisconsin-Madison , Madison Wisconsin 53706 , United States
| | - Nathan A Neff-Mallon
- Department of Chemistry , University of Wisconsin-Madison , Madison Wisconsin 53706 , United States
| | - Emily M Kaufman
- 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
| | - John C Wright
- Department of Chemistry , University of Wisconsin-Madison , Madison Wisconsin 53706 , United States
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6
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Wang Y, Frasconi M, Stoddart JF. Introducing Stable Radicals into Molecular Machines. ACS CENTRAL SCIENCE 2017; 3:927-935. [PMID: 28979933 PMCID: PMC5620985 DOI: 10.1021/acscentsci.7b00219] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Indexed: 06/07/2023]
Abstract
Ever since their discovery, stable organic radicals have received considerable attention from chemists because of their unique optical, electronic, and magnetic properties. Currently, one of the most appealing challenges for the chemical community is to develop sophisticated artificial molecular machines that can do work by consuming external energy, after the manner of motor proteins. In this context, radical-pairing interactions are important in addressing the challenge: they not only provide supramolecular assistance in the synthesis of molecular machines but also open the door to developing multifunctional systems relying on the various properties of the radical species. In this Outlook, by taking the radical cationic state of 1,1'-dialkyl-4,4'-bipyridinium (BIPY•+) as an example, we highlight our research on the art and science of introducing radical-pairing interactions into functional systems, from prototypical molecular switches to complex molecular machines, followed by a discussion of the (i) limitations of the current systems and (ii) future research directions for designing BIPY•+-based molecular machines with useful functions.
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Affiliation(s)
- Yuping Wang
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Marco Frasconi
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, Padova 35131, Italy
| | - J. Fraser Stoddart
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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7
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8
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Jiang W, Li W, Hong Y, Wang S, Fang B. Cloning, Expression, Mutagenesis Library Construction of Glycerol Dehydratase, and Binding Mode Simulation of Its Reactivase with Ligands. Appl Biochem Biotechnol 2015; 178:739-52. [PMID: 26547853 DOI: 10.1007/s12010-015-1906-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/21/2015] [Indexed: 11/26/2022]
Abstract
The production of 1, 3-propanediol (1, 3-PD) and 3-hydroxypropionaldehyde (3-HPA) by enzyme reaction has been a hot field, and glycerol dehydratase (GDHt) is the key and rate-limiting enzyme involved in their biosynthesis. The gldABC gene encoding GDHt was cloned from Klebsiella pneumoniae, and the activity of the corresponding proteins expressed extracellularly and intracellularly was 6.8 and 3.2 U/mg, respectively, about six and three times higher than that of the wild strain. The change of amino acids for the β subunit can adjust the length of the Co-N bond and affect the homolysis rate of the Co-C bond to change GDHt activity. The expression plasmid, pET-32a-gldAC (containing no gldB which encodes the β subunit of GDHt), was constructed to build the mutagenesis library to improve the GDHt activity. The binding models of glycerol dehydratase reactivation factor (GDHtR) with ATP, CTP, or GTP were simulated by semi-flexible docking, respectively, and there was almost no difference between them. This research provided the basis for studying the quantitative structure-activity relationships between GDHtR and its ligands, as well as searching inexpensive ligands to replace ATP. These results and methods are of great use in economical and highly efficient production of 3-HPA and 1, 3-PD by the enzyme method.
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Affiliation(s)
- Wei Jiang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, China
| | - Wenjun Li
- Hangzhou DAC Biotech Co., Ltd, Hangzhou, 310000, China
| | - Yan Hong
- Jingdezhen Ceramic Institute of Materials Science and Engineering, Jingde Zhen, 333000, China
| | - Shizhen Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, China
| | - Baishan Fang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, China.
- The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, Fujian, 361005, China.
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9
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Conrad KS, Jordan CD, Brown KL, Brunold TC. Spectroscopic and Computational Studies of Cobalamin Species with Variable Lower Axial Ligation: Implications for the Mechanism of Co–C Bond Activation by Class I Cobalamin-Dependent Isomerases. Inorg Chem 2015; 54:3736-47. [DOI: 10.1021/ic502665x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Karen S. Conrad
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Christopher D. Jordan
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kenneth L. Brown
- Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, United States
| | - Thomas C. Brunold
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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10
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The entropic contributions in vitamin B12 enzymes still reflect the electrostatic paradigm. Proc Natl Acad Sci U S A 2015; 112:4328-33. [PMID: 25805820 DOI: 10.1073/pnas.1503828112] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The catalytic power of enzymes containing coenzyme B12 has been, in some respects, the "last bastion" for the strain hypothesis. Our previous study of this system established by a careful sampling that the major part of the catalytic effect is due to the electrostatic interaction between the ribose of the ado group and the protein and that the strain contribution is very small. This finding has not been sufficiently appreciated due to misunderstandings of the power of the empirical valence bond (EVB) calculations and the need of sufficient sampling. Furthermore, some interesting new experiments point toward entropic effects as the source of the catalytic power, casting doubt on the validity of the electrostatic idea, at least, in the case of B12 enzymes. Here, we focus on the observation of the entropic effects and on analyzing their origin. We clarify that our EVB approach evaluates free energies rather than enthalpies and demonstrate by using the restraint release (RR) approach that the observed entropic contribution to the activation barrier is of electrostatic origin. Our study illustrates the power of the RR approach by evaluating the entropic contributions to catalysis and provides further support to our paradigm for the origin of the catalytic power of B12 enzymes. Overall, our study provides major support to our electrostatic preorganization idea and also highlights the basic requirements from ab initio quantum mechanics/molecular mechanics calculations of activation free energies of enzymatic reactions.
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11
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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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12
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Blomberg MRA, Borowski T, Himo F, Liao RZ, Siegbahn PEM. Quantum chemical studies of mechanisms for metalloenzymes. Chem Rev 2014; 114:3601-58. [PMID: 24410477 DOI: 10.1021/cr400388t] [Citation(s) in RCA: 431] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
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13
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Kozlowski PM, Kumar M, Piecuch P, Li W, Bauman NP, Hansen JA, Lodowski P, Jaworska M. The Cobalt–Methyl Bond Dissociation in Methylcobalamin: New Benchmark Analysis Based on Density Functional Theory and Completely Renormalized Coupled-Cluster Calculations. J Chem Theory Comput 2012; 8:1870-94. [DOI: 10.1021/ct300170y] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [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,
2320 South Brook St., Louisville, Kentucky 40292, United States
| | - Manoj Kumar
- Department of Chemistry, University
of Louisville,
2320 South Brook St., Louisville, Kentucky 40292, United States
| | - Piotr Piecuch
- Department of Chemistry, Michigan State University,
578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Wei Li
- Department of Chemistry, Michigan State University,
578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Nicholas P. Bauman
- Department of Chemistry, Michigan State University,
578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Jared A. Hansen
- Department of Chemistry, Michigan State University,
578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Piotr Lodowski
- Institute
of Chemistry, University of Silesia, Szkolna
9, PL-40 006 Katowice, Poland
| | - Maria Jaworska
- Institute
of Chemistry, University of Silesia, Szkolna
9, PL-40 006 Katowice, Poland
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14
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Manzerova J, Krymov V, Gerfen GJ. Investigating the intermediates in the reaction of ribonucleoside triphosphate reductase from Lactobacillus leichmannii: An application of HF EPR-RFQ technology. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 213:32-45. [PMID: 21944735 DOI: 10.1016/j.jmr.2011.08.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 08/23/2011] [Indexed: 05/31/2023]
Abstract
In this investigation high-frequency electron paramagnetic resonance spectroscopy (HFEPR) in conjunction with innovative rapid freeze-quench (RFQ) technology is employed to study the exchange-coupled thiyl radical-cob(II)alamin system in ribonucleotide reductase from a prokaryote Lactobacillus leichmannii. The size of the exchange coupling (Jex) and the values of the thiyl radical g tensor are refined, while confirming the previously determined (Gerfen et al. (1996) [20]) distance between the paramagnets. Conclusions relevant to ribonucleotide reductase catalysis and the architecture of the active site are presented. A key part of this work has been the development of a unique RFQ apparatus for the preparation of millisecond quench time RFQ samples which can be packed into small (0.5 mm ID) sample tubes used for CW and pulsed HFEPR--lack of this ability has heretofore precluded such studies. The technology is compatible with a broad range of spectroscopic techniques and can be readily adopted by other laboratories.
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Affiliation(s)
- Julia Manzerova
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, United States
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15
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Hirao H. Which DFT Functional Performs Well in the Calculation of Methylcobalamin? Comparison of the B3LYP and BP86 Functionals and Evaluation of the Impact of Empirical Dispersion Correction. J Phys Chem A 2011; 115:9308-13. [DOI: 10.1021/jp2052807] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Hajime Hirao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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16
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Kamachi T, Kouno T, Doitomi K, Yoshizawa K. Generation of adenosyl radical from S-adenosylmethionine (SAM) in biotin synthase. J Inorg Biochem 2011; 105:850-7. [DOI: 10.1016/j.jinorgbio.2011.03.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 03/16/2011] [Accepted: 03/16/2011] [Indexed: 10/18/2022]
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17
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Robertson WD, Wang M, Warncke K. Characterization of protein contributions to cobalt-carbon bond cleavage catalysis in adenosylcobalamin-dependent ethanolamine ammonia-lyase by using photolysis in the ternary complex. J Am Chem Soc 2011; 133:6968-77. [PMID: 21491908 PMCID: PMC3092035 DOI: 10.1021/ja107052p] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein contributions to the substrate-triggered cleavage of the cobalt-carbon (Co-C) bond and formation of the cob(II)alamin-5'-deoxyadenosyl radical pair in the adenosylcobalamin (AdoCbl)-dependent ethanolamine ammonia-lyase (EAL) from Salmonella typhimurium have been studied by using pulsed-laser photolysis of AdoCbl in the EAL-AdoCbl-substrate ternary complex, and time-resolved probing of the photoproduct dynamics by using ultraviolet-visible absorption spectroscopy on the 10(-7)-10(-1) s time scale. Experiments were performed in a fluid dimethylsulfoxide/water cryosolvent system at 240 K, under conditions of kinetic competence for thermal cleavage of the Co-C bond in the ternary complex. The static ultraviolet-visible absorption spectra of holo-EAL and ternary complex are comparable, indicating that the binding of substrate does not labilize the cofactor cobalt-carbon (Co-C) bond by significantly distorting the equilibrium AdoCbl structure. Photolysis of AdoCbl in EAL at 240 K leads to cob(II)alamin-5'-deoxyadenosyl radical pair quantum yields of <0.01 at 10(-6) s in both holo-EAL and ternary complex. Three photoproduct states are populated following a saturating laser pulse, and labeled, P(f), P(s), and P(c). The relative amplitudes and first-order recombination rate constants of P(f) (0.4-0.6; 40-50 s(-1)), P(s) (0.3-0.4; 4 s(-1)), and P(c) (0.1-0.2; 0) are comparable in holo-EAL and in the ternary complex. Time-resolved, full-spectrum electron paramagnetic resonance (EPR) spectroscopy shows that visible irradiation alters neither the kinetics of thermal cob(II)alamin-substrate radical pair formation, nor the equilibrium between ternary complex and cob(II)alamin-substrate radical pair, at 246 K. The results indicate that substrate binding to holo-EAL does not "switch" the protein to a new structural state, which promptly stabilizes the cob(II)alamin-5'-deoxyadenosyl radical pair photoproduct, either through an increased barrier to recombination, a decreased barrier to further radical pair separation, or lowering of the radical pair state free energy, or a combination of these effects. Therefore, we conclude that such a change in protein structure, which is independent of changes in the AdoCbl structure, and specifically the Co-C bond length, is not a basis of Co-C bond cleavage catalysis. The results suggest that, following the substrate trigger, the protein interacts with the cofactor to contiguously guide the cleavage of the Co-C bond, at every step along the cleavage coordinate, starting from the equilibrium configuration of the ternary complex. The cleavage is thus represented by a diagonal trajectory across a free energy surface, that is defined by chemical (Co-C separation) and protein configuration coordinates.
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Affiliation(s)
| | - Miao Wang
- Department of Physics, Emory University, Atlanta, GA 30322
| | - Kurt Warncke
- Department of Physics, Emory University, Atlanta, GA 30322
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18
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Larsson KM, Logan DT, Nordlund P. Structural basis for adenosylcobalamin activation in AdoCbl-dependent ribonucleotide reductases. ACS Chem Biol 2010; 5:933-42. [PMID: 20672854 DOI: 10.1021/cb1000845] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Class II ribonucleotide reductases (RNR) catalyze the formation of an essential thiyl radical by homolytic cleavage of the Co-C bond in their adenosylcobalamin (AdoCbl) cofactor. Several mechanisms for the dramatic acceleration of Co-C bond cleavage in AdoCbl-dependent enzymes have been advanced, but no consensus yet exists. We present the structure of the class II RNR from Thermotoga maritima in three complexes: (i) with allosteric effector dTTP, substrate GDP, and AdoCbl; (ii) with dTTP and AdoCbl; (iii) with dTTP, GDP, and adenosine. Comparison of these structures gives the deepest structural insights so far into the mechanism of radical generation and transfer for AdoCbl-dependent RNR. AdoCbl binds to the active site pocket, shielding the substrate, transient 5'-deoxyadenosyl radical and nascent thiyl radical from solution. The e-propionamide side chain of AdoCbl forms hydrogen bonds directly to the α-phosphate group of the substrate. This interaction appears to cause a "locking-in" of the cofactor, and it is the first observation of a direct cofactor-substrate interaction in an AdoCbl-dependent enzyme. The structures support an ordered sequential reaction mechanism with release or relaxation of AdoCbl on each catalytic cycle. A conformational change of the AdoCbl adenosyl ribose is required to allow hydrogen transfer to the catalytic thiol group. Previously proposed mechanisms for radical transfer in B12-dependent enzymes cannot fully explain the transfer in class II RNR, suggesting that it may form a separate class that differs from the well-characterized eliminases and mutases.
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Affiliation(s)
- Karl-Magnus Larsson
- Department of Biochemistry
and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Derek T. Logan
- Department of Biochemistry and Structural Biology, Lund University, Box 124, S-221 00 Lund, Sweden
| | - Pär Nordlund
- Department of Biochemistry
and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-171 77 Stockholm, Sweden
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19
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Kuta J, Wuerges J, Randaccio L, Kozlowski PM. Axial bonding in alkylcobalamins: DFT analysis of the inverse versus normal trans influence. J Phys Chem A 2010; 113:11604-12. [PMID: 19848426 DOI: 10.1021/jp901397p] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Density functional theory has been applied to study the origin of the inverse and normal trans influence in alkylcobalamins. In order to cover the X-ray structural data available for alkylcobalamins with a variety of axial substituents, geometries of 28 related corrin-containing models have been optimized and analyzed. The BP86/6-31G(d) level of theory was applied which showed good reliability in reproducing the axial bond lengths. Comparison of experimental and calculated data allowed to conclude that the inverse trans influence is not a general feature of cobalamins, as it appeared from the experimental data analysis alone. Inverse trans influence is observed for the series of R groups with increasing bulk and electron donating ability. For the series of R groups having similar medium bulk, but differing significantly in the electron donating ability, normal trans influence was found. Finally, it was determined, that the axial bond lengths correlate well but differently in the two series of R groups with the orbital energies of the six molecular orbitals essential in axial interligand bonding.
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Affiliation(s)
- Jadwiga Kuta
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA
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20
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21
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Durbeej B, Sandala GM, Bucher D, Smith DM, Radom L. On the importance of ribose orientation in the substrate activation of the coenzyme B12-dependent mutases. Chemistry 2009; 15:8578-8585. [PMID: 19630017 DOI: 10.1002/chem.200901002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The degree to which the corrin ring portion of coenzyme B(12) can facilitate the H-atom-abstraction step in the glutamate mutase (GM)-catalyzed reaction of (S)-glutamate has been investigated with density functional theory. The crystal structure of GM identifies two possible orientations of the ribose portion of coenzyme B(12). In one orientation (A), the OH groups of the ribose extend away from the corrin ring, whereas in the other orientation (B) the OH groups, especially that involving O3', are instead directed towards the corrin ring. Our calculations identify a sizable stabilization amounting to about 30 kJ mol(-1) in the transition structure (TS) complex corresponding to orientation B (TS(B)CorIm). In the TS complex where the ribose instead is positioned in orientation A, no such effect is manifested. The observed stabilization in TS(B)CorIm appears to be the result of favorable interactions involving O3' and the corrin ring, including a C-HO hydrogen bond. We find that the degree of stabilization is not particularly sensitive to the Co-C distance. Our calculations show that any potential stabilization afforded to the H-atom-abstraction step by coenzyme B(12) is sensitive to the orientation of the ribose moiety.
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Affiliation(s)
- Bo Durbeej
- School of Chemistry and ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia.
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22
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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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23
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Li X, Chung LW, Paneth P, Morokuma K. DFT and ONIOM(DFT:MM) studies on Co-C bond cleavage and hydrogen transfer in B12-dependent methylmalonyl-CoA mutase. Stepwise or concerted mechanism? J Am Chem Soc 2009; 131:5115-25. [PMID: 19309090 DOI: 10.1021/ja807677z] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The considerable protein effect on the homolytic Co-C bond cleavage to form the 5'-deoxyadenosyl (Ado) radical and cob(II)alamin and the subsequent hydrogen transfer from the methylmalonyl-CoA substrate to the Ado radical in the methylmalonyl-CoA mutase (MMCM) have been extensively studied by DFT and ONIOM(DFT/MM) methods. Several quantum models have been used to systematically study the protein effect. The calculations have shown that the Co-C bond dissociation energy is very much reduced in the protein, compared to that in the gas phase. The large protein effect can be decomposed into the cage effect, the effect of coenzyme geometrical distortion, and the protein MM effect. The largest contributor is the MM effect, which mainly consists of the interaction of the QM part of the coenzyme with the MM part of the coenzyme and the surrounding residues. In particular, Glu370 plays an important role in the Co-C bond cleavage process. These effects tremendously enhance the stability of the Co-C bond cleavage state in the protein. The initial Co-C bond cleavage and the subsequent hydrogen transfer were found to occur in a stepwise manner in the protein, although the concerted pathway for the Co-C bond cleavage coupled with the hydrogen transfer is more favored in the gas phase. The assumed concerted transition state in the protein has more deformation of the coenzyme and the substrate and has less interaction with the protein than the stepwise route. Key factors and residues in promoting the enzymatic reaction rate have been discussed in detail.
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Affiliation(s)
- Xin Li
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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24
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Kamachi T, Takahata M, Toraya T, Yoshizawa K. What is the Identity of the Metal Ions in the Active Sites of Coenzyme B12-Dependent Diol Dehydratase? A Computational Mutation Analysis. J Phys Chem B 2009; 113:8435-8. [DOI: 10.1021/jp9001737] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takashi Kamachi
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan, and Department of Bioscience and Biotechnology, Okayama University, Okayama 700-8530, Japan
| | - Masanori Takahata
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan, and Department of Bioscience and Biotechnology, Okayama University, Okayama 700-8530, Japan
| | - Tetsuo Toraya
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan, and Department of Bioscience and Biotechnology, Okayama University, Okayama 700-8530, Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan, and Department of Bioscience and Biotechnology, Okayama University, Okayama 700-8530, Japan
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25
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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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26
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The Oniom Method and its Applications to Enzymatic Reactions. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2009. [DOI: 10.1007/978-1-4020-9956-4_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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27
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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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28
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Degtyarenko I, Biarnés X, Nieminen RM, Rovira C. Density-functional molecular dynamics studies of biologically relevant iron and cobalt complexes with macrocyclic ligands. Coord Chem Rev 2008. [DOI: 10.1016/j.ccr.2007.10.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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29
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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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30
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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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31
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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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32
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Sharma PK, Chu ZT, Olsson MHM, Warshel A. A new paradigm for electrostatic catalysis of radical reactions in vitamin B12 enzymes. Proc Natl Acad Sci U S A 2007; 104:9661-6. [PMID: 17517615 PMCID: PMC1887576 DOI: 10.1073/pnas.0702238104] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Indexed: 11/18/2022] Open
Abstract
The catalytic power of enzymes containing coenzyme B(12) cofactor has been, in some respects, the "last bastion" for the strain hypothesis. The present work explores the origin of this effect by using simulation methods that overcome the sampling difficulties of previous energy minimization studies. It is found that the major part of the catalytic effect is due to the electrostatic interaction between the ribose and the protein, and that the strain contribution is very small. Remarkably, enzymes can use electrostatic effects even in a radical process, when the charge distribution of the reacting fragments does not change significantly during the reaction. Electrostatic catalysis can, in such cases, be obtained by attaching a polar group to the leaving fragment and designing an active site that interacts more strongly with this group in the product state than in the reactant state. The finding that evolution had to use this trick provides further evidence to the observation that it is extremely hard to catalyze enzymatic reactions by nonelectrostatic factors. The trick used by B(12) enzymes may, in fact, be a very powerful new strategy in enzyme design.
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Affiliation(s)
- Pankaz K. Sharma
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062
| | - Zhen T. Chu
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062
| | - Mats H. M. Olsson
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062
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33
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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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34
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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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35
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Jensen KP, Ryde U. How the Co-C bond is cleaved in coenzyme B12 enzymes: a theoretical study. J Am Chem Soc 2005; 127:9117-28. [PMID: 15969590 DOI: 10.1021/ja050744i] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The homolytic cleavage of the organometallic Co-C bond in vitamin B12-dependent enzymes is accelerated by a factor of approximately 10(12) in the protein compared to that of the isolated cofactor in aqueous solution. To understand this much debated effect, we have studied the Co-C bond cleavage in the enzyme glutamate mutase with combined quantum and molecular mechanics methods. We show that the calculated bond dissociation energy (BDE) of the Co-C bond in adenosyl cobalamin is reduced by 135 kJ/mol in the enzyme. This catalytic effect can be divided into four terms. First, the adenosine radical is kept within 4.2 angstroms of the Co ion in the enzyme, which decreases the BDE by 20 kJ/mol. Second, the surrounding enzyme stabilizes the dissociated state by 42 kJ/mol using electrostatic and van der Waals interactions. Third, the protein itself is stabilized by 11 kJ/mol in the dissociated state. Finally, the coenzyme is geometrically distorted by the protein, and this distortion is 61 kJ/mol larger in the Co(III) state. This deformation of the coenzyme is caused mainly by steric interactions, and it is especially the ribose moiety and the Co-C5'-C4' angle that are distorted. Without the polar ribose group, the catalytic effect is much smaller, e.g. only 42 kJ/mol for methyl cobalamin. The deformation of the coenzyme is caused mainly by the substrate, a side chain of the coenzyme itself, and a few residues around the adenosine part of the coenzyme.
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Affiliation(s)
- Kasper P Jensen
- Department of Theoretical Chemistry, Lund University, Chemical Center, P.O. Box 124, S-221 00 Lund, Sweden
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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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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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