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Møller MS, Kongsted J, McKenzie CJ. Preparation of organocobalt(iii) complexes via O 2 activation. Dalton Trans 2021; 50:4819-4829. [PMID: 33877179 DOI: 10.1039/d1dt00563d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The coupling of selective C-H activation with O2 activation is an important goal for organic synthesis. New experimental and computational results, along with the results from experimental work accumulated over many decades, now unequivocally link O2 activation with C-H activation by the classic Co(salen) complexes. A common holistic mechanistic framework can rationalise the formation of ostensibly diverse peroxo, superoxo, organo and alkoxide complexes of CoIII(salen). DFT calculations show that cobalt(iii)superoxo, dicobalt(iii)peroxo and cobalt(iii)hydroperoxo complexes are all viable intermediates as participants in hydrogen atom transfer reactions, whereas a Co(iv)oxo intermediate is unlikely. The reaction conditions will determine the pathway followed and all pathways are initiated through the initial formation of a superoxo complex, CoIII(salen)(O2˙)(MeOH) (EPR: g = 2.025, A = 19 G). Organo and alkoxide ligands are derived from solvent media and the trends in reactivity reveal that combination of the pKa and BDE of the C-H of the respective solvent substrates are important. These data explain why landmark, structurally characterized, μ2-η1,η2-peroxide and η1-superoxide Co(salen)-O2 adducts were predominantly isolated from solvents with high C-H pKa values (DMSO, DMF, DMA).
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Affiliation(s)
- Mads Sondrup Møller
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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2
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Liu T, Zhu Z, Ren H, Chen Y, Chen G, Cheng M, Zhao D, Shen J, Zhu W, Xiong B, Chen YL. Efficient syntheses of alpha- and beta-C-nucleosides and the origin of anomeric selectivity. Org Chem Front 2018. [DOI: 10.1039/c8qo00165k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Valuable C-nucleosides are efficiently prepared with excellent anomeric selectivity depending on protecting groups on sugar moiety.
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Crofts TS, Hazra AB, Tran JLA, Sokolovskaya OM, Osadchiy V, Ad O, Pelton J, Bauer S, Taga ME. Regiospecific Formation of Cobamide Isomers Is Directed by CobT. Biochemistry 2014; 53:7805-15. [DOI: 10.1021/bi501147d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Terence S. Crofts
- Department of Plant and Microbial Biology, ∥Department of Chemistry, ⊥QB3 Institute, and #Energy Biosciences Institute, University of California, Berkeley, United States
| | - Amrita B. Hazra
- Department of Plant and Microbial Biology, ∥Department of Chemistry, ⊥QB3 Institute, and #Energy Biosciences Institute, University of California, Berkeley, United States
| | - Jennifer LA Tran
- Department of Plant and Microbial Biology, ∥Department of Chemistry, ⊥QB3 Institute, and #Energy Biosciences Institute, University of California, Berkeley, United States
| | - Olga M. Sokolovskaya
- Department of Plant and Microbial Biology, ∥Department of Chemistry, ⊥QB3 Institute, and #Energy Biosciences Institute, University of California, Berkeley, United States
| | - Vadim Osadchiy
- Department of Plant and Microbial Biology, ∥Department of Chemistry, ⊥QB3 Institute, and #Energy Biosciences Institute, University of California, Berkeley, United States
| | - Omer Ad
- Department of Plant and Microbial Biology, ∥Department of Chemistry, ⊥QB3 Institute, and #Energy Biosciences Institute, University of California, Berkeley, United States
| | - Jeffrey Pelton
- Department of Plant and Microbial Biology, ∥Department of Chemistry, ⊥QB3 Institute, and #Energy Biosciences Institute, University of California, Berkeley, United States
| | - Stefan Bauer
- Department of Plant and Microbial Biology, ∥Department of Chemistry, ⊥QB3 Institute, and #Energy Biosciences Institute, University of California, Berkeley, United States
| | - Michiko E. Taga
- Department of Plant and Microbial Biology, ∥Department of Chemistry, ⊥QB3 Institute, and #Energy Biosciences Institute, University of California, Berkeley, United States
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Friedrich P, Baisch U, Harrington RW, Lyatuu F, Zhou K, Zelder F, McFarlane W, Buckel W, Golding BT. Experimental study of hydrogen bonding potentially stabilizing the 5'-deoxyadenosyl radical from coenzyme B12. Chemistry 2012; 18:16114-22. [PMID: 23080006 DOI: 10.1002/chem.201201840] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 08/21/2012] [Indexed: 01/28/2023]
Abstract
Coenzyme B(12) can assist radical enzymes that accomplish the vicinal interchange of a hydrogen atom with a functional group. It has been proposed that the Co-C bond homolysis of coenzyme B(12) to cob(II)alamin and the 5'-deoxyadenosyl radical is aided by hydrogen bonding of the corrin C19-H to the 3'-O of the ribose moiety of the incipient 5'-deoxyadenosyl radical, which is stabilized by 30 kJ mol(-1) (B. Durbeej et al., Chem. Eur. J. 2009, 15, 8578-8585). The diastereoisomers (R)- and (S)-2,3-dihydroxypropylcobalamin were used as models for coenzyme B(12). A downfield shift of the NMR signal for the C19-H proton was observed for the (R)-isomer (δ=4.45 versus 4.01 ppm for the (S)-isomer) and can be ascribed to an intramolecular hydrogen bond between the C19-H and the oxygen of CHOH. Crystal structures of (R)- and (S)-2,3-dihydroxypropylcobalamin showed C19-H⋅⋅⋅O distances of 3.214(7) Å (R-isomer) and 3.281(11) Å (S-isomer), which suggest weak hydrogen-bond interactions (-ΔG<6 kJ mol(-1)) between the CHOH of the dihydroxypropyl ligand and the C19-H. Exchange of the C19-H, which is dependent on the cobalt redox state, was investigated with cob(I)alamin, cob(II)alamin, and cob(III)alamin by using NMR spectroscopy to monitor the uptake of deuterium from deuterated water in the pH range 3-11. No exchange was found for any of the cobalt oxidation states. 3',5'-Dideoxyadenosylcobalamin, but not the 2',5'-isomer, was found to act as a coenzyme for glutamate mutase, with a 15-fold lower k(cat)/K(M) than 5'-deoxyadenosylcobalamin. This indicates that stabilization of the 5'-deoxyadenosyl radical by a hydrogen bond that involves the C19-H and the 3'-OH group of the cofactor is, at most, 7 kJ mol(-1) (-ΔG). Examination of the crystal structure of glutamate mutase revealed additional stabilizing factors: hydrogen bonds between both the 2'-OH and 3'-OH groups and glutamate 330. The actual strength of a hydrogen bond between the C19-H and the 3'-O of the ribose moiety of the 5'-deoxyadenosyl group is concluded not to exceed 6 kJ mol(-1) (-ΔG).
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Affiliation(s)
- Peter Friedrich
- School of Chemistry, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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5
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Marino N, Rabideau AE, Doyle RP. Trifluoracetic acid-assisted crystallization of vitamin B12 results in protonation of the phosphate group of the nucleotide loop: insight into the influence of crystal packing forces on vitamin B12 structures. Inorg Chem 2010; 50:220-30. [PMID: 21128680 DOI: 10.1021/ic101810v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In the course of experiments concerning our ongoing project on the synthesis of vitamin B(12) (cyanocobalamin, CNCbl) bioconjugates for drug-delivery purposes, we observed the formation of well-shaped red parallelepipeds from a concentrated aqueous solution of the HPLC-purified vitamin. The X-ray structural investigation (MoK(α)) at 98 K on these crystals revealed a CNCbl-TFA salt of formula [CNCbl(H)](TFAc)·14H(2)O (1, where TFA = trifluoracetic acid; TFAc(-) = trifluoracetate anion), in which a proton transfer from the trifluoracetic acid to the phosphate-O4P oxygen atoms is observed. 1 crystallizes in the standard orthorhombic P2(1)2(1)2(1) space group, a = 16.069(2) Å, b = 20.818(2) Å, c = 24.081(2) Å, Z = 4. The final full-matrix least-squares refinements on F(2) converged with R(1) = 4.1% for the 18957 significant reflections, a very low crystallographic residual for cobalamins, which facilitated the analysis of the extensive network of hydrogen bonds within the lattice. To the best of our knowledge, this is the first cobalamin structure to show protonation of the phosphate group of the cobalamin nucleotide loop. In this work, the crystal structure of 1 is analyzed and compared to other CNCbls reported in the literature, namely, CNCbl·3PrOH·12H(2)O (2, PrOH = propyl alcohol), CNCbl·acetone·20H(2)O (3), CNCbl·2LiCl·10.2H(2)O (4), and CNCbl·2KCl·10.6H(2)O (5). The analysis confirmed that protonation of the phosphate leaves the major CNCbl structural parameters unaffected, so that 1 can be considered an "unmodified" Cbl solvate. However, comparison between 1-5 led to interesting findings. In fact, although the cobalt(III) coordination sphere in 1-5 is similar, significant differences could be noted in the upward fold angle of the corrin macrocycle, a parameter commonly related to the steric hindrance of the axial lower "α" nucleotide-base and the electronic trans influence of the upper "β" substituent. This suggests that crystal-packing forces may influence the corrin deformation as well. Herein we explore, on the basis of the newly acquired structure and reported crystallographic data, whether the incongruities among 1-5 have to be attributed to random crystal packing effects or if it is possible to associate them with specific crystal packing (clusters).
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Affiliation(s)
- Nadia Marino
- Department of Chemistry, Syracuse University, Syracuse, New York 13244-4100, USA
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Hassanin HA, Hannibal L, Jacobsen DW, Brown KL, Marques HM, Brasch NE. NMR spectroscopy and molecular modelling studies of nitrosylcobalamin: further evidence that the deprotonated, base-off form is important for nitrosylcobalamin in solution. Dalton Trans 2009:424-33. [PMID: 19122899 PMCID: PMC2754767 DOI: 10.1039/b810895a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structure of nitrosylcobalamin (NOCbl) in solution has been studied by NMR spectroscopy and the 1H and 13C NMR spectra have been assigned. 13C and 31P NMR chemical shifts, the UV-vis spectrum of NOCbl and the observed pKbase-off value of approximately 5.1 for NOCbl provide evidence that a significant fraction of NOCbl is present in the base-off, 5,6-dimethylbenzimidazole (DMB) deprotonated, form in solution. NOE-restrained molecular mechanics modelling of base-on NOCbl gave annealed structures with minor conformational differences in the flexible side chains and the nucleotide loop position compared with the X-ray structure. A molecular dynamics simulation at 300 K showed that DMB remains in close proximity to the alpha face of the corrin in the base-off form of NOCbl. Simulated annealing calculations produced two major conformations of base-off NOCbl. In the first, the DMB is perpendicular to the corrin and its B3 nitrogen is about 3.1 A away from and pointing directly at the metal ion; in the second the DMB is parallel to and tucked beneath the D ring of the corrin.
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Affiliation(s)
- Hanaa A. Hassanin
- Department of Chemistry, School of Biomedical Sciences, Kent State University, Kent, OH44242
| | - Luciana Hannibal
- Department of Chemistry, School of Biomedical Sciences, Kent State University, Kent, OH44242
- School of Biomedical Sciences, Kent State University, Kent, OH 44242. E-mail:
- Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195
| | - Donald W. Jacobsen
- School of Biomedical Sciences, Kent State University, Kent, OH 44242. E-mail:
- Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44106
| | - Kenneth L. Brown
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701
| | - Helder M. Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, PO Wits, Johannesburg, 2050, South Africa. E-mail:
| | - Nicola E. Brasch
- Department of Chemistry, School of Biomedical Sciences, Kent State University, Kent, OH44242
- School of Biomedical Sciences, Kent State University, Kent, OH 44242. E-mail:
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Affiliation(s)
- Tilak Chandra
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701-3132
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Chandra T, Brown KL. Chemoselective deprotection of alpha-indole and imidazole ribonucleosides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2007; 26:1-8. [PMID: 17162582 DOI: 10.1080/15257770601052216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A series of 2 ',3 '-isopropylidene and 5 '-trityl-protected alpha-indole and alpha/beta-benzimidazole and imidazole ribonucleosides were deprotected with different acids. Selectivity was achieved for 5 '-versus 2 ',3 '- deprotection by using formic acid in the alpha-indole ribonucleoside series. Treatment of alpha-indole ribonucleosides with a mixture of formic acid and ether at room temperature afforded 2 ',3 '-deprotected alpha-ribonucleosides, whereas treatment of the alpha-benzimidazole ribonucleosides with the same acid afforded the 5 '-deprotected ribonucleoside without any 2 ', 3 '-deprotected products. The structures of these ribonucleosides were elucidated with 2D (NOESY, COSY, and HMQC) NMR spectroscopy.
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Affiliation(s)
- Tilak Chandra
- Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701-3132, USA
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Cheng MC, Marsh ENG. Evidence for coupled motion and hydrogen tunneling of the reaction catalyzed by glutamate mutase. Biochemistry 2007; 46:883-9. [PMID: 17223710 PMCID: PMC2518312 DOI: 10.1021/bi0616908] [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: 11/30/2022]
Abstract
Glutamate mutase is one of a group of adenosylcobalamin-dependent enzymes that catalyze unusual isomerizations that proceed through organic radical intermediates generated by homolytic fission of the coenzyme's unique cobalt-carbon bond. These enzymes are part of a larger family of enzymes that catalyze radical chemistry in which a key step is the abstraction of a hydrogen atom from an otherwise inert substrate. To gain insight into the mechanism of hydrogen transfer, we previously used pre-steady-state, rapid-quench techniques to measure the alpha-secondary tritium kinetic and equilibrium isotope effects associated with the formation of 5'-deoxyadenosine when glutamate mutase was reacted with [5'-(3)H]adenosylcobalamin and L-glutamate. We showed that both the kinetic and equilibrium isotope effects are large and inverse, 0.76 and 0.72, respectively. We have now repeated these measurements using glutamate deuterated in the position of hydrogen abstraction. The effect of introducing a primary deuterium kinetic isotope effect on the hydrogen transfer step is to reduce the magnitude of the secondary kinetic isotope effect to a value close to unity, 1.05 +/- 0.08, whereas the equilibrium isotope effect is unchanged. The significant reduction in the secondary kinetic isotope effect is consistent with motions of the 5'-hydrogen atoms being coupled in the transition state to the motion of the hydrogen undergoing transfer, in a reaction that involves a large degree of quantum tunneling.
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Affiliation(s)
| | - E. Neil G. Marsh
- Correspondence should be addressed to this author at: Department of Chemistry, University of Michigan, Ann Arbor, MI 48109−1055, USA Tel (734) 763 6096 FAX (734) 764 8815 e-mail
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Chandra T, Zou X, Valente EJ, Brown KL. Regio- and Stereoselective Glycosylation: Synthesis of 5-Haloimidazole α-Ribonucleosides. J Org Chem 2006; 71:5000-3. [PMID: 16776534 DOI: 10.1021/jo060087s] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe the synthesis of novel 5-haloimidazole ribonucleosides as precursors of modified cobalamins. A regio- and stereoselective glycosylation of protected ribose with silylated 4(5)-haloimidazoles produces 5-haloimidazole ribonucleosides predominantly in the alpha-configuration (60-75%) without any 4-substituted imidazole ribonucleoside. The structure of the 5-fluoroimidazole ribonucleoside was confirmed by X-ray crystallography and 2D NMR spectroscopy.
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Affiliation(s)
- Tilak Chandra
- Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, USA
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Using artificial neural networks to develop molecular mechanics parameters for the modelling of metalloporphyrins: Part IV. Five-, six-coordinate metalloporphyrins of Mn, Co, Ni and Cu. J Mol Struct 2006. [DOI: 10.1016/j.molstruc.2005.08.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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12
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Chandra T, Brown KL. Deprotection of α-imidazole/benzimidazole ribonucleosides by catalytic carbon tetrabromide initiated photolysis. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.09.180] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Skopec CE, Robinson JM, Cukrowski I, Marques HM. Using artificial neural networks to develop molecular mechanics parameters for the modelling of metalloporphyrins. III. Five coordinate Zn(II) porphyrins and the metalloprophyrins of the early 3d metals. J Mol Struct 2005. [DOI: 10.1016/j.molstruc.2004.11.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Perry CB, Brown KL, Zou X, Marques HM. The solution structure of some cobalamins determined by NMR-restrained molecular modelling. J Mol Struct 2005. [DOI: 10.1016/j.molstruc.2004.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Brown KL, Zou X, Banka RR, Perry CB, Marques HM. Solution Structure and Thermolysis of Coβ-5‘-Deoxyadenosylimidazolylcobamide, a Coenzyme B12 Analogue with an Imidazole Axial Nucleoside. Inorg Chem 2004; 43:8130-42. [PMID: 15578853 DOI: 10.1021/ic040079z] [Citation(s) in RCA: 16] [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 solution structure of Cobeta-5'-deoxyadenosylimidazolylcobamide, Ado(Im)Cbl, the coenzyme B(12) analogue in which the axial 5,6-dimethylbenzimidazole (Bzm) ligand is replaced by imidazole, has been determined by NMR-restrained molecular modeling. A two-state model, in which a conformation with the adenosyl moiety over the southern quadrant of the corrin and a conformation with the adenosyl ligand over the eastern quadrant of the corrin are both populated at room temperature, was required by the nOe data. A rotation profile and molecular dynamics simulations suggest that the eastern conformation is the more stable, in contrast to AdoCbl itself in which the southern conformation is preferred. Consensus structures of the two conformers show that the axial Co-N bond is slightly shorter and the corrin ring is less folded in Ado(Im)Cbl than in AdoCbl. A study of the thermolysis of Ado(Im)Cbl in aqueous solution (50-125 degrees C) revealed competing homolytic and heterolytic pathways as for AdoCbl but with heterolysis being 9-fold faster and homolysis being 3-fold slower at 100 degrees C than for AdoCbl. Determination of the pK(a)'s for the Ado(Im)Cbl base-on/base-off reaction and for the detached imidazole ribonucleoside as a function of temperature permitted correction of the homolysis and heterolysis rate constants for the temperature-dependent presence of the base-off species of Ado(Im)Cbl. Activation analysis of the resulting rate constants for the base-on species show that the entropy of activation for Ado(Im)Cbl homolysis (13.7 +/- 0.9 cal mol(-1) K(-1)) is identical with that of AdoCbl (13.5 +/- 0.7 cal mol(-1) K(-1)) but that the enthalpy of activation (34.8 kcal mol(-1)) is 1.0 +/- 0.4 kcal mol(-1) larger. The opposite effect is seen for heterolysis, where the enthalpies of activation are identical but the entropy of activation is 5 +/- 1 cal mol(-1) K(-1) less negative for Ado(Im)Cbl. Extrapolation to 37 degrees C provides a rate constant for Ado(Im)Cbl homolysis of 2.1 x 10(-9) s(-1), 4.3-fold smaller than for AdoCbl. Combined with earlier results for the enzyme-induced homolysis of Ado(Im)Cbl by the ribonucleoside triphosphate reductase from Lactobacillus leichmannii, the catalytic efficiency of the enzyme for homolysis of Ado(Im)Cbl at 37 degrees C can be calculated to be 4.0 x 10(8), 3.8-fold, or 0.8 kcal mol(-1), smaller than for AdoCbl. Thus, the bulky Bzm ligand makes at best a <1 kcal mol(-1) contribution to the enzymatic activation of coenzyme B(12).
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Affiliation(s)
- Kenneth L Brown
- Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, USA.
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Brown KL, Zou X, Chen G, Xia Z, Marques HM. Solution structure, enzymatic, and non-enzymatic reactivity of 3-isoadenosylcobalamin, a structural isomer of coenzyme B12 with surprising coenzymic activity. J Inorg Biochem 2004; 98:287-300. [PMID: 14729309 DOI: 10.1016/j.jinorgbio.2003.10.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The coenzymic activity of eight analogs of coenzyme B(12) (5'-deoxyadenosyl-cobalamin, AdoCbl) with structural alterations in the Ado ligand has been investigated with the AdoCbl-dependent ribonucleoside triphosphate reductase (RTPR) from Lactobacillus leichmannii. Six of the analogs were partially active coenzymes, and one, 3-iso-5'-deoxyadenosylcobalamin (3-IsoAdoCbl) was nearly as active as AdoCbl itself. NMR-restrained molecular modeling of 3-IsoAdoCbl revealed a highly conformationally mobile structure which required a four state model to be consistent with the NMR data. Thus, two conformations, one with the IsoAdo ligand over the eastern quadrant of the corrin, and one with the IsoAdo ligand over the northern quadrant, each undergo a facile syn/anti conformational equilibrium in the IsoAdo ligand. Spectrophotometric measurement of the kinetics of RTPR-induced cleavage of the carbon-cobalt bond of 3-IsoAdoCbl showed that it binds to the enzyme with the same affinity as AdoCbl, but its homolysis is only 20% as rapid. Investigation of the non-enzymatic thermolysis of 3-IsoAdoCbl showed that like AdoCbl, 3-IsoAdoCbl decomposes by competing homolytic and heterolytic pathways. A complete temperature-dependent kinetic and product analysis, followed by correction for the base-off species permitted deconvolution of the specific rate constant for both pathways. Eyring plots for the homolysis and heterolysis rate constant cross at 93 degrees C, so that homolysis is the predominant pathway at high temperature, but heterolysis is the predominant pathway at low temperature. At 37 degrees C, the homolysis of 3-IsoAdoCbl is 5.5-fold faster than that of AdoCbl, and the enzyme catalyzes carbon-cobalt bond homolysis in 3-IsoAdoCbl by a factor of 5.9 x 10(7), only 3.9% of the catalytic efficiency with AdoCbl itself. It seems likely that the conformational flexibility of 3-IsoAdoCbl allows it to adopt a coformation in which the hydrogen bonding patterns of the adenine moiety are similar to those of AdoCbl itself, and that this is responsible for the high enzymatic activity of this analog.
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Affiliation(s)
- Kenneth L Brown
- Department of Chemistry and Biochemistry, Clippinger Laboratories, Ohio University, Athens, OH 45701, USA.
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Marques HM, Cukrowski I. Molecular mechanics parameters for the modelling of four-coordinate Zn(ii) porphyrins. Phys Chem Chem Phys 2003. [DOI: 10.1039/b310320j] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Jensen KP, Ryde U. The axial N -base has minor influence on Co–C bond cleavage in cobalamins. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0166-1280(02)00049-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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20
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Marques HM, Brown KL. Molecular mechanics and molecular dynamics simulations of porphyrins, metalloporphyrins, heme proteins and cobalt corrinoids. Coord Chem Rev 2002. [DOI: 10.1016/s0010-8545(01)00411-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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21
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Dybala-Defratyka A, Paneth P. Theoretical evaluation of the hydrogen kinetic isotope effect on the first step of the methylmalonyl-CoA mutase reaction. J Inorg Biochem 2001; 86:681-9. [PMID: 11583786 DOI: 10.1016/s0162-0134(01)00230-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We have calculated hydrogen kinetic isotope effects (KIEs) for the first step of the methylmalonyl-CoA mutase reaction, including multidimensional tunneling correction at the zero curvature (ZCT) level, and compared them with the experimental values. Both alternative mechanisms of this step, concerted and stepwise, can be accommodated. It turned out to be essential to include Arg207 hydrogen-bonded to the reactant in the mechanism predicting simultaneous breaking of the Co-C bond of AdoCbl and hydrogen atom transfer. The consequence of the stepwise mechanism is a much larger facilitation of the homolytic dissociation of the carbon-cobalt bond by the enzyme than currently appreciated; our results suggest lowering of the activation energy by about 23 kcal mol(-1). We have also shown that large hydrogen KIEs of tunneling origin do not necessarily break the Swain-Schaad equation. Furthermore, when this equation does not hold, the exponent may be smaller in the presence of tunneling than it is at the semi-classical limit, indicating that nonclassical behavior may be a more common phenomenon than expected.
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Affiliation(s)
- A Dybala-Defratyka
- Institute of Applied Radiation Chemistry, Department of Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924, Lodz, Poland
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Marques H, Ngoma B, Egan T, Brown K. Parameters for the amber force field for the molecular mechanics modeling of the cobalt corrinoids. J Mol Struct 2001. [DOI: 10.1016/s0022-2860(00)00920-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Brown KL, Marques HM. Molecular modeling of the mechanochemical triggering mechanism for catalysis of carbon-cobalt bond homolysis in coenzyme B12. J Inorg Biochem 2001; 83:121-32. [PMID: 11237251 DOI: 10.1016/s0162-0134(00)00188-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The possible contributions of the mechanochemical triggering effect to the enzymatic activation of the carbon-cobalt bond of coenzyme B12 (5'-deoxyadenosylcobalamin, AdoCbl) for homolytic cleavage have been studied by molecular modeling and semiempirical molecular orbital calculations. Classically, this effect has envisioned enzymatic compression of the axial Co-N bond in the ground state to cause upward folding of the corrin ring and subsequent sterically induced distortion of the Co-C bond leading to its destabilization. The models of this process show that in both methylcobalamin (CH3Cbl) and AdoCbl, compression of the axial Co-N bond does engender upward folding of the corrin ring, and that the extent of such upward folding is smaller in an analog in which the normal 5,6-dimethylbenzimidazole axial ligand is replaced by the sterically smaller ligand, imidazole (CH3(lm)Cbl and Ado(lm)Cbl). Furthermore, in AdoCbl, this upward folding of the corrin is accompanied by increases in the carbon-cobalt bond length and in the Co-C-C bond angle (which are also less pronounced in Ado(Im)Cbl), and which indicate that the Co-C bond is indeed destabilized by this mechanism. However, these effects on the Co-C bond are small, and destabilization of this bond by this mechanism is unlikely to contribute more than ca. 3 kcal mol(-1) towards the enzymatic catalysis of Co-C bond homolysis, far short of the observed ca. 14 kcal mol(-1). A second version of mechanochemical triggering, in which compression of the axial Co-N bond in the transition state for Co-C bond homolysis stabilizes the transition state by increased Co-N orbital overlap, has also been investigated. Stretching the Co-C bond to simulate the approach to the transition state was found to result in an upward folding of the corrin ring, a slight decrease in the axial Co-N bond length, a slight displacement of the metal atom from the plane of the equatorial nitrogens towards the "lower" axial ligand, and a decrease in strain energy amounting to about 8 kcal mol(-1) for both AdoCbl and Ado(Im)Cbl. In such modeled transition states, compression of the axial Co-N bond to just below 2.0 A (the distance subsequently found to provide maximal stabilization of the transition state by increased orbital overlap) required about 4 kcal mol(-1) for AdoCbl, and about 2.5 kcal mol(-1) for Ado(Im)Cbl. ZINDO/1 calculations on slightly simplified structures showed that maximal electronic stabilization of the transition state by about 10 kcal mol(-1) occurred at an axial Co-N bond distance of 1.96 A for both AdoCbl and Ado(Im)Cbl. The net result is that this type of transition state mechanochemical triggering can provide 14 kcal mol(-1) of transition state stabilization for AdoCbl, and about 15.5 kcal mol(-1) for the Ado(Im)Cbl, enough to completely explain the observed enzymatic catalysis. These results are discussed in the light of current knowledge about class I AdoCbl-dependent enzymes, in which the coenzyme is bound in its "base-off" conformation, with the lower axial ligand position occupied by the imidazole moiety of an active site histidine residue, and the class II enzymes, in which AdoCbl binds to the enzyme in its "base-on" conformation, and the pendent 5,6-dimethylbenzimidazole base remains coordinated to the metal during Co-C bond activation.
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Affiliation(s)
- K L Brown
- Department of Chemistry and Biochemistry, Ohio University, Athens 45701-2979, USA.
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Sirovatka JM, Rappé AK, Finke RG. Molecular mechanics studies of coenzyme B12 complexes with constrained CoN(axial-base) bond lengths: introduction of the universal force field (UFF) to coenzyme B12 chemistry and its use to probe the plausibility of an axial-base-induced, ground-state corrin butterfly conformational steric effect. Inorganica Chim Acta 2000. [DOI: 10.1016/s0020-1693(00)00025-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Marques H, Zou X, Brown K. The solution structure of adenosylcobalamin and adenosylcobinamide determined by nOe-restrained molecular dynamics simulations. J Mol Struct 2000. [DOI: 10.1016/s0022-2860(99)00309-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Torrent M, Musaev DG, Morokuma K, Ke SC, Warncke K. Calculation of Nuclear Quadrupole Parameters in Imidazole Derivatives and Extrapolation to Coenzyme B12. A Theoretical Study. J Phys Chem B 1999. [DOI: 10.1021/jp991612c] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Marques HM, Brown KL. The structure of cobalt corrinoids based on molecular mechanics and NOE-restrained molecular mechanics and dynamics simulations. Coord Chem Rev 1999. [DOI: 10.1016/s0010-8545(99)00074-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
In 1997 and the first half of 1998, numerous publications appeared reporting studies of cofactors and their analogues in classical model systems and in enzyme-catalyzed reactions directed at understanding the enzymatic reactions of their natural cofactors. Model systems based on flavins have provided new insights into enzymatic modulation of the flavin reduction potential, and enzymatic reactions of coenzyme A analogues and derivatives have been employed in several studies of coenzyme A utilizing enzymes. Coenzyme B12 analogues have been utilized as alternate cofactors for B12-utilizing enzymes, while pyrroloquinoline quinone esters and analogues have been employed in model studies of the reactions of quinoprotein-catalyzed reactions.
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Affiliation(s)
- P K Mishra
- Department of Chemistry State University of New York at Stony Brook Stony Brook NY 11794-3400 USA
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