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Lundahl MN, Yang H, Broderick WE, Hoffman BM, Broderick JB. Pyruvate formate-lyase activating enzyme: The catalytically active 5'-deoxyadenosyl radical caught in the act of H-atom abstraction. Proc Natl Acad Sci U S A 2023; 120:e2314696120. [PMID: 37956301 PMCID: PMC10665898 DOI: 10.1073/pnas.2314696120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/03/2023] [Indexed: 11/15/2023] Open
Abstract
Enzymes of the radical S-adenosyl-l-methionine (radical SAM, RS) superfamily, the largest in nature, catalyze remarkably diverse reactions initiated by H-atom abstraction. Glycyl radical enzyme activating enzymes (GRE-AEs) are a growing class of RS enzymes that generate the catalytically essential glycyl radical of GREs, which in turn catalyze essential reactions in anaerobic metabolism. Here, we probe the reaction of the GRE-AE pyruvate formate-lyase activating enzyme (PFL-AE) with the peptide substrate RVSG734YAV, which mimics the site of glycyl radical formation on the native substrate, pyruvate formate-lyase. Time-resolved freeze-quench electron paramagnetic resonance spectroscopy shows that at short mixing times reduced PFL-AE + SAM reacts with RVSG734YAV to form the central organometallic intermediate, Ω, in which the adenosyl 5'C is covalently bound to the unique iron of the [4Fe-4S] cluster. Freeze-trapping the reaction at longer times reveals the formation of the peptide G734• glycyl radical product. Of central importance, freeze-quenching at intermediate times reveals that the conversion of Ω to peptide glycyl radical is not concerted. Instead, homolysis of the Ω Fe-C5' bond generates the nominally "free" 5'-dAdo• radical, which is captured here by freeze-trapping. During cryoannealing at 77 K, the 5'-dAdo• directly abstracts an H-atom from the peptide to generate the G734• peptide radical trapped in the PFL-AE active site. These observations reveal the 5'-dAdo• radical to be a well-defined intermediate, caught in the act of substrate H-atom abstraction, providing new insights into the mechanistic steps of radical initiation by RS enzymes.
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Affiliation(s)
- Maike N. Lundahl
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT59717
| | - Hao Yang
- Department of Chemistry, Northwestern University, Evanston, IL60208
| | - William E. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT59717
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL60208
| | - Joan B. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT59717
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2
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Abstract
Radical S-adenosylmethionine (SAM) enzymes use a site-differentiated [4Fe-4S] cluster and SAM to initiate radical reactions through liberation of the 5'-deoxyadenosyl (5'-dAdo•) radical. They form the largest enzyme superfamily, with more than 700,000 unique sequences currently, and their numbers continue to grow as a result of ongoing bioinformatics efforts. The range of extremely diverse, highly regio- and stereo-specific reactions known to be catalyzed by radical SAM superfamily members is remarkable. The common mechanism of radical initiation in the radical SAM superfamily is the focus of this review. Most surprising is the presence of an organometallic intermediate, Ω, exhibiting an Fe-C5'-adenosyl bond. Regioselective reductive cleavage of the SAM S-C5' bond produces 5'-dAdo• to form Ω, with the regioselectivity originating in the Jahn-Teller effect. Ω liberates the free 5'-dAdo• as the catalytically active intermediate through homolysis of the Fe-C5' bond, in analogy to Co-C5' bond homolysis in B12, which was once viewed as biology's choice of radical generator.
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Affiliation(s)
- Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - William E Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA;
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA;
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3
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Broderick JB, Broderick WE, Hoffman BM. Radical SAM enzymes: Nature's choice for radical reactions. FEBS Lett 2023; 597:92-101. [PMID: 36251330 PMCID: PMC9894703 DOI: 10.1002/1873-3468.14519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/05/2022] [Indexed: 02/04/2023]
Abstract
Enzymes that use a [4Fe-4S]1+ cluster plus S-adenosyl-l-methionine (SAM) to initiate radical reactions (radical SAM) form the largest enzyme superfamily, with over half a million members across the tree of life. This review summarizes recent work revealing the radical SAM reaction pathway, which ultimately liberates the 5'-deoxyadenosyl (5'-dAdo•) radical to perform extremely diverse, highly regio- and stereo-specific, transformations. Most surprising was the discovery of an organometallic intermediate Ω exhibiting an Fe-C5'-adenosyl bond. Ω liberates 5'-dAdo• through homolysis of the Fe-C5' bond, in analogy to Co-C5' bond homolysis in B12 , previously viewed as biology's paradigmatic radical generator. The 5'-dAdo• has been trapped and characterized in radical SAM enzymes via a recently discovered photoreactivity of the [4Fe-4S]+ /SAM complex, and has been confirmed as a catalytically active intermediate in enzyme catalysis. The regioselective SAM S-C bond cleavage to produce 5'-dAdo• originates in the Jahn-Teller effect. The simplicity of SAM as a radical precursor, and the exquisite control of 5'-dAdo• reactivity in radical SAM enzymes, may be why radical SAM enzymes pervade the tree of life, while B12 enzymes are only a few.
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Affiliation(s)
- Joan B. Broderick
- Department of Chemistry & Biochemistry, 103 CBB, Montana State University, Bozeman, MT 59717
| | - William E. Broderick
- Department of Chemistry & Biochemistry, 103 CBB, Montana State University, Bozeman, MT 59717
| | - Brian M. Hoffman
- Department of Chemistry, 2145 Sheridan Rd, Northwestern University, Evanston, IL. 60208
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Ghosh AP, Lodowski P, Kozlowski PM. Aerobic photolysis of methylcobalamin: unraveling the photoreaction mechanism. Phys Chem Chem Phys 2022; 24:6093-6106. [PMID: 35212341 DOI: 10.1039/d1cp02013g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photo-reactivity of cobalamins (Cbls) is influenced by the nature of axial ligands and the cofactor's environment. While the biologically active forms of Cbls with alkyl axial ligands, such as methylcobalamin (MeCbl) and adenosylcobalamin (AdoCbl), are considered to be photolytically active, in contrast, the non-alkyl Cbls are photostable. In addition to these, the photolytic properties of Cbls can also be modulated in the presence of molecular oxygen, i.e., under aerobic conditions. Herein, the photoreaction of the MeCbl in the presence of oxygen has been explored using density functional theory (DFT) and time-dependent DFT (TD-DFT). The first stage of the aerobic photoreaction is the activation of the Co-C bond and the formation of the ligand field (LF) electronic state through the displacement of axial bonds. Once the photoreaction reaches the LF excited state, three processes can occur: namely the formation of OO-CH3 through the reaction of CH3 with molecular oxygen, de-activation of the {Im⋯[CoII(corrin)]⋯CH3}+ sub-system from the LF electronic state by changing the electronic configuration from (dyz)1(dz2)2 to (dyz)2(dz2)1 and the formation of the deactivation complex (DC) complex via the recombination of OO-CH3 species with the de-excited [CoII(corrin)] system. In the proposed mechanism, the deactivation of the [CoII(corrin)] subsystem may coexist with the formation of OO-CH3, followed by immediate relaxation of the subsystems in the ground state. Moreover, the formation of the OO-CH3 species followed by the formation of the {[CoIII(corrin)]-OO-CH3}+ complex stabilizes the system compared to the reactant complex.
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Affiliation(s)
- Arghya Pratim Ghosh
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA.
| | - Piotr Lodowski
- Institute of Chemistry, University of Silesia in Katowice, Szkolna 9, PL-40 006 Katowice, Poland
| | - Pawel M Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA.
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Ghosh AP, Toda MJ, Kozlowski PM. Photolytic properties of B 12-dependent enzymes: A theoretical perspective. VITAMINS AND HORMONES 2022; 119:185-220. [PMID: 35337619 DOI: 10.1016/bs.vh.2022.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The biologically active vitamin B12 derivates, methylcobalamin (MeCbl) and adenosylcobalamin (AdoCbl), are ubiquitous organometallic cofactors. In addition to their key roles in enzymatic catalysis, B12 cofactors have complex photolytic properties which have been the target of experimental and theoretical studies. With the recent discovery of B12-dependent photoreceptors, there is an increased need to elucidate the underlying photochemical mechanisms of these systems. This book chapter summarizes the photolytic properties of MeCbl- and AdoCbl-dependent enzymes with particular emphasis on the effect of the environment of the cofactor on the excited state processes. These systems include isolated MeCbl and AdoCbl as well as the enzymes, ethanolamine ammonia-lyase (EAL), glutamate mutase (GLM), methionine synthase (MetH), and photoreceptor CarH. Central to determining the photodissociation mechanism of each system is the analysis of the lowest singlet excited state (S1) potential energy surface (PES). Time-dependent density functional theory (TD-DFT), employing BP86/TZVPP, is widely used to construct such PESs. Regardless of the environment, the topology of the S1 PES of AdoCbl or MeCbl is marked by characteristic features, namely the metal-to-ligand charge transfer (MLCT) and ligand field (LF) regions. Conversely, the relative energetics of these electronic states are affected by the environment. Applications and outlooks for Cbl photochemistry are also discussed.
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Affiliation(s)
- Arghya Pratim Ghosh
- Department of Chemistry, University of Louisville, Louisville, KY, United States
| | - Megan J Toda
- 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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Toda MJ, Mamun AA, Lodowski P, Kozlowski PM. Why is CarH photolytically active in comparison to other B12-dependent enzymes? JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2020; 209:111919. [DOI: 10.1016/j.jphotobiol.2020.111919] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 12/23/2022]
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7
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Ghosh AP, Lodowski P, Bazarganpour A, Leks M, Kozlowski PM. Aerobic photolysis of methylcobalamin: structural and electronic properties of the Cbl-O-O-CH 3 intermediate. Dalton Trans 2020; 49:4114-4124. [PMID: 32142090 DOI: 10.1039/c9dt03740c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Photolysis of methylcobalamin (MeCbl) in the presence of molecular oxygen (O2) has been investigated using density functional theory (DFT) and time-dependent DFT (TD-DFT). The key step involves the formation of the Cbl-O-O-CH3 intermediate as a result of triplet O2 insertion in the Co-C bond in the presence of light. Analysis of low-lying excited states shows that the presence of light is only needed to activate the Co-C bond via the formation of the ligand field (LF) state. The insertion of O2, as well as the change in the spin state, takes place in the ground state. The analysis of the structural and electronic properties of the Cbl-O-O-CH3 intermediate is presented and possible decomposition also discussed.
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Affiliation(s)
- Arghya Pratim Ghosh
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA.
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8
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Yang H, Impano S, Shepard EM, James CD, Broderick WE, Broderick JB, Hoffman BM. Photoinduced Electron Transfer in a Radical SAM Enzyme Generates an S-Adenosylmethionine Derived Methyl Radical. J Am Chem Soc 2019; 141:16117-16124. [PMID: 31509404 DOI: 10.1021/jacs.9b08541] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Radical SAM (RS) enzymes use S-adenosyl-l-methionine (SAM) and a [4Fe-4S] cluster to initiate a broad spectrum of radical transformations throughout all kingdoms of life. We report here that low-temperature photoinduced electron transfer from the [4Fe-4S]1+ cluster to bound SAM in the active site of the hydrogenase maturase RS enzyme, HydG, results in specific homolytic cleavage of the S-CH3 bond of SAM, rather than the S-C5' bond as in the enzyme-catalyzed (thermal) HydG reaction. This result is in stark contrast to a recent report in which photoinduced ET in the RS enzyme pyruvate formate-lyase activating enzyme cleaved the S-C5' bond to generate a 5'-deoxyadenosyl radical, and provides the first direct evidence for homolytic S-CH3 bond cleavage in a RS enzyme. Photoinduced ET in HydG generates a trapped •CH3 radical, as well as a small population of an organometallic species with an Fe-CH3 bond, denoted ΩM. The •CH3 radical is surprisingly found to exhibit rotational diffusion in the HydG active site at temperatures as low as 40 K, and is rapidly quenched: whereas 5'-dAdo• is stable indefinitely at 77 K, •CH3 quenches with a half-time of ∼2 min at this temperature. The rapid quenching and rotational/translational freedom of •CH3 shows that enzymes would be unable to harness this radical as a regio- and stereospecific H atom abstractor during catalysis, in contrast to the exquisite control achieved with the enzymatically generated 5'-dAdo•.
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Affiliation(s)
- Hao Yang
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Stella Impano
- Department of Chemistry & Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Eric M Shepard
- Department of Chemistry & Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Christopher D James
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - William E Broderick
- Department of Chemistry & Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Joan B Broderick
- Department of Chemistry & Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Brian M Hoffman
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
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9
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Toda MJ, Lodowski P, Mamun AA, Jaworska M, Kozlowski PM. Photolytic properties of the biologically active forms of vitamin B12. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2018.12.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Mamun AA, Toda MJ, Lodowski P, Kozlowski PM. Photolytic Cleavage of Co–C Bond in Coenzyme B12-Dependent Glutamate Mutase. J Phys Chem B 2019; 123:2585-2598. [DOI: 10.1021/acs.jpcb.8b07547] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Abdullah Al Mamun
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
| | - Megan J. Toda
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
| | - Piotr Lodowski
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia in Katowice, Szkolna 9, PL-40 006 Katowice, Poland
| | - Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
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11
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Mamun AA, Toda MJ, Kozlowski PM. Can photolysis of the Co C bond in coenzyme B12-dependent enzymes be used to mimic the native reaction? JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2019; 191:175-184. [DOI: 10.1016/j.jphotobiol.2018.12.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 12/22/2022]
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12
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Ucuncuoglu N, Warncke K. Protein Configurational States Guide Radical Rearrangement Catalysis in Ethanolamine Ammonia-Lyase. Biophys J 2018; 114:2775-2786. [PMID: 29925015 DOI: 10.1016/j.bpj.2018.03.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 03/15/2018] [Accepted: 03/20/2018] [Indexed: 01/14/2023] Open
Abstract
The adenosylcobalamin- (coenzyme B12) dependent ethanolamine ammonia-lyase (EAL) plays a key role in aminoethanol metabolism, associated with microbiome homeostasis and Salmonella- and Escherichia coli-induced disease conditions in the human gut. To gain molecular insight into these processes toward development of potential therapeutic targets, reactions of the cryotrapped (S)-2-aminopropanol substrate radical EAL from Salmonella typhimurium are addressed over a temperature (T) range of 220-250 K by using T-step reaction initiation and time-resolved, full-spectrum electron paramagnetic resonance spectroscopy. The observed substrate radical reaction kinetics are characterized by two pairs of biexponential processes: native decay to diamagnetic products and growth of a non-native radical species and Co(II) in cobalamin. The multicomponent low-T kinetics are simulated by using a minimal model, in which the substrate-radical macrostate, S⋅, is partitioned by a free-energy barrier into two sequential microstates: 1) S1⋅, a relatively high-entropy/high-enthalpy microstate with a protein configuration that captures the nascent substrate radical in the terminal step of radical-pair separation; and 2) S2⋅, a relatively low-enthalpy/low-entropy microstate with a protein configuration that enables the rearrangement reaction. The non-native, destructive reaction of S1⋅ at T ≤ 250 K is caused by a prolonged lifetime in the substrate-radical capture state. Monotonic S⋅ decay over 278-300 K indicates that the free-energy barrier to S1⋅ and S2⋅ interconversion is latent at physiological T-values. Overall, the low-temperature studies reveal two protein-configuration microstates and connecting protein-configurational transitions that specialize the S⋅ macrostate for the dual functional roles of radical capture and rearrangement enabling. The identification of new, to our knowledge, intermediate states and specific protein-fluctuation contributions to the reaction coordinate represent an advance toward development of novel therapeutic targets in EAL.
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Affiliation(s)
| | - Kurt Warncke
- Department of Physics, Emory University, Atlanta, Georgia.
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13
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Mamun AA, Toda MJ, Lodowski P, Jaworska M, Kozlowski PM. Mechanism of Light Induced Radical Pair Formation in Coenzyme B12-Dependent Ethanolamine Ammonia-Lyase. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00120] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Abdullah Al Mamun
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
| | - Megan J. Toda
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
| | - Piotr Lodowski
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia in Katowice, Szkolna 9, PL-40 006 Katowice, Poland
| | - Maria Jaworska
- Department of Theoretical Chemistry, Institute of Chemistry, University of Silesia in Katowice, Szkolna 9, PL-40 006 Katowice, Poland
| | - Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
- Department of Food Sciences, Medical University of Gdansk, Al. Gen. J. Hallera 107, 80-416 Gdansk, Poland
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14
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Garabato BD, Lodowski P, Jaworska M, Kozlowski PM. Mechanism of Co-C photodissociation in adenosylcobalamin. Phys Chem Chem Phys 2016; 18:19070-82. [PMID: 27356617 DOI: 10.1039/c6cp02136k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A mechanism of Co-C bond photodissociation in the base-on form of adenosylcobalamin (AdoCbl) was investigated by time-dependent density functional theory (TD-DFT). The key mechanistic step involves singlet radical pair (RP) generation from the first electronically excited state (S1). To connect TD-DFT calculations with ultra-fast excited state dynamics, the potential energy surface (PES) of the S1 state was constructed using Co-C and Co-NIm axial coordinates. The S1 PES can be characterized by two minima separated by a seam resulting from the crossing of two surfaces, of metal-to-ligand charge transfer (MLCT) character near the minimum, and a shallow ligand field (LF) surface at elongated axial bond distances. Only one possible pathway for photolysis (path A) was identified based on energetic grounds. This pathway is characterized by the first elongation of the Co-C bond, followed by photolysis from an LF state where the axial base is partially detached. A new perspective on the photolysis of AdoCbl is then gained by connecting TD-DFT results with available experimental observations.
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Affiliation(s)
- Brady D Garabato
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40202, USA.
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15
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Kozlowski PM, Garabato BD, Lodowski P, Jaworska M. Photolytic properties of cobalamins: a theoretical perspective. Dalton Trans 2016; 45:4457-70. [PMID: 26865262 DOI: 10.1039/c5dt04286k] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This Perspective Article highlights recent theoretical developments, and summarizes the current understanding of the photolytic properties of cobalamins from a computational point of view. The primary focus is on two alkyl cobalamins, methylcobalamin (MeCbl) and adenosylcobalamin (AdoCbl), as well as two non-alkyl cobalamins, cyanocobalamin (CNCbl) and hydroxocobalamin (HOCbl). Photolysis of alkyl cobalamins involves low-lying singlet excited states where photodissociation of the Co-C bond leads to formation of singlet-born alkyl/cob(ii)alamin radical pairs (RPs). Potential energy surfaces (PESs) associated with cobalamin low-lying excited states as functions of both axial bonds, provide the most reliable tool for initial analysis of their photochemical and photophysical properties. Due to the complexity, and size limitations associated with the cobalamins, the primary method for calculating ground state properties is density functional theory (DFT), while time-dependent DFT (TD-DFT) is used for electronically excited states. For alkyl cobalamins, energy pathways on the lowest singlet surface, connecting metal-to-ligand charge transfer (MLCT) and ligand field (LF) minima, can be associated with photo-homolysis of the Co-C bond observed experimentally. Additionally, energy pathways between minima and seams associated with crossing of S1/S0 surfaces, are the most efficient for internal conversion (IC) to the ground state. Depending on the specific cobalamin, such IC may involve simultaneous elongation of both axial bonds (CNCbl), or detachment of axial base followed by corrin ring distortion (MeCbl). The possibility of intersystem crossing, and the formation of triplet RPs is also discussed based on Landau-Zener theory.
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Affiliation(s)
- Pawel M Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA.
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16
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Wang M, Zhu C, Kohne M, Warncke K. Resolution and Characterization of Chemical Steps in Enzyme Catalytic Sequences by Using Low-Temperature and Time-Resolved, Full-Spectrum EPR Spectroscopy in Fluid Cryosolvent and Frozen Solution Systems. Methods Enzymol 2015; 563:59-94. [PMID: 26478482 PMCID: PMC6186429 DOI: 10.1016/bs.mie.2015.08.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Approaches to the resolution and characterization of individual chemical steps in enzyme catalytic sequences, by using temperatures in the cryogenic range of 190-250 K, and kinetics measured by time-resolved, full-spectrum electron paramagnetic resonance spectroscopy in fluid cryosolvent and frozen solution systems, are described. The preparation and performance of the adenosylcobalamin-dependent ethanolamine ammonia-lyase enzyme from Salmonella typhimurium in the two systems exemplifies the biochemical and spectroscopic methods. General advantages of low-temperature studies are (1) slowing of reaction steps, so that measurements can be made by using straightforward T-step kinetic methods and commercial instrumentation, (2) resolution of individual reaction steps, so that first-order kinetic analysis can be applied, and (3) accumulation of intermediates that are not detectable at room temperatures. The broad temperature range from room temperature to 190 K encompasses three regimes: (1) temperature-independent mean free energy surface (corresponding to native behavior); (2) the narrow temperature region of a glass-like transition in the protein, over which the free energy surface changes, revealing dependence of the native reaction on collective protein/solvent motions; and (3) the temperature range below the glass transition region, for which persistent reaction corresponds to nonnative, alternative reaction pathways, in the vicinity of the native configurational envelope. Representative outcomes of low-temperature kinetics studies are portrayed on Eyring and free energy surface (landscape) plots, and guidelines for interpretations are presented.
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Affiliation(s)
- Miao Wang
- Department of Physics, Emory University, N201 Mathematics and Science Center, Atlanta, Georgia, USA
| | - Chen Zhu
- Department of Physics, Emory University, N201 Mathematics and Science Center, Atlanta, Georgia, USA
| | - Meghan Kohne
- Department of Physics, Emory University, N201 Mathematics and Science Center, Atlanta, Georgia, USA
| | - Kurt Warncke
- Department of Physics, Emory University, N201 Mathematics and Science Center, Atlanta, Georgia, USA.
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17
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The photochemical mechanism of a B12-dependent photoreceptor protein. Nat Commun 2015; 6:7907. [PMID: 26264192 PMCID: PMC4557120 DOI: 10.1038/ncomms8907] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 06/23/2015] [Indexed: 01/01/2023] Open
Abstract
The coenzyme B12-dependent photoreceptor protein, CarH, is a bacterial transcriptional regulator that controls the biosynthesis of carotenoids in response to light. On binding of coenzyme B12 the monomeric apoprotein forms tetramers in the dark, which bind operator DNA thus blocking transcription. Under illumination the CarH tetramer dissociates, weakening its affinity for DNA and allowing transcription. The mechanism by which this occurs is unknown. Here we describe the photochemistry in CarH that ultimately triggers tetramer dissociation; it proceeds via a cob(III)alamin intermediate, which then forms a stable adduct with the protein. This pathway is without precedent and our data suggest it is independent of the radical chemistry common to both coenzyme B12 enzymology and its known photochemistry. It provides a mechanistic foundation for the emerging field of B12 photobiology and will serve to inform the development of a new class of optogenetic tool for the control of gene expression. Coenzyme B12 traditionally acts as cofactor to light-independent metabolic enzymes in bacteria and humans. Here, Kutta et al. present a time-resolved photochemical description of a B12-dependent photoreceptor protein, which represents a mechanistic foundation for B12 photobiology.
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Mori K, Oiwa T, Kawaguchi S, Kondo K, Takahashi Y, Toraya T. Catalytic Roles of Substrate-Binding Residues in Coenzyme B12-Dependent Ethanolamine Ammonia-Lyase. Biochemistry 2014; 53:2661-71. [DOI: 10.1021/bi500223k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Koichi Mori
- Department
of Bioscience
and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Toshihiro Oiwa
- Department
of Bioscience
and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Satoshi Kawaguchi
- Department
of Bioscience
and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Kyosuke Kondo
- Department
of Bioscience
and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Yusuke Takahashi
- Department
of Bioscience
and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Tetsuo Toraya
- Department
of Bioscience
and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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19
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Cobalamin-dependent dehydratases and a deaminase: Radical catalysis and reactivating chaperones. Arch Biochem Biophys 2014; 544:40-57. [DOI: 10.1016/j.abb.2013.11.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 11/04/2013] [Accepted: 11/08/2013] [Indexed: 01/12/2023]
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20
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Photolytic cleavage of Co–C bond: A mechanistic study for the formation of solvent coordinated cobalt(II) complex. J Organomet Chem 2014. [DOI: 10.1016/j.jorganchem.2013.09.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Lodowski P, Jaworska M, Andruniów T, Garabato BD, Kozlowski PM. Mechanism of the S1 excited state internal conversion in vitamin B12. Phys Chem Chem Phys 2014; 16:18675-9. [DOI: 10.1039/c4cp02465f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To explain the photostability of vitamin B12, internal conversion of the S1 state was investigated using TD-DFT.
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Affiliation(s)
- Piotr Lodowski
- Department of Theoretical Chemistry
- Institute of Chemistry
- University of Silesia
- PL-40 006 Katowice, Poland
| | - Maria Jaworska
- Department of Theoretical Chemistry
- Institute of Chemistry
- University of Silesia
- PL-40 006 Katowice, Poland
| | - Tadeusz Andruniów
- Institute of Physical and Theoretical Chemistry
- Department of Chemistry
- Wroclaw University of Technology
- 50-370 Wroclaw, Poland
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22
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Wang M, Warncke K. Entropic origin of cobalt-carbon bond cleavage catalysis in adenosylcobalamin-dependent ethanolamine ammonia-lyase. J Am Chem Soc 2013; 135:15077-84. [PMID: 24028405 PMCID: PMC3839591 DOI: 10.1021/ja404467d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Adenosylcobalamin-dependent enzymes accelerate the cleavage of the cobalt-carbon (Co-C) bond of the bound coenzyme by >10(10)-fold. The cleavage-generated 5'-deoxyadenosyl radical initiates the catalytic cycle by abstracting a hydrogen atom from substrate. Kinetic coupling of the Co-C bond cleavage and hydrogen-atom-transfer steps at ambient temperatures has interfered with past experimental attempts to directly address the factors that govern Co-C bond cleavage catalysis. Here, we use time-resolved, full-spectrum electron paramagnetic resonance spectroscopy, with temperature-step reaction initiation, starting from the enzyme-coenzyme-substrate ternary complex and (2)H-labeled substrate, to study radical pair generation in ethanolamine ammonia-lyase from Salmonella typhimurium at 234-248 K in a dimethylsulfoxide/water cryosolvent system. The monoexponential kinetics of formation of the (2)H- and (1)H-substituted substrate radicals are the same, indicating that Co-C bond cleavage rate-limits radical pair formation. Analysis of the kinetics by using a linear, three-state model allows extraction of the microscopic rate constant for Co-C bond cleavage. Eyring analysis reveals that the activation enthalpy for Co-C bond cleavage is 32 ± 1 kcal/mol, which is the same as for the cleavage reaction in solution. The origin of Co-C bond cleavage catalysis in the enzyme is, therefore, the large, favorable activation entropy of 61 ± 6 cal/(mol·K) (relative to 7 ± 1 cal/(mol·K) in solution). This represents a paradigm shift from traditional, enthalpy-based mechanisms that have been proposed for Co-C bond-breaking in B12 enzymes. The catalysis is proposed to arise from an increase in protein configurational entropy along the reaction coordinate.
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Affiliation(s)
- Miao Wang
- Department of Physics, Emory University, Atlanta, GA 30322, United States
- Current Address: Wilmad-LabGlass, 1172 NW Boulevard, Vineland, NJ 08360
| | - Kurt Warncke
- Department of Physics, Emory University, Atlanta, GA 30322, United States
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23
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Jones AR, Levy C, Hay S, Scrutton NS. Relating localized protein motions to the reaction coordinate in coenzyme B12-dependent enzymes. FEBS J 2013; 280:2997-3008. [DOI: 10.1111/febs.12223] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Revised: 02/27/2013] [Accepted: 02/27/2013] [Indexed: 01/27/2023]
Affiliation(s)
| | - Colin Levy
- Manchester Institute of Biotechnology and Faculty of Life Sciences; The University of Manchester; Manchester; UK
| | - Sam Hay
- Manchester Institute of Biotechnology and Faculty of Life Sciences; The University of Manchester; Manchester; UK
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology and Faculty of Life Sciences; The University of Manchester; Manchester; UK
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24
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Bucher D, Sandala GM, Durbeej B, Radom L, Smith DM. The Elusive 5′-Deoxyadenosyl Radical in Coenzyme-B12-Mediated Reactions. J Am Chem Soc 2012; 134:1591-9. [DOI: 10.1021/ja207809b] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Denis Bucher
- School of Chemistry and ARC Centre of Excellence
for Free Radical Chemistry
and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
| | - Gregory M. Sandala
- School of Chemistry and ARC Centre of Excellence
for Free Radical Chemistry
and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
- Division of Organic
Chemistry and Biochemistry, Ruđer Bošković Institute, 10002 Zagreb, Croatia
| | - Bo Durbeej
- Division of Computational
Physics, IFM Theory and Modelling, Linköping University, SE-581 83 Linköping, Sweden
| | - Leo Radom
- School of Chemistry and ARC Centre of Excellence
for Free Radical Chemistry
and Biotechnology, University of Sydney, Sydney, NSW 2006, Australia
| | - David M. Smith
- Division of Organic
Chemistry and Biochemistry, Ruđer Bošković Institute, 10002 Zagreb, Croatia
- Computer-Chemie-Centrum, University of Erlangen-Nürnberg, 91052 Erlangen, Germany
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25
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Jones AR, Hardman SJO, Hay S, Scrutton NS. Is There a Dynamic Protein Contribution to the Substrate Trigger in Coenzyme B12-Dependent Ethanolamine Ammonia Lyase? Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201105132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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26
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Jones AR, Hardman SJO, Hay S, Scrutton NS. Is there a dynamic protein contribution to the substrate trigger in coenzyme B12-dependent ethanolamine ammonia lyase? Angew Chem Int Ed Engl 2011; 50:10843-6. [PMID: 21948289 DOI: 10.1002/anie.201105132] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Indexed: 11/07/2022]
Affiliation(s)
- Alex R Jones
- Faculty of Life Sciences, Photon Science Institute and Manchester Interdisciplinary Biocentre, University of Manchester, Manchester M1 7DN, UK
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27
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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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28
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Knör G, Monkowius U. Photosensitization and photocatalysis in bioinorganic, bio-organometallic and biomimetic systems. ADVANCES IN INORGANIC CHEMISTRY 2011. [DOI: 10.1016/b978-0-12-385904-4.00005-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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29
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Jones AR, Woodward JR, Scrutton NS. Continuous wave photolysis magnetic field effect investigations with free and protein-bound alkylcobalamins. J Am Chem Soc 2010; 131:17246-53. [PMID: 19899795 DOI: 10.1021/ja9059238] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The activation of the Co-C bond in adenosylcobalamin-dependent enzymes generates a singlet-born Co(II)-adenosyl radical pair. Two of the salient questions regarding this process are: (1) What is the origin of the considerable homolysis rate enhancement achieved by this class of enzyme? (2) Are the reaction dynamics of the resultant radical pair sensitive to the application of external magnetic fields? Here, we present continuous wave photolysis magnetic field effect (MFE) data that reveal the ethanolamine ammonia lyase (EAL) active site to be an ideal microreactor in which to observe enhanced magnetic field sensitivity in the adenosylcobalamin radical pair. The observed field dependence is in excellent agreement with that calculated from published hyperfine couplings for the constituent radicals, and the magnitude of the MFE (<18%) is almost identical to that observed in a solvent containing 67% glycerol. Similar augmentation is not observed, however, in the equivalent experiments with EAL-bound methylcobalamin, where all field sensitivity observed in the free cofactor is washed out completely. Parallels are drawn between the latter case and the loss of field sensitivity in the EAL holoenzyme upon substrate binding (Jones et al. J. Am. Chem. Soc. 2007, 129, 15718-15727). Both are attributed to the rapid removal of the alkyl radical immediately after homolysis, such that there is inadequate radical pair recombination for the observation of field effects. Taken together, these results support the notion that rapid radical quenching, through the coupling of homolysis and hydrogen abstraction steps, and subsequent radical pair stabilization make a contribution to the observed rate acceleration of Co-C bond homolysis in adenosylcobalamin-dependent enzymes.
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Affiliation(s)
- Alex R Jones
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester M1 7DN, United Kingdom
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