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Wojdyla Z, Maldonado-Domínguez M, Bharadwaz P, Culka M, Srnec M. Elucidation of factors shaping reactivity of 5'-deoxyadenosyl - a prominent organic radical in biology. Phys Chem Chem Phys 2024. [PMID: 39041228 DOI: 10.1039/d4cp01725k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
This study investigates the factors modulating the reactivity of 5'-deoxyadenosyl (5'dAdo˙) radical, a potent hydrogen atom abstractor that forms in the active sites of radical SAM enzymes and that otherwise undergoes a rapid self-decay in aqueous solution. Here, we compare hydrogen atom abstraction (HAA) reactions between native substrates of radical SAM enzymes and 5'dAdo˙ in aqueous solution and in two enzymatic microenvironments. With that we reveal that HAA efficiency of 5'dAdo˙ is due to (i) the in situ formation of 5'dAdo˙ in a pre-ordered complex with a substrate, which attenuates the unfavorable effect of substrate:5'dAdo˙ complex formation, and (ii) the prevention of the conformational changes associated with self-decay by a tight active-site cavity. The enzymatic cavity, however, does not have a strong effect on the HAA activity of 5'dAdo˙. Thus, we performed an analysis of in-water HAA performed by 5'dAdo˙ based on a three-component thermodynamic model incorporating the diagonal effect of the free energy of reaction, and the off-diagonal effect of asynchronicity and frustration. To this aim, we took advantage of the straightforward relationship between the off-diagonal thermodynamic effects and the electronic-structure descriptor - the redistribution of charge between the reactants during the reaction. It allows to access HAA-competent redox and acidobasic properties of 5'dAdo˙ that are otherwise unavailable due to its instability upon one-electron reduction and protonation. The results show that all reactions feature a favourable thermodynamic driving force and tunneling, the latter of which lowers systematically barriers by ∼2 kcal mol-1. In addition, most of the reactions experience a favourable off-diagonal thermodynamic contribution. In HAA reactions, 5'dAdo˙ acts as a weak oxidant as well as a base, also 5'dAdo˙-promoted HAA reactions proceed with a quite low degree of asynchronicity of proton and electron transfer. Finally, the study elucidates the crucial and dual role of asynchronicity. It directly lowers the barrier as a part of the off-diagonal thermodynamic contribution, but also indirectly increases the non-thermodynamic part of the barrier by presumably controlling the adiabatic coupling between proton and electron transfer. The latter signals that the reaction proceeds as a hydrogen atom transfer rather than a proton-coupled electron transfer.
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Affiliation(s)
- Zuzanna Wojdyla
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18200 Prague, Czech Republic.
| | - Mauricio Maldonado-Domínguez
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18200 Prague, Czech Republic.
| | - Priyam Bharadwaz
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18200 Prague, Czech Republic.
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague, Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18200 Prague, Czech Republic.
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Yamauchi R, Fujisawa M, Koyanagi S, Muramatsu A, Kobayashi T, Wada Y, Akama K, Tanaka M, Kurashige H, Sato A, Horiuchi H, Mukai T, Yamamoto Y, Sasaki Y. Formate-producing capacity provided by reducing ability of Streptococcus thermophilus nicotinamide adenine dinucleotide oxidase determines yogurt acidification rate. J Dairy Sci 2023; 106:6710-6722. [PMID: 37211485 DOI: 10.3168/jds.2023-23245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/19/2023] [Indexed: 05/23/2023]
Abstract
Yogurt is made by fermenting milk with 2 lactic acid bacteria, Lactobacillus delbrueckii ssp. bulgaricus and Streptococcus thermophilus. To comprehensively understand the protocooperation mechanism between S. thermophilus and L. bulgaricus in yogurt fermentation, we examined 24 combinations of cocultures comprising 7 fast- or slow-acidifying S. thermophilus strains with 6 fast- or slow-acidifying L. bulgaricus strains. Furthermore, 3 NADH oxidase (Nox)-deficient mutants (Δnox) and one pyruvate formate-lyase deficient mutant (ΔpflB) of S. thermophilus were used to evaluate the factor that determines the acidification rate of S. thermophilus. The results revealed that the acidification rate of S. thermophilus monoculture determined the yogurt fermentation rates, despite the coexistence of L. bulgaricus, whose acidification rate was either fast or slow. Significant correlation was found between the acidification rate of S. thermophilus monoculture and the amount of formate production. Result using ΔpflB showed that the formate was indispensable for the acidification of S. thermophilus. Moreover, results of the Δnox experiments revealed that formate production required Nox activity, which not only regulated dissolved oxygen, but also the redox potential. The Nox provided the large decrease in redox potential required by pyruvate formate-lyase to produce formate. A highly significant correlation was found between formate accumulation and Nox activity in S. thermophilus. In conclusion, the formate production ability provided by the action of Nox activity determines the acidification rate of S. thermophilus, and consequently, regulates yogurt coculture fermentation.
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Affiliation(s)
- R Yamauchi
- Graduate School of Agriculture, University of Meiji, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - M Fujisawa
- Graduate School of Agriculture, University of Meiji, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - S Koyanagi
- Graduate School of Agriculture, University of Meiji, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - A Muramatsu
- Graduate School of Agriculture, University of Meiji, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - T Kobayashi
- Graduate School of Agriculture, University of Meiji, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Y Wada
- Graduate School of Agriculture, University of Meiji, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - K Akama
- Graduate School of Agriculture, University of Meiji, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - M Tanaka
- Graduate School of Agriculture, University of Meiji, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - H Kurashige
- Department of Animal Science, School of Veterinary Medicine, Kitasato University, 35-1 Higashi 23, Towada, Aomori 034-8628, Japan
| | - A Sato
- Department of Animal Science, School of Veterinary Medicine, Kitasato University, 35-1 Higashi 23, Towada, Aomori 034-8628, Japan
| | - H Horiuchi
- Food Science and Technology Research Laboratories, R&D Division, Meiji Co. Ltd., 1-29-1 Nanakuni, Hachioji, Tokyo 192-0919, Japan
| | - T Mukai
- Department of Animal Science, School of Veterinary Medicine, Kitasato University, 35-1 Higashi 23, Towada, Aomori 034-8628, Japan
| | - Y Yamamoto
- Department of Animal Science, School of Veterinary Medicine, Kitasato University, 35-1 Higashi 23, Towada, Aomori 034-8628, Japan
| | - Y Sasaki
- Graduate School of Agriculture, University of Meiji, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan.
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Sen A, Ansari A, Swain A, Pandey B, Rajaraman G. Probing the Origins of Puzzling Reactivity in Fe/Mn-Oxo/Hydroxo Species toward C-H Bonds: A DFT and Ab Initio Perspective. Inorg Chem 2023; 62:14931-14941. [PMID: 37650771 DOI: 10.1021/acs.inorgchem.3c01632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Activation of C-H bonds using an earth-abundant metal catalyst is one of the top challenges of chemistry, where high-valent Mn/Fe-oxo(hydroxo) biomimic species play an important role. There are several open questions related to the comparative oxidative abilities of these species, and a unifying concept that could accommodate various factors influencing reactivity is lacking. To shed light on these open questions, here, we have used a combination of density functional theory (DFT) (B3LYP-D3/def2-TZVP) and ab initio (CASSCF/NEVPT2) calculations to study a series of high-valent metal-oxo species [Mn+H3buea(O/OH)] (M = Mn and Fe, n = II to V; H3buea = tris[(N'-tert-butylureaylato)-N-ethylene)]aminato towards the activation of dihydroanthracene (DHA). The H-bonding network in the ligand architecture influences the ground state-excited state gap and brings several excited states of the same spin multiplicity closer in energy, which triggers reactivity via one of those excited states, reducing the kinetic barriers for the C-H bond activation and rationalizing several puzzling reactivity trends observed in various high-valent Mn/Fe-oxo(hydroxo) species.
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Affiliation(s)
- Asmita Sen
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai400076, India
| | - Azaj Ansari
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai400076, India
| | - Abinash Swain
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai400076, India
| | - Bhawana Pandey
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai400076, India
| | - Gopalan Rajaraman
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai400076, India
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Bím D, Alexandrova AN. Local Electric Fields as a Natural Switch of Heme-Iron Protein Reactivity. ACS Catal 2021; 11:6534-6546. [PMID: 34413991 DOI: 10.1021/acscatal.1c00687] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Heme-iron oxidoreductases operating through the high-valent FeIVO intermediates perform crucial and complicated transformations, such as oxidations of unreactive saturated hydrocarbons. These enzymes share the same Fe coordination, only differing by the axial ligation, e.g., Cys in P450 oxygenases, Tyr in catalases, and His in peroxidases. By examining ~200 heme-iron proteins, we show that the protein hosts exert highly specific intramolecular electric fields on the active sites, and there is a strong correlation between the direction and magnitude of this field and the protein function. In all heme proteins, the field is preferentially aligned with the Fe-O bond ( Fz ). The Cys-ligated P450 oxygenases have the highest average Fz of 28.5 MV cm-1, i.e., most enhancing the oxyl-radical character of the oxo group, and consistent with the ability of these proteins to activate strong C-H bonds. In contrast, in Tyr-ligated proteins, the average Fz is only 3.0 MV cm-1, apparently suppressing single-electron off-pathway oxidations, and in His-ligated proteins, Fz is -8.7 MV cm-1. The operational field range is given by the trade-off between the low reactivity of the FeIVO Compound I at the more negative Fz , and the low selectivity at the more positive Fz . Consequently, a heme-iron site placed in the field characteristic of another heme-iron protein class loses its canonical function, and gains an adverse one. Thus, electric fields produced by the protein scaffolds, together with the nature of the axial ligand, control all heme-iron chemistry.
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Affiliation(s)
- Daniel Bím
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Anastassia N. Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
- California NanoSystems Institute, University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, California 90095-1569, United States
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