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Methane Generation Via Intraprotein C-S Bond Cleavage in Cytochrome

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Methane Generation Via Intraprotein C-S Bond Cleavage in Cytochrome Journal of Organometallic Chemistry 901 (2019) 120945 Contents lists available at ScienceDirect Journal of Organometallic Chemistry journal homepage: www.elsevier.com/locate/jorganchem Methane generation via intraprotein CeS bond cleavage in cytochrome b562 reconstituted with nickel didehydrocorrin * ** Yuta Miyazaki a, Koji Oohora a, b, , Takashi Hayashi a, a Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan b Frontier Research Base for Global Young Researchers, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan article info abstract II Article history: Cytochrome b562 (Cyt b562) reconstituted with nickel didehydrocorrin (Ni (DDHC)), a protein-based Received 20 August 2019 functional model of methyl-coenzyme M reductase (MCR), was investigated to demonstrate methane Received in revised form generation via intraprotein cleavage of a CeS bond. NiII(DDHC) was synthesized as a model complex of an 16 September 2019 MCR cofactor known as F430 and found to show NiII/NiI redox behavior with a potential of À0.61 V vs. Accepted 18 September 2019 AgjAgCl. This potential is slightly positive-shifted compared to that of F430 without protein. Conjugation Available online 19 September 2019 II II of Ni (DDHC) with the apo-form of Cyt b562 provides reconstituted Cyt b562 (rCyt b562(Ni (DDHC))) which II was characterized by spectroscopic measurements. Photoirradiation of rCyt b562(Ni (DDHC)) generates Keywords: 0 Hemoprotein methane gas in the presence of tris(2,2 -bipyridine)ruthenium(II) chloride as a photosensitizer and so- fi MCR dium ascorbate as a sacri cial reagent. Further experiments using Cyt b562 mutants indicate that F430 methane is derived from the CH3S group of the methionine residue in the heme-binding site where Methane thioether, thiol and the nickel center are precisely arranged. The present study demonstrates the first Nickel corrinoid example of methane generation via intraprotein cleavage of a CeS bond using a functional model of MCR. © 2019 Elsevier B.V. All rights reserved. 1. Introduction this moment, two plausible mechanisms have been proposed which include formation of an organometallic methyleNi(III) in- Methane has been investigated both as an alternative fuel and a termediate or a methyl radical intermediate [5]. In the former case, greenhouse gas. Most of the methane gas in nature is generated as the stable methyleNi(III) intermediate is detected in a reaction of an end-product of decomposition of organic compounds by archaea the active Ni(I) species of MCR with methyl iodide [13e17]. The under anaerobic conditions [1,2]. Methanogenic archaea are known latter mechanism is more plausible according to a recent study to possess the enzyme methyl-coenzyme M reductase (MCR) which which included a detailed analysis of single turnover reaction of catalyzes the final and rate-limiting step of biological methane MCR with substrates possessing the CH3S group, which are similar generation [3e5]. This reaction is promoted by a nickel hydro- to native substrates [22]. In this context, an appropriate model corphinoid cofactor known as F430 in the active site. Methyl- complex of F430 has been required to properly assess the physi- coenzyme M (CH3SeCoM) and coenzyme B (HSeCoB) are con- cochemical properties and reactivity of F430 [28e32]. Although verted to methane and the heterodisulfide compound some model complexes generate methane from activated methyl (CoMeSeSeCoB) by the active Ni(I) intermediate in the enzymatic donors, examples of methane generation via cleavage of a CeS reaction (Fig. 1). bond have been quite limited. Jaun and co-workers reported that In spite of investigations in various experimental and theoretical photoirradiation of a Ni(II) complex with a thiolate-thioether studies, the reaction mechanism of MCR has not yet been fully ligand, bis{1-[2-(methylthio)ethyl]cyclohexanethiolato)nickel, in elucidated because of the complicated structure of MCR [6e27]. At the presence of the corresponding thiol-thioether substrate, 1-[2- (methylthio)ethyl]cyclohexanethiol, generated methane gas and the disulfide 1,2-dithiaspiro[4.5]decane, via cleavage of the CeS * Corresponding author. Department of Applied Chemistry, Graduate School of bond [30]. Tatsumi and co-workers also reported that chemical Engineering, Osaka University, Suita, 565-0871, Japan. reduction of Ni(II) complexes with thioether ligands, 1,8-dimethyl- ** Corresponding author. 4,11-bis{(2-methylthio)ethyl}-1,4,8,11-tetraaza-1,4,8,11- E-mail addresses: [email protected] (K. Oohora), thayashi@chem. cyclotetradecane and 1,8-{bis(2-methylthio)ethyl}-1,4,8,11- eng.osaka-u.ac.jp (T. Hayashi). https://doi.org/10.1016/j.jorganchem.2019.120945 0022-328X/© 2019 Elsevier B.V. All rights reserved. 2 Y. Miyazaki et al. / Journal of Organometallic Chemistry 901 (2019) 120945 Fig. 1. (a) Molecular structure of cofactor F430. (b) Methane generation catalyzed by methyl-coenzyme M reductase (MCR) in methanogenic archaea. tetraaza-1,4,8,11-cyclotetradecane, generates methane and ethane species of Ni(DDHC) is expected to be a more reactive intermediate gases via intramolecular cleavage of the CeS bond. The further than the Ni(I) species of Ni(TDHC). Previous investigations have addition of a thiol compound, 2,6-dimesitylbenzenethiol, promotes found that the nucleophilicity of the Co(I) species of cobalt dide- methane generation [31]. These model systems mimicking the hydrocorrin (Co(DDHC)) is enhanced relative to the Co(I) species of enzymatic reaction have provided important insights into our un- cobalt tetradehydrocorrin (Co(TDHC)) [34,35]. In addition, Cyt b562 derstanding of the reaction mechanism of MCR. is a suitable protein matrix because the CH3S group of the methi- In our previous work, we have reported a protein-based func- onine residue, Met7, is located close to the metal center in the heme tional MCR model which is prepared by myoglobin reconstituted pocket. In this paper, methane generation by present functional with nickel tetradehydrocorrin (Ni(TDHC)) as a model complex of model via intraprotein cleavage of the CeS bond of Met7 upon F430 [33]. The active Ni(I) species was confirmed in the presence photoreduction of the nickel complex is demonstrated in recon- and absence of the protein matrix of myoglobin. The protein-based stituted Cyt b562 as shown in Fig. 2. functional model was found to promote methane gas generation from methyl iodide, whereas the bare Ni(TDHC) complex does not 2. Experimental generate any significant amounts of methane gas under the same condition, indicating the importance of a protein matrix. However, 2.1. Instruments even the Ni(I) species of Ni(TDHC) in the protein matrix of myoglobin appears to be insufficient to activate a substrate UVevis spectral measurements were carried out with a involving a CH3S group as seen in catalysis by MCR. Thus, to BioSpec-nano spectrophotometer (Shimadzu) or a V-670 spectro- enhance the reactivity of the Ni(I) species, we have recently con- photometer (JASCO). CD spectra were recorded on a J-820AC structed a different type of protein-based functional model of MCR spectropolarimeter (JASCO). ESI-TOF MS analyses were performed by conjugation of nickel didehydrocorrin (Ni(DDHC)) and the apo- with a micrOTOF-II mass spectrometer (Bruker). 1H NMR spectrum form of cytochrome b562 (Cyt b562) in an effort to replicate methane was collected on an Avance III (600 MHz) spectrometer (Bruker). generation via CeS bond cleavage (Fig. 2). This is because the Ni(I) The 1H NMR chemical shift values are reported in ppm relative to a Fig. 2. (a) Structure of Cyt b562 (PDB ID: 1QPU). (b) Schematic representation of the reconstitution of Cyt b562 with Ni(DDHC). Y. Miyazaki et al. / Journal of Organometallic Chemistry 901 (2019) 120945 3 residual solvent peak. ICP-OES was performed on an ICPS-7510 2.4. Protein sequence of Cyt b562 and its mutants emission spectrometer (Shimadzu). Electrochemical studies were performed using a potentiostat (CompactStat, Ivium Technologies). 2.4.1. Cyt b562 A single-compartment cell was used for all cyclic voltammetry (CV) ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATP experiments with a polished Pt working electrode, a Pt wire PKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQ counter electrode and an AgjAgCl (3 M NaCl) reference electrode LKTTRNAYHQKYR (ALS Co., Ltd.). All electrochemical experiments were performed with 100 mM tetrabutylammonium hexafluorophosphate (TBAPF ) M7L 6 2.4.2. Cyt b562 as a supporting electrolyte. All solutions were purged with N2 ADLEDNLETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPP before CV measurements. Air-sensitive manipulations were per- KLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLK fi formed in a UNILab glove box (MBRAUN). Puri cation by HPLC was TTRNAYHQKYR conducted with a HPLC Prominence System (Shimadzu). Size exclusion chromatographic (SEC) purification was performed using 2.4.3. Cyt b L3C € fi 562 an AKTApuri er system (GE Healthcare). The pH measurements ADCEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATP were made with an F-72 pH meter (Horiba). Photoirradiation re- PKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQL action was conducted using an Optical Modulex (USHIO Inc.) KTTRNAYHQKYR equipped with a 500 W Xe arc lamp, a cold filter (Asahi Spectra Co., Ltd.) and a 420 nm sharp cut filter (SIGMAKOKI Co., Ltd.) to produce 2.5. Expression and purification of Cyt b and its mutants light in the range of 420 l 750 nm for 2 h at 25 C in a cryostat 562 (CoolSpeK, UNISOKU Co., Ltd.)
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