Friday, May 3, 2024
5/3/2024
Project Summary Archaea in the human gut express methyl-coenzyme M reductase (MCR) to catalyze the last step of methanogenesis and the first step of the anaerobic oxidation of methane. These reactions occur at F430, a nickel cofactor whose first coordination sphere — the ligands directly bound to it — includes the four nitrogen atoms of a unique anionic macrocycle. This center reversibly cleaves the thioether methyl-coenzyme M (CoM– SMe) to release methyl radical, which combines with thiol coenzyme B (HS–CoB) in the second coordination sphere — the residues proximal to but not bonded to the active site — to liberate methane and the disulfide CoM–S–S–CoB. The first and second coordination spheres of nickel in several MCR states are intractable, which motivates us to synthesize tractable small molecules that recapitulate active-site features proposed for these contentious states. Comparing data for models and MCR tells us how plausible these proposals are. Our long-term goal is to synthesize high-fidelity models that help us understand how MCR makes and breaks the C–H bonds in methane. Towards this goal, the objective of this project is to prepare, and spectroscopically and chemically interrogate macrocyclic nickel complexes with very similar ligand environments to F430 in different MCR states. The central hypothesis is that to mimic MCR spectroscopy a nickel complex needs a high-fidelity first coordination sphere, while to mimic MCR function and cleave methane it further requires a second-coordination-sphere radical. In preliminary work, we prepared and crystallized four-coordinate nickel complexes of a readily tunable anionic macrocycle. Our density functional theory calculations predict that one such complex should bind thiolate to mimic the first coordination sphere of F430 in the methane-cleaving step. Further calculations predict that a related complex with a pendant thiyl radical near the thiolate is both plausible and thermodynamically favored to cleave methane. The rationale is that tunable models will let us tease out the motifs necessary for C–H activation. We will test our hypothesis by focusing on two specific aims. Aim 1: Model the first coordination sphere of nickel in MCR to mimic spectroscopy and Aim 2: Model the second coordination sphere of nickel in MCR to mimic function. Towards Aim 1 we will: (a) prepare and characterize nickel complexes of anionic macrocycles, and (b) bind these complexes to water, thioether, thiolate, thiol, methyl or hydride ligands. These ligands have been proposed to bind the MCR active site but evidence, particularly for the last three ligands, is scarce, so our models will identify plausible first coordination spheres. Towards Aim 2 we will: (a) further develop the nickel complexes to feature a thiolate and a proximal thiyl radical, and (b) investigate the chemistry of this thiolate–thiyl species towards methane and other alkanes. The macrocylic nickel complexes and their adducts will be the highest-fidelity synthetic models reported and their activation of methane would be unprecedented for such nickel macrocycles. Overall, this work will complement biochemical studies to fill in our mechanistic picture for MCR, a central metabolic enzyme.
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