Effect of the Methyl-Coenzyme-M Reductase Protein Matrix on the Hole-Size and Nonplanar Deformations of Coenzyme F430

Myoglobin Reconstituted with Ni Tetradehydrocorrin as a Methane-Generating Model of Methyl-coenzyme M Reductase

Myoglobin reconstituted with Ni tetradehydrocorrin was investigated as a model of F430-containing methyl-coenzyme M reductase, which catalyzes anaerobic methane generation. The Ni^II tetradehydrocorrin complex has a Ni^II /Ni^I redox potential of -0.34 V vs. SHE and EPR spectroscopy indicates the formation of a Ni^I species upon reduction by dithionite. This redox potential is approximately 0.31 V more positive than that of F430. The Ni^I tetradehydrocorrin moiety is bound to the apo-form of myoglobin to yield the reconstituted protein. Methane gas is generated in the reaction of the model with methyl iodide in the presence of the reconstituted protein under reductive conditions, whereas the Ni^I complex itself does not produce methane gas. This is the first example of a protein-based functional model of F430-containing methyl-coenzyme M reductase.

Conformational control of cofactors in nature - the influence of protein-induced macrocycle distortion on the biological function of tetrapyrroles

Tetrapyrrole-containing proteins are one of the most fundamental classes of enzymes in nature and it remains an open question to give a chemical rationale for the multitude of biological reactions that can be catalyzed by these pigment-protein complexes. There are many fundamental processes where the same (i.e., chemically identical) porphyrin cofactor is involved in chemically quite distinct reactions. For example, heme is the active cofactor for oxygen transport and storage (hemoglobin, myoglobin) and for the incorporation of molecular oxygen in organic substrates (cytochrome P450). It is involved in the terminal oxidation (cytochrome c oxidase) and the metabolism of H2O2 (catalases and peroxidases) and catalyzes various electron transfer reactions in cytochromes. Likewise, in photosynthesis the same chlorophyll cofactor may function as a reaction center pigment (charge separation) or as an accessory pigment (exciton transfer) in light harvesting complexes (e.g., chlorophyll a). Whilst differences in the apoprotein sequences alone cannot explain the often drastic differences in physicochemical properties encountered for the same cofactor in diverse protein complexes, a critical factor for all biological functions must be the close structural interplay between bound cofactors and the respective apoprotein in addition to factors such as hydrogen bonding or electronic effects. Here, we explore how nature can use the same chemical molecule as a cofactor for chemically distinct reactions using the concept of conformational flexibility of tetrapyrroles. The multifaceted roles of tetrapyrroles are discussed in the context of the current knowledge on distorted porphyrins. Contemporary analytical methods now allow a more quantitative look at cofactors in protein complexes and the development of the field is illustrated by case studies on hemeproteins and photosynthetic complexes. Specific tetrapyrrole conformations are now used to prepare bioengineered designer proteins with specific catalytic or photochemical properties.

A new mechanism for methane production from methyl-coenzyme M reductase as derived from density functional calculations

We propose a new DFT-based mechanism for methane production using the full F430 cofactor of MCR (methyl-coenzyme M reductase) along with a coordinated O=CH2CH2C(H)NH2C(H)O (surrogate for glutamine) as a model of the active site for conversion of CH3SCoM(-) (CH3SCH2CH2SO3(-)) + HSCoB to methane plus the corresponding heterodisulfide. The cycle begins with the protonation of F430, either on Ni or on the C-ring nitrogen of the tetrapyrrole ring, both of which are nearly equally favorable. The C-ring protonated form is predicted to oxidatively add CH3SCoM(-) to give a 4-coordinate Ni center where the Ni moves out of the plane of the four ring nitrogens. The movement of Ni (and the attached CH3 and SCH2CH2SO3(2-) ligands) toward the SCoB(-) (deprotonated HSCoB) cofactor allows a 2c-3e interaction to form between the two sulfur atoms. The release of the heterodisulfide yields a Ni(III) center with a methyl group attached. The concerted elimination of methane, where the methyl group coordinated to Ni abstracts the proton from the C-ring nitrogen, has a very small calculated activation barrier (5.4 kcal/mol). The NPA charge on Ni for the various reaction steps indicates that the oxidation state changes occur largely on the attached ligands.

Monocopper center embedded in a biomimetic cavity: from supramolecular control of copper coordination to redox regulation

The electrochemical behavior of diversely substituted Cu-N3-calix[6]arene, enzyme-like, "funnel" complexes is analyzed. The Cu(II)/Cu(I) redox process is regulated by the supramolecular organization of the Cu coordination. The presence of a "shoetree" alkyl nitrile guest molecule inside the host cavity is a prerequisite for a dynamic redox behavior. Combination of supramolecular CH-pi weak interactions with the calixarene cavity and electronic/steric effects from the N3 substituting groups (pyridine, imidazole, pyrrolidine) enforces the preferential geometrical pattern adopted by Cu. This dictates the pathway of the electron-transfer process and, thus, the thermodynamics and kinetics of the redox reaction in the framework of a square-scheme mechanism. The present observations recall strongly the redox control exerted by the protein matrix on copper proteins through biological concepts such as induced fit mechanism, protein foldings, and entatic and allosteric effects.