Atomically defined mechanism for proton transfer to a buried redox centre in a protein

Abstract

The basis of the chemiosmotic theory is that energy from light or respiration is used to generate a trans-membrane proton gradient. This is largely achieved by membrane-spanning enzymes known as 'proton pumps. There is intense interest in experiments which reveal, at the molecular level, how protons are drawn through proteins. Here we report the mechanism, at atomic resolution, for a single long-range electron-coupled proton transfer. In Azotobacter vinelandii ferredoxin I, reduction of a buried iron-sulphur cluster draws in a solvent proton, whereas re-oxidation is 'gated' by proton release to the solvent. Studies of this 'proton-transferring module' by fast-scan protein film voltammetry, high-resolution crystallography, site-directed mutagenesis and molecular dynamics, reveal that proton transfer is exquisitely sensitive to the position and pK of a single amino acid. The proton is delivered through the protein matrix by rapid penetrative excursions of the side-chain carboxylate of a surface residue (Asp 15), whose pK shifts in response to the electrostatic charge on the iron-sulphur cluster. Our analysis defines the structural, dynamic and energetic requirements for proton courier groups in redox-driven proton-pumping enzymes.

Proton-Coupled Electron Transfer in Organic Synthesis: Fundamentals, Applications, and Opportunities

“…These experiments elucidate not only the role for hydrogen bonding in proton transfer, but also corroborate work by Thomas demonstrating increased stability of hydrogen-bound phenoxyl radicals [129]. Proton movement in PCET processes is limited to short (i.e., hydrogenbonding contact) distances [130]; however, hydrogen-bonding networks are frequently used as "proton wires" [131] to accomplish long-range proton transfer and are well documented in GFP [132], ferredoxin I of Azotobacter vinelandii [133], cytochrome c oxidase [134], and numerous other proteins [135]. In a notable example, a hydrogen-bonding network between Tyr122 and Cys439 in ribonucleotide reductase (RNR) allows for a net proton transfer over > 30 Å [136].…”

De Novo Design of a CytochromebMaquette for Electron Transfer and Coupled Reactions on Electrodes

“…Similar pK a 's are found here, close to 7 for reduced heme and 4 for oxidized heme. Although relatively little is presently known about the proton translocation in natural proteins, in a few systems certain carboxylate residues with unusually high pK values were proven to be part of protontransfer pathway, such as ferredoxin I, 22 bacteriorhodopsin, 46 photosynthetic reaction center, 47 and cytochrome c oxidase. 48 The films of cyt b maquettes after reduction, were able to bind CO reversibly.…”

“…Electron-transfer rates between the electrode metal and the redox centers in the proteins can be calculated by simulating the potential-scan-rate-dependent voltammograms and comparing to the experimental data. 17,[22][23][24][25] In nature, electron transfer reactions are often coupled to other chemical events that are critical for physiological function and its regulation. For example, oxidation/reduction of redox cofactors in proteins is frequently coupled to proton binding/ release.…”

First principles study of electronic structure for cubane-like and ring-shaped structures of M4O4, M4S4 clusters (M = Mn, Fe, Co, Ni, Cu)

“…22,23 Our aim, in this work, will be, therefore, to perform a rigorous relative structural stability analysis of each M 4 X 4 cluster between the two commonly found geometrical blocks, namely a 2D rhombus-like planar structure versus a 3D cubane-like structure. The special interest in these two structures, is mainly motivated by their relevance to multi-electron transfer centers in biological systems, 24,25 their interesting magnetic and optical properties, [26][27][28][29] as well as to their potential relevance to inorganic solids. 30 Many poly-nuclear complexes containing cubane-type M 4 O 4 /M 4 S 4 core units, have been studied extensively during the last decade.…”