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Electron Transfer Coupled to Conformational Dynamics in Cell Respiration.

ABSTRACT: Cellular respiration is a fundamental process required for energy production in many organisms. The terminal electron transfer complex in mitochondrial and many bacterial respiratory chains is cytochrome c oxidase (CcO). This converts the energy released in the cytochrome c/oxygen redox reaction into a transmembrane proton electrochemical gradient that is used subsequently to power ATP synthesis. Despite detailed knowledge of electron and proton transfer paths, a central question remains as to whether the coupling between electron and proton transfer in mammalian mitochondrial forms of CcO is mechanistically equivalent to its bacterial counterparts. Here, we focus on the conserved span between H376 and G384 of transmembrane helix (TMH) X of subunit I. This conformationally-dynamic section has been suggested to link the redox activity with the putative H pathway of proton transfer in mammalian CcO. The two helix X mutants, Val380Met (V380M) and Gly384Asp (G384D), generated in the genetically-tractable yeast CcO, resulted in a respiratory-deficient phenotype caused by the inhibition of intra-protein electron transfer and CcO turnover. Molecular aspects of these variants were studied by long timescale atomistic molecular dynamics simulations performed on wild-type and mutant bovine and yeast CcOs. We identified redox- and mutation-state dependent conformational changes in this span of TMH X of bovine and yeast CcOs which strongly suggests that this dynamic module plays a key role in optimizing intra-protein electron transfers.

SUBMITTER: Reidelbach M

PROVIDER: S-EPMC8378252 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Tyrosyl radicals play essential roles in biological proton-coupled electron transfer (PCET) reactions. Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides and is vital in DNA replication in all organisms. Class Ia RNRs consist of ?2 and ?2 homodimeric subunits. In class Ia RNR, such as the E. coli enzyme, an essential tyrosyl radical (Y122O(•))-diferric cofactor is located in ?2. Although Y122O(•) is extremely stable in free ?2, Y122O(•) is highly reactive in the quaternary substrate-?2?2 complex and serves as a radical initiator in catalytic PCET between ?2 and ?2. In this report, we investigate the structural interactions that control the reactivity of Y122O(•) in a model system, isolated E. coli ?2. Y122O(•) was reduced with hydroxyurea (HU), a radical scavenger that quenches the radical in a clinically relevant reaction. In the difference FT-IR spectrum, associated with this PCET reaction, amide I (CO) and amide II (CN/NH) bands were observed. Specific (13)C-labeling of the tyrosine C1 carbon assigned a component of these bands to the Y122-T123 amide bond. Comparison to density functional calculations on a model dipeptide, tyrosine-threonine, and structural modeling demonstrated that PCET is associated with a Y122 rotation and a 7.2 Å translation of the Y122 phenolic oxygen. To test for the functional consequences of this structural change, a proton inventory defined the origin of the large solvent isotope effect (SIE = 16.7 ± 1.0 at 25 °C) on this reaction. These data suggest that the one-electron, HU-mediated reduction of Y122O(•) is associated with two, rate-limiting (full or partial) proton transfer reactions. One is attributable to HU oxidation (SIE = 11.9, net H atom transfer), and the other is attributable to coupled, hydrogen-bonding changes in the Y122O(•)-diferric cofactor (SIE = 1.4). These results illustrate the importance of redox-linked changes to backbone and ring dihedral angles in high potential PCET and provide evidence for rate-limiting, redox-linked hydrogen-bonding interactions between Y122O(•) and the iron cluster.

Project description:The effect of molecular topology, and conformation on the dynamics of photoinduced electron transfer (ET) processes has been studied in interlocked electron donor-acceptor systems, specifically rotaxanes with zinc(II)-tetraphenylporphyrin (ZnP) electron donor and [60]fullerene (C(60)) as the electron acceptor. Formation or cleavage of coordinative bonds was used to induce major topological and conformational changes in the interlocked architecture. In the first approach, the tweezers-like structure created by the two ZnP stopper groups on the thread was used as a recognition site for complexation of 1,4-diazabicyclo[2.2.2]octane (DABCO), which creates a bridge between the two ZnP moieties on the rotaxane, generating a catenane structure. The photoinduced processes in the DABCO-complexed (ZnP)(2)-[2]catenate-C(60) system were compared with those of the (ZnP)(2)-rotaxane-C(60) precursor and the previously reported ZnP-[2]catenate-C(60). Steady-state emission and transient absorption studies showed that a similar multistep ET pathway emerged for rotaxanes and catenanes upon photoexcitation at various wavelengths, ultimately resulting in a long-lived ZnP(•+)/C(60) (•-) charge separated radical pair state. However, the decay kinetics of the latter states clearly reflect the topological differences between the rotaxane, the catenate, and DABCO-complexed-catenate architectures. The lifetime of the long-distance ZnP(•+)-[Cu(I)phen(2)](+)-C(60) (•-) charge separated state is more than four times longer in 3 (1.03 µs) than in 1 (0.24 µs) and approaches that in catenate 2 (1.1 µs). The results clearly showed that adoption of a catenane from a rotaxane topology inhibits the charge recombination process. In a second approach, the Cu(I) ion used as template to assemble the (ZnP)(2)-[Cu(I)phen(2)](+)-C(60) rotaxane was removed, and structural analysis suggested a major topographical change occurred, such that charge separation between the chromophores was no longer observed upon photoexcitation in nonpolar as well as polar solvents. Only ZnP and C(60) triplet excited states were observed upon laser excitation. These results highlighted the critical importance of the central Cu(I) ion for long range ET processes in these large interlocked electron donor-acceptor systems.

Project description:The coupling between electrons and protons and the long-range transport of protons play important roles throughout biology. Biomimetic systems derived from benzimidazole-phenol (BIP) constructs have been designed to undergo proton-coupled electron transfer (PCET) upon electrochemical or photochemical oxidation. Moreover, these systems can transport protons along hydrogen-bonded networks or proton wires through multiproton PCET. Herein, the nonequilibrium dynamics of both single and double proton transfer in BIP molecules initiated by oxidation are investigated with first-principles molecular dynamics simulations. Although these processes are concerted in that no thermodynamically stable intermediate is observed, the simulations predict that they are predominantly asynchronous on the ultrafast time scale. For both systems, the first proton transfer typically occurs ∼100 fs after electron transfer. For the double proton transfer system, typically the second proton transfer occurs hundreds of femtoseconds after the initial proton transfer. A machine learning algorithm was used to identify the key molecular vibrational modes essential for proton transfer: a slow, in-plane bending mode that dominates the overall inner-sphere reorganization, the proton donor-acceptor motion that leads to vibrational coherence, and the faster donor-hydrogen stretching mode. The asynchronous double proton transfer mechanism can be understood in terms of a significant mode corresponding to the two anticorrelated proton donor-acceptor motions, typically decreasing only one donor-acceptor distance at a time. Although these PCET processes appear concerted on the time scale of typical electrochemical experiments, attaching these BIP constructs to photosensitizers may enable the detection of the asynchronicity of the electron and multiple proton transfers with ultrafast two-dimensional spectroscopy. Understanding the fundamental PCET mechanisms at this level will guide the design of PCET systems for catalysis and energy conversion processes.

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Electron Transfer Coupled to Conformational Dynamics in Cell Respiration.

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