Modeling and computations of the intramolecular electron transfer process in the two-heme protein cytochrome c(4)

Mechano-control of Extracellular Electron Transport Rate via Modification of Inter-heme Coupling in Bacterial Surface Cytochrome

Bacterial outer-membrane multi-heme cytochromes (OMCs) mediate extracellular electron transport (EET). While heme alignment dictates the rate of EET, control of inter-heme coupling in a single OMC remains challenging, especially in intact cells. Given that OMCs diffuse and collide without aggregation on the cell surface, the overexpression of OMCs could increase such mechanical stress to impact the OMCs' protein structure. Here, the heme coupling is modified via mechanical interactions among OMCs by controlling their concentrations. Employment of whole-cell circular dichroism (CD) spectra of genetically engineered Escherichia coli reveals that the OMC concentration significantly impacts the molar CD and redox property of OMCs, resulting in a 4-fold change of microbial current production. The overexpression of OMCs increased the conductive current across the biofilm on an interdigitated electrode, indicating that a higher concentration of OMCs causes more lateral inter-protein electron hopping via collision on the cell surface. The present study would open a novel strategy to increase microbial current production by mechanically enhancing the inter-heme coupling.

Structure and redox properties of the diheme electron carrier cytochrome c4 from Pseudomonas aeruginosa

At low oxygen concentrations, respiration of Pseudomonas aeruginosa (Pa) and other bacteria relies on activity of cytochrome cbb₃ oxidases. A diheme cytochrome c₄ (cyt c₄) donates electrons to Pa cbb₃ oxidases to enable oxygen reduction and proton pumping by these enzymes. Given the importance of this redox pathway for bacterial pathogenesis, both cyt c₄ and cbb₃ oxidase are potential targets for new antibacterial strategies. The structural information about these two proteins, however, is scarce, and functional insights for Pa and other bacteria have been primarily drawn from analyses of the analogous system from Pseudomonas stutzeri (Ps). Herein, we describe characterization of structural and redox properties of cyt c₄ from Pa. The crystal structure of Pa cyt c₄ has revealed that this protein is organized in two monoheme domains. The interdomain interface is more hydrophobic in Pa cyt c₄, and the protein surface does not show the dipolar distribution of charges found in Ps cyt c₄. The reduction potentials of the two hemes are similar in Pa cyt c₄ but differ by about 100 mV in Ps cyt c₄. Analyses of structural models of these and other cyt c₄ proteins suggest that multiple factors contribute to the potential difference of the two hemes in these proteins, including solvent accessibility of the heme group, the distribution of surface charges, and the nature of the interdomain interface. The distinct properties of cyt c₄ proteins from closely-related Pa and Ps bacteria emphasize the importance of examining the cbb₃/cyt c₄ redox pathway in multiple species.

Charge-patching method for the calculation of electronic structure of polypeptides

Based on the CPM method, the charge densities of polypeptides can be generated and their electronic structure can be further calculated.

Chiral Selectivity in Inter-reactant Recognition and Electron Transfer of the Oxidation of Horse Heart Cytochrome c by Trioxalatocobaltate(III)

Outer-sphere electron transfer (ET) between optically active transition-metal complexes and either other transition-metal complexes or metalloproteins is a prototype reaction for kinetic chirality. Chirality as the ratio between bimolecular rate constants of two enantiomers mostly amounts to 1.05-1.2 with either the Λ or Δ form the more reactive, but the origin of chirality in ET parameters such as work terms, electronic transmission coefficient, and nuclear reorganization free energy has not been addressed. We report a study of ET between the Λ-/Δ-[Co(Ox)3](3-) pair (Ox = oxalate) and horse heart cytochrome c (cyt c). This choice is prompted by strong ion-pair formation that enables separation into inter-reactant interaction (chiral "recognition") and ET within the ion pair ("stereoselectivity"). Chiral selectivity was first addressed experimentally. Λ-[Co(Ox)3](3-) was found to be both the more strongly bound and faster reacting enantiomer expressed respectively by the ion-pair formation constant KX and ET rate constant kET(X) (X = Λ and Δ), with KΛ/KΔ and kET(Λ)/kET(Δ) both ≈1.1-1.2. rac-[Co(Ox)3](3-) behavior is intermediate between those of Λ- and Δ-[Co(Ox)3](3-). Chirality was next analyzed by quantum-mechanical ET theory combined with density functional theory and statistical mechanical computations. We also modeled the ion pair K(+)·[Co(Ox)3](3-) in order to address the influence of the solution ionic strength. The complex structure of cyt c meant that this reactant was represented solely by the heme group including the chiral axial ligands L-His and L-Met. Both singlet and triplet hemes as well as hemes with partially deprotonated propionic acid side groups were addressed. The computations showed that the most favorable inter-reactant configuration involved a narrow distance and orientation space very close to the contact distance, substantiating the notion of a reaction complex and the equivalence of the binding constant to a bimolecular reaction volume. The reaction is significantly diabatic even at these short inter-reactant distances, with electronic transmission coefficients κel(X) = 10(-3)-10(-2). The computations demonstrated chirality in both KX and κel(X) but no chirality in the reorganization and reaction free energy (driving force). As a result of subtle features in both KX and κel(X) chirality, the "operational" chirality κET(Λ)KΛ/κET(Δ)KΔ emerges larger than unity (1.1-1.2) from the molecular modeling as in the experimental data.

Progress and challenges in simulating and understanding electron transfer in proteins

This Review presents an overview of the most common numerical simulation approaches for the investigation of electron transfer (ET) in proteins. We try to highlight the merits of the different approaches but also the current limitations and challenges. The article is organized into three sections. Section 2 deals with direct simulation algorithms of charge migration in proteins. Section 3 summarizes the methods for testing the applicability of the Marcus theory for ET in proteins and for evaluating key thermodynamic quantities entering the reaction rates (reorganization energies and driving force). Recent studies interrogating the validity of the theory due to the presence of non-ergodic effects or of non-linear responses are also described. Section 4 focuses on the tunneling aspects of electron transfer. How can the electronic coupling between charge transfer states be evaluated by quantum chemistry approaches and rationalized? What interesting physics regarding the impact of protein dynamics on tunneling can be addressed? We will illustrate the different sections with examples taken from the literature to show what types of system are currently manageable with current methodologies. We also take care to recall what has been learned on the biophysics of ET within proteins thanks to the advent of atomistic simulations.

Axial iron coordination and spin state change in a heme c upon electrostatic protein-SAM interaction

A bacterial di-heme cytochrome c binds electrostatically to a gold electrode surface coated with a negatively charged COOH-terminated SAM adopting a sort of 'perpendicular' orientation. Cyclic voltammetry, Resonance Raman and SERRS spectroscopies indicate that the high-potential C-terminal heme center proximal to the SAM's surface undergoes an adsorption-induced swapping of one axial His ligand with a water molecule, which is probably lost in the reduced form, and a low- to high-spin transition. This coordination change for a bis-His ligated heme center upon an electrostatically-driven molecular recognition is as yet unprecedented, as well as the resulting increase in reduction potential. We discuss it in comparison with the known methionine ligand lability in monoheme cytochromes c occurring upon interaction with charged molecular patches. One possible implication of this finding in biological ET is that mobile redox partners do not behave as rigid and invariant bodies, but in the ET complex are subjected to molecular changes and structural fluctuations that affect in a complex way the thermodynamics and the kinetics of the process.