Structural Determinants of Redox Conduction Favor Robustness over Tunability in Microbial Cytochrome Nanowires

Cytochrome "nanowires" are physically limited to sub-picoamp currents that suffice for cellular respiration

Mineral-respiring microorganisms from hydrothermal vents to terrestrial soils express filaments that electrically connect intracellular respiration to extracellular geochemistry. Filaments dubbed "cytochrome nanowires" (CNs) have been resolved by CryoEM, but whether they are the two-decades-long sought-after physiological "nanowires" remains unproven. To assess their functional competence, we analyzed biological redox conduction in all CNs by computing driving forces in the presence of redox anti-cooperativities, reorganization energies with electronic polarizability, and Marcus rates for diffusive and protein-limited flux models. The chain of heme cofactors in any CN must be densely packed to realize weak (≤0.01 eV) electronic coupling for electron transfer, as evidenced by a single Soret band produced from coincidental absorptions on multiple hemes. Dense packing, in turn, has three consequences: (1) limited driving forces (≤|0.3| eV) due to shared electrostatic microenvironments, (2) strong (≤0.12 eV) redox anti-cooperativities that would accentuate the free energy landscape if the linear heme arrangement did not dictate a contra-thermodynamic oxidation order, and (3) an entropic penalty that is offset by thioether 'tethers' of the hemes to the protein backbone. These linkages physically necessitate the rate-throttling T-stacked motif (10-fold slower than the other highly conserved slip-stacked motif). If the sequence of slip- and T-stacked hemes in the CNs had the fastest known nanosecond rates at every step, a micron-long filament would carry a diffusive 0.02 pA current at a physiological 0.1 V, or a protein-limited current of 0.2 pA. Actual CNs have sub-optimal (≤102-fold lower), but sufficient conductivities for cellular respiration, with at most thousands of filaments needed for total cellular metabolic flux. Reported conductivities once used to argue for metallic-like pili against the cytochrome hypothesis and now attributed to CNs remain inconsistent by 102-105-fold with the physical constraints on biological redox conduction through multiheme architectures.

Delineating redox cooperativity in water-soluble and membrane multiheme cytochromes through protein design

Nature has evolved diverse electron transport proteins and multiprotein assemblies essential to the generation and transduction of biological energy. However, substantially modifying or adapting these proteins for user-defined applications or to gain fundamental mechanistic insight can be hindered by their inherent complexity. De novo protein design offers an attractive route to stripping away this confounding complexity, enabling us to probe the fundamental workings of these bioenergetic proteins and systems, while providing robust, modular platforms for constructing completely artificial electron-conducting circuitry. Here, we use a set of de novo designed mono-heme and di-heme soluble and membrane proteins to delineate the contributions of electrostatic micro-environments and dielectric properties of the surrounding protein medium on the inter-heme redox cooperativity that we have previously reported. Experimentally, we find that the two heme sites in both the water-soluble and membrane constructs have broadly equivalent redox potentials in isolation, in agreement with Poisson-Boltzmann Continuum Electrostatics calculations. BioDC, a Python program for the estimation of electron transfer energetics and kinetics within multiheme cytochromes, also predicts equivalent heme sites, and reports that burial within the low dielectric environment of the membrane strengthens heme-heme electrostatic coupling. We conclude that redox cooperativity in our diheme cytochromes is largely driven by heme electrostatic coupling and confirm that this effect is greatly strengthened by burial in the membrane. These results demonstrate that while our de novo proteins present minimalist, new-to-nature constructs, they enable the dissection and microscopic examination of processes fundamental to the function of vital, yet complex, bioenergetic assemblies.

Controlling heme redox properties in peptide amphiphile fibers with sequence and heme loading ratio

Controlling the reduction midpoint potential of heme B is a key factor in many bioelectrochemical reactions, including long-range electron transport. Currently, there are a number of globular model protein systems to study this biophysical parameter; however, there are none for large polymeric protein model systems (e.g., the OmcS protein from G. sulfurreducens). Peptide amphiphiles, short peptides with a lipid tail that polymerize into fibrous structures, fill this gap. Here, we show a peptide amphiphile model system where one can tune the electrochemical potential of heme B by changing the loading ratio and peptide sequence. Changing the loading ratio resulted in the most significant increase, with values as high as -22 mV down to -224 mV. Circular dichroism spectra of certain sequences show Cotton effects at lower loading ratios that disappear as more heme B is added, indicating an ordered environment that becomes disrupted if heme B is overpacked. These findings can contribute to the design of functional self-assembling biomaterials.

To be or not to be a cytochrome: electrical characterizations are inconsistent with Geobacter cytochrome 'nanowires'

Geobacter sulfurreducens profoundly shapes Earth's biogeochemistry by discharging respiratory electrons to minerals and other microbes through filaments of a two-decades-long debated identity. Cryogenic electron microscopy has revealed filaments of redox-active cytochromes, but the same filaments have exhibited hallmarks of organic metal-like conductivity under cytochrome denaturing/inhibiting conditions. Prior structure-based calculations and kinetic analyses on multi-heme proteins are synthesized herein to propose that a minimum of ~7 cytochrome 'nanowires' can carry the respiratory flux of a Geobacter cell, which is known to express somewhat more (≥20) filaments to increase the likelihood of productive contacts. By contrast, prior electrical and spectroscopic structural characterizations are argued to be physiologically irrelevant or physically implausible for the known cytochrome filaments because of experimental artifacts and sample impurities. This perspective clarifies our mechanistic understanding of physiological metal-microbe interactions and advances synthetic biology efforts to optimize those interactions for bioremediation and energy or chemical production.