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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Electron Transfer Beyond the Outer Membrane: Putting Electrons to Rest

Extracellular electron transfer (EET) is the physiological process that enables the reduction or oxidation of molecules and minerals beyond the surface of a microbial cell. The first bacteria characterized with this capability were Shewanella and Geobacter, both reported to couple their growth to the reduction of iron or manganese oxide minerals located extracellularly. A key difference between EET and nearly every other respiratory activity on Earth is the need to transfer electrons beyond the cell membrane. The past decade has resolved how well-conserved strategies conduct electrons from the inner membrane to the outer surface. However, recent data suggest a much wider and less well understood collection of mechanisms enabling electron transfer to distant acceptors. This review reflects the current state of knowledge from Shewanella and Geobacter, specifically focusing on transfer across the outer membrane and beyond—an activity that enables reduction of highly variable minerals, electrodes, and even other organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Robust measurement of microbial reduction of graphene oxide nanoparticles using image analysis

ABSTRACT Shewanella oneidensis ( S. oneidensis ) has the capacity to reduce electron acceptors within a medium and is thus used frequently in microbial fuel generation, pollutant breakdown, and nanoparticle fabrication. Microbial fuel setups, however, often require costly or labor-intensive components, thus making optimization of their performance onerous. For rapid optimization of setup conditions, a model reduction assay can be employed to allow simultaneous, large-scale experiments at lower cost and effort. Since S. oneidensis uses different extracellular electron transfer pathways depending on the electron acceptor, it is essential to use a reduction assay that mirrors the pathways employed in the microbial fuel system. For microbial fuel setups that use nanoparticles to stimulate electron transfer, reduction of graphene oxide provides a more accurate model than other commonly used assays as it is a bulk material that forms flocculates in solutions with a large ionic component. However, graphene oxide flocculates can interfere with traditional absorbance-based measurement techniques. This study introduces a novel image analysis method for quantifying graphene oxide reduction, showing improved performance and statistical accuracy over traditional methods. A comparative analysis shows that the image analysis method produces smaller errors between replicates and reveals more statistically significant differences between samples than traditional plate reader measurements under conditions causing graphene oxide flocculation. Image analysis can also detect reduction activity at earlier time points due to its use of larger solution volumes, enhancing color detection. These improvements in accuracy make image analysis a promising method for optimizing microbial fuel cells that use nanoparticles or bulk substrates. IMPORTANCE Shewanella oneidensis ( S. oneidensis ) is widely used in reduction processes such as microbial fuel generation due to its capacity to reduce electron acceptors. Often, these setups are labor-intensive to operate and require days to produce results, so use of a model assay would reduce the time and expenses needed for optimization. Our research developed a novel digital analysis method for analysis of graphene oxide flocculates that may be utilized as a model assay for reduction platforms featuring nanoparticles. Use of this model reduction assay will enable rapid optimization and drive improvements in the microbial fuel generation sector.

Bennett, Danielle T. (ORCID:0009000188748827)↗
DOE OSTI2020

Organic Microbial Electrochemical Transistor Monitoring Extracellular Electron Transfer

Abstract Extracellular electron transfer (EET) denotes the process of microbial respiration with electron transfer to extracellular acceptors and has been exploited in a range of microbial electrochemical systems (MESs). To further understand EET and to optimize the performance of MESs, a better understanding of the dynamics at the microscale is needed. However, the real‐time monitoring of EET at high spatiotemporal resolution would require sophisticated signal amplification. To amplify local EET signals, a miniaturized bioelectronic device, the so‐called organic microbial electrochemical transistor (OMECT), is developed, which includes Shewanella oneidensis MR‐1 integrated onto organic electrochemical transistors comprising poly(3,4‐ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) combined with poly(vinyl alcohol) (PVA). Bacteria are attached to the gate of the transistor by a chronoamperometric method and the successful attachment is confirmed by fluorescence microscopy. Monitoring EET with the OMECT configuration is achieved due to the inherent amplification of the transistor, revealing fast time‐responses to lactate. The limits of detection when using microfabricated gates as charge collectors are also investigated. The work is a first step toward understanding and monitoring EET in highly confined spaces via microfabricated organic electronic devices, and it can be of importance to study exoelectrogens in microenvironments, such as those of the human microbiome.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

The transformation of U(VI) and V(V) in carnotite group minerals during dissimilatory respiration by a metal reducing bacterium

Recent results from laboratory and field studies support that dissimilatory metal reducing (DMR) bacteria influence the fate and transport of uranium in anaerobic subsurface environments. To date, most research efforts have focused on the reduction of soluble U(VI) by DMR bacteria to form insoluble uraninite (UO 2 ). Subsurface environments harbor, however, large reservoirs of U(VI) in solid or mineral form. Uranium that is structure-bound in minerals is expected to be more refractory to microbial reduction than soluble U, based on analogy with Fe respiration. The reducibility of U(VI) could impact the fate of U(IV) by controlling mineral precipitation reactions, which has implications for the long-term immobilization of U in subsurface environments. Here, we studied anoxic cultures of Shewanella putrefaciens CN32 incubated with natural carnotite-group minerals by X-ray diffraction, electron microscopy, scanning transmission X-ray microscopy (STXM). Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy measurements at U-N 4,5 , V-L 2,3 , and O-K edges on cultures incubated up to 10 months show that V(V) was reduced to V(IV), whereas U was not reduced. In contrast, V(V) and U(VI) in solution were both completely reduced to lower oxidation states by CN32, as precipitates within the exopolymer surrounding the bacteria. Assays for the toxicity of U and V to CN32 showed that biofilm formation was stimulated at 0.001 M U(VI), and growth was inhibited at concentrations of U(VI) greater than 0.001 M. Vanadium did not inhibit growth or stimulate biofilm formation at any concentration tested. Investigations of the bacteria-mineral and bacteria-metal interface at the nanometer and molecular scales provide new insights into the co-respiration of V and U that help explain their biogeochemical cycling and have implications for subsurface bioremediation of these elements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Bioelectrochemical crossbar architecture screening platform for extracellular electron transfer

Electroactive microbes can serve as living components in bioelectronic devices, where their unique ability to transfer electrons enables applications in sensing, energy conversion, and synthesis, but they remain challenging to engineer because the bioelectrochemical systems (BESs) used for characterization are low throughput. Here, we present a bioelectrochemical crossbar architecture screening platform (BiCASP) that uses stacked and orthogonally arrayed electrodes to enable individual sample selection for characterization in arrayed formats. This device reports on the current generated by electroactive bacteria on the minute timescale, decreasing the time for data acquisition by several orders of magnitude compared to conventional BESs. This device increases the throughput of screening engineered biological components in cells, identifying mutants of the membrane protein wire MtrA in Shewanella oneidensis that retain the ability to support extracellular electron transfer (EET). BiCASP may be integrated with bioelectronics that need directed evolution of electroactive proteins.

Shewanella↗
DOE OSTI2021

Lignin-enhanced reduction of structural Fe(III) in nontronite: Dual roles of lignin as electron shuttle and donor

Lignin is a major component of plant-derived soil organic matter (SOM) in soils and sediments. Fe-bearing clay minerals are widely distributed in these environments and often co-exist with lignin. While previous studies have reported the electron shuttling and donating roles of certain redox-active SOM in the dissimilatory reduction of structural Fe(III) in Fe-bearing clay minerals, the role of lignin in this process remains unknown. Here we studied this role by incubating an Fe-rich smectite (nontronite NAu-2) with two types of lignin (soluble and insoluble) in the absence and presence of an Fe(III)-reducing bacterium Shewanella putrefaciens CN32 under anaerobic condition. Labile carbon source (i.e., lactate) was added in some experiments as an extra electron donor. The results demonstrated that both soluble and insoluble lignins abiotically reduced structural Fe(III) in NAu-2. The reduction extent was proportional to lignin concentration. After abiotic reaction, lignin served as either electron shuttle or electron donor in the presence of CN32: (1) When lactate was present, lignin served as an electron shuttle to enhance the rate of Fe(III) reduction; (2) When lactate was absent, lignin served as an electron donor for Fe(III) reduction. Although the biotic Fe(III) reduction extents were similar in the presence of either soluble or insoluble lignin, the reduction rates with soluble lignin were always higher than those with insoluble lignin, likely owing to their different electron transfer mechanisms. After interaction with NAu-2 and/or CN32, soluble lignin structure largely remained intact, but with some decreases of humic/fulvic acid-like and protein-like compounds, aromatic functional groups (e.g., C-H, C=O, COOH), and aliphatic/aromatic compounds. An increase of semiquinone-like organic radicals was observed after lignin interaction with NAu-2. These chemical changes of lignin were likely coupled with reduction of structural Fe(III) in nontronite. The nontronite structure remained largely unchanged without much dissolution and mineral transformation. The findings of this study provide insights into the role of lignin in promoting mineral-microbe interactions and have significant implications for coupled Fe and C biogeochemical cycles in soils and sediments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Single molecule tracking of bacterial cell surface cytochromes reveals dynamics that impact long-distance electron transport

Using a series of multiheme cytochromes, the metal-reducing bacterium Shewanella oneidensis MR-1 can perform extracellular electron transfer (EET) to respire redox-active surfaces, including minerals and electrodes outside the cell. While the role of multiheme cytochromes in transporting electrons across the cell wall is well established, these cytochromes were also recently found to facilitate long-distance (micrometer-scale) redox conduction along outer membranes and across multiple cells bridging electrodes. Recent studies proposed that long-distance conduction arises from the interplay of electron hopping and cytochrome diffusion, which allows collisions and electron exchange between cytochromes along membranes. However, the diffusive dynamics of the multiheme cytochromes have never been observed or quantified in vivo, making it difficult to assess their hypothesized contribution to the collision-exchange mechanism. Here, we use quantum dot labeling, total internal reflection fluorescence microscopy, and single-particle tracking to quantify the lateral diffusive dynamics of the outer membrane-associated decaheme cytochromes MtrC and OmcA, two key components of EET in S. oneidensis. We observe confined diffusion behavior for both quantum dot-labeled MtrC and OmcA along cell surfaces (diffusion coefficients D MtrC = 0.0192 ± 0.0018 µm 2 /s, D OmcA = 0.0125 ± 0.0024 µm 2 /s) and the membrane extensions thought to function as bacterial nanowires. We find that these dynamics can trace a path for electron transport via overlap of cytochrome trajectories, consistent with the long-distance conduction mechanism. The measured dynamics inform kinetic Monte Carlo simulations that combine direct electron hopping and redox molecule diffusion, revealing significant electron transport rates along cells and membrane nanowires.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Solution-Deposited and Patternable Conductive Polymer Thin-Film Electrodes for Microbial Bioelectronics

Microbial bioelectronic devices integrate naturally occurring or synthetically engineered electroactive microbes with microelectronics. These devices have a broad range of potential applications, but engineering the biotic–abiotic interface for biocompatibility, adhesion, electron transfer, and maximum surface area remains a challenge. Prior approaches to interface modification lack simple processability, the ability to pattern the materials, and/or a significant enhancement in currents. We report a novel conductive polymer coating that significantly enhances current densities relative to unmodified electrodes in microbial bioelectronics is reported. The coating is based on a blend of poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS) crosslinked with poly(2-hydroxyethylacrylate) (PHEA) along with a thin polydopamine (PDA) layer for adhesion to an underlying indium tin oxide (ITO) electrode. When used as an interface layer with the current-producing bacterium Shewanella oneidensis MR-1, this material produces a 178-fold increase in the current density compared to unmodified electrodes, a current gain that is higher than previously reported thin-film 2D coatings and 3D conductive polymer coatings. The chemistry, morphology, and electronic properties of the coatings are characterized and the implementation of these coated electrodes for use in microbial fuel cells, multiplexed bioelectronic devices, and organic electrochemical transistor based microbial sensors are demonstrated. It is envisioned that this simple coating will advance the development of microbial bioelectronic devices.

patterned bioelectronics↗
DOE OSTI2022

In Situ Optical Quantification of Extracellular Electron Transfer Using Plasmonic Metal Oxide Nanocrystals**

Extracellular electron transfer (EET) is a critical form of microbial metabolism that enables respiration on a variety of inorganic substrates, including metal oxides. However, quantifying current generated by electroactive bacteria has been predominately limited to biofilms formed on electrodes. To address this, we developed a platform for quantifying EET flux from cell suspensions using aqueous dispersions of infrared plasmonic tin-doped indium oxide nanocrystals. Furthermore, tracking the change in optical extinction during electron transfer enabled quantification of current generated by planktonic Shewanella oneidensis cultures. Using this method, we differentiated between starved and actively respiring cells, cells of varying genotype, and cells engineered to differentially express a key EET gene using an inducible genetic circuit. Overall, our results validate the utility of colloidally stable plasmonic metal oxide nanocrystals as quantitative biosensors in aqueous environments and contribute to a fundamental understanding of planktonic S. oneidensis electrophysiology using simple in situ spectroscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

A hybrid cyt c maturation system enhances the bioelectrical performance of engineered Escherichia coli by improving the rate-limiting step

Bioelectronic devices can use electron flux to enable communication between biotic components and abiotic electrodes. We have modified Escherichia coli to electrically interact with electrodes by expressing the cytochrome c from Shewanella oneidensis MR-1. However, we observe inefficient electrical performance, which we hypothesize is due to the limited compatibility of the E. coli cytochrome c maturation (Ccm) systems with MR-1 cytochrome c. Here we test whether the bioelectronic performance of E. coli can be improved by constructing hybrid Ccm systems containing protein domains from both E. coli and S. oneidensis MR-1. The hybrid CcmH increased cytochrome c expression by increasing the abundance of CymA 60%, while only slightly changing the abundance of the other cytochromes c. Electrochemical measurements showed that the overall current from the hybrid ccm strain increased 121% relative to the wildtype ccm strain, with an electron flux per cell of 12.3 ± 0.3 fA·cell -1 . Additionally, the hybrid ccm strain doubled its electrical response with the addition of exogenous flavin, and quantitative analysis of this demonstrates CymA is the rate-limiting step in this electron conduit. These results demonstrate that this hybrid Ccm system can enhance the bioelectrical performance of the cyt c expressing E. coli, allowing the construction of more efficient bioelectronic devices.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Reduction of selenite by bacterial exudates

Bacterial reduction of Se(IV) is a significant component of the global selenium cycle, and hence affects the fate and transport of selenium in both natural and contaminated environments. However, it is unknown whether bacterially-produced exudates are capable of reducing selenium independent of bacterial cells. In this study, we measured the rate and extent of Se(IV) reduction by exudates from three bacterial species, and we determined the importance of exudate sulfhydryl sites by conducting parallel experiments after treatment of the exudates with a sulfhydryl-specific blocking molecule. Here, we also conducted experiments with whole cell biomass for each of the three bacterial species to determine the importance of exudate-only reduction relative to whole biomass-promoted reduction. Under our experimental conditions, exudates from Bacillus subtilis and Pseudomonas putida remove Se(IV) from solution after an approximately 20-24 h lag period, but exudates from Shewanella oneidensis are ineffective at Se(IV) removal, except when the cells are grown in the presence of Se(IV). For both B. subtilis and P. putida , pretreatment blocking of the sulfhydryl sites on the exudate molecules dramatically decreases the rate and extent of Se(IV) removal, strongly suggesting that sulfhydryl groups on the exudate molecules play a key role in the Se(IV) reduction mechanism. The behavior of S. oneidensis exudates indicates that up-regulation of the Se(IV) reduction mechanism can occur in response to the Se content of the medium in which the cells grow. Our results demonstrate the capacity of some bacterial exudates to reduce Se(IV), and suggest that the activity of bacterial exudates should be accounted for when modeling selenium cycling in natural and engineered environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Microbial diversity analysis of two full-scale seawater desalination treatment trains provides insights into detrimental biofilm formation

Detrimental biofilms on RO membranes remain a crucial challenge for seawater desalination. Comparative analysis of 16S rRNA gene amplicon sequencing data revealed differences and commonalities of biofilm communities associated with unit operations in the two largest seawater desalination facilities in the U.S., the Claude "Bud" Lewis Carlsbad Desalination Plant and the Tampa Bay Seater Desalination facility. At both plants, feedwater collected at a single time point was a poor indicator of the RO membrane communities, which showed far greater taxa diversity. The analysis of prefilter cartridges from the Carlsbad plant revealed similarly high taxon diversity as the RO module biofilms, with relevant differences. Algal sequences were enriched on the prefilter cartridges as were sequences representing Bdellovibrionota, which are predatory bacteria. Sequences representing opportunistic Gammaproteobacteria (i.e., Shewanella, Woesia) were present in significantly higher relative abundance on the RO membranes than in the prefilter cartridges, suggesting growth of certain taxa in the RO modules. Untargeted metabolomics distinguished intra- and inter-desalination plant biofilm samples, highlighting the potential value of this tool for biofilm monitoring. These findings underscore the value of omics tools for effective microbial monitoring, to understand biofouling dynamics within RO desalination plants, and to provide insight for the development of ecologically-informed biofilm control measures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Oxidation of biogenic U(IV) mediated by iron-bearing clay minerals, iron-reducing bacteria, and organic ligands

Bioreduction of hexavalent uranium (U(VI)) to tetravalent uranium (U(IV)) by dissimilatory metal-reducing bacteria (DMRB) is considered an effective strategy for uranium immobilization in contaminated environments. However, U(IV) can be reoxidized to U(VI) under fluctuating redox conditions and remobilized. This work investigates the oxidation behavior of biogenic U(IV) in the presence of bioreduced iron-bearing clay minerals (rNAu-2), iron-reducing bacteria (Shewanella putrefaciens CN32), and organic ligands (ethylenediaminetetraacetic acid (EDTA) and citrate). Results demonstrate that the presence of CN32 significantly inhibits U(IV) oxidation. rNAu-2 exerted a context-dependent influence on U(IV) oxidation: its effect was masked by bicarbonate-promoted U(VI) mobilization in the absence of active CN32, but became detectable when CN32-mediated microbial protection slowed U(IV) oxidation. EDTA and citrate markedly accelerate U(IV) oxidation via formation of soluble U(IV)-ligand complexes, changing U(IV) redox potentials, and by promoting clay mineral dissolution that enhances Fe(II)/Fe(III) redox cycling. Collectively, our findings constrain the roles that clay minerals, iron-reducing bacteria, and organic ligands play in governing U(IV) stability, emphasizing the need to account for these factors in developing robust bioremediation strategies.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2021

Combined Effects of Fe(III)-Bearing Clay Minerals and Organic Ligands on U(VI) Bioreduction and U(IV) Speciation

Reduction of U(VI) to U(IV) drastically reduces its solubility and has been proposed as a method for remediation of uranium contamination. However, much is still unknown about the kinetics, mechanisms, and products of U(VI) bioreduction in complex systems. In this work, U(VI) bioreduction experiments were conducted with Shewanella putrefaciens strain CN32 in the presence of clay minerals and two organic ligands: citrate and EDTA. In reactors with U and Fe(III)-clay minerals, the rate of U(VI) bioreduction was enhanced due to the presence of ligands, likely because soluble Fe 3+ - and Fe 2+ -ligand complexes served as electron shuttles. In the presence of citrate, bioreduced U(IV) formed a soluble U(IV)-citrate complex in experiments with either Fe-rich or Fe-poor clay mineral. In the presence of EDTA, U(IV) occurred as a soluble U(IV)-EDTA complex in Fe-poor montmorillonite experiments. However, U(IV) remained associated with the solid phase in Fe-rich nontronite experiments through the formation of a ternary U(IV)-EDTA-surface complex, as suggested by the EXAFS analysis. Our study indicates that organic ligands and Fe(III)-bearing clays can significantly affect the microbial reduction of U(VI) and the stability of the resulting U(IV) phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Coupling flux balance analysis with reactive transport modeling through machine learning for rapid and stable simulation of microbial metabolic switching

Integrating genome-scale metabolic networks with reactive transport models (RTMs) provides a detailed description of the dynamic changes in microbial growth and metabolism. Despite promising demonstrations in the past, computational inefficiency has been pointed out as a critical issue to overcome because it requires repeated application of linear programming (LP) to obtain flux balance analysis (FBA) solutions in every time step and spatial grid. To address this challenge, we propose a new simulation method where we train and validate artificial neural networks (ANNs) using randomly sampled FBA solutions and incorporate the resulting surrogate FBA model (represented as algebraic equations) into RTMs as source/sink terms. We demonstrate the efficiency of our method via a case study of Shewanella oneidensis MR-1. During aerobic growth on lactate, S. oneidensis produces metabolic byproducts (such as pyruvate and acetate), which are subsequently consumed as alternative carbon sources when the preferred nutrients are depleted. To effectively simulate these complex dynamics, we used a cybernetic approach that models metabolic switches as the outcome of dynamic competition among multiple growth options. In both zero-dimensional batch and one-dimensional column configurations, the ANN-based surrogate models achieved substantial reduction of computational time by several orders of magnitude compared to the original LP-based FBA models. Moreover, the ANN models produced robust solutions without any special measures to prevent numerical instability. These developments significantly promote our ability to utilize genome-scale networks in complex, multi-physics, and multi-dimensional ecosystem modeling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Influence of aluminum incorporation and aqueous conditions on metal ion release of high-Ni transition metal oxide nanomaterials

Developing a materials perspective of how to control the degradation and negative impact of complex metal oxides requires an integrated understanding of how these nanomaterials transform in the environment and interact with biological systems. Doping with aluminum is known to stabilize oxide materials, but has not been assessed cohesively from synthesis to environmental fate and biological impact. In the present study, the influence of aluminum doping on metal ion release from transition metal oxides was investigated by comparing aqueous transformations of lithium nickel cobalt aluminum oxide (LiNi 0.82 Co 0.15 Al 0.03 O 2 ; NCA) and lithium nickel cobalt oxide (LiNi 0.80 Co 0.20 O 2 ; NC) nanoparticles and by calculating the energetics of metal release using a density functional theory (DFT) and thermodynamics method. Two model environmental organisms were used to assess biological impact, and metal ion release was compared for NCA and NC nanoparticles incubated in their respective growth media: moderately hard reconstituted water (MHRW) for the freshwater invertebrate Daphnia magna (D. magna) and minimal growth medium for the Gram-negative bacterium Shewanella oneidensis MR-1 (S. oneidensis). Further, the amount of metal ions released was reduced for NCA compared to NC in MHRW, which correlated to changes in the modeled energetics of release upon Al substitution in the lattice. In minimal medium, metal ion release was approximately an order of magnitude higher compared to MHRW and was similar to the stoichiometry of the bulk nanoparticles for both NCA and NC. Interpretation of the release profiles and modeling indicated that the increase in total metal ion release and the reduced influence of Al doping arises from lactate complexation of metal ions in solution. The relative biological impacts of NC and NCA exposure for both S. oneidensis and D. magna were consistent with the metal release trends observed for minimal medium and MHRW, respectively. Together, these results demonstrate how a combined experimental and computational approach provides valuable insight into the aqueous transformations and biological impacts of complex metal oxide nanoparticles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Electron transfer in a crystalline cytochrome with four hemes

Diffusion of electrons over distances on the order of 100 μm has been observed in crystals of a small tetraheme cytochrome (STC) from Shewanella oneidensis [J. Huang et al . J. Am. Chem. Soc. 142, 10459–10467 (2020)]. Electron transfer between hemes in adjacent subunits of the crystal is slower and more strongly dependent on temperature than had been expected based on semiclassical electron-transfer theory. Here, in this work, we explore explanations for these findings by molecular-dynamics simulations of crystalline and monomeric STC. New procedures are developed for including time-dependent quantum mechanical energy differences in the gap between the energies of the reactant and product states and for evaluating fluctuations of the electronic-interaction matrix element that couples the two hemes. Rate constants for electron transfer are calculated from the time- and temperature-dependent energy gaps, coupling factors, and Franck–Condon-weighted densities of states using an expression with no freely adjustable parameters. Back reactions are considered, as are the effects of various protonation states of the carboxyl groups on the heme side chains. Interactions with water are found to dominate the fluctuations of the energy gap between the reactant and product states. The calculated rate constant for electron transfer from heme IV to heme Ib in a neighboring subunit at 300 K agrees well with the measured value. However, the calculated activation energy of the reaction in the crystal is considerably smaller than observed. We suggest two possible explanations for this discrepancy. The calculated rate constant for transfer from heme I to II within the same subunit of the crystal is about one-third that for monomeric STC in solution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP

YiiP is a secondary transporter that couples Zn 2+ transport to the proton motive force. Structural studies of YiiP from prokaryotes and Znt8 from humans have revealed three different Zn 2+ sites and a conserved homodimeric architecture. These structures define the inward-facing and outward-facing states that characterize the archetypal alternating access mechanism of transport. To study the effects of Zn 2+ binding on the conformational transition, we use cryo-EM together with molecular dynamics simulation to compare structures of YiiP from Shewanella oneidensis in the presence and absence of Zn 2+ . To enable single-particle cryo-EM, we used a phage-display library to develop a Fab antibody fragment with high affinity for YiiP, thus producing a YiiP/Fab complex. To perform MD simulations, we developed a nonbonded dummy model for Zn 2+ and validated its performance with known Zn 2+ -binding proteins. Using these tools, we find that, in the presence of Zn 2+ , YiiP adopts an inward-facing conformation consistent with that previously seen in tubular crystals. After removal of Zn 2+ with high-affinity chelators, YiiP exhibits enhanced flexibility and adopts a novel conformation that appears to be intermediate between inward-facing and outward-facing states. This conformation involves closure of a hydrophobic gate that has been postulated to control access to the primary transport site. Comparison of several independent cryo-EM maps suggests that the transition from the inward-facing state is controlled by occupancy of a secondary Zn 2+ site at the cytoplasmic membrane interface. This work enhances our understanding of individual Zn 2+ binding sites and their role in the conformational dynamics that govern the transport cycle.

59 BASIC BIOLOGICAL SCIENCES↗