The Molecular Basis for Binding of an Electron Transfer Protein to a Metal Oxide Surface

Electron Transfer Mechanism at the Interface of Multi-Heme Cytochromes and Metal Oxide

Electroactive microbial cells have evolved unique extracellular electron transfer to conduct the reactions via redox outer-membrane (OM) proteins. However, the electron transfer mechanism at the interface of OM proteins and nanomaterial remains unclear. In this study, the mechanism for the electron transfer at biological/inorganic interface is investigated by integrating molecular modeling with electrochemical and spectroscopic measurements. For this purpose, a model system composed of OmcA, a typical OM protein, and the hexagonal tungsten trioxide (h-WO3 ) with good biocompatibility is selected. The interfacial electron transfer is dependent mainly on the special molecular configuration of OmcA and the microenvironment of the solvent exposed active center. Also, the apparent electron transfer rate can be tuned by site-directed mutagenesis at the axial ligand of the active center. Furthermore, the equilibrium state of the OmcA/h-WO3 systems suggests that their attachment is attributed to the limited number of residues. The electrochemical analysis of OmcA and its variants reveals that the wild type exhibits the fastest electron transfer rate, and the transient absorption spectroscopy further shows that the axial histidine plays an important role in the interfacial electron transfer process. This study provides a useful approach to promote the site-directed mutagenesis and nanomaterial design for bioelectrocatalytic applications.

Goethite Formed in the Periplasmic Space of Pseudomonas sp. JM-7 during Fe Cycling Enhances Its Denitrification in Water

Denitrification-driven Fe(II) oxidation is an important microbial metabolism that connects iron and nitrogen cycling in the environment. The formation of Fe(III) minerals in the periplasmic space has a significant effect on microbial metabolism and electron transfer, but direct evidence of iron ions entering the periplasm and resulting in periplasmic mineral precipitation and electron conduction properties has yet to be conclusively determined. Here, we investigated the pathways and amounts of iron, with different valence states and morphologies, entering the periplasmic space of the denitrifier Pseudomonas sp. JM-7 (P. JM-7), and the possible effects on the electron transfer and the denitrifying ability. When consistently provided with Fe(II) ions (from siderite (FeCO3)), the dissolved Fe(II) ions entered the periplasmic space and were oxidized to Fe(III), leading to the formation of a 25 nm thick crystalline goethite crust, which functioned as a semiconductor, accelerating the transfer of electrons from the intracellular to the extracellular matrix. This consequently doubled the denitrification rate and increased the electron transport capacity by 4-30 times (0.015-0.04 μA). However, as the Fe(II) concentration further increased to above 4 mM, the Fe(II) ions tended to preferentially nucleate, oxidize, and crystallize on the outer surface of P. JM-7, leading to the formation of a densely crystallized goethite layer, which significantly slowed down the metabolism of P. JM-7. In contrast to the Fe(II) conditions, regardless of the initial concentration of Fe(III), it was challenging for Fe(III) ions to form goethite in the periplasmic space. This work has shed light on the likely effects of iron on environmental microorganisms, improved our understanding of globally significant iron and nitrogen geochemical cycles in water, and expanded our ability to study and control these important processes.

Molecular Insights of Cellobiose Dehydrogenase Adsorption on Self-Assembled Monolayers

Cellobiose dehydrogenase (CDH) is capable of direct electron transfer (DET) on electrodes and is a promising redox enzyme for bioelectrochemical applications. Its unique two-domain structure makes the function of CDH adsorbed on the surface of the electrode deeply affected by the external environment, such as ion species, strength, pH, and surface charge density. To date, however, the exact mechanism of how the external environment tailors the structure and dynamics of CDH adsorbed on the electrode surface still remains poorly understood. Here, multiscale simulations were performed to look for insight into the effect of Na⁺ and Ca²⁺ ions on the activation of CDH on oppositely charged self-assembled monolayer (NH₂-SAM and COOH-SAM) surfaces with different surface charge densities (SCDs). Both Na⁺ and Ca²⁺ can promote CDH conformation switch from the open state to the closed state, while the promotion effect of Ca²⁺ is stronger than that of Na⁺ at the same conditions. However, the high ionic strength (IS) of Ca²⁺ renders the cytochrome (CYT) domain of CDH away from the NH₂-SAM with low SCD. In contrast, whatever the IS, the NH₂-SAM surface with high SCD can not only enhance the CYT-surface interaction but also achieve a closed-state conformation due to a similar role of Ca²⁺. Overall, this study gains molecular-level insights into the role of ion species and surface charge in modulating the structure and conformation of CDH on the SAM surface, thereby tailoring its activity.

In Situ Microscopic Studies on the Interaction of Multi-Principal Element Nanoparticles and Bacteria

Multi-principal element nanoparticles are an emerging class of materials with potential applications in medicine and biology. However, it is not known how such nanoparticles interact with bacteria at nanoscale. In the present work, we evaluated the interaction of multi-principal elemental alloy (FeNiCu) nanoparticles with Escherichia coli (E. coli) bacteria using the in situ graphene liquid cell (GLC) scanning transmission electron microscopy (STEM) approach. The imaging revealed the details of bacteria wall damage in the vicinity of nanoparticles. The chemical mappings of S, P, O, N, C, and Cl elements confirmed the cytoplasmic leakage of the bacteria. Our results show that there is selective release of metal ions from the nanoparticles. The release of copper ions was much higher than that for nickel while the iron release was the lowest. In addition, the binding affinity of bacterial cell membrane protein functional groups with Cu, Ni, and Fe cations is found to be the driving force behind the selective metal cations' release from the multi-principal element nanoparticles. The protein functional groups driven dissolution of multielement nanoparticles was evaluated using the density functional theory (DFT) computational method, which confirmed that the energy required to remove Cu atoms from the nanoparticle surface was the least in comparison with those for Ni and Fe atoms. The DFT results support the experimental data, indicating that the energy to dissolve metal atoms exposed to oxidation and/or the to presence of oxygen atoms at the surface of the nanoparticle catalyzes metal removal from the multielement nanoparticle. The study shows the potential of compositional design of multi-principal element nanoparticles for the controlled release of metal ions to develop antibacterial strategies. In addition, GLC-STEM is a promising approach for understanding the nanoscale interaction of metallic nanoparticles with biological structures.

Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity

OmcZ nanowires produced by Geobacter species have high electron conductivity (>30 S cm-1). Of 111 cytochromes present in G. sulfurreducens, OmcZ is the only known nanowire-forming cytochrome essential for the formation of high-current-density biofilms that require long-distance (>10 µm) extracellular electron transport. However, the mechanisms underlying OmcZ nanowire assembly and high conductivity are unknown. Here we report a 3.5-Å-resolution cryogenic electron microscopy structure for OmcZ nanowires. Our structure reveals linear and closely stacked haems that may account for conductivity. Surface-exposed haems and charge interactions explain how OmcZ nanowires bind to diverse extracellular electron acceptors and how organization of nanowire network re-arranges in different biochemical environments. In vitro studies explain how G. sulfurreducens employ a serine protease to control the assembly of OmcZ monomers into nanowires. We find that both OmcZ and serine protease are widespread in environmentally important bacteria and archaea, thus establishing a prevalence of nanowire biogenesis across diverse species and environments.

Modulating the adsorption orientation of methionine-rich laccase by tailoring the surface chemistry of single-walled carbon nanotubes

Achieving fast electron transfer process between oxidoreductase and electrodes is pivotal for the biocathode of enzymatic biofuel cells (EBFCs). However, in-depth understanding of the interplay mechanism between enzymes and electrode materials remains challenging when designing and constructing EBFCs. Herein, atomic-scale insight into the direct electron transfer (DET) behavior of Thermus thermophilus laccase (TtLac) with a special methionine-rich β-hairpin motif adsorbed on the carboxyl-functionalized carbon nanotube (COOH-CNT) and amino-functionalized carbon nanotube (NH₂-CNT) surfaces were disclosed by multi-scale molecular simulations. Simulation results reveal that electrostatic modification is an effective way to tune the DET behavior for TtLac on the modified-CNTs electrode surface. Surprisingly, the positively charged TtLac can be attracted by both negatively charged COOH-CNT and positively charged NH₂-CNT surfaces, yet only the latter is capable to trigger the DET process due to the 'lying-on' adsorption orientation. Specifically, the T1 copper site is near the methionine-rich β-hairpin motif, which is the key binding site for TtLac binding onto the NH₂-CNT surface via electrostatic interaction, π-π stacking and cation-π interaction. Moreover, TtLac on the NH₂-CNT surface undergoes less conformational changes than those on the COOH-CNT surface, which allows the laccase stability and catalytic efficiency to be well preserved. These findings provide a fundamental guidance for future design and fabrication of methionine-rich laccase-based EBFCs with high power output and long lifespan.

Light driven Aspergillus niger-ZnS nanobiohybrids for degradation of methyl orange

Inorganic-microbial hybrid systems have potential to be sustainable, efficient and versatile chemical synthesis platforms by integrating the light-harvesting properties of semiconductors with microbial cells. Here, we demonstrate light-driven photocatalytic semiconducting Aspergillus niger cells-ZnS nanoparticles for enhanced removal of the dye methyl orange. Chemically synthesized ZnS nanoparticles exhibited a zinc blende pattern in X-ray diffraction, had a dimension of 20-90 nm with a band gap (E_bg) of 3.4 eV at 1.83 × 10¹⁸ photons/second. Biologically synthesized ZnS nanoparticles of 40-90 nm showed a hexagonal pattern in the X-ray powder diffraction spectra with an E_bg 3.7 eV at 1.68 × 10¹⁸ photons/second. At a methyl orange (MO) concentration of 100 mg/L, dosage of 0.5 × 10⁵ mol catalyst and pH 4, a 97.5% and 98% removal efficiency of MO was achieved in 90 min and 60 min for, respectively, chemically and biologically synthesized ZnS nanobiohybrids in the presence of UV-A light. The major degradation products of photocatalysis for chemically synthesized ZnS nanobiohybrids were naphtholate (C₁₀H₇O m/z 143) and hydroquinone (C₉H₅m/z 113). For the biologically synthesized ZnS nanobiohybrids, the degradation products were hydroquinone (C₉H₅m/z 113) and 2-phenylphenol (C₁₂H₁₀O m/z 170).

Determinants of Multiheme Cytochrome Extracellular Electron Transfer Uncovered by Systematic Peptide Insertion

The multiheme cytochrome MtrA enables microbial respiration by transferring electrons across the outer membrane to extracellular electron acceptors. While structural studies have identified residues that mediate the binding of MtrA to hemes and to other cytochromes that facilitate extracellular electron transfer (EET), the relative importance of these interactions for EET is not known. To better understand EET, we evaluated how insertion of an octapeptide across all MtrA backbone locations affects Shewanella oneidensis MR-1 respiration on Fe(III). The EET efficiency was found to be inversely correlated with the proximity of the insertion to the heme prosthetic groups. Mutants with decreased EET efficiencies also arose from insertions in a subset of the regions that make residue-residue contacts with the porin MtrB, while all sites contacting the extracellular cytochrome MtrC presented high peptide insertion tolerance. MtrA variants having peptide insertions within the CXXCH motifs that coordinate heme cofactors retained some ability to support respiration on Fe(III), although these variants presented significantly decreased EET efficiencies. Furthermore, the fitness of cells expressing different MtrA variants under Fe(III) respiration conditions correlated with anode reduction. The peptide insertion profile, which represents the first comprehensive sequence-structure-function map for a multiheme cytochrome, implicates MtrA as a strategic protein engineering target for the regulation of EET.

Coupled- and Independent-Trajectory Approaches Based on the Exact Factorization Using the PyUNIxMD Package

We present mixed quantum-classical approaches based on the exact factorization framework. The electron-nuclear correlation term in the exact factorization enables us to deal with quantum coherences by accounting for electronic and nuclear nonadiabatic couplings effectively within classical nuclei approximation. We compare coupled- and independent-trajectory approximations with each other to understand algorithms in description of the bifurcation of nuclear wave packets and the correct spatial distribution of electronic wave functions along with nuclear trajectories. Finally, we show numerical results for comparisons of coupled- and independent-trajectory approaches for the photoisomerization of a protonated Schiff base from excited state molecular dynamics (ESMD) simulations with the recently developed Python-based ESMD code, namely, the PyUNIxMD program.

Iron Cycle Tuned by Outer-Membrane Cytochromes of Dissimilatory Metal-Reducing Bacteria: Interfacial Dynamics and Mechanisms In Vitro

The biogeochemical cycle of iron is of great importance to living organisms on Earth, and dissimilatory metal-reducing bacteria (DMRB) with the capability of reducing hematite (α-Fe2O3) by outer-membrane (OM) cytochromes play a great role in the iron cycle. However, the dynamic binding of cytochromes to α-Fe2O3 at the molecular level and the resulting impact on the photon-to-electron conversion of α-Fe2O3 for the iron cycle are not fully understood. To address these issues, two-dimensional IR correlation analysis coupled with molecular dynamics (MD) simulations was conducted for an OmcA-Fe2O3 system as OmcA bonds stronger with hematite in a typical DMRB,Shewanella. The photoelectric response of α-Fe2O3 with the OmcA coating was evaluated at three different potentials. Specifically, the binding groups from OmcA to α-Fe2O3 were in the sequence of carboxyl groups, amide II, and amide I. Further MD analysis reveals that both electrostatic interactions and hydrogen bonds played essential roles in the binding process, leading to the structural changes of OmcA to facilitate iron reduction. Moreover, the OmcA coating could store the photogenerated electrons from α-Fe2O3 like a capacitor and utilize the stored electrons for α-Fe2O3 reduction in dark and anoxic environments, further driving the biogeochemical cycle of iron. These investigations give the dynamic information on the OM protein/hematite interaction and provide fundamental insights into the biogeochemical cycle of iron by taking the photon-induced redox chemistry of iron oxide into consideration.

Boosting the anode performance of microbial fuel cells with a bacteria-derived biological iron oxide/carbon nanocomposite catalyst

Modifying the electrodes of microbial fuel cells (MFCs) with iron oxides can improve the bacterial attachment performances and electrocatalytic activities for energy conversion, which is of significance in the fabrication of MFCs. However, the conventional modification methods usually result in the aggregation of iron sites, producing the electrodes of poor qualities. Herein, we report a novel method for the modification of electrochemical electrodes to boost the anode performance of MFC. The Shewanella precursor adhered on carbon felt electrode was directly carbonized to form a bacteria-derived biological iron oxide/carbon (Bio-FeOx/C) nanocomposite catalyst. The large spatial separation between the bacteria, as well as those between the iron containing proteins in the bacteria, deliver a highly dispersed Bio-FeOx/C nanocomposite with good electrocatalytic activities. The excellent microbial attachment performance and electron transfer rate of the Bio-FeOx/C modified electrode significantly promote the transfer of produced electrons between bacteria and electrode. Accordingly, the MFC with the Bio-FeOx/C electrode exhibits the maximum power density of 797.0 mW m^-2, much higher than that obtained with the conventional carbon felt anode (226.1 mW m^-2). Our works have paved a new avenue to the conversion of the natural bacterial precursors into active iron oxide nanoparticles as the anode catalyst of MFCs. The high catalytic activity of the prepared Bio-FeOx endows it great application potentials in the construction of high-performance electrodes.

Nanomaterials Facilitating Microbial Extracellular Electron Transfer at Interfaces

Electrochemically active bacteria can transport their metabolically generated electrons to anodes, or accept electrons from cathodes to synthesize high-value chemicals and fuels, via a process known as extracellular electron transfer (EET). Harnessing of this microbial EET process has led to the development of microbial bio-electrochemical systems (BESs), which can achieve the interconversion of electrical and chemical energy and enable electricity generation, hydrogen production, electrosynthesis, wastewater treatment, desalination, water and soil remediation, and sensing. Here, the focus is on the current understanding of the microbial EET process occurring at both the bacteria-electrode interface and the biotic interface, as well as some attempts to improve the EET by using various nanomaterials. The behavior of nanomaterials in different EET routes and their influence on the performance of BESs are described. The inherent mechanisms will guide rational design of EET-related materials and lead to a better understanding of EET mechanisms.

Coating iron oxide nanoparticles with mesoporous silica reduces their interaction and impact on S. oneidensis MR-1

Here, we investigate the impact of iron oxide nanoparticles (IONPs) and mesoporous silica-coated iron oxide nanoparticles (msIONPs) on Shewanella oneidensis in an aerobic environment, which is likely the main environment where such nanoparticles will end up after use in consumer products or biomedical applications. Monitoring the viability of S. oneidensis, a model environmental organism, after exposure to the nanoparticles reveals that IONPs promote bacterial survival, while msIONPs do not impact survival. These apparent impacts are correlated with association of the nanoparticles with the bacterial membrane, as revealed by TEM and ICP-MS studies, and upregulation of membrane-associated genes. However, similar survival in bacteria was observed when exposed to equivalent concentrations of released ions from each nanomaterial, indicating that aqueous nanoparticle transformations are responsible for the observed changes in bacterial viability. Therefore, this work demonstrates that a simple mesoporous silica coating can control the dissolution of the IONP core by greatly reducing the amount of released iron ions, making msIONPs a more sustainable option to reduce perturbations to the ecosystem upon release of nanoparticles into the environment.

Controlling protein assembly on inorganic crystals through designed protein interfaces

The ability of proteins and other macromolecules to interact with inorganic surfaces is critical to biological function. The proteins involved in these interactions are highly charged and often rich in carboxylic acid side chains^1-5, but the structures of most protein-inorganic interfaces are unknown. We explored the possibility of systematically designing structured protein-mineral interfaces guided by the example of ice-binding proteins, which present arrays of threonine residues matched to the ice lattice that order clathrate waters into an ice-like structure⁶. We designed proteins displaying arrays of up to 54 carboxylate residues geometrically matched to the K⁺ sublattice on muscovite mica (001). At low [K⁺] individual molecules bind independently to mica in the designed orientations, while at high [K⁺], the designs form 2D liquid-crystal phases, which accentuate the inherent structural bias in the muscovite lattice to produce protein arrays ordered over tens of millimeters. Incorporation of designed protein-protein interactions preserving the match between the proteins and the K⁺ lattice led to extended self-assembled structures on mica: designed end-to-end interactions produced micron long single protein-diameter wires, and a designed trimeric interface yielded extensive honeycomb arrays. The nearest neighbor distances in these hexagonal arrays could be set digitally between 7.5 and 15.9 nm with 2.1 nm selectivity by changing the number of repeat units in the monomer. These results demonstrate that protein-inorganic lattice interactions can be systematically programmed and set the stage for designing protein-inorganic hybrid materials.

Geometrical Changes in the Hemes of Bacterial Surface c-Type Cytochromes Reveal Flexibility in Their Binding Affinity with Minerals

Microbial extracellular electron transport occurs via the physical and electrical association of outer-membrane c-type cytochromes (OM c-Cyts) with extracellular solid surfaces. However, studies investigating the characteristics of cytochrome binding with solid materials have been limited to the use of purified units of OM c-Cyts dissolved in solution, rather than OM c-Cyts in intact cells, because of the lack of a methodology that specifically allows for the monitoring of OM c-Cyts in whole-cells. Here, we utilized circular dichroism (CD) spectroscopy to examine the molecular mechanisms and binding characteristics of the interaction between MtrC, a unit of OM c-Cyts, in whole Shewanella oneidensis MR-1 cells and hematite nanoparticles. The addition of hematite nanoparticles significantly decreased the intensity of the Soret CD peaks, indicating geometrical changes in the hemes in MtrC associated with their physical contact with hematite. The binding affinity of MtrC estimated using CD spectra changed predominantly depending upon the redox state of MtrC and the concentration of the hematite nanoparticles. In contrast, purified MtrC demonstrated a constant binding affinity following a Langmuir isotherm, with a standard Gibbs free energy of -43 kJ mol^-1, suggesting that the flexibility in the binding affinity of MtrC with hematite was specific in membrane-bound protein complex conditions. Overall, these findings suggest that the binding affinity as well as the heme geometry of OM c-Cyts are flexibly modulated in the membrane complex associated with microbe-mineral interactions.

Detection of the conformational changes of Discosoma red fluorescent proteins adhered on silver nanoparticles-based nanocomposites via surface-enhanced Raman scattering

Description of the relationship between protein structure and function remains a primary focus in molecular biology, biochemistry, protein engineering and bioelectronics. Moreover, the investigation of the protein conformational changes after adhesion and dehydration is of importance to tackle problems related to the interaction of proteins with solid surfaces. In this paper the conformational changes of wild-type Discosoma recombinant red fluorescent proteins (DsRed) adhered on silver nanoparticles (AgNPs)-based nanocomposites are explored via surface-enhanced Raman scattering (SERS). Originality in the present approach is to work on dehydrated DsRed thin protein layers in link with natural conditions during drying. To enable the SERS effect, plasmonic substrates consisting of a single layer of AgNPs encapsulated by an ultra-thin silica cover layer were elaborated by plasma process. The achieved enhancement of the electromagnetic field in the vicinity of the AgNPs is as high as 105. This very strong enhancement factor allowed detecting Raman signals from discontinuous layers of DsRed issued from solution with protein concentration of only 80 nM. Three different conformations of the DsRed proteins after adhesion and dehydration on the plasmonic substrates were identified. It was found that the DsRed chromophore structure of the adsorbed proteins undergoes optically assisted chemical transformations when interacting with the optical beam, which leads to reversible transitions between the three different conformations. The proposed time-evolution scenario endorses the dynamical character of the relationship between protein structure and function. It also confirms that the conformational changes of proteins with strong internal coherence, like DsRed proteins, are reversible.

Extracellular Electron Transfer by Shewanella oneidensis Controls Palladium Nanoparticle Phenotype

The relative scarcity of well-defined genetic and metabolic linkages to material properties impedes biological production of inorganic materials. The physiology of electroactive bacteria is intimately tied to inorganic transformations, which makes genetically tractable and well-studied electrogens, such as Shewanella oneidensis, attractive hosts for material synthesis. Notably, this species is capable of reducing a variety of transition-metal ions into functional nanoparticles, but exact mechanisms of nanoparticle biosynthesis remain ill-defined. We report two key factors of extracellular electron transfer by S. oneidensis, the outer membrane cytochrome, MtrC, and soluble redox shuttles (flavins), that affect Pd nanoparticle formation. Changes in the expression and availability of these electron transfer components drastically modulated particle synthesis rate and phenotype, including their structure and cellular localization. These relationships may serve as the basis for biologically tailoring Pd nanoparticle catalysts and could potentially be used to direct the biogenesis of other metal nanomaterials.

Surface Hopping Dynamics beyond Nonadiabatic Couplings for Quantum Coherence

Description of correct electron-nuclear couplings is crucial in modeling of nonadiabatic dynamics. Within traditional semiclassical or mixed quantum-classical dynamics, the coupling between quantum electronic states and classical nuclear trajectories is governed by nonadiabatic coupling vectors coupled to classical nuclear momenta. This enables us to develop a very powerful nonadiabatic dynamics algorithm, namely, surface hopping dynamics, which can describe the splitting of nuclear wave packets and detailed balance. Despite its efficiency and practicality, it suffers from the lack of quantum decoherence due to incorrect accounts for the electron-nuclear coupling. Here we present a new surface hopping algorithm based on the exact electron-nuclear correlation from the exact factorization of molecular wave functions. This algorithm demands comparable computational costs to existing surface hopping methods. Numerical simulations with two-state models and a multidimensional multistate realistic molecule show that the electron-nuclear coupling beyond the nonadiabatic coupling terms can describe the quantum coherence properly.