Spatially Resolved Chemical Analysis of Geobacter sulfurreducens Cell Surface.

Geobacter sulfurreducens is of interest for the highest efficiency of power generation and extremely long extracellular electron transfer (EET) between the bacterium and electrodes. Despite more than 15 years of intensive molecular biological research, there is still no clear answer which molecules are responsible for these processes. In the present work, we look at the problem from another (atomic) perspective and identify the location and shape of the compounds that are known to be conductive, particularly those containing Fe atoms.

Internal Redox Polarity of an Individual G. sulfurreducens Bacterial Cell Attached to an Inorganic Substrate.

Bacterial cell polarity is an internal asymmetric distribution of subcellular components, including proteins, lipids, and other molecules that correlates with the cell ability to sense energy and metabolite sources, chemical signals, quorum signals, toxins, and movement in the desired directions. This ability also plays central role in cell attachment to various surfaces and biofilm formation. Mechanisms and factors controlling formation of this cell internal asymmetry are not completely understood.

Effect of iron doping on protein molecular conductance.

Protein molecular conductance has attracted attention from researchers for the possibility of constructing innovative flexible biocompatible nanoscale electronic devices and smart hybrid materials. Due to protein complexity, most evaluations of protein conductivity are based on the simple estimation of protein's molecular orbital energy levels and spatial distributions without analysing its protein interaction with electrodes and the calculation of the rates of electron transfer (ET). In the present work, we included in our density functional theory (DFT) analysis an approach based on the non-equilibrium Green's function (NEGF) allowing for calculation from the first principles the molecular interaction with electrodes and thus the role of electrode materials, Fermi level, the thermal distribution of electronic energy levels, and the coupling efficiency between the molecule and the electrodes.

Redox-gradient driven electron transport in a mixed community anodic biofilm.

Here, we describe the long-distance (multi-cell-length) extracellular electron transport (LD-EET) that occurs in an anode-grown mixed community biofilm (MCB) enriched from river sediment that contains 3%-45% Geobacter spp. High signal-to-noise temperature-dependent electrochemical gating measurements (EGM) using interdigitated microelectrode arrays reveal a peak-shaped electrical conductivity vs. potential dependency, indicating MCB acts as a redox conductor, similar to pure culture anode-grown Geobacter sulfurreducens biofilms (GSB).

On the relationship between long-distance and heterogeneous electron transfer in electrode-grown Geobacter sulfurreducens biofilms.

The ability of certain microorganisms to live in a multi-cell thick, electrode-grown biofilm by utilizing the electrode as a metabolic electron acceptor or donor requires electron transfer across cell membranes, through the biofilm, and across the biofilm/electrode interface. Even for the most studied system, anode-grown Geobacter sulfurreducens, the mechanisms underpinning each process and how they connect is largely unresolved. Here we report on G.

A virus-based nanoplasmonic structure as a surface-enhanced Raman biosensor.

Fabrication of nanoscale structures with localized surface plasmons allows for substantial increase in sensitivity of chem/bio sensors. The main challenge for realizing complex nanoplasmonic structures in solution is the high level of precision required at the nanoscale to position metal nanoparticles in 3D. In this study, we report a virus-like particle (VLP) for building a 3D plasmonic nanostructure in solution in which gold nanoparticles are precisely positioned on the VLP by directed self-assembly techniques.

Integrated metagenomic and metaproteomic analyses of marine biofilm communities.

Metagenomic and metaproteomic analyses were utilized to determine the composition and function of complex air-water interface biofilms sampled from the hulls of two US Navy destroyers. Prokaryotic community analyses using PhyloChip-based 16S rDNA profiling revealed two significantly different and taxonomically rich biofilm communities (6,942 taxa) in which the majority of unique taxa were ascribed to members of the Gammaproteobacteria, Alphaproteobacteria and Clostridia. Although metagenomic sequencing indicated that both biofilms were dominated by prokaryotic sequence reads (> 91%) with the majority of the bacterial reads belonging to the Alphaproteobacteria, the Ship-1 metagenome harbored greater organismal and functional diversity and was comparatively enriched for sequences from Cyanobacteria, Bacteroidetes and macroscopic eukaryotes, whereas the Ship-2 metagenome was enriched for sequences from Proteobacteria and microscopic photosynthetic eukaryotes.

Spatially resolved confocal resonant Raman microscopic analysis of anode-grown Geobacter sulfurreducens biofilms.

When grown on the surface of an anode electrode, Geobacter sulfurreducens forms a multi-cell thick biofilm in which all cells appear to couple the oxidation of acetate with electron transport to the anode, which serves as the terminal metabolic electron acceptor. Just how electrons are transported through such a biofilm from cells to the underlying anode surface over distances that can exceed 20 microns remains unresolved. Current evidence suggests it may occur by electron hopping through a proposed network of redox cofactors composed of immobile outer membrane and/or extracellular multi-heme c-type cytochromes.

Adaptation of the black yeast Wangiella dermatitidis to ionizing radiation: molecular and cellular mechanisms.

Observations of enhanced growth of melanized fungi under low-dose ionizing radiation in the laboratory and in the damaged Chernobyl nuclear reactor suggest they have adapted the ability to survive or even benefit from exposure to ionizing radiation. However, the cellular and molecular mechanism of fungal responses to such radiation remains poorly understood. Using the black yeast Wangiella dermatitidis as a model, we confirmed that ionizing radiation enhanced cell growth by increasing cell division and cell size.

Function and regulation of Vibrio campbellii proteorhodopsin: acquired phototrophy in a classical organoheterotroph.

Proteorhodopsins (PRs) are retinal-binding photoproteins that mediate light-driven proton translocation across prokaryotic cell membranes. Despite their abundance, wide distribution and contribution to the bioenergy budget of the marine photic zone, an understanding of PR function and physiological significance in situ has been hampered as the vast majority of PRs studied to date are from unculturable bacteria or culturable species that lack the tools for genetic manipulation. In this study, we describe the presence and function of a horizontally acquired PR and retinal biosynthesis gene cluster in the culturable and genetically tractable bioluminescent marine bacterium Vibrio campbellii.

Structural reorganizations control intermolecular conductance and charge trapping in paraquat-tetraphenylborate inverse photochemical cell.

Miniaturization of electronic devices to the level of single molecules requires detailed understanding of the mechanisms of their operation. One of the questions here is the identification of the role of structural alterations in charge separation and stabilization in photoactive complexes. To address this question, we calculate optimized molecular and electronic structures, and optical and vibrational spectra of l,l'-dimethyl 4,4'-bipyridinium-bis tetraphenylborate PQ(BPh(4))(2) complex ab initio using density functional theory approach and compare them with the experimentally observed UV-Vis and Raman spectra of the molecules in solid-state films.

Observation of two discrete conductivity states in quinone-oligo(phenylene vinylene).

The single-molecule conductivity of quinone-oligo(phenylene vinylene) (Q-OPV) attached to a gold substrate was studied using electrochemical scanning tunnelling microscopy. The results show that the molecule has two discrete conductivity states: a low-conductivity state, when it is oxidized, and a high-conductivity state, when reduced. The electron transport through the molecule in both states occurs via coherent tunnelling.

Electrochemically controlled conductance switching in a single molecule: quinone-modified oligo(phenylene vinylene).

Reversible conductance switching in single quinone-oligo(phenylene vinylene) (Q-OPV) molecules was demonstrated using electrochemical STM. The switching was achieved by application of electrochemical potential to the substrate supporting the molecule. The ratio of conductances between the high- and low-conductivity states is over 40.

Proteomic analysis and identification of the structural and regulatory proteins of the Rhodobacter capsulatus gene transfer agent.

The gene transfer agent of Rhodobacter capsulatus (GTA) is a unique phage-like particle that exchanges genetic information between members of this same species of bacterium. Besides being an excellent tool for genetic mapping, the GTA has a number of advantages for biotechnological and nanoengineering purposes. To facilitate the GTA purification and identify the proteins involved in GTA expression, assembly and regulation, in the present work we construct and transform into R.

Photoprotective role of NADPH:protochlorophyllide oxidoreductase A.

A homology model of NADPH:protochlorophyllide (Pchlide) oxidoreductase A (POR; E.C. 1.

Increasing efficiency of photoelectronic conversion by encapsulation of photosynthetic reaction center proteins in arrayed carbon nanotube electrode.

The construction of efficient light energy converting (photovoltaic and photoelectronic) devices is a current and great challenge in science and technology and one that will have important economic consequences. Here we show that the efficiency of these devices can be improved by the utilization of a new type of nano-organized material having photosynthetic reaction center proteins encapsulated inside carbon nanotube arrayed electrodes. In this work, a generically engineered bacterial photosynthetic reaction center protein with specifically synthesized organic molecular linkers were encapsulated inside carbon nanotubes and bound to the inner tube walls in unidirectional orientation.

Surface reactivity of the quinone/hydroquinone redox center tethered to gold: comparison of delocalized and saturated bridges.

We found that when a quinone headgroup, present in a mixed self-assembled monolayer on gold, reacts with a nucleophile, dissolved in the bulk phase, the reaction rate widely depends on the chemical nature of the tether, being 7 times faster for quinones attached via a delocalized bridge as compared to a saturated alkane chain. Cyclic voltammetry (CV) of the quinone/hydroquinone redox couple was used to monitor the nucleophilic addition, while simulated CVs compared to experimental runs permitted the determination of rate constants. Analysis of CV data also suggests that the delocalized oligo(phenylene ethynylene) bridge facilitates the addition of two mercaptoethanol molecules as compared to the alkane bridge, where only one molecule is being added.

In vitro assembly of a prohead-like structure of the Rhodobacter capsulatus gene transfer agent.

The gene transfer agent (GTA) is a phage-like particle capable of exchanging double-stranded DNA fragments between cells of the photosynthetic bacterium Rhodobacter capsulatus. Here we show that the major capsid protein of GTA, expressed in E. coli, can be assembled into prohead-like structures in the presence of calcium ions in vitro.

Rapid proton-coupled electron-transfer of hydroquinone through phenylenevinylene bridges.

We describe the synthesis of two oligo(phenylene vinylene)s (OPVs) with a hydroquinone moiety and a thiol anchor group: 4-(2',5'-dihydroxystyryl)benzyl thioacetate and 4-[4'-(2' ',5' '-dihydroxystyryl)styryl]benzyl thioacetate. Monolayers on gold of these molecules were examined by electrochemical techniques to determine the electron transfer kinetics of the hydroquinone functionality (H2Q) through these delocalized tethers ("molecular wires") as a function of pH. Between pH 4 and 9, rate constants were ca.

Conductive wiring of immobilized photosynthetic reaction center to electrode by cytochrome C.

The photosynthetic reaction center (RC) found in photosynthetic bacteria is one of the most advanced photoelectronic devices developed by nature. However, after immobilization on the electrode surface, the efficiency of electron transfer (ET) between the RC and the electrode is relatively low. This inefficiency has limited the possibility of using the RC for technological applications.

Fluorescent signal amplification of carbocyanine dyes using engineered viral nanoparticles.

We report enhancement in the fluorescent signal of the carbocyanine dye Cy5 by using an engineered virus as a scaffold to attach >40 Cy5 reporter molecules at fixed locations on the viral capsid. Although cyanine dye loading is often accompanied by fluorescence quenching, our results demonstrate that organized spatial distribution of Cy5 reporter molecules on the capsid obviates this commonly encountered problem. In addition, we observe energy transfer from the virus to adducted dye molecules, resulting in a highly fluorescent viral nanoparticle.

POR structural domains important for the enzyme activity in R. capsulatus complementation system.

NADPH:protochlorophyllide oxidoreductase (POR) catalyzes hydrogen transfer from NADPH to protochlorophyllide (PChlide) in the course of chlorophyll biosynthesis in photosynthetic organisms and is involved in the regulation of the development of photosynthetic apparatus in higher plants, algae and cyanobacteria. To approach molecular factors determining the enzyme activity in a living cell, several mutants of POR from pea (Pisum sativum) with site-directed modifications in different parts of the enzyme were generated. The mutant enzymes were expressed in a R.

Effect of protein orientation on electron transfer between photosynthetic reaction centers and carbon electrodes.

A new type of monolayer of photosynthetic reaction centers (RC) with the primary donor facing the carbon electrode has been constructed using a new bifunctional linker and genetically engineered protein. Comparison of protein in two different orientations with linkers binding to the opposite sides of the protein demonstrates the possibility of utilizing the constructed surfaces as photoelectronic devices. The results show improvement of the electron transfer efficiency when RC is bound with the primary donor (P) facing the electrode (P-side).

Orientated binding of photosynthetic reaction centers on gold using Ni-NTA self-assembled monolayers.

Coupling of photosynthetic reaction centers (RCs) with inorganic surfaces is attractive for the identification of the mechanisms of interprotein electron transfer (ET) and for possible applications in construction of photo- and chemosensors. Here we show that RCs from Rhodobacter sphaeroides can be immobilized on gold surfaces with the RC primary donor looking towards the substrate by using a genetically engineered poly-histidine tag (His(7)) at the C-terminal end of the M-subunit and a Ni-NTA terminated self-assembled monolayer (SAM). In the presence of an electron acceptor, ubiquinone-10, illumination of this RC electrode generates a cathodic photocurrent.