Elucidating the Roles of Conserved Active Site Amino Acids in the Escherichia coli Cytochrome c Nitrite Reductase

The periplasmic cytochrome c nitrite reductase NrfA is a homodimeric protein containing ten c-type cytochromes. NrfA catalyses the six electron reduction of nitrite to ammonia which in turn facilitates anaerobic respiration. NrfA also reduces nitric oxide and hydroxylamine to ammonium. The reduction of substrate is carried out at the distal position of a lysine ligated heme and in an active site cavity dominated by a conserved catalytic triad of histidine, tyrosine and arginine residues. The role of the catalytic triad of Escherichia coli NrfA has been explored by generating NrfA variants. Three NrfA variants were studied in which a single active site residue was substituted: arginine to lysine (R106K), tyrosine to phenylalanine (Y216F) and histidine to asparagine (H264N). These NrfA variants were then compared to the wild type enzyme. The comparison of the crystal structures revealed the substituted residues in the NrfA variants adopted similar positions to the native residues. The ability of the NrfA proteins to reduce nitrogenous substrates was characterised by both solution assay and protein film electrochemistry (PFE). The results revealed that R106K and Y216F NrfA maintained the ability to reduce nitrite whereas the H264N NrfA did not. Further characterisation of H264N NrfA using PFE identified that not only was nitrite no longer a substrate, it could instead act as an inhibitor of hydroxylamine reduction. A fourth variant of E. coli NrfA, in which the lysine ligand was substituted for a histidine residue (K126H), attempted to examine the importance of lysine ligation to the active site heme. The crystal structure of the K126H variant revealed the histidine was not ligating the heme iron. However, spectroscopy of the K126H NrfA was unable to confirm the presence of a tetra-coordinated heme. The substitution of the four key residues resulted in proteins with different characteristics to the wild type enzyme and to each other. This offered an insight into role these residues play in the reaction mechanism of NrfA

Resolution of Key Roles for the Distal Pocket Histidine in Cytochrome c Nitrite Reductases

Cytochrome c nitrite reductases perform a key step in the biogeochemical N-cycle by catalyzing the six-electron reduction of nitrite to ammonium. These multi-heme cytochromes contain a number of His/His ligated c-hemes for electron transfer and a structurally differentiated heme that provides the catalytic center. The catalytic heme has proximal ligation from lysine, or histidine, and an exchangeable distal ligand bound within a pocket that includes a conserved histidine. Here we describe properties of a penta-heme cytochrome c nitrite reductase in which the distal His has been substituted by Asn. The variant is unable to catalyze nitrite reduction despite retaining the ability to reduce a proposed intermediate in that process, namely, hydroxylamine. A combination of electrochemical, structural and spectroscopic studies reveals that the variant enzyme simultaneously binds nitrite and electrons at the catalytic heme. As a consequence the distal His is proposed to play a key role in orienting the nitrite for N-O bond cleavage. The electrochemical experiments also reveal that the distal His facilitates rapid nitrite binding to the catalytic heme of the native enzyme. Finally it is noted that the thermodynamic descriptions of nitrite- and electron-binding to the active site of the variant enzyme are modulated by the prevailing oxidation states of the His/His ligated hemes. This is behavior that is likely to be displayed by other multi-centered redox enzymes such that there are wide implications for considering the determinants of catalytic activity in this important and varied group of oxidoreductases

The Effect of Blade Alignment on Kinematics and Plantar Pressure during the Execution of Goaltender-Specific Movement Patterns: A Case Study.

Innovations in material properties of goaltender skates have improved the protective characteristics of the boot, leading to redesign of the blade holder to resemble players' holders. The redesigned blade holder introduces the ability to customize blade alignment, which may grant a performance advantage. We investigated the effect of blade alignment on kinematics and plantar pressure during the execution of two different goaltender-specific movement patterns: (1) the butterfly drop to recovery and (2) the lateral butterfly slide to recovery. The main objective of this study was to investigate the effect of three blade alignment conditions. The secondary objective was to compare two neutral alignment conditions, which was facilitated by studying the effects of two different holders on kinematics and plantar pressure during two goaltender-specific techniques. A male goaltender with professional experience completed an A-B-A design, executing five trials of A, B, and A for both movements with each blade alignment condition (n = 30 per collection, n = 90 overall) on synthetic ice in a controlled lab environment. Blade alignment conditions were defined by the alignment of the blade holder on the boot and the type of blade holder. Kinematic and plantar pressure data were collected simultaneously using 3D motion capture and in-skate pressure insoles, respectively. Increased butterfly drop velocity (2.07 ± 0.09 m/s) and peak plantar pressure (77.19 ± 2.67 psi) were revealed when executing the butterfly drop with medial alignment. This work suggests medial blade alignment may enable the goaltender to drop into the butterfly position faster, potentially increasing the likelihood of making a save.The Brock Library Open Access Publishing Fun

Purification and characterization of the isoprene monooxygenase from Rhodococcus sp. strain AD45

Isoprene (2-methyl-1,3-butadiene) is a climate-active gas released to the atmosphere in large quantities, comparable to methane in magnitude. Several bacteria have been isolated which can grow on isoprene as a sole carbon and energy source, but very little information is available about the degradation of isoprene by these bacteria at the biochemical level. Isoprene utilization is dependent on a multistep pathway, with the first step being the oxidation of isoprene to epoxy-isoprene. This is catalyzed by a four-component soluble diiron monooxygenase, isoprene monooxygenase (IsoMO). IsoMO is a six-protein complex comprising an oxygenase (IsoABE), containing the di-iron active site, a Rieske-type ferredoxin (IsoC), a NADH reductase (IsoF), and a coupling/effector protein (IsoD), homologous to the soluble methane monooxygenase and alkene/aromatic monooxygenases. Here, we describe the purification of the IsoMO components from Rhodococcus sp. AD45 and reconstitution of isoprene-oxidation activity in vitro. Some IsoMO components were expressed and purified from the homologous host Rhodococcus sp. AD45-ID, a Rhodococcus sp. AD45 strain lacking the megaplasmid which contains the isoprene metabolic gene cluster. Others were expressed in Escherichia coli and purified as fusion proteins. We describe the characterization of these purified components and demonstrate their activity when combined with Rhodococcus sp. AD45 cell lysate. Demonstration of IsoMO activity in vitro provides a platform for further biochemical and biophysical characterization of this novel soluble diiron center monooxygenase, facilitating new insights into the enzymatic basis for the bacterial degradation of isoprene

Structural modeling of an outer membrane electron conduit from a metal-reducing bacterium suggests electron transfer via periplasmic redox partners

Many subsurface microorganisms couple their metabolism to the reduction or oxidation of extracellular substrates. For example, anaerobic mineral-respiring bacteria can use external metal oxides as terminal electron acceptors during respiration. Porin–cytochrome complexes facilitate the movement of electrons generated through intracellular catabolic processes across the bacterial outer membrane to these terminal electron acceptors. In the mineral-reducing model bacterium Shewanella oneidensis MR-1, this complex is composed of two decaheme cytochromes (MtrA and MtrC) and an outer-membrane β-barrel (MtrB). However, the structures and mechanisms by which porin–cytochrome complexes transfer electrons are unknown. Here, we used small-angle neutron scattering (SANS) to study the molecular structure of the transmembrane complexes MtrAB and MtrCAB. Ab initio modeling of the scattering data yielded a molecular envelope with dimensions of ∼105 × 60 × 35 Å for MtrAB and ∼170 × 60 × 45 Å for MtrCAB. The shapes of these molecular envelopes suggested that MtrC interacts with the surface of MtrAB, extending ∼70 Å from the membrane surface and allowing the terminal hemes to interact with both MtrAB and an extracellular acceptor. The data also reveal that MtrA fully extends through the length of MtrB, with ∼30 Å being exposed into the periplasm. Proteoliposome models containing membrane-associated MtrCAB and internalized small tetraheme cytochrome (STC) indicate that MtrCAB could reduce Fe(III) citrate with STC as an electron donor, disclosing a direct interaction between MtrCAB and STC. Taken together, both structural and proteoliposome experiments support porin–cytochrome–mediated electron transfer via periplasmic cytochromes such as STC

Photoreduction of Shewanella oneidensis Extracellular Cytochromes by Organic Chromophores and Dye-Sensitized TiO2.

The transfer of photoenergized electrons from extracellular photosensitizers across a bacterial cell envelope to drive intracellular chemical transformations represents an attractive way to harness nature's catalytic machinery for solar-assisted chemical synthesis. In $\textit{Shewanella oneidensis}$ MR-1 (MR-1), trans-outer-membrane electron transfer is performed by the extracellular cytochromes MtrC and OmcA acting together with the outer-membrane-spanning porin$\cdot$cytochrome complex (MtrAB). Here we demonstrate photoreduction of solutions of MtrC, OmcA, and the MtrCAB complex by soluble photosensitizers: namely, eosin Y, fluorescein, proflavine, flavin, and adenine dinucleotide, as well as by riboflavin and flavin mononucleotide, two compounds secreted by MR-1. We show photoreduction of MtrC and OmcA adsorbed on Ru$^{\text{II}}$-dye-sensitized TiO$_2$ nanoparticles and that these protein-coated particles perform photocatalytic reduction of solutions of MtrC, OmcA, and MtrCAB. These findings provide a framework for informed development of strategies for using the outer-membrane-associated cytochromes of MR-1 for solar-driven microbial synthesis in natural and engineered bacteria.This work was supported by the UK Biotechnology and Biological Sciences Research Council (grants BB/K009753/1, BB/K010220/1, BB/K009885/1, and BB/K00929X/1), the Engineering and Physical Sciences Research Council (EP/M001989/1, PhD studentship 1307196 to E.V.A.), a Royal Society Leverhulme Trust Senior Research Fellowship to J.N.B., the Christian Doppler Research Association, and OMV group

A Decaheme Cytochrome as a Molecular Electron Conduit in Dye-Sensitized Photoanodes.

In nature, charge recombination in light-harvesting reaction centers is minimized by efficient charge separation. Here, it is aimed to mimic this by coupling dye-sensitized TiO2 nanocrystals to a decaheme protein, MtrC from Shewanella oneidensis MR-1, where the 10 hemes of MtrC form a ≈7-nm-long molecular wire between the TiO2 and the underlying electrode. The system is assembled by forming a densely packed MtrC film on an ultra-flat gold electrode, followed by the adsorption of approximately 7 nm TiO2 nanocrystals that are modified with a phosphonated bipyridine Ru(II) dye (RuP). The step-by-step construction of the MtrC/TiO2 system is monitored with (photo)electrochemistry, quartz-crystal microbalance with dissipation (QCM-D), and atomic force microscopy (AFM). Photocurrents are dependent on the redox state of the MtrC, confirming that electrons are transferred from the TiO2 nanocrystals to the surface via the MtrC conduit. In other words, in these TiO2/MtrC hybrid photodiodes, MtrC traps the conduction-band electrons from TiO2 before transferring them to the electrode, creating a photobioelectrochemical system in which a redox protein is used to mimic the efficient charge separation found in biological photosystems.This work was supported by the BBSRC (grants BB/K009753/1, BB/K010220/1, and BB/K009885/1), the EPSRC (EP/H00338X/2; PhD studentship to Emma Ainsworth), the Christian Doppler Research Association and the OMV Group. The authors appreciate Dr. Liang Shi (PNNL) and Dr. Marcus Edwards (UEA) for providing the S. oneidensis strain and the protocol allowing for purification of MtrC.This is the final published version of the article. It was originally published in Advanced Functional Materials (Hwang ET, Sheikh K, Orchard KL, Hojo D, Radu V, Lee C-Y, Ainsworth E, Lockwood C, Gross MA, Adschiri T, Reisner E, Butt JN, Jeuken LJC, Advanced Functional Materials 2015, 25, 2308–2315, doi: 10.1002/adfm.201404541) http://dx.doi.org/10.1002/adfm.201404541

Genetic code expansion in Shewanella oneidensis MR-1 allows site-specific incorporation of bioorthogonal functional groups into a c-type Cytochrome

Genetic code expansion has enabled cellular synthesis of proteins containing unique chemical functional groups to allow understanding and modulation of biological systems and engineer new biotechnology. Here we report the development of efficient methods for site-specific incorporation of structurally diverse non-canonical amino acids (ncAAs) into proteins expressed in the electroactive bacterium Shewanella oneidensis MR-1. We demonstrate that the biosynthetic machinery for ncAA incorporation is compatible and orthogonal to endogenous pathways of S. oneidensis MR-1 for protein synthesis, maturation of c-type cytochromes, and protein secretion. This allowed efficient synthesis of a c-type cytochrome, MtrC, containing site-specifically incorporated ncAA in S. oneidensis MR-1 cells. We demonstrate that site-specific replacement of surface residues in MtrC with ncAAs does not influence its three-dimensional structure and redox properties. We also demonstrate that site-specifically incorporated biorthogonal functional groups could be used for efficient site-selective labelling of MtrC with fluorophores. These synthetic biology developments pave the way to expand the chemical repertoire of designer proteins expressed in S. oneidensis MR-1

Changes in weight loss, body composition and cardiovascular disease risk after altering macronutrient distributions during a regular exercise program in obese women

<p>Abstract</p> <p>Background</p> <p>This study's purpose investigated the impact of different macronutrient distributions and varying caloric intakes along with regular exercise for metabolic and physiological changes related to weight loss.</p> <p>Methods</p> <p>One hundred forty-one sedentary, obese women (38.7 ± 8.0 yrs, 163.3 ± 6.9 cm, 93.2 ± 16.5 kg, 35.0 ± 6.2 kg•m^-2, 44.8 ± 4.2% fat) were randomized to either no diet + no exercise control group (CON) a no diet + exercise control (ND), or one of four diet + exercise groups (high-energy diet [HED], very low carbohydrate, high protein diet [VLCHP], low carbohydrate, moderate protein diet [LCMP] and high carbohydrate, low protein [HCLP]) in addition to beginning a 3x•week^-1supervised resistance training program. After 0, 1, 10 and 14 weeks, all participants completed testing sessions which included anthropometric, body composition, energy expenditure, fasting blood samples, aerobic and muscular fitness assessments. Data were analyzed using repeated measures ANOVA with an alpha of 0.05 with LSD post-hoc analysis when appropriate.</p> <p>Results</p> <p>All dieting groups exhibited adequate compliance to their prescribed diet regimen as energy and macronutrient amounts and distributions were close to prescribed amounts. Those groups that followed a diet and exercise program reported significantly greater anthropometric (waist circumference and body mass) and body composition via DXA (fat mass and % fat) changes. Caloric restriction initially reduced energy expenditure, but successfully returned to baseline values after 10 weeks of dieting and exercising. Significant fitness improvements (aerobic capacity and maximal strength) occurred in all exercising groups. No significant changes occurred in lipid panel constituents, but serum insulin and HOMA-IR values decreased in the VLCHP group. Significant reductions in serum leptin occurred in all caloric restriction + exercise groups after 14 weeks, which were unchanged in other non-diet/non-exercise groups.</p> <p>Conclusions</p> <p>Overall and over the entire test period, all diet groups which restricted their caloric intake and exercised experienced similar responses to each other. Regular exercise and modest caloric restriction successfully promoted anthropometric and body composition improvements along with various markers of muscular fitness. Significant increases in relative energy expenditure and reductions in circulating leptin were found in response to all exercise and diet groups. Macronutrient distribution may impact circulating levels of insulin and overall ability to improve strength levels in obese women who follow regular exercise.</p