Full Text Journal Articles by
Author Thomas A Clarke


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Which Multi-Heme Protein Complex Transfers Electrons More Efficiently? Comparing MtrCAB from Shewanella with OmcS from Geobacter.

Xiuyun Jiang, Jessica H van Wonderen, Julea N Butt, Marcus J Edwards, Thomas A Clarke, Jochen Blumberger,

Microbial nanowires are fascinating biological structures that allow bacteria to transport electrons over micrometers for reduction of extracellular substrates. It was recently established that the nanowires of both Shewanella and Geobacter are made of multi-heme proteins; but, while Shewanella employs the 20-heme protein complex MtrCAB, Geobacter uses a redox polymer ... Read more >>

J Phys Chem Lett (The journal of physical chemistry letters)
[2020, :9421-9425]

Cited: 0 times

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Uncovering nature's electronics.

Thomas A Clarke, Marcus J Edwards,

Nat. Chem. Biol. (Nature chemical biology)
[2020, 16(10):1041-1042]

Cited: 0 times

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Treatment of hallux valgus by Scarf osteotomy - rates and reasons for recurrence and rates of avascular necrosis: A systematic review.

Thomas A C Clarke, Simon R Platt,

BACKGROUND:We reviewed the rates of and reasons for hallux valgus (HV) recurrence and the rates of avascular necrosis following Scarf osteotomy. METHODS:We searched the Cochrane Library, PubMed, and Embase databases for studies reporting operative management of HV using Scarf osteotomy. The primary endpoints were reasons for and rates of HV ... Read more >>

Foot Ankle Surg (Foot and ankle surgery : official journal of the European Society of Foot and Ankle Surgeons)
[2020, :]

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Whole-cell circular dichroism difference spectroscopy reveals an in vivo-specific deca-heme conformation in bacterial surface cytochromes.

Yoshihide Tokunou, Punthira Chinotaikul, Shingo Hattori, Thomas A Clarke, Liang Shi, Kazuhito Hashimoto, Kazuyuki Ishii, Akihiro Okamoto,

We established whole-cell circular dichroism difference spectroscopy to identify the inter-heme interaction in deca-heme cytochrome protein MtrC in whole cell. Our data showed that the heme alignment of reduced MtrC in whole cell is distinct from that in purified one, suggesting the in vivo specific electron transport kinetics. ... Read more >>

Chem. Commun. (Camb.) (Chemical communications (Cambridge, England))
[2018, 54(99):13933-13936]

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His/Met heme ligation in the PioA outer membrane cytochrome enabling light-driven extracellular electron transfer by Rhodopseudomonas palustris TIE-1.

Dao-Bo Li, Marcus J Edwards, Anthony W Blake, Simone E Newton-Payne, Samuel E H Piper, Leon P Jenner, Katarzyna P Sokol, Erwin Reisner, Jessica H Van Wonderen, Thomas A Clarke, Julea N Butt,

A growing number of bacterial species are known to move electrons across their cell envelopes. Naturally this occurs in support of energy conservation and carbon-fixation. For biotechnology it allows electron exchange between bacteria and electrodes in microbial fuel cells and during microbial electrosynthesis. In this context Rhodopseudomonas palustris TIE-1 is ... Read more >>

Nanotechnology (Nanotechnology)
[2020, 31(35):354002]

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The Crystal Structure of a Biological Insulated Transmembrane Molecular Wire.

Marcus J Edwards, Gaye F White, Julea N Butt, David J Richardson, Thomas A Clarke,

A growing number of bacteria are recognized to conduct electrons across their cell envelope, and yet molecular details of the mechanisms supporting this process remain unknown. Here, we report the atomic structure of an outer membrane spanning protein complex, MtrAB, that is representative of a protein family known to transport ... Read more >>

Cell (Cell)
[2020, 181(3):665-673.e10]

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Role of multiheme cytochromes involved in extracellular anaerobic respiration in bacteria.

Marcus J Edwards, David J Richardson, Catarina M Paquete, Thomas A Clarke,

Heme containing proteins are involved in a broad range of cellular functions, from oxygen sensing and transport to catalyzing oxidoreductive reactions. The two major types of cytochrome (b-type and c-type) only differ in their mechanism of heme attachment, but this has major implications for their cellular roles in both localization ... Read more >>

Protein Sci (Protein science : a publication of the Protein Society)
[2020, 29(4):830-842]

Cited: 1 time

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Ultrafast Light-Driven Electron Transfer in a Ru(II)tris(bipyridine)-Labeled Multiheme Cytochrome.

Jessica H van Wonderen, Christopher R Hall, Xiuyun Jiang, Katrin Adamczyk, Antoine Carof, Ismael Heisler, Samuel E H Piper, Thomas A Clarke, Nicholas J Watmough, Igor V Sazanovich, Michael Towrie, Stephen R Meech, Jochen Blumberger, Julea N Butt,

Multiheme cytochromes attract much attention for their electron transport properties. These proteins conduct electrons across bacterial cell walls and along extracellular filaments and when purified can serve as bionanoelectronic junctions. Thus, it is important and necessary to identify and understand the factors governing electron transfer in this family of proteins. ... Read more >>

J Am Chem Soc (Journal of the American Chemical Society)
[2019, 141(38):15190-15200]

Cited: 2 times

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An electrogenic redox loop in sulfate reduction reveals a likely widespread mechanism of energy conservation.

Américo G Duarte, Teresa Catarino, Gaye F White, Diana Lousa, Sinje Neukirchen, Cláudio M Soares, Filipa L Sousa, Thomas A Clarke, Inês A C Pereira,

The bioenergetics of anaerobic metabolism frequently relies on redox loops performed by membrane complexes with substrate- and quinone-binding sites on opposite sides of the membrane. However, in sulfate respiration (a key process in the biogeochemical sulfur cycle), the substrate- and quinone-binding sites of the QrcABCD complex are periplasmic, and their ... Read more >>

Nat Commun (Nature communications)
[2018, 9(1):5448]

Cited: 1 time

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Photosensitised Multiheme Cytochromes as Light-Driven Molecular Wires and Resistors.

Jessica H van Wonderen, Daobo Li, Samuel E H Piper, Cheuk Y Lau, Leon P Jenner, Christopher R Hall, Thomas A Clarke, Nicholas J Watmough, Julea N Butt,

Multiheme cytochromes possess closely packed redox-active hemes arranged as chains spanning the tertiary structure. Here we describe five variants of a representative multiheme cytochrome engineered as biohybrid phototransducers for converting light into electricity. Each variant possesses a single Cys sulfhydryl group near a terminus of the heme chain, and this ... Read more >>

Chembiochem (Chembiochem : a European journal of chemical biology)
[2018, 19(20):2206-2215]

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Membrane-spanning electron transfer proteins from electrogenic bacteria: Production and investigation.

Colin W J Lockwood, Jessica H van Wonderen, Marcus J Edwards, Samuel E H Piper, Gaye F White, Simone Newton-Payne, David J Richardson, Thomas A Clarke, Julea N Butt,

Certain bacterial species have a natural ability to exchange electrons with extracellular redox partners. This behavior allows coupling of catalytic transformations inside bacteria to complementary redox transformations of catalysts and electrodes outside the cell. Electricity generation can be coupled to waste-water remediation. Industrially relevant oxidation reactions can proceed exclusively when ... Read more >>

Meth. Enzymol. (Methods in enzymology)
[2018, 613:257-275]

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Extracellular reduction of solid electron acceptors by Shewanella oneidensis.

Sebastian Beblawy, Thea Bursac, Catarina Paquete, Ricardo Louro, Thomas A Clarke, Johannes Gescher,

Shewanella oneidensis is the best understood model organism for the study of dissimilatory iron reduction. This review focuses on the current state of our knowledge regarding this extracellular respiratory process and highlights its physiologic, regulatory and biochemical requirements. It seems that we have widely understood how respiratory electrons can reach ... Read more >>

Mol Microbiol (Molecular microbiology)
[2018, 109(5):571-583]

Cited: 6 times

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Electron transfer process in microbial electrochemical technologies: The role of cell-surface exposed conductive proteins.

Nazua L Costa, Thomas A Clarke, Laura-Alina Philipp, Johannes Gescher, Ricardo O Louro, Catarina M Paquete,

Electroactive microorganisms have attracted significant interest for the development of novel biotechnological systems of low ecological footprint. These can be used for the sustainable production of energy, bioremediation of metal-contaminated environments and production of added-value products. Currently, almost 100 microorganisms from the Bacterial and Archaeal domains are considered electroactive, given ... Read more >>

Bioresour. Technol. (Bioresource technology)
[2018, 255:308-317]

Cited: 8 times

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Redox Linked Flavin Sites in Extracellular Decaheme Proteins Involved in Microbe-Mineral Electron Transfer.

Marcus J Edwards, Gaye F White, Michael Norman, Alice Tome-Fernandez, Emma Ainsworth, Liang Shi, Jim K Fredrickson, John M Zachara, Julea N Butt, David J Richardson, Thomas A Clarke,

Extracellular microbe-mineral electron transfer is a major driving force for the oxidation of organic carbon in many subsurface environments. Extracellular multi-heme cytochromes of the Shewenella genus play a major role in this process but the mechanism of electron exchange at the interface between cytochrome and acceptor is widely debated. The ... Read more >>

Sci Rep (Scientific reports)
[2015, 5:11677]

Cited: 36 times

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Identification of furfural resistant strains of Saccharomyces cerevisiae and Saccharomyces paradoxus from a collection of environmental and industrial isolates.

Sarah J Field, Peter Ryden, David Wilson, Stephen A James, Ian N Roberts, David J Richardson, Keith W Waldron, Thomas A Clarke,

BACKGROUND:Fermentation of bioethanol using lignocellulosic biomass as a raw material provides a sustainable alternative to current biofuel production methods by utilising waste food streams as raw material. Before lignocellulose can be fermented, it requires physical, chemical and enzymatic treatment in order to release monosaccharides, a process that causes the chemical ... Read more >>

(Biotechnology for biofuels)
[2015, 8:33]

Cited: 13 times

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A trans-outer membrane porin-cytochrome protein complex for extracellular electron transfer by Geobacter sulfurreducens PCA.

Yimo Liu, Zheming Wang, Juan Liu, Caleb Levar, Marcus J Edwards, Jerome T Babauta, David W Kennedy, Zhi Shi, Haluk Beyenal, Daniel R Bond, Thomas A Clarke, Julea N Butt, David J Richardson, Kevin M Rosso, John M Zachara, James K Fredrickson, Liang Shi,

The multi-heme, outer membrane c-type cytochrome (c-Cyt) OmcB of Geobacter sulfurreducens was previously proposed to mediate electron transfer across the outer membrane. However, the underlying mechanism has remained uncharacterized. In G. sulfurreducens, the omcB gene is part of two tandem four-gene clusters, each is predicted to encode a transcriptional factor (OrfR/OrfS), ... Read more >>

Environ Microbiol Rep (Environmental microbiology reports)
[2014, 6(6):776-785]

Cited: 45 times

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Characterization of MtoD from Sideroxydans lithotrophicus: a cytochrome c electron shuttle used in lithoautotrophic growth.

Christopher R Beckwith, Marcus J Edwards, Matthew Lawes, Liang Shi, Julea N Butt, David J Richardson, Thomas A Clarke,

The autotrophic Sideroxydans lithotrophicus ES-1 can grow by coupling the oxidation of ferrous iron to the reduction of oxygen. Soluble ferrous iron is oxidized at the surface of the cell by an MtoAB porin-cytochrome complex that functions as an electron conduit through the outer membrane. Electrons are then transported to ... Read more >>

(Frontiers in microbiology)
[2015, 6:332]

Cited: 7 times

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Resolution of key roles for the distal pocket histidine in cytochrome C nitrite reductases.

Colin W J Lockwood, Bénédicte Burlat, Myles R Cheesman, Melanie Kern, Jörg Simon, Thomas A Clarke, David J Richardson, Julea N Butt,

Cytochrome c nitrite reductases perform a key step in the biogeochemical N-cycle by catalyzing the six-electron reduction of nitrite to ammonium. These multiheme 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 ... Read more >>

J. Am. Chem. Soc. (Journal of the American Chemical Society)
[2015, 137(8):3059-3068]

Cited: 1 time

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The X-ray crystal structure of Shewanella oneidensis OmcA reveals new insight at the microbe-mineral interface.

Marcus J Edwards, Nanakow A Baiden, Alexander Johs, Stephen J Tomanicek, Liyuan Liang, Liang Shi, Jim K Fredrickson, John M Zachara, Andrew J Gates, Julea N Butt, David J Richardson, Thomas A Clarke,

The X-ray crystal structure of Shewanella oneidensis OmcA, an extracellular decaheme cytochrome involved in mineral reduction, was solved to a resolution of 2.7 Å. The four OmcA molecules in the asymmetric unit are arranged so the minimum distance between heme 5 on adjacent OmcA monomers is 9 Å, indicative of ... Read more >>

FEBS Lett. (FEBS letters)
[2014, 588(10):1886-1890]

Cited: 21 times

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Analysis of structural MtrC models based on homology with the crystal structure of MtrF.

Marcus J Edwards, James K Fredrickson, John M Zachara, David J Richardson, Thomas A Clarke,

The outer-membrane decahaem cytochrome MtrC is part of the transmembrane MtrCAB complex required for mineral respiration by Shewanella oneidensis. MtrC has significant sequence similarity to the paralogous decahaem cytochrome MtrF, which has been structurally solved through X-ray crystallography. This now allows for homology-based models of MtrC to be generated. The ... Read more >>

Biochem. Soc. Trans. (Biochemical Society transactions)
[2012, 40(6):1181-1185]

Cited: 10 times

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Development of a proteoliposome model to probe transmembrane electron-transfer reactions.

Gaye F White, Zhi Shi, Liang Shi, Alice C Dohnalkova, James K Fredrickson, John M Zachara, Julea N Butt, David J Richardson, Thomas A Clarke,

The mineral-respiring bacterium Shewanella oneidensis uses a protein complex, MtrCAB, composed of two decahaem cytochromes brought together inside a transmembrane porin to transport electrons across the outer membrane to a variety of mineral-based electron acceptors. A proteoliposome system has been developed that contains Methyl Viologen as an internalized electron carrier ... Read more >>

Biochem. Soc. Trans. (Biochemical Society transactions)
[2012, 40(6):1257-1260]

Cited: 7 times

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Molecular structure and free energy landscape for electron transport in the decahaem cytochrome MtrF.

Marian Breuer, Piotr Zarzycki, Liang Shi, Thomas A Clarke, Marcus J Edwards, Julea N Butt, David J Richardson, James K Fredrickson, John M Zachara, Jochen Blumberger, Kevin M Rosso,

The free energy profile for electron flow through the bacterial decahaem cytochrome MtrF has been computed using thermodynamic integration and classical molecular dynamics. The extensive calculations on two versions of the structure help to validate the method and results, because differences in the profiles can be related to differences in ... Read more >>

Biochem. Soc. Trans. (Biochemical Society transactions)
[2012, 40(6):1198-1203]

Cited: 10 times

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The impact of copper, nitrate and carbon status on the emission of nitrous oxide by two species of bacteria with biochemically distinct denitrification pathways.

Heather Felgate, Georgios Giannopoulos, Matthew J Sullivan, Andrew J Gates, Thomas A Clarke, Elizabeth Baggs, Gary Rowley, David J Richardson,

Denitrifying bacteria convert nitrate (NO(3) (-) ) to dinitrogen (N(2) ) gas through an anaerobic respiratory process in which the potent greenhouse gas nitrous oxide (N(2) O) is a free intermediate. These bacteria can be grouped into classes ... Read more >>

Environ Microbiol (Environmental microbiology)
[2012, 14(7):1788-1800]

Cited: 23 times

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The crystal structure of the extracellular 11-heme cytochrome UndA reveals a conserved 10-heme motif and defined binding site for soluble iron chelates.

Marcus J Edwards, Andrea Hall, Liang Shi, James K Fredrickson, John M Zachara, Julea N Butt, David J Richardson, Thomas A Clarke,

Members of the genus Shewanella translocate deca- or undeca-heme cytochromes to the external cell surface thus enabling respiration using extracellular minerals and polynuclear Fe(III) chelates. The high resolution structure of the first undeca-heme outer membrane cytochrome, UndA, reveals a crossed heme chain with four potential electron ingress/egress sites arranged within ... Read more >>

Structure (Structure (London, England : 1993))
[2012, 20(7):1275-1284]

Cited: 27 times

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Exploring the biochemistry at the extracellular redox frontier of bacterial mineral Fe(III) respiration.

David J Richardson, Marcus J Edwards, Gaye F White, Nanakow Baiden, Robert S Hartshorne, Jim Fredrickson, Liang Shi, John Zachara, Andrew J Gates, Julea N Butt, Thomas A Clarke,

Many species of the bacterial Shewanella genus are notable for their ability to respire in anoxic environments utilizing insoluble minerals of Fe(III) and Mn(IV) as extracellular electron acceptors. In Shewanella oneidensis, the process is dependent on the decahaem electron-transport proteins that lie at the extracellular face of the outer membrane ... Read more >>

Biochem. Soc. Trans. (Biochemical Society transactions)
[2012, 40(3):493-500]

Cited: 11 times

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