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    Article

    Allen, William J. and Phan, Gilles and Waksman, Gabriel (2012) Pilus biogenesis at the outer membrane of Gram-negative bacterial pathogens. Current Opinion in Structural Biology 22 (4), pp. 500-506. ISSN 0959-440X.

    Ashford, Paul and Moss, David S. and Alex, A. and Yeap, S.K. and Povia, Alice and Nobeli, Irene and Williams, Mark A. (2012) Visualization of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets. BMC Bioinformatics 13 , p. 39. ISSN 1471-2105.

    Bowles, M. and Lally, J. and Fadden, A.J. and Mouilleron, S. and Hammonds, T. and McDonald, Neil Q. (2012) Fluorescence-based incision assay for human XPF-ERCC1 activity identifies important elements of DNA junction recognition. Nucleic Acids Research 40 (13), e101. ISSN 0305-1048.

    Busch, Andreas and Waksman, Gabriel (2012) Chaperone-usher pathways: diversity and pilus assembly mechanism. Philosophical Transactions of the Royal Society B: Biological Sciences 367 (1592), pp. 1112-1122. ISSN 0962-8436.

    Chauviac, Francois-Xavier and Bommer, M. and Yan, Jun and Parkin, G. and Daviter, Tina and Lowden, Philip A.S. and Raven, E. L. and Thalassinos, Konstantinos and Keep, Nicholas H. (2012) Crystal structure of reduced MsAcg a putative nitroreductase from Mycobacterium smegmatis, and a close homologue of Mycobacterium tuberculosis Acg. Journal of Biological Chemistry 287 , pp. 44372-44383. ISSN 0021-9258.

    Clare, Daniel K. and Vasishtan, Daven and Stagg, S. and Quispe, J. and Farr, G.W. and Topf, Maya and Horwich, A.L. and Saibil, Helen R. (2012) ATP-triggered conformational changes delineate substrate-binding and -folding mechanics of the GroEL Chaperonin. Cell 149 (1), pp. 113-123. ISSN 0092-8674.

    Clark, Alice R. and Lubsen, N.H. and Slingsby, Christine (2012) sHSP in the eye lens: crystallin mutations, cataract and proteostasis. The International Journal of Biochemistry & Cell Biology 44 (10), pp. 1687-1697. ISSN 1357-2725.

    Coll, F. and Mallard, K. and Preston, M. and Bentley, S. and Parkhill, J. and McNerney, R. and Martin, Nigel and Clark, T. (2012) SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences. Bioinformatics 28 (22), pp. 2991-2993. ISSN 1367-4803.

    Cordeiro de Amorim, Renato and Mirkin, Boris (2012) Minkowski metric, feature weighting and anomalous cluster initializing in K-Means clustering. Pattern Recognition 45 (3), pp. 1061-1075. ISSN 0031-3203.

    Cozens, C. and Pinheiro, Vitor B. and Vaisman, A. and Woodgate, R. and Holliger, P. (2012) A short adaptive path from DNA to RNA polymerases. Proceedings of the National Academy of Sciences of the United States of America 109 (21), pp. 8067-8072. ISSN 0027-8424.

    Czarnecki, Jan M. and Nobeli, Irene and Smith, Adrian M.L. and Shepherd, Adrian J. (2012) A text-mining system for extracting metabolic reactions from full-text articles. BMC Bioinformatics 13 (172), ISSN 1471-2105.

    Dumoux, Maud and Clare, Daniel K. and Saibil, Helen R. and Hayward, Richard D. (2012) Chlamydiae assemble a pathogen synapse to hijack the host endoplasmic reticulum. Traffic 13 (12), pp. 1612-1617. ISSN 1398-9219.

    Erdmanis, L. and O’Reilly, Andrias O. and Williamson, M.S. and Field, L.M. and Turberg, A. and Wallace, Bonnie A. (2012) Association of Neonicotinoid insensitivity with a conserved residue in the Loop D binding region of the Tick Nicotinic Acetylcholine Receptor. Biochemistry 51 (23), pp. 4627-4629. ISSN 0006-2960.

    Fogl, C. and Puckey, Loretto and Hinssen, U. and Zaleska, M. and el-Mezgueldi, M. and Croasdale, R. and Bowman, A. and Matsukawa, A. and Samani, N.J. and Savva, Renos and Pfuhl, M. (2012) A structural and functional dissection of the cardiac stress response factor MS1. Proteins: Structure, Function, and Bioinformatics 80 (2), pp. 398-409. ISSN 0887-3585.

    Ford, B. and Verger, D. and Dodson, K. and Volkan, E. and Kostakioti, M. and Elam, J. and Pinkner, J. and Waksman, Gabriel and Hultgren, S. (2012) The structure of the PapD-PapGII pilin complex reveals an open and flexible P5 pocket. Journal of Bacteriology 194 (23), pp. 6390-6397. ISSN 0021-9193.

    Gasset, M. and Fra, A.M. and Gooptu, Bibek and Ferrarotti, I. and Miranda, E. and Scabini, R. and Ronzoni, R. and Benini, F. and Corda, L. and Medicina, D. and Luisetti, M. and Schiaffonati, L. (2012) Three new Alpha1-Antitrypsin deficiency variants help to define a C-Terminal region regulating conformational change and polymerization. PLoS One 7 (6), ISSN 1932-6203.

    Gill, J.L. and James, Victoria M. and Carta, E. and Harris, D. and Topf, Maya and Scholes, S.F.E. and Hateley, G. and Harvey, R.J. (2012) Identification of congenital muscular dystonia 2 associated with an inherited GlyT2 defect in Belgian Blue cattle from the United Kingdom. Animal Genetics 43 (3), pp. 267-270. ISSN 0268-9146.

    Gonen, T. and Waksman, Gabriel (2012) Recent progress in membrane protein structures and investigation methods. Current Opinion in Structural Biology 22 (4), pp. 467-468. ISSN 0959-440X.

    Gouge, Jerome and Ralec, C. and Henneke, G. and Delarue, M. (2012) Molecular recognition of canonical and deaminated bases by P. abyssi family B DNA polymerase. Journal of Molecular Biology 423 (3), pp. 315-36. ISSN 0022-2836.

    Goulet, Adeline and Behnke-Parks, W.M. and Sindelar, C.V. and Major, J. and Rosenfeld, S.S. and Moores, Carolyn A. (2012) The structural basis of force generation by the Mitotic motor Kinesin-5. Journal of Biological Chemistry 287 , pp. 44654-44666. ISSN 0021-9258.

    Gupta, Antima and Bhakta, Sanjib (2012) An integrated surrogate model for screening of drugs against Mycobacterium tuberculosis. Journal of Antimicrobial Chemotherapy 67 (6), pp. 1380-1391. ISSN 0305-7453.

    Gupta, Antima and Kaul, Akshay and Tsolaki, A.G. and Kishore, U. and Bhakta, Sanjib (2012) Mycobacterium tuberculosis: immune evasion, latency and reactivation. Immunobiology 217 (3), pp. 363-374. ISSN 0171-2985.

    Guzman, Juan D. and Gupta, Antima and Bucar, F. and Gibbons, S. and Bhakta, Sanjib (2012) Antimycobacterials from natural sources: ancient times, antibiotic era and novel scaffolds. Frontiers in Bioscience 17 (1), pp. 1861-1881. ISSN 1093-9946.

    Janes, R.W. and Miles, Andrew J. and Woollett, Benjamin and Whitmore, Lee and Klose, D. and Wallace, Bonnie A. (2012) Circular Dichroism Spectral Data and Metadata in the Protein Circular Dichroism Data Bank (PCDDB): a tutorial guide to accession and deposition. Chirality 24 (9), pp. 751-763. ISSN 0899-0042.

    Klose, D.P. and Wallace, Bonnie A. and Janes, R.W. (2012) DichroMatch: a website for similarity searching of circular dichroism spectra. Nucleic Acids Research 40 (W1), W547-W552. ISSN 0305-1048.

    Kottakota, S.K. and Benton, M. and Evangelopoulos, Dimitrios and Guzman, Juan D. and Bhakta, Sanjib and McHugh, T.D. and Gray, M. and Groundwater, P.W. and Marrs, E.C.L. and Perry, J.D. and Harburn, J.J. (2012) Versatile routes to marine sponge metabolites through Benzylidene Rhodanines. Organic Letters 14 (24), pp. 6310-6313. ISSN 1523-7060.

    Lander, G.C. and Saibil, Helen R. and Nogales, E. (2012) Go hybrid: EM, crystallography, and beyond. Current Opinion in Structural Biology 22 (5), pp. 627-635. ISSN 0959-440X.

    Liu, J.S. and Schubert, C.R. and Fu, X. and Fourniol, Franck J. and Jaiswal, J.K. and Houdusse, A. and Stultz, C.M. and Moores, Carolyn A. and Walsh, C.A. (2012) Molecular basis for specific regulation of neuronal Kinesin-3 motors by Doublecortin family proteins. Molecular Cell 47 (5), pp. 707-721. ISSN 1097-2765.

    Malet, Hélène and Canellas, F. and Sawa, J. and Yang, J. and Thalassinos, Konstantinos and Ehrmann, M. and Clausen, T. and Saibil, Helen R. (2012) Newly folded substrates inside the molecular cage of the HtrA chaperone DegQ. Nature Structural & Molecular Biology 19 , pp. 152-157. ISSN 1545-9993.

    Maurer, S.P. and Fourniol, Franck J. and Bohner, G. and Moores, Carolyn A. and Surrey, T. (2012) EBs recognize a nucleotide-dependent structural cap at growing microtubule ends. Cell 149 (2), pp. 371-382. ISSN 0092-8674.

    McCusker, Emily C. and Bagneris, Claire and Naylor, Claire E. and Cole, Ambrose R. and d'Avanzo, N. and Nichols, C.G. and Wallace, Bonnie A. (2012) Structure of a bacterial voltage-gated sodium channel pore reveals mechanisms of opening and closing. Nature Communications 3 , ISSN 2041-1723.

    Meier, C. and Brookings, D.C. and Ceska, T.A. and Doyle, C. and Gong, H. and McMillan, D. and Saville, G.P. and Mushtaq, A. and Knight, D. and Reich, S. and Pearl, L.H. and Powell, K.A. and Savva, Renos and Allen, R.A. (2012) Engineering human MEK-1 for structural studies: a case study of combinatorial domain hunting. Journal of Structural Biology 177 (2), pp. 329-334. ISSN 1047-8477.

    Milanesi, Lilia and Sheynis, T. and Xue, W.-F. and Orlova, Elena and Hellewell, A.L. and Jelinek, R. and Hewitt, E.W. and Radford, S.E. and Saibil, Helen R. (2012) Direct three-dimensional visualization of membrane disruption by amyloid fibrils. Proceedings of the National Academy of Sciences of the United States of America 109 (50), pp. 20455-20460. ISSN 0027-8424.

    Mirkin, Boris and Nascimento, S. (2012) Additive spectral method for fuzzy cluster analysis of similarity data including community structure and affinity matrices. Information Sciences 183 (1), pp. 16-34. ISSN 0020-0255.

    Moores, Carolyn A. (2012) Dynein: a force (generation mechanism) to be reckoned with. Structure 20 (10), pp. 1611-1612. ISSN 0969-2126.

    Morrissey, B. and Leney, A.C. and Toste Rego, A. and Phan, G. and Allen, W.J. and Verger, D. and Waksman, Gabriel and Ashcroft, A.E. and Radford, S.E. (2012) The role of chaperone-subunit usher domain interactions in the mechanism of bacterial pilus biogenesis revealed by ESI-MS. Molecular & Cellular Proteomics 11 (7), ISSN 1535-9476.

    Mouilleron, S. and Wiezlak, M. and O’Reilly, N. and Treisman, R. and McDonald, Neil Q. (2012) Structures of the Phactr1 RPEL domain and RPEL motif complexes with G-Actin reveal the molecular basis for Actin Binding Cooperativity. Structure 20 (11), pp. 1960-1970. ISSN 0969-2126.

    Nyon, Mun Peak and Kirkpatrick, J. and Cabrita, L.D. and Christodoulou, John and Gooptu, Bibek (2012) 1H, 15N and 13C backbone resonance assignments of the archetypal serpin α1-antitrypsin. Biomolecular NMR Assignments 6 (2), pp. 153-156. ISSN 1874-2718.

    Nyon, Mun Peak and Segu, Lakshmi and Cabrita, L.D. and Lévy, Géraldine R. and Kirkpatrick, J. and Roussel, B.D. and Patschull, Anathe O.M. and Barrett, Tracey E. and Ekeowa, U.I. and Kerr, R. and Waudby, Christopher A. and Kalsheker, N. and Hill, M. and Thalassinos, Konstantinos and Lomas, D.A. and Christodoulou, John and Gooptu, Bibek (2012) Structural dynamics associated with intermediate formation in an archetypal conformational disease. Structure 20 (3), pp. 504-512. ISSN 0969-2126.

    O’Brien, E.P. and Christodoulou, John and Vendruscolo, M. and Dobson, C.M. (2012) Trigger factor slows co-translational folding through kinetic trapping while sterically protecting the nascent chain from aberrant Cytosolic interactions. Journal of the American Chemical Society 134 (26), pp. 10920-10932. ISSN 0002-7863.

    Pandurangan, Arun and Topf, Maya (2012) Finding rigid bodies in protein structures: application to flexible fitting into cryoEM maps. Journal of Structural Biology 177 (2), pp. 520-531. ISSN 1047-8477.

    Pandurangan, Arun and Topf, Maya (2012) RIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps. Bioinformatics 28 (18), pp. 2391-2393. ISSN 1367-4803.

    Patel, N.A. and Crombie, A. and Slade, S.E. and Thalassinos, Konstantinos and Hughes, C. and Connolly, J.B. and Langridge, J. and Murrell, J.C. and Scrivens, J.H. (2012) Comparison of one- and two-dimensional liquid chromatography approaches in the label-free quantitative analysis of methylocella silvestris. Journal of Proteome Research 11 (9), pp. 4755-4763. ISSN 1535-3893.

    Patschull, Anathe O.M. and Gooptu, Bibek and Ashford, Paul and Daviter, Tina and Nobeli, Irene (2012) In silico assessment of potential druggable pockets on the surface of α1-Antitrypsin conformers. PLoS One 7 (5), ISSN 1932-6203.

    Petukhov, M. and Dagkessamanskaja, A. and Bommer, M. and Barrett, Tracey E. and Tsaneva, I.R. and Yakimov, A. and Quéval, R. and Shvetsov, A. and Khodorkovskiy, M. and Käs, E. and Grigoriev, M. (2012) Large-scale conformational flexibility determines the properties of AAA+ TIP49 ATPases. Structure 20 (8), pp. 1321-1331. ISSN 0969-2126.

    Pinheiro, Vitor B. and Holliger, P. (2012) The XNA world: progress towards replication and evolution of synthetic genetic polymers. Current Opinion in Chemical Biology 16 (3/4), pp. 245-252. ISSN 1367-5931.

    Pinheiro, Vitor B. and Loakes, D. and Holliger, P. (2012) Synthetic polymers and their potential as genetic materials. BioEssays 35 (2), pp. 113-122. ISSN 0265-9247.

    Pinheiro, Vitor B. and Taylor, A.I. and Cozens, C. and Abramov, M. and Renders, M. and Zhang, S. and Chaput, J.C. and Wengel, J. and Peak-Chew, S.-Y. and McLaughlin, S.H. and Herdewijn, P. and Holliger, P. (2012) Synthetic genetic polymers capable of heredity and evolution. Science 336 (6079), pp. 341-344. ISSN 0036-8075.

    Powl, Andrew M. and Miles, Andrew J. and Wallace, Bonnie A. (2012) Transmembrane and extramembrane contributions to membrane protein thermal stability: studies with the NaChBac sodium channel. Biochimica et Biophysica Acta (BBA) - Biomembranes 1818 (3), pp. 889-895. ISSN 0006-3002.

    Prohens, R. and Portell, A. and Puigjaner, C. and Barbas, R. and Alcobé, X. and Font-Bardia, M. and Tomas, Salvador (2012) Cooperative induction in double H-bonding donor/acceptor compounds: chains vs. ribbons. CrystEngComm 18 , pp. 5745-5748.

    Saibil, Helen R. and Seybert, A. and Habermann, A. and Winkler, J. and Eltsov, M. and Perkovic, M. and Castano-Diez, D. and Scheffer, M.P. and Haselmann, U. and Chlanda, P. and Lindquist, S. and Tyedmers, J. and Frangakis, A.S. (2012) Heritable yeast prions have a highly organized three-dimensional architecture with interfiber structures. Proceedings of the National Academy of Sciences of the United States of America 109 (37), pp. 14906-14911. ISSN 0027-8424.

    Sivalingam, G.N. and Shepherd, Adrian J. (2012) An analysis of B-cell epitope discontinuity. Molecular Immunology 51 (3-4), pp. 304-309. ISSN 0161-5890.

    Slingsby, Christine and Clark, Alice R. (2012) Breaking down order to keep cells tidy. Chemistry & Biology 19 (5), pp. 547-548. ISSN 1074-5521.

    Thalassinos, Konstantinos and Vissers, J.P.C. and Tenzer, S. and Levin, Y. and Thompson, J.W. and Daniel, D. and Mann, D. and DeLong, M.R. and Moseley, M.A. and America, A.H. and Ottens, A.K. and Cavey, G.S. and Efstathiou, G. and Scrivens, J.H. and Langridge, J.I. and Geromanos, S.J. (2012) Design and application of a data-independent precursor and product ion repository. Journal of The American Society for Mass Spectrometry 23 (10), pp. 1808-1820. ISSN 1044-0305.

    Toste-Rêgo, Ana and Johnson, J.G. and Geibel, Sebastien and Enguita, F.J. and Clegg, S. and Waksman, Gabriel (2012) Crystal structure of the MrkD1P receptor binding domain of Klebsiella pneumoniae and identification of the human collagen V binding interface. Molecular Microbiology 86 (4), pp. 882-893. ISSN 0950-382X.

    Volkan, E. and Ford, B.A. and Pinkner, J.S. and Dodson, K.W. and Henderson, N.S. and Thanassi, D.G. and Waksman, Gabriel and Hultgren, S.J. (2012) Domain activities of PapC usher reveal the mechanism of action of an Escherichia coli molecular machine. Proceedings of the National Academy of Sciences of the United States of America 109 (24), pp. 9563-9568. ISSN 0027-8424.

    Waksman, Gabriel (2012) Bacterial secretion comes of age. Philosophical Transactions of the Royal Society B: Biological Sciences 367 (1592), pp. 1014-1015. ISSN 0962-8436.

    Walldén, Karin and Williams, Robert and Yan, Jun and Lian, Pei W. and Wang, Luchun and Thalassinos, Konstantinos and Orlova, Elena and Waksman, Gabriel (2012) Structure of the VirB4 ATPase, alone and bound to the core complex of a type IV secretion system. Proceedings of the National Academy of Sciences of the United States of America 109 (28), pp. 11348-11353. ISSN 0027-8424.

    Waudby, Christopher A. and Christodoulou, John (2012) An analysis of NMR sensitivity enhancements obtained using non-uniform weighted sampling, and the application to protein NMR. Journal of Magnetic Resonance 219 , pp. 46-52. ISSN 1090-7807.

    Waudby, Christopher A. and Mantle, M.D. and Cabrita, L.D. and Gladden, L.F. and Dobson, C.M. and Christodoulou, John (2012) Rapid Distinction of Intracellular and Extracellular Proteins Using NMR Diffusion Measurements. Journal of the American Chemical Society 134 (28), pp. 11312-11315. ISSN 0002-7863.

    Webster, Matthew P. and Jukes, R. and Zamfir, V.S. and Kay, Christopher W.M. and Bagneris, Claire and Barrett, Tracey E. (2012) Crystal structure of the UvrB dimer: insights into the nature and functioning of the UvrAB damage engagement and UvrB-DNA complexes. Nucleic Acids Research 40 (17), pp. 8743-8758. ISSN 0305-1048.

    White, Helen E. and Sherman, M.B. and Brasiles, S. and Jacquet, E. and Seavers, P. and Tavares, P. and Orlova, Elena (2012) Capsid structure and its stability at the late stages of bacteriophage SPP1 assembly. Journal of Virology 86 (12), pp. 6768-6777. ISSN 0022-538X.

    Book Section

    Horwich, A.L. and Buchner, J. and Smock, R.G. and Gierasch, L.M. and Saibil, Helen R. (2012) Chaperones and protein folding. In: UNSPECIFIED (ed.) Comprehensive Biophysics. New York, U.S.: Elsevier, pp. 212-237. ISBN 9780080957180.

    Itzhaki, L.S. and Lowe, Alan R. (2012) From artificial antibodies to nanosprings: the biophysical properties of repeat proteins. In: Matthews, Jaqueline M. (ed.) Protein Dimerization and Oligomerization in Biology. Austin, USA: Landes Bioscience, pp. 153-166. ISBN 9781461432289.

    Orlova, Elena (2012) Bacteriophages and their structural organisation. In: Kurtboke, I. (ed.) Bacteriophages. Rijeka, Croatia: InTech, pp. 3-30. ISBN 9789535102724.

    Pinheiro, Vitor B. and Ong, J.L. and Holliger, P. (2012) Polymerase engineering: from PCR and sequencing to synthetic biology. In: Lutz, S. and Bornscheuer, U.T. (eds.) Protein Engineering Handbook. Weinheim: Wiley-VCH. ISBN 9783527331239.

    Wang, J. and Martin, Nigel and Poulovassilis, Alexandra (2012) An ontology-based quality framework for data integration. In: Niedrite, L. and Strazdina, R. and Wangler, B. (eds.) Workshops on Business Informatics Research. Lecture Notes in Business Information Processing 106. Berlin, Germany: Springer Verlag, pp. 196-208. ISBN 9783642292309.

    This list was generated on Mon Oct 18 06:37:38 2021 BST.