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ISMB Member Publications 2011


Dr Jim Anderson [top]


Anderson, J. C., Stepney, G. J., Mills, M. R., Horsfall, L. R., Blake, A. J., Lewis, W. (2011). Enantioselective Conjugate Addition Nitro-Mannich Reactions: Solvent Controlled Synthesis of Acyclic anti- and syn-β-Nitroamines with Three Contiguous Stereocenters. J Org Chem doi:10.1021/jo102408u

Dr Erik Arstad [top]


Smith, G., Zhao, Y., Leyton, J., Shan, B., Nguyen, Q. D., Perumal, M., Turton, D., Årstad, E., Luthra, S. K., Robins, E. G., Aboagye, E. O. (2011). Radiosynthesis and pre-clinical evaluation of [(18)F]fluoro-[1,2-(2)H(4)]choline. Nucl Med Biol 38(1), 39-51

Dr James Baker [top]


In situ maleimide bridging of disulfides and a new approach to protein PEGylation. (2011) Schumacher FF, Nobles M, Ryan CP, Smith ME, Tinker A, Caddick S, Baker JR. Bioconjug Chem.  2011 Feb 16;22(2):132-6.

The design, synthesis and pharmacological characterization of novel β(2) -adrenoceptor antagonists. Hothersall JD, Black J, Caddick S, Vinter JG, Tinker A, Baker JR. Br J Pharmacol. 2011 Feb 16. doi: 10.1111/j.1476-5381.2011.01269.x. [Epub ahead of print]

Dr Tracey Barrett [top]

Bagnéris C, Briggs LC, Savva R, Ebrahimi B, Barrett TE. (2011) Crystal structure of a KSHV-SOX-DNA complex: insights into the molecular mechanisms underlying DNase activity and host shutoff. Nucleic Acids Res. 2011 Mar 17. [Epub ahead of print]

Shimizu A, Baratchian M, Takeuchi Y, Escors D, Macdonald D, Barrett T, Bagneris C, Collins M, Noursadeghi M. J Virol. 'Kaposi's sarcoma-associated herpesvirus vFLIP and human T cell lymphotropic virus type 1 Tax oncogenic proteins activate IkappaB kinase subunit gamma by different mechanisms independent of the physiological cytokine-induced pathways.' (2011) Jul;85(14):7444-8. Epub 2011 May 18.

Bagnéris C, Briggs LC, Savva R, Ebrahimi B, Barrett TE. Nucleic Acids Res. (2011) Jul;39(13):5744-56. Epub 2011 Mar 17. Crystal structure of a KSHV-SOX-DNA complex: insights into the molecular mechanisms underlying DNase activity and host shutoff.

Patschull AO, Segu L, Nyon MP, Lomas DA, Nobeli I, Barrett TE, Gooptu B. 'Therapeutic target-site variability in α1-antitrypsin characterized at high resolution.' Acta Crystallogr Sect F Struct Biol Cryst Commun. (2011) Dec 1;67(Pt 12):1492-7. Epub 2011 Nov 25.

Dr Sanjib Bhakta [top]

Evangelopoulos D, Cronin N, Daviter T, Sim E, Keep NH and Bhakta S* (2011) Characterization of an oxidoreductase from the arylamine N-acetyltransferase operon in Mycobacterium smegmatis. FEBS J. 278(24):4824-32. DOI: 10.1111/j.1742-4658.2011.08382.x

Guzman JD, Wube A, Evangelopoulos D, Gupta A, Hüfner A, Basavannacharya C, Rahman MM, Thomaschitz C, Bauer R, McHugh TD, Nobeli I, Prieto JM, Gibbons S, Bucar F and Bhakta S* (2011) Interaction of N-methyl-2-alkenyl-4-quinolones with ATP-dependent MurE ligase of Mycobacterium tuberculosis: antibacterial activity, molecular docking and inhibition kinetics. J Antimicrob Chemother. 66(8):1766-72. DOI: 10.1093/jac/dkr203

Dr Emmanuel Boucrot [top]

Thiery J., Keefe D., Boulant S., Boucrot E., Walch M., Martinvalet D., Goping I.S., Bleackley R.C., Kirchhausen T. and Lieberman J. (2011) 'Perforin pores in the endosomal membrane trigger release of endocytosed granzyme B to the cytosol of target cells'  Nat Immunol  12(8):770-7

Boucrot E., Howes M.T., Kirchhausen T. and Parton R.G. (2011) ‘Redistribution of caveolae during mitosis’ J Cell Sci  124(Pt 15):1965-72

Dr Kate Bowers [top]


Professor Jeremy Brockes [top]

Kumar A, Delgado JP, Gates PB, Neville G, Forge A, Brockes JP. (2011) 'The aneurogenic limb identifies developmental cell interactions underlying vertebrate limb regeneration.' PNAS (USA) 108, 13588-13593

Shaikh N, Gates PB, Brockes JP. (2011) 'The Meis homeoprotein regulates the axolotl Prod 1 promoter during limb regeneration.' Gene 484, 69-74

Blassberg RA, Garza-Garcia A, Janmohamed A, Gates PB, Brockes JP. (2011) 'Functional convergence of signalling by GPI-anchored and anchorless forms of a salamander protein implicated in limb regeneration.' J Cell Sci 124, 47-56


Professor Steve Caddick [top]

The design, synthesis and pharmacological characterization of novel β(2) -adrenoceptor antagonists. Hothersall JD, Black J, Caddick S, Vinter JG, Tinker A, Baker JR. Br J Pharmacol. 2011 Feb 16. [Epub ahead of print]

Functionalisation of aldehydes via aerobic hydroacylation of azodicarboxylates 'on' water. (2011) Chudasama V, Ahern JM, Dhokia DV, Fitzmaurice RJ, Caddick S. Chem Commun (Camb). 2011 Mar 21;47(11):3269-71.

In situ maleimide bridging of disulfides and a new approach to protein PEGylation. (2011) Schumacher FF, Nobles M, Ryan CP, Smith ME, Tinker A, Caddick S, Baker JR. Bioconjug Chem. 2011 Feb 16;22(2):132-6.

A novel synthesis of (di)-benzazocinones via an endocyclic N-acyliminium ion cyclisation. (2011) King FD, Aliev AE, Caddick S, Tocher DA. Org Biomol Chem. 2011 Mar 7;9(5):1547-54.

New Scenarios of Protein Folding Can Occur on the Ribosome. (2011) O'Brien EP, Christodoulou J, Vendruscolo M, Dobson CM. J Am Chem Soc. 2011 Jan 4. [Epub ahead of print]

Wan, S., Coveney, P. V. (2011). Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs. J R Soc Interface

Professor Richard Catlow [top]


Dr John Christodoulou [top]

New Scenarios of Protein Folding Can Occur on the Ribosome. (2011) O'Brien EP, Christodoulou J, Vendruscolo M, Dobson CM. J Am Chem Soc. 2011 Jan 4. [Epub ahead of print]

Professor Peter Coveney [top]

Wan, S., Coveney, P. V. (2011). Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs. J R Soc Interface

D. Groen, J. Suter, P. V. Coveney, "Modelling Distributed Multiscale Simulation Performance: An Application to Nanocomposites," esciencew, pp.105-111, 2011 IEEE Seventh International Conference on e-Science Workshops, (2011)

D. Groen, S. J. Zasada, P. V. Coveney, "Taxonomy of Multiscale Computing Communities," esciencew, pp.120-127, 2011 IEEE Seventh International Conference on e-Science Workshops, (2011)

D. Wright and P. V. Coveney, "Resolution of Discordant HIV-1 Protease Resistance Rankings Using Molecular Dynamics Simulations", Journal of Chemical Information and Modeling, (2011), 51(10), 2636-49

S. J. Zasada , T. Wang , A. Haidar , E. Liu, B. Graf, G. Clapworthy, S. Manos, P. V. Coveney, "IMENSE: An e-Infrastructure Environment for Patient Specific Multiscale Modelling and Treatment", Journal of Computational Science, (2011)

T. Hewer, M. Nekovee, P. V. Coveney, "Universality of Performance Parameters in Vehicular ad hoc Networks", IEEE Communications Letters, (2011), 15 (9), 947 - 949

C. Sansom, M. Mendes, P. V. Coveney, "Modelling the Virtual Physiological Human", BioTechnologia, (2011) 92 (3), 225-229.

N. Shublaq, S. Zasada, P. V. Coveney, "Exciting Times in Computational Science", Journal of Computational Science, (2011), 2(4), 315, DOI: 10.1016/j.jocs.2011.11.001

P. V Coveney, R. Kenway, R. Perott, D. de Roure, A. Trefethen, D. Groen, N. Shublaq et al., "Strategy for the UK Research Computing Ecosystem", (2011), Available Online. K. Sadiq, B. Konnyu, V. Muller, P. V. Coveney, "Reaction Kinetics of Catalyzed Competitive Heteropolymer Cleavage", The Journal of Physical Chemistry B, (2011), 115 (37), 11017–11027, DOI: 10.1021/jp206321b

J. L. Suter , P. V. Coveney , R. L. Anderson , H. C. Greenwell and S. Cliffe, "Rule based design of clay-swelling inhibitors" Energy Environ. Sci., 2011,4, 4572-4586, DOI: 10.1039/C1EE01280K S. J. Zasada, A. N. Haidar, and P. V. Coveney, "On the Usability of Grid Middleware and Security Mechanisms", Philosophical Transactions of the Royal Society A, (2011), 369, 3413-3428 , DOI: 10.1098/rsta.2011.0131

S. Wan and P. V. Coveney, "Molecular Dynamics Simulation Reveals Structural and Thermodynamic Features of Kinase Activation by Cancer Mutations within the Epidermal Growth Factor Receptor", J. Comput. Chem., (2011), Published Online, DOI: 10.1002/jcc.21866 L. Biferale, P. V. Coveney, S. Ubertini and S. Succi, "Discrete simulation of fluid dynamics: methods", Phil. Trans. R. Soc. A, (2011), 369, 2152-2154, DOI: 10.1098/rsta.2011.0101

B. M. Boghosian, L. M. Fazendeiro, J. Latt, H. Tang and P. V. Coveney, "New variational principles for locating periodic orbits of differential equations", Phil. Trans. R. Soc. A, (2011), 369, 2211-2218, DOI: 10.1098/rsta.2011.0066.

B. M. Boghosian, A. Brown, J. Latt, H. Tang, L. M. Fazendeiro and P. V. Coveney, "Unstable periodic orbits in the Lorenz attractor", Phil. Trans. R. Soc. A, (2011), 369, 2345-2353, DOI: 10.1098/rsta.2011.0067.

P. V. Coveney, V. Diaz, P. Hunter, P. Kohl, and M. Viceconti, "The Virtual Physiological Human" Interface Focus June 6, (2011) 1:281-285; published online before print March 31, 2011, DOI: 10.1098/rsfs.2011.0020.

K. Marias, D. Dionysiou, V. Sakkalis, N. Graf, R. M. Bohle, P. V. Coveney, S. Wan, A. Folarin, P. Büchler, M. Reyes, G. Clapworthy, E. Liu, J. Sabczynski, T. Bily, A. Roniotis, M. Tsiknakis, E. Kolokotroni, S. Giatili, C. Veith, E. Messe, H. Stenzhorn, Yoo-Jin Kim, S. Zasada, A. N. Haidar, C. May, S. Bauer, T. Wang, Y. Zhao, M. Karasek, R. Grewer, A. Franz, and G. Stamatakos, "Clinically driven design of multi-scale cancer models: the ContraCancrum project paradigm", Interface Focus June 6, 2011 1:450-461; published online before print March 30, (2011), DOI:10.1098/rsfs.2010.0037.

A. N. Haidar, S. J. Zasada, P. V. Coveney, A. E. Abdallah, B. Beckles, and M. A. S. Jones, "Audited credential delegation: a usable security solution for the virtual physiological human toolkit", Interface Focus June 6, 2011 1:462-473; published online before print March 30, (2011), DOI: 10.1098/rsfs.2010.0026.

S. Wan, P. V. Coveney, "Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs", J. R. Soc. Interface, 8, 1114-1127, (2011)

Dr Martin Crompton [top]



Prof Chris Danpure [top]



Dr Snezana Djordjevic [top]

Tsai ML, Cronin N, Djordjevic S. (2011) The structure of human leucine carboxyl methyltransferase 1 that regulates protein phosphatase PP2A. Acta Crystallogr D Biol Crystallogr. 2011 Jan;67(Pt 1):14-24.

Dr Paul Driscoll [top]


Professor Jasminka Godovac-Zimmerman [top]

Radulovic, M., Godovac-zimmermann, J. (2011). Proteomic approaches to understanding the role of the cytoskeleton in host-defense mechanisms. Expert Rev Proteomics. 2011 Feb;8(1):117-26.

Dr Bibek Gooptu [top]

1H, 15N and 13C backbone resonance assignments of the archetypal serpin α1-antitrypsin MP Nyon, J Kirkpatrick, LD Cabrita, J Christodoulou, B Gooptu (2011) Biomolecular NMR Assignments, Epub ahead of print

Therapeutic target site variability in α1-antitrypsin characterized at high resolution AOM Patschull, L Segu, MP Nyon, DA Lomas, I Nobeli, TE Barrett, B Gooptu (2011)

Acta Crystallographica F, 67:1492-1497

The structural biology of α1-antitrypsin and the serpinopathies B Gooptu and DA Lomas

in “Methods in Protein Biochemistry” (2011)

Edited by Prof Harald Tschesche, De Gruyter, Berlin, New York

The serpinopathies: Studying serpin polymerisation in vivo

JA Irving, UI Ekeowa, D Belorgey, I Haq, B Gooptu, E Miranda, J Pérez, BD Roussel, A Ordóñez, LE Dalton, SE Thomas, SJ Marciniak, H Parfrey, ER Chilvers, JH Teckman, S Alam, R Mahadeva, ST Rashid, L Vallier, DA Lomas (2011)

Methods in Enzymology, 501:421-66

Targeting serpins in high-throughput and structure-based drug design YP Chang, R Mahadeva, AOM Patschull, I Nobeli, AR McKay, K Thalassinos, JA Irving, I Haq, MP Nyon, J Christodoulou, UI Ekeowa, A Ordóñez, E Miranda, B Gooptu (2011)

Methods in Enzymology, 501:139-75


Dr Ivan Gout [top]


Dr Helen Hailes [top]

Goodworth, K. J., Hervé, A., Stavropoulos, E., Hervé, G., Casades, I., Hill, A. M., Weingarten, G. G., Tascon, R. E., Colston, M. J., Hailes, H. C. (2011). Synthesis and in vivo biological activity of large-ringed calixarenes against Mycobacterium tuberculosis. Tetrahedron 67(2), 373-382

Pesnot, T., Gershater, M. C., Ward, J. M., Hailes, H. C. (2011). Phosphate mediated biomimetic synthesis of tetrahydroisoquinoline alkaloids. Chem Commun (Camb) 47(11), 3242-3244.

Tagalakis, A. D., Grosse, S. M., Meng, Q. H., Mustapa, M. F., Kwok, A., Salehi, S. E., Tabor, A. B., Hailes, H. C., Hart, S. L. (2011). Integrin-targeted nanocomplexes for tumour specific delivery and therapy by systemic administration. Biomaterials 32(5), 1370-1376


L. Kudsiova, J. Ho, B. Fridrich, R. Harvey, M. Keppler, T. Ng, S. L. Hart, A. B. Tabor, H. C. Hailes, M. J. Lawrence, “Lipid Chain Geometry of C14 Glycerol-based Lipids: Effect on Lipoplex Structure and Transfection” Mol. BioSyst., 2011, 7, 422–436.

G. J. Lye, P. A. Dalby, F. Baganz, J. M. Ward, H. C. Hailes, “Biocatalysis is the future- the future is now!, The Chemical Engineer, 2011, 839, 36–38.

V. G. H. Lafitte, A. E. Aliev, E. Greco, K. Bala, P. Golding, H. C. Hailes, “Quadruple Hydrogen Bonded Cytosine Modules: N-1 Functionalised Arrays, New J. Chem., 2011, 35, 1522–1527.

L. Kudsiova, B. Fridrich, J. Ho, M. F. M. Mustapa, F. Campbell, K. Welser, D. Barlow, M. Keppler, T. Ng, D. Barlow, A. B. Tabor, H. C. Hailes, M. J. Lawrence, "Lipopolyplex Ternary Delivery Systems Incorporating C14 Glycerol-Based Lipids", Mol. Pharm., 2011, 8, 1831–1847.

L. Rios-Solis, M. Halim, A. Cázares, P. Morris, J. M. Ward, H. C. Hailes, P. A. Dalby, F. Baganz, G. J. Lye, “A toolbox approach for the rapid evaluation of multi-step enzymatic synthesis comprising a ‘mix and match’ E. coli expression system with microscale experimentation”, Biocatalysis and Biotransformation, 2011, 29, 192–203.

M. D. I. Manunta, R. J. McAnulty, A. D. Tagalakis, S. E. Bottoms, F. Campbell, H. C. Hailes, A. B. Tabor, G. J. Laurent, C. O’Callaghan, S. L. Hart, “Nebulisation of Receptor-Targeted Nanocomplexes for Gene Delivery to the Airway Epithelium”, PLoS ONE, 2011, 6, e26768.


Dr Flemming Hansen [top]

Guillaume Bouvignies, Pramodh Vallurupalli, Matthew H Cordes, D. Flemming Hansen, Lewis E. Kay “Measuring 1HN temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy.” J. Biomol. NMR. 50 p. 13-18 (2011).

D. Flemming Hansen, Lewis E. Kay “Determining valine side-chain rotamer conformations in proteins from methyl 13C chemical shifts: application to the 360 kDa half-proteasome.” J. Am. Chem. Soc. 133 p. 8272-8281 (2011).

Guillaume Bouvignies, Pramodh Vallurupalli, D. Flemming Hansen, Bruno E. Correia, Oliver Lange, Alaji Bah, Robert Vernon, Frederick W. Dahlquist, David Baker, Lewis E. Kay “Solution structure of a minor and transiently formed state of a T4 lysozyme mutant.” Nature. 477 p. 111-114 (2011).
Professor Elizabeth Hounsell [top]


Dr Richard Hayward [top]


Brinkworth AJ, Malcolm DS, Pedrosa AT, Roguska K, Shahbazian S, Graham JE, Hayward RD, Carabeo RA (2011)
Chlamydia trachomatis Slc1 is a type III secretion chaperone that enhances the translocation of its invasion effector substrate TARP. Molecular Microbiology 82: 131-144


Dr Stefan Howorka [top]

Nguyen, G., Howorka, S., Siwy, Z. S. (2011). DNA strands attached inside single conical nanopores: ionic pore characteristics and insight into DNA biophysics. J Membr Biol 239(1-2), 105-113

Leitner, M., N. Mitchell, M. Kastner, R. Schlapak, H. J. Gruber, P. Hinterdorfer, S. Howorka, A. Ebner (2011) Single-Molecule AFM Characterization of Individual Chemically Tagged DNA Tetrahedra, ACS Nano, 5(9):7048-54

Pavkov-Keller, T., S. Howorka, W. Keller, (2011) “The Structure of Bacterial S-Layer Proteins”,  In: “Molecular Assembly in Natural and Engineered Systems”, Series title: Progress in Molecular Biology and Translational Science, Academic Press, Editor: S. Howorka

S. Howorka (2011) Rationally engineering natural protein assemblies in nanobiotechnology. Curr. Opin. Biotechnol., 22: 485-491

M., C. Rankl, A. Ebner, P. D. Pollheimer, S. Howorka, H. J. Gruber, D. Blaas, P. Hinterdorfer (2011) Nanoimaging, Molecular Interaction, and Nanotemplating of Human Rhinovirus Nanopores: Kastner, In: Scanning Probe Microscopy in Nanoscience and Nanotechnology, Vol.2., Editor, B. Bhushan, Springer-Verlag, Heidelberg

Nguyen, G., S. Howorka, Z. S. Siwy (2011) DNA Strands Attached inside Single Conical Nanopores: Ionic Pore Characteristics and Insight into DNA Biophysics J. Membr. Biol., 239(1-2):105-13

Professor David Jones [top]

Nan R, Farabella I, Schumacher FF, Miller A, Gor J, Martin AC, Jones DT, Lengyel I, Perkins SJ.(2011) Zinc Binding to the Tyr402 and His402 Allotypes of Complement Factor H: Possible Implications for Age-Related Macular Degeneration. J Mol Biol. 2011 Mar 16.

Lise S, Buchan D, Pontil M, Jones DT. (2011) Predictions of hot spot residues at protein-protein interfaces using support vector machines. PLoS One. 2011 Feb 28;6(2):e16774.

Nugent T, Ward S, Jones DT (2011) The MEMPACK alpha-helical transmembrane protein structure prediction server. Bioinformatics. 2011 Feb 23.

Nan, R., Farabella, I., Schumacher, F.F., Miller, A., Gor, J., Martin. A.C., Jones, D.T., Lengyel, I. & Perkins, S.J. (2011) Zinc binding to the Tyr402 and His402 allotypes of complement factor H: possible implications for age-related macular degeneration. J. Mol. Biol. 408, 714-735.

Cuff, A.L., Sillitoe, I., Lewis, T., Clegg, A.B., Rentzsch, R,, Furnham, N., Pellegrini-Calace, M., Jones, D., Thornton, J. & Orengo, C.A. (2011) Extending CATH: increasing coverage of the protein structure universe and linking structure with function. Nucl. Acids Res. 39, D420-D426.

Dr Christopher Kay [top]

Naik,A.J.T., Ismail,S., Kay,C.W.M., Wilson,M., Parkin, I.P. (2011) 'Antimicrobial activity of polyurethane embedded with methylene blue, toluidene blue and gold nanoparticles against Staphylococcus aureus; illuminated with white light. Materials Chemistry and Physics' 129, 446-450.

Phan,G., Remaut,H., Wang,T., Allen, W., Pirker,K.F., Lebedev,A., Henderson,N., Geibel,S., Volkan,E., Yan,J., Kunze,M.B.A., Pinkner,J., Ford,B., Kay,C.W.M., Li, H., Hultgren, S., Thanassi,D., Waksman,G. (2011) 'Crystal structure of the FimD usher bound to its cognate FimC:FimH substrate.' Nature 474, 47-53.

Dr Nick Keep [top]

Clark AR, Naylor CE, Bagneris, C., Keep NH  & Slingsby, C.  (2011) Crystal Structure of R120G Disease Mutant of Human alpha B-Crystallin Domain Dimer Shows Closure of a Groove. J.Mol. Biol. 408, 118-134

Evangelopoulos,  D., Cronin, N., Daviter, T., Sim, E., Keep, N.H., Bhakta, S. (2011) Characterization of an oxidoreductase from the arylamine N-acetyltransferase operon in Mycobacterium smegmatis. FEBS J.   278 , 4824-32

Dr Philip Lowden [top]

Taylor, D.M., Balabadra, U., Xiang, Z., Woodman, B., Meade, S., Amore, A., Maxwell, M.M., Reeves, S., Bates, G.P., Luthi-Carter, R., Lowden, P.A.S., Kazantsev, A.G. (2011)

A Brain-Permeable Small Molecule Reduces Neuronal Cholesterol by Inhibiting Activity of Sirtuin 2 Deacetylase Taylor, D.M., Balabadra, U., Xiang, Z., Woodman, B., Meade, S., Amore, A., Maxwell, M.M., Reeves, S., Bates, G.P., Luthi-Carter, R., Lowden, P.A.S., Kazantsev, A.G. ACS Chemical Biology 2011, Vol. 6, Iss. 6, Pages 540-546.
DOI: 10.1021/cb100376q
 

Dr Derek MacMillan [top]

Richardson JP, Macmillan D. (2011) Semi-synthesis of glycoproteins from E. coli through native chemical ligation. Methods Mol Biol. 2011;705:151-74.

Professor Charles Marson [top]


Dr Andrew Martin [top]

Nan R, Farabella I, Schumacher FF, Miller A, Gor J, Martin AC, Jones DT, Lengyel I, Perkins SJ. (2011) Zinc Binding to the Tyr402 and His402 Allotypes of Complement Factor H: Possible Implications for Age-Related Macular Degeneration. J Mol Biol. 2011 Mar 16. [Epub ahead of print]

Martin AC, Besag FM, Berry DJ, Besag FP. (2011) The effect of lamotrigine on valproic acid concentrations. Curr Drug Saf. 2011 Feb 1;6(1):23-9.

Izarzugaza, J.M.G., Hopcroft, L.E.M., Baresic, A., Orengo, C.A., Martin, A.C.R. and Valencia, A. (2011) Characterizing Pathogenic Germline Deviations in Human Protein Kinases. BMC Bioinformatics (special issue - Proceedings of the European Conference on Computational Biology (ECCB) 2010 Workshop: Annotation, interpretation and management of mutation (AIMM)) 12 Suppl.4, S1.

Baresic, A. and Martin, A.C.R. (2011) Compensated Pathogenic Mutations, Biomolecular Concepts 2,281-292. DOI: 10.1515/BMC.2011.025

Henderson, B. and Martin, A.C.R. (2011) Bacterial Virulence in the Moonlight: Multitasking Bacterial Moonlighting Proteins are Virulence
Determinants in Infectious Disease, Infection and Immunity, 79, 3476-91. DOI:10.1128/IAI.00179-11

Henderson, B. and Martin, A.C.R. (2011) Bacterial Moonlighting Proteins and Bacterial Virulence, Current Topics in Microbiology and Immunology, [EPub ahead of print]

Dr Nigel Martin [top]


Dr Neil McDonald [top]

Boeda B, Knowles PP, Briggs D, Murray-Rust J, Soriano E, Garvalov BK, McDonald NQ, Way M.(2011) Molecular recognition of the Tes LIM2-3 domains by the actin-related protein Arp7A. J Biol Chem. 2011 Jan 29. [Epub ahead of print]

Dr Adam MacKay [top]



Professor Boris Mirkin [top]


Dr Carolyn Moores [top]

Behnke-Parks, W.M. Vendomme, J., Honig, B., Maliga, Z., Moores, C., and Rosenfeld, S.S. (2011) Loop L5 acts as a conformational latch in the mitotic kinesin Eg5. J. Biol. Chem. 286, 5242-5253.


Fourniol F. and Moores C.A. (2011). “Snapshots of kinesin motors on microtubule tracks” in “Single Molecule Enzymology: Methods and Protocols”. 778, 57-70.


Professor David Moss [top]

Structure of the food-poisoning Clostridium perfringens enterotoxin reveals similarity to the aerolysin-like pore-forming toxins. Briggs D C, Naylor C E, Smedley, J G III, Lukoyanova N, Robertson S, Moss D S, McClane B A and Basak A K, Journal of Molecular Biology, (2011) 413, 138-149. doi:10.1016/j.jmb.2011.07.066

Analysis of antigenically important residues in human influenza A virus in terms of B-cell epitopes. Lees W D, Moss D S and Shepherd A J, Journal of Virology, (2011), 85, 8548-8555. doi:10.1128/JVI.00579-11

Dr Sylvia Nagl [top]


Dr Irilenia Nobeli [top]

Favia, AD, Bottegoni, G, Nobeli, I, Bisignano, P, Cavalli, A (2011). 'SERAPhiC: a Benchmark for in Silico Fragment-Based Drug Design.' J. Chem. Inf. Model. 51, 2882-2896.

Patschull, AOM, Segu, L, Nyon, MP, Lomas, DA, Nobeli, I, Barrett, TE, Gooptu, B (2011). '1.8 Ang X-ray crystallographic structure of alpha1-antitrypsin characterizes variable features of an important site for allosteric drug design.' Acta Cryst. F67, 1492-1497.

Chang, Y-P, Mahadeva, R, Patschull, AO, Nobeli, I, Ekeowa, UI, McKay AR, Thalassinos, K, Irving, JA, Haq, I, Nyon, MP, Christodoulou, J, Ordonez, A, Miranda, E, Gooptu, E (2011). 'Targeting serpins in high-throughput and structure-based drug design.' Methods in Enzymology, 501, 139-175.

Guzman, J.D., Wube, A., Evangelopoulos, D., Gupta, A., Hufner, A., Basavannacharrya, C., Rahman, Md M., Thomaschitz, C., Bauer, R., McHugh, T.D., Nobeli, I., Prieto, J.M., Gibbons, S., Bucar, F., Bhakta, S. (2011). 'Interaction of N-methyl-2-alkenyl-4-quinolones with ATP-dependent MurE ligase of Mycobacterium tuberculosis: antibacterial activity, molecular docking and inhibition kinetics.' J. Antimicrob. Chemother., 66, 1766-1772
.

Professor Christine Orengo [top]


Cuff A.L, Sillitoe I, Lewis T, Clegg AB, Rentzsch R, Furnham N, Pellegrini-Calace M, Jones D, Thornton J, Orengo CA. (2011) Extending CATH: increasing coverage of the protein structure universe and linking structure with function. Nucleic Acids Res. 39:D420-6.

Yu C, Sonnen AF, George R, Dessailly BH, Stagg L.J, Evans E.J, Orengo C.A, Stuart DI, Ladbury JE, Ikemizu S, Gilbert RJ, Davis SJ. (2011) Rigid-body ligand recognition drives cytotoxic T-lymphocyte antigen 4 (CTLA-4) receptor triggering. J Biol Chem. 286(8):6685-96.

Lee D, de Beer T.A, Laskowski RA, Thornton JM, Orengo CA. (2011) 1,000 structures and more from the MCSG. BMC Struct Biol. 11:2.

Lees JG, Heriche JK, Morilla I, Ranea JA, Orengo CA. (2011) Systematic computational prediction of protein interaction networks. Phys Biol. 8:035008.

Yeats C, Lees J, Carter P,  Sillitoe I, Orengo C. (2011) The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences. Nucleic Acids Res. 39:W546-50.

Dawes J.M, Calvo M, Perkins J.R, Paterson K.J, Kiesewetter H, Hobbs C, Kaan T.K, Orengo C, Bennett D.L, McMahon S.B. (2011) CXCL5 mediates UVB irradiation-induced pain. Sci Transl Med. 3(90):90ra60.

Izarzugaza JM, Hopcroft L.E, Baresic A, Orengo C.A, Martin A.C, Valencia A. (2011) Characterization of pathogenic germline mutations in human protein kinases. BMC Bioinformatics.12 Suppl 4:S1

Dr Elena Orlova [top]

R. Aramayo, M. B. Sherman, K. Brownless, A. L. Okorokov and E. V. Orlova. Quaternary structure of the specific p53-DNA complex reveals the mechanism of p53 mutant dominance. (2011)  NAR, 39 (20), 8960-8971

Dr Andrew Osborne [top]


Professor Steve Perkins [top]

Nan, R., Farabella, I., Schumacher, F., Miller, A., Gor, J., Martin, A.C.R., Jones, D.T., Lengyel, I. & Perkins, S. J. (2011). Localisation of the major zinc-binding site of complement Factor H to the SCR-6/8 domains: possible implications for age-related macular degeneration. J. Mol. Biol. 408, 714-735.

Perkins, S. J., Nan, R., Li, K., Khan, S. & Abe, Y. (2011). Analytical ultracentrifugation combined with X-ray and neutron scattering: experiment and modeling. Modern Analytical Ultracentrifugation Methods (Eds. Schuck, P. & Zhao, J.), Methods, 54, 181-199.

Khan, S., Rodriguez, E., Patel, R., Gor, J., Mulloy, B. & Perkins, S. J. (2011). The solution structure of heparan sulphate differs from that of heparin: implications for function. J. Biol. Chem. 286, 24842-24854.


Dr Saul Purton [top]


Professor Peter Rich [top]

Rich, P.R (2011) Editorial for Special Section: Peter Mitchell - 50th anniversary of the chemiosmotic theory, Biochim. Biophys. Acta Bioenergetics, 1807, 1505-1506.

Maréchal, A. and Rich, P.R. (2011) Water molecule reorganization in cytochrome c oxidase revealed by FTIR spectroscopy, Proc. Natl. Acad. Sci. USA, 108, 8634-8638.

Professor David Saggerson [top]


Professor Helen Saibil [top]

Freir D, Nicoll A, Kluybin I, Panico S, McDonald J, Risse E, Asante E, Farrow M, Clarke A, Saibil H, Sessions R, Rowan M, Walsh D, Collinge J (2011) Interaction between prion protein and toxic amyloid β assemblies can be therapeutically targeted at multiple sites. Nature Commun 2, 336.

Book chapter: Horwich & Saibil, in Frank, J, Ed. (2011) Molecular machines in biology: Workshop of the cell. Cambridge University Press. ISBN-10: 0521194288 | ISBN-13: 978-0521194280

Orlova EV, Saibil HR. (2011) Structural Analysis of Macromolecular Assemblies by Electron Microscopy. Chem. Rev. 111, 7710-7748.

Dr Joanne Santini [top]

Lett MC, Muller D, Lièvremont D, Silver S, Santini JM. (2011). Unified nomenclature for genes involved in prokaryotic aerobic arsenite oxidation.  J. Bacteriol.(4) [Epub ahead of print]


Dr Renos Savva [top]

Maclagan K., Tommasi R., Laurine E., Prodromou C., Driscoll P.C., Pearl L.H., Reich S., Savva R. (2011). A combinatorial method to enable detailed investigation of protein-protein interactions. Future Med. Chem., 3, 271-282.

Fogl C, Puckey L, Hinssen U, Zaleska M, El-Mezgueldi M, Croasdale R, Bowman A, Matsukawa A, Samani NJ, Savva R, Pfuhl M. (2011). A structural and functional dissection of the cardiac stress response factor MS1. Proteins, 19: 398-409 doi: 10.1002/prot.23201

Bagnéris C, Briggs LC, Savva R, Ebrahimi B, Barrett TE. (2011). Crystal structure of a KSHV–SOX–DNA complex: insights into the molecular mechanisms underlying DNase activity and host shutoff. Nucleic Acids Res, 39: 5744–5756. doi: 10.1093/nar/gkr111

Dr David Selwood [top]


Professor Elizabeth Shephard [top]

Cain A, Shephard E. Enhanced engagement in the undergraduate laboratory practical experience (HEA). Bolsover SR, Shephard EA, White HA, Hyams JS (2011). Cell Biology: a short course 3e.

Phillips IR, Shephard EA. Trimethylaminuria in: GeneReviews at GeneTests: Medical Genetics Information Resource [database online www.ncbi.nlm.nih.gov/books/NBK1103/]. Copyright University of Washington, Seattle.

Dr Adrian Shepherd [top]

Lees, W.D., Moss, D.S., Shepherd, A.J. (2011). Analysis of antigenically important residues in human influenza A in terms of B-cell epitopes. Journal of Virology 85: 8548-8555

Nan, R., Farabella, I., Schumacher, F., Miller, A., Gor, J., Martin, A.C.R., Jones, D.T., Lengyel, I. & Perkins, S. J. (2011). Localisation of the major zinc-binding site of complement Factor H to the SCR-6/8 domains: possible implications for age-related macular degeneration. J. Mol. Biol. 408, 714-735.  Pubmed 21396937.

Perkins, S. J., Nan, R., Li, K., Khan, S. & Abe, Y. (2011). Analytical ultracentrifugation combined with X-ray and neutron scattering: experiment and modeling. Modern Analytical Ultracentrifugation Methods (Eds. Schuck, P. & Zhao, J.), Methods, 54, 181-199. Pubmed 21256219.

Khan, S., Rodriguez, E., Patel, R., Gor, J., Mulloy, B. & Perkins, S. J. (2011). The solution structure of heparan sulphate differs from that of heparin: implications for function. J. Biol. Chem. 286, 24842-24854.  Pubmed 21576246.

Dr Christine Slingsby [top]

Crystal Structure of R120G Disease Mutant of Human alphaB-Crystallin Domain Dimer Shows Closure of a Groove. Clark, A.R., Naylor, C.E., Bagnéris, C., Keep, N.H. and Slingsby, C. (2011) J. Mol. Biol. 408:118-134. DOI: 10.1016/j.jmb.2011.02.020

Dr Alona Sosinsky [top]


Prof Kaila Srai [top]


Dr Alethea Tabor [top]

Tagalakis, A. D., Grosse, S. M., Meng, Q. H., Mustapa, M. F., Kwok, A., Salehi, S. E., Tabor, A. B., Hailes, H. C., Hart, S. L. Integrin-targeted nanocomplexes for tumour specific delivery and therapy by systemic administration (2011). Biomaterials 32(5), 1370-1376. 

Kudsiova, L., Ho, J., Fridrich, B., Harvey, R., Keppler, M., Ng, T., Hart, S. L., Tabor, A. B., Hailes, H. C., Lawrence, M. J. Lipopolyplex Ternary Delivery Systems Incorporating C14 Glycerol-Based Lipids (2011). Mol Biosyst 7(2), 422-436.  

Kudsiova, L., Fridrich, B., Ho, J., Mustapa, M. F., Campbell, F., Welser, K., Keppler, M., Ng, T., Barlow, D. J., Tabor, A. B., Hailes, H. C., Lawrence, M. J. (2011).   Mol Pharm 8(5), 1831-1847.

Tabor, A. B.  The challenge of the lantibiotics: synthetic approaches to thioether-bridged peptides (2011) Org Biomol Chem 9(22), 7606-7628. 
Mothia, B., Appleyard, A. N., Wadman, S., Tabor, A. B. Synthesis of Peptides Containing Overlapping Lanthionine Bridges on the Solid Phase: An Analogue of Rings D and E of the Lantibiotic Nisin (2011)  Org Lett 13(16), 4216-4219.  

Manunta, M. D., McAnulty, R. J., Tagalakis, A. D., Bottoms, S. E., Campbell, F., Hailes, H. C., Tabor, A. B., Laurent, G. J., O'Callaghan, C., Hart, S. L. Nebulisation of Receptor-Targeted Nanocomplexes for Gene Delivery to the Airway Epithelium (2011) PLoS One 6(10), e26768-

Tulone, C., Sponaas, A. M., Raiber, E. A., Tabor, A. B., Langhorne, J., Chain, B. M. Differential Requirement for Cathepsin D for Processing of the Full Length and C-Terminal Fragment of the Malaria Antigen MSP1 (2011).   PLoS One 6(10), e24886-  


Dr Konstantinos Thalassinos [top]

Chang, Y.P., Mahadeva, R., Patschull, A.O.M. Nobeli, I., Ekeowa, U.I., McKay, A.R., Thalassinos, K., Irving, J.A., Haq, I., Nyon, M.P., Christodoulou, J., Ordóñez, A., Miranda, E. and Gooptu. B. Targeting Serpins in High-Throughput and Structure-Based Drug Design (Chapter 8) Methods in Enzymology (2011) 501:139–175.

Harvey, D.J., Sobott, F., Crispin, M., Wrobel, A., Bonomelli, C., Vasiljevic, S., Scanlan, C.N., Scarff, C.A., Thalassinos, K. and Scrivens J.H. Ion Mobility Mass Spectrometry for Extracting Spectra of N-Glycans Directly from Incubation Mixtures Following Glycan Release: Application to Glycans from Engineered Glycoforms of Intact, Folded HIV gp120 Journal of the American Society for Mass Spectrometry (2011) 22:568-581.

Dr Geraint Thomas [top]



Dr Katherine Thompson [top]

Evidence for a non-base stacking effect for the environment sensitive fluorescent base pyrrolocytosine ⎯ comparison with 2-aminopurine Samantha J. O. Hardman, Stanley W. Botchway and Katherine C. Thompson,* Photochemistry and Photobiology, 84(6), 1473−1479, 2008 DOI: 10.1111/j.1751-1097.2008.00368.x

Dr Salvador Tomas [top]

Cooperativity in Solid-State SquaramideJournal: Authors (corresponding author(s) noted with an asterisk (*)): R. Prohens*, A.  Portell, C.  Puigjaner*, R. Barbas, S. Tomas*, X. Alcobe, M. Font-Bardia, K.  Harris*  Journal: Crystal Growth & Design 2011, 11, 3725-3730, DOI: 10.1021/cg200772e

Versatile low-molecular-weight hydrogelators: achieving multiresponsiveness through a modular design. Authors (corresponding author(s) noted with an asterisk (*)):L. Milanesi*, C. A. Hunter, N. Tzokova, J. P. Waltho, S. Tomas*, Chemistry, a European Journal 2011, 17, 9753-9761  DOI: 10.1002/chem.201100640


Dr Maya Topf [top]

Vasishtan D, Topf M. Scoring functions for cryoEM density fitting. (2011) J Struct Biol 174:333-343. doi:10.1016/j.jsb.2011.01.012

Gill JL, James VM, Carta E, Harris D, Topf M, Scholes SFE, Hateley G, Harvey RJ. (2011)  Identification of congenital muscular dystonia 2 associated with an inherited GlyT2 defect in Belgian Blue cattle from the United Kingdom. Animal Genetics 43(3):267-70.

Yuan S, Yu X, Topf M, Dorstyn L, Kumar S, Ludtke SJ, Akey CW. (2011). Structure of the Drosophila apoptosome at 6.9 Å resolution. Structure 19:128-140.

James VM, Gill JL, Topf M, Harvey RJ. (2011) Molecular mechanisms of glycine transporter GlyT2 mutations in startle disease. Biol Chem 393:283–289.

Beck M, Topf M, Frazier Z, Tjong H, Xu M, Zhang S, Alber F. (2011) Exploring the spatial and temporal organization of a cell’s proteome. J Struct Biol  173:483-96.


Dr Andrea Townsend-Nicholson [top]


Dr Irina Tsaneva [top]


Dr Cara Vaughan [top]

Threonine 22 phosphorylation attenuates Hsp90 interaction with cochaperones and affects its chaperone activity. Mollapour M, Tsutsumi S, Truman AW, Xu W, Vaughan CK, Beebe K, Konstantinova A, Vourganti S, Panaretou B, Piper PW, Trepel JB, Prodromou C, Pearl LH, Neckers L. Mol Cell. 2011 Mar 18;41(6):672-81.

β-amylase-like proteins function as transcription factors in Arabidopsis, controlling shoot growth and development. Reinhold H, Soyk S, Simková K, Hostettler C, Marafino J, Mainiero S, Vaughan CK, Monroe JD, Zeeman SC. Plant Cell. 2011 Apr;23(4):1391-403.

Professor Gabriel Waksman [top]


Professor Bonnie Wallace [top]

Whitmore, L., Woollett, B., Miles, A.J., Klose, D.P.,  Janes, R.W., and Wallace, B.A.(2011) PCDDB: The Protein Circular Dichroism Data Bank, A Repository for Circular Dichroism Spectral and Metadata, Nucleic Acids Research 39: D480-D486.

McCusker, E.C., D’Avanzo, N., Nichols, C.G., and Wallace, B.A. (2011) Simplified Bacterial “Pore” Provides Insight into the Assembly, Stability and Structure of Sodium Channels. J. Biol. Chem. 286:16386-1639.

Abdul-Gader, A., Miles, A.J., and Wallace, B.A.  (2011) A reference dataset for the analyses of membrane protein secondary structures and transmembrane residues using circular dichroism spectroscopy. Bioinformatics 27:1630-1636.


Miles, A.J., Wallace, B.A. and Essman, M. (2011) Correlation of structural and functional thermal stability of the integral membrane protein Na,K-ATPase. Biophys. Biochim. Acta (Biomembranes) 1808:2573-2580. [doi: /10.1016/j.bbamem.2011.06.009]

Prof John Ward [top]

Hunter SJ, Easton S, Booth V,  Henderson B, Wade WG, John M. Ward JM (2011). Selective Removal of Human DNA from Metagenomic DNA Samples Extracted from Dental Plaque. J Basic Microbiol. 51. 1-5
 
Pesnot T, Gershater MC, John M. Ward  JM and Helen C. Hailes HC (2011) Phosphate mediated biomimetic synthesis of tetrahydroisoquinoline alkaloids. Chem Comm. 47.  3242-3244

Branston S, Stanley E, Ward J, Keshavarz-Moore E. (2011) Study of robustness of filamentous bacteriophages for industrial applications. Biotechnol Bioeng. 108. 1468-1472.
 
Rios-Solis L, Halim M, Cázares A, Morris P, Ward JM, Hailes HC,  Dalby PA, Baganz F and Lye GJ (2011) A toolbox approach for the rapid evaluation of multi-step enzymatic syntheses comprising a ³mix and match² E. coli expression system with microscale experimentation. Biocat. Biotrans. 29. 192-203
 
 Parker BM, Ian Taylor I,  Woodley JM, Ward JM and Dalby PA (2011) Directed evolution of a thermostable L-aminoacylase biocatalyst. J.Biotechnol. 155. 396-405

Branston, S. Stanley, E., Keshavarz-Moore, E. and Ward, J (2011) Precipitation of filamentous bacteriophages for their selective recovery in primary purification. Biotech. Prog. 28.  129-136

Strafford J, Payongsri P, Hibbert EG, Sukhjeet SB, Steadman D, Smith MEB, Ward J, Hailes HC, Dalby  PA. (2011) Directed evolution to re-adapt a co-evolved network within an enzyme. J. Biotechnol. 157. 237-245

Nesbeth, D, Pardo, MA,  Ali, S, Ward, J, Keshavarz-Moore, E (2012) Growth and Productivity Impacts of Periplasmic Nuclease Expression in an Escherichia coli Fab¹ Fragment Production Strain. Biotech. Bioeng. 109. 517-527

Sehl T, Simon R, Hailes HC,  Ward JM,  Pohl M, Rother D (2011) TTC-based screening assay for w-transaminases: a rapid method to detect reduction of 2-hydroxy ketones. J. Biotechnol 139. 47-54

Dartnell LR, Storrie-Lombardi MC, Mullineaux CM, Ruban AV, Wright G, Griffiths AD, Muller JP,6 and Ward JM. (2011) Degradation of Cyanobacterial Biosignatures by Ionizing Radiation. Astrobiology. 11. 997-1016

Mukhopadhyay TK, Allison N, Charlton S, Ward JM and Lye GJ (2011) Use of microwells to investigate the effect of quorum sensing on growth and antigen production in Bacillus anthracis Sterne 34F2. J. Appl. Microbiol. 111. 1224-1234


Dr Finn Werner [top]

Grohmann D, Nagy J, Chakraborty A, Klose D, Fielden D, Ebright RH, Michaelis J,Werner F. The initiation factor TFE and the elongation factor Spt4/5 compete for the RNAP clamp during transcription initiation and elongation. Mol Cell. 2011 Jul 22;43(2):263-74.

Grohmann D, Werner F. Curr Recent advances in the understanding of archaeal transcription. Opin Microbiol. 2011 Jun;14(3):328-34. Epub 2011 May 17. Review.

Werner F, Grohmann D. Evolution of multisubunit RNA polymerases in the three domains of life. Nat Rev Microbiol. 2011 Feb;9(2):85-98. Review.

Grohmann D, Werner F. Cycling through transcription with the RNA polymerase F/E (RPB4/7) complex: structure, function and evolution of archaeal RNA polymerase. Res Microbiol. 2011 Jan;162(1):10-8. Epub 2010 Sep 21. Review.


Dr Lorenz Wernisch [top]


Dr Jonathan Wilden [top]


Dr Mark Williams [top]

Olsson TSG, Ladbury JE, Pitt WR, Williams MA (2011).  The extent of enthalpy-entropy compensation in protein-ligand interactions.  Protein Science 20,1607-1618.

da Fonseca PCA, Kong EH, Zhang Z, Schreiber A, Williams MA, Morris EP, Barford D (2011). Structures of APC/C-CDH1 with substrates identify Cdh1 and Apc10 as the D-box co-receptor. Nature 470, 274-278..

Edwards MJ, Williams MA, Maxwell AJ, Adam McKay A (2011). Mass spectrometry reveals that the antibiotic simocyclinone D8 binds to DNA gyrase in a "bent-over" conformation: evidence for positive cooperativity in binding. Biochemistry 50, 3432-3440.

Henderson B, Nair S, Pallas J, Williams MA (2011). Fibronectin: a multidomain host adhesin targeted by bacterial fibronectin-binding proteins. FEMS Microbiology Reviews 35, 147-200.


Dr Steve Wood [top]


Dr Xuemei Yuan [top]




 





 
 
   
     
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