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ISMB member publications in 2006



Dr James Baker [top]

Baker JR, Woolfson DN, Muskett FW, Stoneman RG, Urbaniak MD, Caddick S. (2007) Protein-small molecule interactions in neocarzinostatin, the prototypical enediyne chromoprotein antibiotic.Chembiochem. 8(7):704-17.

Baker,J.R., Thominet,O., Britton,H., Caddick,S. (2007). An Efficient Synthesis of Epoxydiynes and a Key Fragment of Neocarzinostatin Chromophore. Organic Letters 9(1), 45-48.

Gulten,S., Sharpe,A., Baker,J. R., Booker-Milburn,K. I. (2007). Use of Temporary Tethers in the Intramolecular [2+2] Photocycloaddition Reactions of Tetrahydrophtalimide Derivatives: A New Approach to Complex Tricyclic Lactones. Tetrahedron Letters 63, 3659-3671.

Hickford,P.J., Baker,J.R., Bruce,I., Booker-Milburn,K.I. (2007). Acid catalyzed rearrangement of fused alkylideneoxetanols. Organic Letters 9(23), 4681-4684.

Thominet,O., Baker,J.R., Britton H., Etheridge,Z., Soscia,M., G.Caddick,S. (2007). Synthetic Strategies to Epoxydiynes and a Key Synthon of the Neocarzinostatin Chromophore. Organic and Biomolecular Chemistry 5(22), 3703-3712.


Dr Tracey Barrett [top]

N/A


Dr Sanjib Bhakta [top]


Madikane VE, Bhakta S, Russell AJ, Campbell WE, Claridge TD, Elisha BG, Davies SG, Smith P, Sim E. (2007) Inhibition of mycobacterial arylamine N-acetyltransferase contributes to anti-mycobacterial activity of Warburgia salutaris. Bioorg Med Chem. 15(10):3579-86.

Smellie I, Bhakta S, Sim E, Fairbanks A (2007) Synthesis of putative chain terminators of mycobacterial arabinan biosynthesis. Organic and Biomolecular Chemistry 5 (14): 2257-66.


Professor Jeremy Brockes [top]

Kumar,A., Gates,P.B., Brockes,J.P. (2007). Positional identity of adult stem cells in salamander limb regeneration. C.R. Biol. 330, 485-490.

Kumar,A., Godwin,J.W., Gates,P.B., Garza-Garcia,A.A., Brockes,J.P., (2007). Molecular Basis for the Nerve Dependence of Limb Regeneration in an Adult Vertebrate. Science 318(5851), 772-777.

Kumar,A., Brockes,J.P. (2007). Preparation of cultured myofibers from larval salamander limbs for cellular plasticity studies. Nat Protoc. 209, 939-947.


Professor Steve Caddick [top]



Gois P.M.P, Veiros L.F, Afonso C.A.M., Caddick S., Cloke F.G.N.(2007) Tuning the Reactivity of Di-rhodium (II) Complexes with Axial NHC Ligands: Arylation of Aldehydes. Angew. Chem. Int. Ed. Eng. 2007, 46, 5750-5753

Wilden,J.D., Geldeard,L., Lee,C.C., Judd,D.B., Caddick,S. (2007). Trichlorophenol (TCP) Sulfonate Esters: A Selective Alternative to Pentafluorophenol Esters and Sulfonyl Chlorides for the Preparation of Sulfonamides. Chemical Communications (10), 1074-1076.

Esposito O, Lewis AK, Hitchcock PB, Caddick S, Cloke FG. (2007) Synthesis and reactivity of alkyl-palladium N-heterocyclic carbene complexes.Chem Commun. (11):1157-1159.

Morris T, Sandham D, Caddick S. (2007) A microwave enhanced cross-metathesis approach to peptidomimetics.Org Biomol Chem. 5(7):1025-7.

Baker JR, Woolfson DN, Muskett FW, Stoneman RG, Urbaniak MD, Caddick S. (2007) Protein-small molecule interactions in neocarzinostatin, the prototypical enediyne chromoprotein antibiotic.Chembiochem. 8(7):704-17.

Thominet,O., Baker,J.R., Britton H., Etheridge,Z., Soscia,M., G.Caddick,S. (2007). Synthetic Strategies to Epoxydiynes and a Key Synthon of the Neocarzinostatin Chromophore. Organic and Biomolecular Chemistry 5(22), 3703-3712.

Baker,J.R., Thominet,O., Britton,H., Caddick,S. (2007). A New Synthesis of Diyne Epoxides. Organic Letters 9(1), 45-48.


Professor Richard Catlow [top]


French,S.A., Di Tommaso,D., Zanotti-Gerosa,A., Hancock,F., Catlow,C.R.A. (2007). New insights into the enantioselectivity in the hydrogenation of prochiral ketones. Chemical Communications 23, 2381-2383.

Grau-Crespo,R., Catlow,C.R.A., de Leeuw,N.H. (2007). A computer modeling study of redox processes on the FeSbO4 (100) surface. Journal of Catalysis 248(1), 77-88.

O'Brien,M.G., Sanchez-Sanchez,M., Beale,A.M., Lewis,D.W., Sankar,G., Catlow,C.R.A. (2007). Effect of Organic Templates on the Kinetics and Crystallization of Microporous Metal-Substituted Aluminophosphates. Journal of Physical Chemistry C 111(45), 16951-16961.

Goumans,T.P.M., Wander,A., Catlow,C.R.A., Brown,W.A. (2007). Silica grain catalysis of methanol formation. Monthly notices of the royal astronomical society 382, 1829-1832.

Goumans,T.P.M, Wander,A., Brown,W.A., Catlow,C.R.A. (2007). Structure and stability of the (001) alpha-quartz surface. Physical Chemistry Chemical Physics 9(17), 2146-2152.


Professor Peter Coveney [top]


Coveney,P.V., Saksena,R.S., Zasada,S.J., McKeown,M., Pickles,S. (2007). The application hosting environmnet: Lightweight middleware for grid-based computational science. Computer Physics Communications 176, 406-418.

De Fabritiis G, Serrano M, Delgado-Buscalioni R, Coveney PV. (2007) Fluctuating hydrodynamic modeling of fluids at the nanoscale. Phys Rev E Stat Nonlin Soft Matter Phys. 75(2 Pt 2):026307.

Fowler PW, Balali-Mood K, Deol S, Coveney PV, Sansom MS. (2007) Monotopic enzymes and lipid bilayers: a comparative study.Biochemistry. 46(11):3108-15.

Giupponi G, De Fabritiis G, Coveney PV. (2007) Hybrid method coupling fluctuating hydrodynamics and molecular dynamics for the simulation of macromolecules. J Chem Phys. 126(15):154903.

Harting J, Giupponi G, Coveney PV. (2007) Structural transitions and arrest of domain growth in sheared binary immiscible fluids and microemulsions. Phys Rev E Stat Nonlin Soft Matter Phys. 75(4 Pt 1):041504. Erratum in: Phys Rev E Stat Nonlin Soft Matter Phys. 2007 May;75(5 Pt 2):059901.

Sadiq SK, Wan S, Coveney PV.(2007) Insights into a Mutation-Assisted Lateral Drug Escape Mechanism from the HIV-1 Protease Active Site. Biochemistry. 46(51):14865-77.

Suter,J.L., Coveney,P.V., Greenwell,H.C., Thyveetil,M. (2007). Large-scale molecular dynamics study of montmorillonite clay: Emergence of undulatory fluctuations and determination of material properties. Journal of Physical Chemistry C 111, 8248-8259.

Wattis JA, Coveney PV. (2007) Sequence selection during copolymerization. J Phys Chem B. 111(32):9546-62.



Dr Snezana Djordjevic [top]


N/A


Dr Paul Driscoll [top]

Bayliss,R., Harris,R., Coutte,L., Monier,A., Fronzes,R., Christie,P.J., Driscoll,P.C., Waksman,G. (2007). NMR structure of a complex between the VirB9/VirB7 interaction domains of the pKM101 type IV secretion system. Proc Natl Acad Sci U S A. 104(5), 1673-1678.

Ferguson,B.J., Esposito,D., Jovanovic,J., Sankar,A., Driscoll,P.C., Mehmet,H. (2007). Biophysical and cell-based evidence for differential interactions between the death domains of CD95/Fas and FADD. Cell Death and Differentiation 14(9), 1717-1719.

Prodromou, C.; Savva, R. and Driscoll, P.C. (2007) DNA fragmentation-based combinatorial approaches to soluble protein expression: Part I. Generating DNA fragment libraries. Drug Discovery Today. 12, 931-938.

Savva, R.; Prodromou, C. and Driscoll, P.C. (2007) DNA fragmentation based combinatorial approaches to soluble protein expression: Part II: Library expression, screening and scale-up. Drug Discovery Today. 12, 939-947.


Professor Jasminka Godovac-Zimmerman [top]

Fischer A, Radulovic M, Schrick C, Sananbenesi F, Godovac-Zimmermann J, Radulovic J. (2007) Hippocampal Mek/Erk signaling mediates extinction of contextual freezing behavior. Neurobiology of Learning and Memory. 87(1): p.149-58

Godovac-Zimmermann J, Mulvey C, Konstantoulaki M, Sainsbury R, Brown LR. (2007) Promise of multiphoton detection in discovery and diagnostic proteomics. Expert Rev Proteomics. 4(2):161-73. Review.

Guerrera IC, Keep NH, Godovac-Zimmermann J. (2007) Proteomics study reveals cross-talk between Rho guanidine nucleotide dissociation inhibitor 1 post-translational modifications in epidermal growth factor stimulated fibroblasts. J Proteome Res. 6(7):2623-30.


Dr Bibek Gooptu [top]


N/A


Dr Helen Hailes [top]

Hailes H.C, Dalby P.A, and Woodley J.M (2007) Integration of biocatalytic conversions into chemical syntheses. J. Chem. Tech. Biotech. 2007, 82, 1063-1066.

Hailes H.C. (2007). Reaction Solvent Selection: The Potential of Water as a Solvent for Organic Transformations. Org. Process Res. Dev. 11, 114-120.

Hibbert EG, Senussi T, Costelloe SJ, Lei W, Smith ME, Ward JM, Hailes HC, Dalby PA. (2007) Directed evolution of transketolase activity on non-phosphorylated substrates.J Biotechnol. 131(4):425-32.

Ingram,C.U., Bommer,M., Smith,M.E.B., Dalby,P.A., Ward,J.M., Hailes,H., Lye,G.J. (2007). One-pot synthesis of amino-alcohols using a de-novo transketolase and ß-alanine:pyruvate transaminase pathway in Escherichia coli. Biotechnology and Bioengineering 96(3), 559-569.

Kaulmann U., Smithies K., Smith M.E.B., Hailes H.C., and Ward,J.M. (2007). Substrate spectrum of Š-transaminase from Chromobacterium violaceum DSM30191 and its potential for biocatalysis. Enz. Microb. Tech. 41, 628-637.

Mustapa,F.M., Bell,P.C., Hurley,C.A., Nicol,A., Guénin,E., Sarkar,S., Writer,M.J., Barker,S.E., Wong,J.B., Pilkington-Miksa,M.A., Papahadjopoulos-Sternberg,B., Shamlou,P.A., Hailes,H.C., Hart,S.L., Zicha,D., Tabor,A.B. (2007). Biophysical characterisation of an integrin-targeted lipopolyplex gene delivery vector. Biochemistry 46(45), 12930-12944.

Pilkington-Miksa MA, Writer MJ, Sarkar S, Meng QH, Barker SE, Shamlou PA, Hailes HC, Hart SL, Tabor AB. (2007) Targeting lipopolyplexes using bifunctional peptides incorporating hydrophobic spacer amino acids: synthesis, transfection, and biophysical studies. Bioconjug Chem. 18(6):1800-10.

Tranchant I, Hervé AC, Carlisle S, Lowe P, Slevin CJ, Forssten C, Dilleen J, Tabor AB, Williams DE, Hailes HC. (2007) Applications of tailored ferrocenyl molecules as electrochemical probes of biochemical interactions.Bioconjug Chem. 18(1):199-208.



Professor Elizabeth Hounsell [top]


Hounsell, E.F. (2007) NMR of Carbohydrates, lipids and membranes. In: RSC Specialist Reports in Nuclear Magnetic Resonance Spectroscopy 36, 285-308.


Dr Stefan Howorka [top]

Astier,Y., Kainov,D.E., Bayley,H., Tuma,R., Howorka,S. (2007). Stochastic Detection of Motor Protein-RNA Complexes by Single-Channel Current Recording. ChemPhysChem 8(15), 2189-2194.

Drbal,K., Moertelmaier,M., Holzhauser,C., Muhammad,A., Fuertbauer,E., Howorka,S., Hinterberger,M, Stockinger,H., Schutz,G.J. (2007). Single-molecule microscopy reveals heterogeneous dynamics of lipid raft components upon TCR engagement. International Immunology 19(5), 675-684.

Howorka,S. (2007). Creating regular arrays of nanoparticles with self-assembling protein building blocks. Journal of Materials Chemistry 17(20), 2049-2053.

Martin,H., Kinns,H., Mitchell,N., Astier,Y., Howorka,S. (2007). Nanoscale protein pores modified with PAMAM dendrimers. J. Am. Chem. Soc. 129, 9640-9649.

Schlapak,R., Armitage,D., Saucedo-Zeni,N., Hohage,M., Howorka,S. (2007). Dense passivating poly(ethylene glycol) films on indium tin oxide substrates. Langmuir 23(20), 10244-10253.

Schlapak,R., Armitage,D., Saucedo-Zeni,N., Latini,G., Gruber,H.J., Mesquida,P., Samotskaya,Y., Hohage,M., Cacialli,F., Howorka,S. (2007). Preparation and characterization of dense films of poly(amidoamine) dendrimers on indium tin oxide. Langmuir 23(17), 8916-8924.

Schlapak,R., Kinns,H., Wechselberger,C., Hesse,J., Howorka,S. (2007). Sizing trinucleotide repeat sequences by single-molecule analysis of fluorescence brightness. ChemPhysChem 8(11), 1618-1621.



Professor David Jones [top]


Bryson, K., Cozzetto, D. & Jones, D.T. (2007) Computer-assisted protein domain boundary prediction using the DomPred server. Curr Protein Pept Sci., 8, 181-188.

Jones, D.T. (2007) Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics. 23, 538-544.

Tress, M.L., Martelli, P.L., Frankish, A., Reeves, G.A., Wesselink, J.J., Yeats, C., Olason, P.L., Albrecht, M., Hegyi, H., Giorgetti, A., Raimondo, D., Lagarde, J., Laskowski, R.A., Lopez, G., Sadowski, M.I., Watson, J.D., Fariselli, P., Rossi, I., Nagy, A., Kai, W., Storling, Z., Orsini, M., Assenov, Y., Blankenburg, H., Huthmacher C, Ramirez, F., Schlicker, A., Denoeud, F., Jones, P., Kerrien, S., Orchard, S., Antonarakis, S.E., Reymond, A., Birney, E., Brunak, S., Casadio, R., Guigo, R. , Harrow, J., Hermjakob, H., Jones, D.T., Lengauer, T., Orengo, C.A., Patthy, L., Thornton, J.M, Tramontano, A. & Valencia, A. (2007) The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A. 104, 5495-5500.


Dr Cristopher Kay [top]


Kay,C.W.M., El Mkami,E., Cammack,R., Evans,R.W. (2007). Pulsed ELDOR determination of the intramolecular distance between the metal binding sites in Dicupric human serum transferrin and lactoferrin. Journal of the American Chemical Society USA 129(16), 4868-4868.

Kay,C.W.M, Grishin, Yu.,A., Weber,S.Möbius,K. (2007). An Improved TM110 Resonator for Continuous-Wave ENDOR Studies at X-Band. Applied Magnetic Resonance 31(3-4), 599-609.

Kay C.W.M., El Mkami H, Molla G, Pollegioni L, Ramsay RR. (2007) Characterization of the covalently bound anionic flavin radical in monoamine oxidase a by electron paramagnetic resonance. J Am Chem Soc. 129(51):16091-7.

Schleicher,E., Hitomi,K., Kay,C.W.M., Getzoff,E.D., Todo,T., Weber,S. (2007). Electron nuclear double resonance differentiates complementary roles for active site histidines in (6-4) photolyase. The Journal of Biological Chemistry 282(7), 4738-4747.


Dr Nick Keep [top]

Guerrera, I. C, Keep, N. H and Godovac-Zimmermann, J. (2007). Proteomics Study Reveals Cross-Talk between Rho Guanidine Nucleotide Dissociation Inhibitor 1 Post-Translational Modifications in Epidermal Growth Factor Stimulated Fibroblasts. J. Proteome Res. 6; 2623-2630.

Morris, J.R, Pagnon, L, Boutell, C, Katagiri, T., Keep, N.H and Solomon, E., (2006). Genetic analysis of BRCA1 ubiquitin ligase activity and its relationship to breast cancer susceptibility. Human Molecular Genetics 15, 599–606.

Professor John Ladbury [top]

Ababou A, Ladbury JE.Survey of the year 2005: literature on applications of isothermal titration calorimetry.J Mol Recognit. 2007 Jan-Feb;20(1):4-14. Review.

Impagliazzo A, Blok AJ, Cliff MJ, Ladbury JE, Ubbink M (2007). Redox-state-dependent complex formation between pseudoazurin and nitrite reductase. J Am Chem Soc. 129(1):226-33.

Ladbury JE (2007). Measurement of the formation of complexes in tyrosine kinase-mediated signal transduction. Acta Crystallogr D Biol Crystallogr. 63(Pt 1):26-31.

Schüller AC, Ahmed Z, Ladbury JE (2007). Extracellular point mutations in FGFR2 result in elevated Erk1/2 activation and perturbation of neuronal differentiation. Biochem J.

Taylor JD, Gilbert PJ, Williams MA, Pitt WR, Ladbury JE (2007). Identification of novel fragment compounds targeted against the pY pocket of v-Src SH2 by computational and NMR screening and thermodynamic evaluation. Proteins. 67(4):981-90.


Dr Philip Lowden [top]

N/A


Dr Derek MacMillan [top]

Chalmers S, Olson ML, MacMillan D, Rainbow RD, McCarron JG. (2007) Ion channels in smooth muscle: regulation by the sarcoplasmic reticulum and mitochondria. Cell Calcium. 42(4-5):447-66.

Cardoso MJ, Cardoso J, Amaral N, Azevedo I, Barreau L, Bernardo M, Christie D, Costa S, Fitzal F, Fougo JL, Johansen J, Macmillan D, Mano MP, Regolo L, Rosa J, Teixeira L, Vrieling C. (2007) Turning subjective into objective: the BCCT.core software for evaluation of cosmetic results in breast cancer conservative treatment. Breast. 16(5):456-61.

Macmillan D, Currie S, McCarron JG.(2007) FK506-binding protein (FKBP12) regulates ryanodine receptor-evoked Ca(2+) release in colonic but not aortic smooth muscle.Cell Calcium. 43(6):539-49

McCarron JG, Olson ML, Rainbow RD, Macmillan D, Chalmers S. (2007) Ins(1,4,5)P(3) receptor regulation during 'quantal' Ca(2+) release in smooth muscle. Trends Pharmacol Sci. 28(6):271-9.


Professor Charles Marson [top]

Marson,C.M., Edaan,E., Morrell,J.M., Coles,S.J., Hursthouse,M.B., Davies,D.T. (2007). A catalytic asymmetric protocol for the enantioselective synthesis of 3(2H)-furanones. Chemical Communications 24, 2494-2496.

Marson,C.M., Mahadevan,T., Dines,J., Sengmany,S., Morrell,J.M., Alao,J.P., Joel,S.P., Vigushin,D.M., Coombes,R.C. (2007). Structure-activity relationships of aryloxyalkanoic acid hydroxyamides as potent inhibitors of histone deacetylase. Bioorganic & Medicinal Chemistry Letters 17(1), 136-141.


Dr Andrew Martin [top]


Abhinandan, K. R. and Martin, Andrew C. R. (2007) Analyzing the 'degree of humanness' of antibody sequences. J. Mol. Biol 369, 852-862.

Churamani,D., Boulware,M.J., Geach,T.J., Martin,A.C.R., Moy,G.W., Su,Y-H., Vacquier,V.D., Marchant,J.S., Dale,L., Patel,S. (2007). Molecular characterization of a novel intracellular ADP-ribosyl cyclase. PLoS ONE 2(8), e797.


Merelli, E., Armano, G., Cannata, N., Corradini, F., d'Inverno, M., Doms, A., Lord, P., Martin, A., Milanesi, L., Moeller, S., Schroeder, M. and Luck, M. (2007) Agents in Bioinformatics, Computational and Systems Biology. Briefings in Bioinformatics, 8, 45-59


Dr Nigel Martin [top]


Zamboulis L., Martin N., Poulovassilis A. (2007). Bioinformatics Service Reconciliation By Heterogeneous Schema Transformation. Proc. 4th International Workshop Data Integration in the Life Sciences DILS. 89-104.


Dr Neil McDonald [top]

Boëda B, Briggs DC, Higgins T, Garvalov BK, Fadden AJ, McDonald NQ, Way M. (2007) Tes, a Specific Mena Interacting Partner, Breaks the Rules for EVH1 Binding. Mol Cell. 28(6):1071-82.

Ciccia, A, Ling, C, Coulthard, R, Yan, Z, Xue, Y, Meetei, AR, Laghmani, EH, McDonald, NQ, de Winter, JP, Wang, W, & West, SC (2007). Identification of FAAP24, a Novel Fanconi Anemia Core Complex Protein that Interacts with FANCM. Molecular Cell 25, 331-343.

Fox,G, Shafiq, M, Briggs, D., Knowles, P., Collister, M., Didmon, M. , Tilley, S., Stewart, A., Keyse, S.M. & McDonald, NQ (2007). Redox-mediated substrate recognition by Sdp1 defines a new group of tyrosine phosphatases. Nature 447:487-492.

Leiper J, Nandi M, Torondel B, Murray-Rust J, Malaki M, O’hara B, Rossiter S, Anthony S, Madhani M, Selwood D, Smith C, Wojciak-Stothard B, Rudiger A, Stidwill R, McDonald NQ, Vallance P (2007). Disruption of methylarginine metabolism impairs vascular homeostasis. Nature Medicine 13, 198 - 203

Plun-Favreau H, Klupsch K, Moisoi N, Gandhi S, Kjaer S, Frith D, Harvey K, Deas E, Harvey RJ, McDonald N, Wood NW, Martins LM, Downward J. (2007) The mitochondrial protease HtrA2 is regulated by Parkinson's disease-associated kinase PINK1. Nat Cell Biol. 9(11):1243-52.

Rosivatz E, Matthews JG, McDonald NQ, Mulet X, Ho KK, Lossi N, Schmid AC, Mirabelli M, Pomeranz KM, Erneux C, Lam EW, Vilar R, Woscholski R (2007). A small molecule inhibitor for phosphatase and tensin homologue deleted on chromosome 10 (PTEN). ACS Chem Biol. 3;1(12):780-90.


Professor Boris Mirkin [top]

N/A


Dr Carolyn Moores [top]

Moores C.A. (In press) Studying microtubules by electron microscopy in “Introduction to Electron Microscopy for Biologists” (ed. T.D. Allen). Academic Press, Elsevier, Inc.


Professor David Moss [top]

Davies, M N, Lamikanra, A, Sansom, C E, Flower, D R, Moss, D S and Travers, P J (2007). Identification of the HLA-DM/HLA-DR interface. Molecular Immunology. 45(4):1063-70.

Todman S J, Halling-Brown M D, Davies M N, Flower D R and Moss D S (2007) Toward the atomistic simulation of T cell epitopes. Automated construction of HLA:peptide Structures for free energy calculations. Journal of Molecular Graphics and Modelling. 26(6):957-61.


Dr Sylvia Nagl [top]

Baleizão C, Nagl S, Borisov SM, Schäferling M, Wolfbeis OS, Berberan-Santos MN. (2007) An optical thermometer based on the delayed fluorescence of C70. Chemistry. 13(13):3643-51.

Nagl S, Wolfbeis OS. (2007) Optical multiple chemical sensing: status and current challenges. Analyst. 132(6):507-11.


Professor Christine Orengo [top]


Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, Dibley M, Redfern O, Pearl F, Nambudiry R, Reid A, Sillitoe I, Yeats C, Thornton JM, Orengo CA. (2007) The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res. 35(Database issue):D291-7.

Harrison AP, Johnston CE, Orengo CA. (2007) Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips. BMC Bioinformatics. 8:195.

Lobley A, Swindells MB, Orengo CA, Jones DT. (2007) Inferring function using patterns of native disorder in proteins. PLoS Comput Biol. 3(8):e162.

Redfern OC, Harrison A, Dallman T, Pearl FM, Orengo CA. (2007) CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures. PLoS Comput Biol. 3(11):e232.

Marsden RL, Lewis TA, Orengo CA.(2007) Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint. BMC Bioinformatics. 8:86.

Mulder, Orengo, C, N, Yeats et al. (2007) New Developments in the InterPro Database. Nuclei Acids Res. D224-8.

Ranea JA, Yeats C, Grant A, Orengo CA. (2007) Predicting protein function with hierarchical phylogenetic profiles: the Gene3D Phylo-Tuner method applied to eukaryotic genomes. PLoS Comput Biol. 3(11):e237.

Reid A and Orengo C. (2007) Structural annotation of genomes. in Structural Bioinformatics. Editors Phil Bourne and Helge Weissig. Wiley-Liss. Lee D, Redfern O, Orengo. C. (2007) Predicting protein function from sequence and structure. Nat Rev Mol Cell Biol. 8:995-1005.

Reid AJ, Yeats C, Orengo CA. (2007) Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone. Bioinformatics. 23(18):2353-60.

Tress, M., Thornton, J., Valencia A., Orengo, C, Jones, D. et al. (2007) The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci 104:5495-500.

Watson JD, Sanderson S, Ezersky A, Savchenko A, Edwards A, Orengo C, Joachimiak A, Laskowski RA, Thornton JM. (2007) Towards Fully Automated Structure-based Function Prediction in Structural Genomics: A Case Study. J Mol Biol. 367:1511-22. .


Dr Elena Orlova [top]

Elad N, Clare DK, Saibil HR, Orlova EV.(2007) Detection and separation of heterogeneity in molecular complexes by statistical analysis of their two-dimensional projections. J Struct Biol. 162(1):108-20

Elad N, Farr GW, Clare DK, Orlova EV, Horwich AL, Saibil HR (2007). Topologies of a substrate protein bound to the chaperonin GroEL. Mol Cell. 26, 415-426.

Lebedev AA, Krause MH, Isidro AL, Vagin AA, Orlova EV, Turner J, Dodson EJ, Tavares P, Antson AA (2007). Structural framework for DNA translocation via the viral portal protein. EMBO J. 26, 1984-1994.

Okorokov AL, Waugh A, Hodgkinson J, Murthy A, Hong HK, Leo E, Sherman MB, Stoeber K, Orlova EV, Williams GH.(2007) Hexameric ring structure of human MCM10 DNA replication factor. EMBO Rep. 8(10), 925-930

Plisson C, White HE, Auzat I, Zafarani A, São-José C, Lhuillier S, Tavares P, Orlova EV (2007). Structure of bacteriophage SPP1 tail reveals trigger for DNA ejection. EMBO J. 26,3720-3728



Professor Steve Perkins [top]


Barlow, P. N., Lea, S. M. & Perkins, S. J. (2007). Structural analysis of complement proteins: a brief comparison of available approaches. Focus On Complement, Issue 6. Pages 2-5.

Bonner, A., Perrier, C., Corthésy, B. & Perkins, S. J. (2007). Solution structure of human secretory component and implications for biological function. J. Biol. Chem. 282, 16969 - 16980.

Fernando, A. N., Furtado, P. B., Clark, S. J., Gilbert, H. E., Day, A. J., Sim, R. B. & Perkins, S. J. (2007). Associative and structural properties of the region of complement Factor H encompassing the Tyr402His disease-related polymorphism and its interactions with heparin J Mol Biol., 368, 564-581.

Saunders, R. E. Abarrategui-Garrido, C., Frémeaux-Bacchi, V., Goicoechea de Jorge, E., Goodship, T. H. J., López Trascasa, M., Noris, M., Ponce Castro, I. M., Remuzzi, G., Rodríguez de Córdoba, S., Sánchez-Corral, P., Skerka, C., Zipfel, P. F. & Perkins, S. J. (2007). The interactive Factor H - atypical Haemolytic Uraemic Syndrome mutation database and website: Update and integration of Membrane Cofactor Protein and Factor I mutations with structural models. Human Mutation, 28, 222-234.


Professor Peter Rich [top]

Iwaki, M. and Rich, P.R. (2007) An IR Study of Protonation Changes Associated with Heme-Heme Electron Transfer in Bovine Cytochrome c Oxidase, J. Amer. Chem. Soc., 129, 2923-2929.

Rich, P.R. and Iwaki, M. (2007) A Comparison of Catalytic Site Intermediates of Cytochrome c Oxidase and Peroxidases. Biochemistry (Moscow), 72, 1047-1055.

Rich, P.R. and Iwaki, M. (2007) Probing protein transitions with ATR infrared spectroscopy, "HIGHLIGHT" article, Molecular Biosystems. 3, 398-407.


Professor David Saggerson [top]

N/A


Professor Helen Saibil [top]

Elad N, Farr GW, Clare DK, Orlova EV, Horwich AL, Saibil HR. (2007). Topologies of a substrate protein bound to the chaperonin GroEL. Mol Cell. 26(3):415-26.

Elad N, Clare DK, Saibil HR, Orlova EV.(2007) Detection and separation of heterogeneity in molecular complexes by statistical analysis of their two-dimensional projections. J Struct Biol. 162(1):108-20

Puri T, Wendler P, Sigala B, Saibil H, Tsaneva IR.(2007). Dodecameric Structure and ATPase Activity of the Human TIP48/TIP49 Complex. J Mol Biol. 366(1):179-92.

Wendler P, Shorter J, Plisson C, Cashikar AG, Lindquist SL, Saibil HR (2007) Atypical AAA+ subunit packing creates an expanded cavity for disaggregation by the protein-remodeling factor Hsp104. Cell, 131(7):1366-77.


Dr Renos Savva [top]

Prodromou, C.; Savva, R. and Driscoll, P.C. (2007) DNA fragmentation-based combinatorial approaches to soluble protein expression: Part I. Generating DNA fragment libraries. Drug Discovery Today. 12, 931-938.

Savva, R.; Prodromou, C. and Driscoll, P.C. (2007) DNA fragmentation based combinatorial approaches to soluble protein expression: Part II: Library expression, screening and scale-up. Drug Discovery Today. 12, 939-947.


Dr David Selwood [top]

Hartzoulakis B, Rossiter S, Gill H, O'Hara B, Steinke E, Gane PJ, Hurtado-Guerrero R, Leiper JM, Vallance P, Rust JM, Selwood DL (2007). Discovery of inhibitors of the pentein superfamily protein dimethylarginine dimethylaminohydrolase (DDAH), by virtual screening and hit analysis. Bioorg Med Chem Lett. 17(14):3953-6.

Hoi PM, Visintin C, Okuyama M, Gardiner SM, Kaup SS, Bennett T, Baker D, Selwood DL, Hiley CR (2007). Vascular pharmacology of a novel cannabinoid-like compound, 3-(5-dimethylcarbamoyl-pent-1-enyl)-N-(2-hydroxy-1-methyl-ethyl)benzamide (VSN16) in the rat. Br J Pharmacol. 152(5):751-64.

Leiper J, Nandi M, Torondel B, Murray-Rust J, Malaki M, O'Hara B, Rossiter S, Anthony S, Madhani M, Selwood D, Smith C, Wojciak-Stothard B, Rudiger A, Stidwill R, McDonald NQ, Vallance P (2007). Disruption of methylarginine metabolism impairs vascular homeostasis. Nat Med. 13(2):198-203

Okuyama M, Laman H, Kingsbury SR, Visintin C, Leo E, Eward KL, Stoeber K, Boshoff C, Williams GH, Selwood DL (2007). Small-molecule mimics of an alpha-helix for efficient transport of proteins into cells.Nat Methods. 4(2):153-9.


Professor Elizabeth Shephard [top]

Allerston CK, Shimizu M, Fujieda M, Shephard EA, Yamazaki H, Phillips IR. (2007) Molecular evolution and balancing selection in the flavin-containing monooxygenase 3 gene (FMO3). Pharmacogenet Genomics. 17(10):827-39.

Shephard,E.A., Chandan,P., Stevanovic-Walker,M., Edwards,M., Phillips,I.R., (2007). Alternative promoters and repetitive DNA elements define the species-dependent tissue-specific expression of the FMO1 gene of human and mouse. Biochem. J. 406(3), 491-499


Dr Adrian Shepherd
[top]

Clegg AB, Shepherd AJ (2007): Benchmarking natural-language parsers for biological applications using dependecy graphs. BMC Bioinformatics. 8(1):24


Dr Christine Slingsby [top]

Evans, P., Bateman, O.A., Slingsby, C. and Wallace, B.A. (2007) A reference dataset for circular dichroism spectroscopy tailored for the bg-crystallin lens proteins. Experimental Eye Research. 84: 1001-1008.

Purkiss, A.G., Bateman, O.A., Wyatt, K., Wilmarth, W.A., David, L.L., Wistow, G.J. & Slingsby, C. (2007) Biophysical properties of gC-crystallin in human and mouse eye lens: the role of molecular dipoles. J. Mol. Biol. 372: 205-222.

Smith, M.A., Bateman, O.A., Jaenicke, R. and Slingsby, C. (2007) Mutation of interfaces in domain swapped human bB2-crystallin. Protein Science, 16: 615-625 (front cover)


Dr Alethea Tabor [top]


Mustapa,F.M., Bell,P.C., Hurley,C.A., Nicol,A., Guénin,E., Sarkar,S., Writer,M.J., Barker,S.E., Wong,J.B., Pilkington-Miksa,M.A., Papahadjopoulos-Sternberg,B., Shamlou,P.A., Hailes,H.C., Hart,S.L., Zicha,D., Tabor,A.B. (2007). Biophysical characterisation of an integrin-targeted lipopolyplex gene delivery vector. Biochemistry 46(45), 12930-12944.

Pilkington-Miksa MA, Writer MJ, Sarkar S, Meng QH, Barker SE, Shamlou PA, Hailes HC, Hart SL, Tabor AB. (2007) Targeting lipopolyplexes using bifunctional peptides incorporating hydrophobic spacer amino acids: synthesis, transfection, and biophysical studies. Bioconjug Chem. 18(6):1800-10.

Tranchant I, Hervé AC, Carlisle S, Lowe P, Slevin CJ, Forssten C, Dilleen J, Tabor AB, Williams DE, Hailes HC. (2007) Applications of tailored ferrocenyl molecules as electrochemical probes of biochemical interactions.Bioconjug Chem. 18(1):199-208.


Dr Salvador Tomas [top]


Battaglia G., Tomas S, Ryan A.J (2007) Lamellarsomes: metastable polymeric multilamellar aggregates. Soft Matter 3, 470.


Dijkstra H.P.,Hutchinson J.J, Hunter C.A, Qin H., Tomas S., Webb S.J, Williams N.H. (2007). Transmission of binding information across lipid bilayers. Chem.-Eur. J. 13, 7215.


Dr Maya Topf [top]


N/A


Professor Gabriel Waksman [top]


Bayliss R. , R. Harris, L. Coutte, A. Monier, R. Fronzes, P.J. Christie, P. Driscoll, and G. Waksman* (2007). NMR structure of a complex between the VirB9/VirB7 interaction domains of the pKM101 type IV secretion system. Proc. Natl. Acad. Sci. USA. 104(5):1673-1678.

Fowler P.W, S. Geroult, S. Jha, G. Waksman, and PV. Coveney* (2007) Rapid, Accurate, and Precise Calculation of Relative Binding Affinities for the SH2 Domain Using a Computational Grid. J. Chem. Theory Comput. 3:1193-1202.

Geroult S., M. Hooda, S. Virdee and G. Waksman* (2007). Prediction of solvation sites at the interface of Src SH2 domain complexes using molecular dynamics simulations. Chemical Biology and Drug Design. 70:87-99.

Hare S. , W. Fischer, R. Williams, L. Terradot, R. Bayliss, R. Haas, and G. Waksman* (2007). Identification, structure and mode of action of a new regulator of the Helicobacter pylori HP0525 ATPase. EMBO Journal. In Press.

Rothwell P. and G. Waksman* (2007). A pre-equilibrium before nucleotide binding limits fingers subdomain closure by Klentaq1. J. Biol. Chem. 282, 28884-28892. Verger D. , E. Bullitt*, S. Hultgren* and G. Waksman* (2007). Crystal structure of the P pilus rod subunit. PLoS Pathogens. 3(5):e73;001-009.

Verger D. , E. Bullitt*, S. Hultgren* and G. Waksman* (2007). Crystal structure of the P pilus rod subunit. PLoS Pathogens. 3(5):e73;001-009..


Professor Bonnie Wallace [top]

Evans P, Bateman OA, Slingsby C, Wallace BA. (2007) A reference dataset for circular dichroism spectroscopy tailored for the betagamma-crystallin lens proteins. Exp Eye Res. 84(5):1001-8

McKibbin, C., Farmer, N.A., Jeans, C., Reeves, P.J., Khorana, H.G., Wallace, B.A., Edwards, P.C., Villa, C., and Booth, P.J. (2007) Opsin Stability and Folding: Modulation by Phospholipid Bicelles. J. Mol. Biol. 374:1319–1332.



Dr Finn Werner [top]


N/A


Dr Lorenz Wernisch [top]

N/A

Dr Jonathan Wilden [top]

Wilden,J.D., Geldeard,L., Lee,C.C., Judd,D.B., Caddick,S. (2007). Trichlorophenol (TCP) Sulfonate Esters: A Selective Alternative to Pentafluorophenol Esters and Sulfonyl Chlorides for the Preparation of Sulfonamides. Chemical Communications (10), 1074-1076.


Dr Mark Williams [top]

Taylor JD, Gilbert PJ, Williams MA, Pitt WR and Ladbury JE (2007). Identification and thermodynamic analysis of novel small molecules targeted against the pY pocket of the Src SH2 domain. Proteins: Struct. Funct. Gen. 67, 981-990

John E. Ladbury and Mark A. Williams (2007). Application of isothermal titration calorimetry in exploring the extending interface. In Protein Interactions: Biophysical Approaches for the Study of Multi-Component Systems editor P Schuck, in press.



 





 
 
   
     
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