ISMB member publications in 2004

Dr Richard Bayliss

Bayliss R, Sardon T, Vernos I, Conti E (2003) Structural Basis of Aurora-A Activation by TPX2 at the Mitotic Spindle. Mol.Cell. 12: 851-62.

Professor Jeremy Brockes

Bettencourt-Dias M, Mittnacht S, Brockes JP. Links Heterogeneous proliferative potential in regenerative adult newt cardiomyocytes. J Cell Sci. 2003 Oct 1;116(19): 4001-9.

Imokawa Y, Brockes JP. Selective activation of thrombin is a critical determinant for vertebrate lens regeneration.Curr Biol. 2003 May 13;13(10):877-81.

Professor Steve Caddick

A Generic Approach for the Catalytic Reduction of Nitriles. S. Caddick, D. B. Judd, A. K. de K. Lewis, M. T. Reich, M. R. V. Williams, Tetrahedron, 2003, 59, 5417 – 5423

Synthesis of Functionalised Sulfonamides via 1,3-Dipolar Cycloaddition of Pentafluorophenyl Vinylsulfonates. S. Caddick, H. D. Bush, Organic Lett. 2003, 5, 2489 - 2492

Studies on High Temperature Amination of Aromatic Chlorides using Palladium-N-Heterocyclic-Carbene Complexes. S. Caddick, A. K. de K. Lewis, D. Sandham, L. R. Titcomb, A. McCarroll, B. P. Davies, F. G. N. Cloke. Molecular Diversity, 2003, 7, 115-123

Synthetic, Structural, and Mechanistic Studies on the Oxidative Addition of Aromatic Chlorides to a Palladium (N-Heterocyclic-Carbene) Complex: Relevance to Catalytic Amination. A. K. De Lewis, S. Caddick, F. G. N. Cloke, N. C. Billingham, P. B. Hitchcock, J. Leonard, J. Am. Chem. Soc. 2003, 125, 10066-10073

Chemical Synthesis and Cyotoxicity of Dihydroxylated Cyclopentenone Analogues of Neocarzinostatin Chromophore. M. D. Urbaniak, L. M. Frost, J. P. Bingham, L. R. Kelland, J. A. Hartley, D. N. Woolfson, S. Caddick. Bioorganic and Medicinal Chemistry Lett. 2003, 13, 2025 – 2027.

Professor Richard Catlow [top]

Not yet available

Professor Peter Coveney

E. S. Boek, J. Chin and P. V. Coveney, "Lattice Boltzmann Simulation of the Flow of Non-Newtonian Fluids in Porous Media," International Journal of Modern Physics B, 17, Nos. 1 & 2, 99-102 (2003); available online as a PS file (210KB).

B. M. Boghosian, P. J. Love, P. V. Coveney, I. V. Karlin, S. Succi, and J. Yepez, "Galilean-Invariant Lattice-Boltzmann Models with H-Theorem," Phys. Rev. E, 68, 025103(R) (2003); DOI: 10.1103/PhysRevE.68.025103.

A. A. Bowden, P. Boulet, P. V. Coveney and A. Whiting, "Combined experimental and theoretical investigations of clay-polymer nanocomposites: intercalation of single bifunctional organic compounds in Na+-montmorillonite and Na+-hectorite clays for the design of new materials," J. Mater. Chem., 13, 2540-2550 (2003); DOI: 10.1039/b307752g.

J. M. Brooke, P. V. Coveney, J. Harting, S. Jha, S. M. Pickles, R. L. Pinning, A. R. Porter, "Computational Steering in RealityGrid," Proceedings of the UK e-Science All Hands Meeting 2003, published online at, article is available here.

J. Chin, J. Harting, S. Jha, P. V. Coveney, A. R. Porter, and S. M. Pickles, "Steering in computational science: mesoscale modelling and simulation," Contemporary Physics, 44, 417-434 (2003); DOI: 10.1080/00107510310001605046.

P. V. Coveney, "Modeling structure and properties in mesoscale fluid systems," Fiona Case and Paschalis Alexandridis, eds., Mesoscale Phenomena in Fluid Systems, 206-226, (ACS Symposium Series), Oxford University Press 2003.

P. V. Coveney, "Self-organization and complexity: a new age for theory, computation and experiment," Phil. Trans. R. Soc. Lond. A 361, Number 1807, 1057 (2003); available online.

R. Delgado-Buscalioni and P. V. Coveney, "Continuum-particle hybrid coupling for mass, momentum, and energy transfers in unsteady fluid flow," Phys. Rev. E 67, 046704 (2003); available online from the American Physical Society.

R. Delgado-Buscalioni and P. V. Coveney, "USHER: An algorithm for particle insertion in dense fluids," J. Chem. Phys. 119, 2, 978-987 (2003); available online from the American Institute of Physics.

G. De Fabritiis and P. V. Coveney, "Dynamical geometry for multiscale dissipative particle dynamics," Comp. Phys. Commun., 153, Issue 2, 209-226 (2003); DOI: 10.1016/S0010-4655(03)00199-1 .

D. Flower, H. McSparron, M. J. Blythe, C. Zygouri, D. Taylor, P. Guan, S. Wan, P. V. Coveney, V. Walshe, P. Borrow, and I. A. Doytchinova, "Computational vaccinology: quantitative approaches," Novartis Found. Symp., 254, 102-20 (2003); discussion 120-5, 216-22, 250-2; abstract available online.

N. González-Segredo, M. Nekovee, and P. V. Coveney, "Three-dimensional lattice-Boltzmann simulations of critical spinodal decomposition in binary immiscible fluids," Phys. Rev. E 67, 046304 (2003); available online from the American Physical Society.

H. C. Greenwell, W. Jones, S. P. Newman, and P. V. Coveney, "Computer simulation of interlayer arrangement in cinnamate intercalated layered double hydroxides," J. Mol. Struct. 647, 75 (2003).

H. C. Greenwell, S. Stackhouse, P. V. Coveney, and W. Jones, "A density functional theory study of catalytic trans-esterification by tert-butoxide MgAl anionic clays," J. Phys. Chem. B 107, 3476 (2003); DOI: 10.1021/jp027663i.

J. Harting, S. Wan, and P. V. Coveney, "RealityGrid: high performance computing, visualisation, computational steering and teragrids", Capability Computing: The newsletter of the HPCx community, issue 2, 4-7 (2003); available online .

P. J. Love, M. Nekovee, P. V. Coveney, J. Chin, N. González-Segredo, and J. M. R. Martin, "Simulations of amphiphilic fluids using mesoscale lattice-Boltzmann and lattice-gas methods," Comp. Phys. Commun.153, Issue 3, 340-358 (2003); DOI: 10.1016/S0010-4655(03)00200-5.

J. Skår and P. V. Coveney, eds., "Self-organization: the quest for the origin and evolution of structure." Proceedings of the 2002 Nobel Symposium on self-organization. Phil. Trans. R. Soc. Lond. A 361, Number 1807 (2003); available from the Royal Society.

J. Skår and P. V. Coveney, "Preface," Phil. Trans. R. Soc. Lond. A 361, Number 1807, 1047 (2003); available online.

J. Skår and P. V. Coveney, "Developmental and physiological circuits: dissecting complexity. A report on a talk given by Dr Leroy Hood," Phil. Trans. R. Soc. Lond. A 361, Number 1807, 1313 (2003); available online.

D. A. Tilbrook, G. J. Pearson, M. Braden, and P. V. Coveney, "Prediction of polymerisation shrinkage using molecular modelling," J. Polym. Sci. Part B: Polym. Phys. 41, 528 (2003).

Dr Rainer Cramer [top]

On-target oxidation of methionine residues using hydrogen peroxide for composition-restricted matrix-assisted laser desorption/ionisation peptide mass mapping" S. Corless, R. Cramer, Rapid Commun. Mass Spectrom. 2003, 17, 1212-1215.

Phosphorylation of the WASP-VCA domain increases its affinity for the Arp2/3 complex and enhances actin polymerization by WASP G. O. C. Cory, R. Cramer, L. Blanchoin, A. J. Ridley Mol. Cell 2003, 11, 1229-1239."

Sample preparation of gel electrophoretically separated protein binding partners for analysis by mass spectrometry R. Cramer, M. Saxton, K. Barnouin Methods in Molecular Biology: Protein-Protein Interactions: Methods and Protocols, H. Fu (Ed.); Humana Press, Totowa, New Jersey 2003, in press.

Urinary proteomics of renal Fanconi syndrome, P. R. Cutillas, A. G. W. Norden, R. Cramer, A. L. Burlingame, R. J. Unwin, Contributions to Nephrology, Vol. 141: Proteomics in Nephrology, V. Thongboonkerd, J. B. Klein (Eds.); Karger, Basel, Switzerland 2003, 155-169.

Detection and analysis of urinary peptides by on-line liquid chromatography and mass spectrometry: application to patients with renal Fanconi syndrome, P. R. Cutillas, A. G. W. Norden, R. Cramer, A. L. Burlingame, R. J. Unwin, Clin. Sci. 2003, 104, 483-490.

Proteomics in the analysis of prostate cancer, S. Naaby-Hansen, K. Nagano, P. Gaffney, J. Masters, R. Cramer, Methods in Molecular Medicine, Vol. 81: Prostate Cancer Methods and Protocols, P. J. Russell, P. Jackson, E. A. Kingsley (Eds.); Humana Press, Totowa, New Jersey 2003, 277-297.

Characterization of protein phosphorylation by mass spectrometry using immobilized metal ion affinity chromatography with on-resin b-elimination and Michael addition, A. J. Thompson, S. R. Hart, C. Franz, K. Barnouin, A. Ridley, R. Cramer, Anal. Chem. 2003, 75, 3232-3243.

Protein kinase C phosphorylates ribosomal protein S6 kinase bII and regulates its subcellular localization, T. Valovka, F. Verdier, R. Cramer, A. Zhyvoloup, T. Fenton, H. Rebholz, M.-L. Wang, M. Gzhegotsky, A. Lutsyk, G. Matsuka, V. Filonenko, L. Wang, C. G. Proud, P. J. Parker, I. T. Gout, Mol. Cell. Biol. 2003, 23, 852-863.

Localization of a highly active pool of type II phosphatidylinositol 4-kinase in a p97/VCP-rich fraction of the endoplasmic reticulum, M. G. Waugh, S. Minogue, J. S. Anderson, A. Balinger, D. Blumenkrantz, D. P. Calnan, R. Cramer, J. J. Hsuan, Biochem. J. 2003, 373, 57-63.

Dr Andrew Dingley [top]

Dingley, A.J., Steger, G., Esters, B., Riesner, D., Grzesiek, S. (2003). Structural characterization of the 69-nt left terminal domain of the potato spindle tuber viroid by NMR and thermodynamic analysis. Journal of Molecular Biology 334(4), 751-767

Grzesiek,S.,Cordier,F.,Dingley,A.J. (2003). Hydrogen bond scalar couplings - A new tool for biomolecular NMR. in Rama Krishna,N.,Berliner,L.J. (ed.) Biological magnetic resonance: Protein NMR for the millenium. New York: Kluwer Academic/Plenum, 255-283

Dr Snezana Djordjevic [top]

Koshkin A, Nunn CM, Djordjevic S, Ortiz de Montellano PR. 'The mechanism of Mycobacterium tuberculosis alkylhydroperoxidase AhpD as defined by mutagenesis, crystallography, and kinetics.' 2003, J Biol Chem. 278:29502-8.

Dr Paul Driscoll [top]

Galbraith T. P., R. Harris, P. C. Driscoll and B. A. Wallace, Solution NMR studies of antiamoebin, a membrane channel-forming polypeptide.(2003) Biophys. J. 84, 185-194.

Mustapa M. F. M., R. Harris, S.L. Elliot, M. F. A. Groussier, J. Mould, D. Schultz, N. A. L. Chubb, P.R. J. Gaffney, P. C. Driscoll and A. B. Tabor, Synthesis of orthogonally protected lanthionines, (2003) J. Org. Chem. 68, 8185-8192.

Mustapa M. F. M., R. Harris, D. Esposito, J. Mould, N. A. L. Chubb, D. Schultz, P. C. Driscoll and A. B. Tabor, Synthesis of a cyclic peptide containing nor-lanthionine: effect of the thioether bridge on peptide conformation, (2003) J. Org. Chem. 68, 8193-8198.

Professor Jasminka Godovac-Zimmerman [top]

Armbruster, A., Biler, S. M., Koch, M. H. J., Coskum, U., and Godovac-Zimmermann, J., and Gruber, G. Dimer Formation of Subunit G of the Yeast V-ATPase (2003) Febs. Lett. 546, 395-400

Godovac-Zimmermann, J., and Brown, L. R. Proteomics Approaches to Elucidation of Signal Transduction Pathways. (2003) Current Opin. Mol. Therapeut. 5, 241-249.

Paclet, M.H., Davis, C., Kotsonis, P., Godovac-Zimmermann, J., Segal, A. W., and Dekker, L. V. N-formypeptide receptor subtypes in human neutrophils activate L-plastin phosphorylation through different signal transduction intermediates. (2003) Biochem. J. 377, 469-477.

Reeves, I., Nagl, M., Godovac-Zimmermann, J. and Segal, A. W. Reassesment of the microbicidal activity of reactive oxygen species and hypochlorous acid with reference to the phagocytic vacuole of the neutrophil granulocyte (2003) J. Med. Micr. 52, 643-651

Stannard, C., V., Lehenkari, P., and Godovac-Zimmermann, J. Functional Diversity of Endothelin Pathways in Human Lung Fibroblasts May be Based on Structural Diversity of the Endothelin receptors. (2003) Biochemistry 42, 13909-13918

Stannard, C., Soskic, V., and Godovac-Zimmermann, J. Rapid Changes in Protein Phosphorylation Show Diverse Cellular response Following Stimulation of Human Lung Fibroblasts with Endothelin-1. (2003) Biochemistry 42, 13919-13928

Dr Helen Hailes [top]

Helen C. Hailes, Ben Isaac and M. Hashim Javaid, ""The Synthesis of 2-Alkylated Cyclopentene-1,3-Diones: Novel Compounds with Olfactory Properties"", Syn. Commun., 2003, 33, 29-41.

G Herve, D Uwe Hahn, H C Hailes, A-C Herve, K J Goodworth and A M Hill. The Selective Functionalisation and Difunctionalisation of p-Substituted Calix[6]arene and Calix[8]arenes using Hydrophilic Moieties, Org. Biomol.
., 2003, 1, 427-435

M. A. Pilkington-Miksa, A. B. Tabor, H. C. Hailes, S. L. Hart, M. Writer, P. A. Shamlou and S. Sarkhar. Synthesis of Unusual Integrin-Binding Peptides for Inclusion into LID Transfection Complexes, Molecular Therapy, 2003, 3, S217.

Supti Sarkar, Hu Zhang, Stephen, L. Hart, Helen C. Hailes, Alethea B. Tabor, Parviz Ayazi Shamlou, M. Susana Levy. Impact of Biophysical and Chemical Properties of Non-viral Vector, AICHE Topical Conference Proceedings paper, 2003.

Sarkar S., Zhang H, Hart , SL, Hailes HC, Tabor AB, Ayazi Shamlou P. Prediction of size distribution of lipid-peptide-DNA vector particles using Monte Carlo simulation techniques, Biotechn. Appl. Biochem., 2003, 38, 95-102.

Professor Karl Hale [top]

Not yet available

Professor Elizabeth Hounsell [top]

Hounsell EF (2003) NMR of Carbohydrates, lipids and membranes. RSC Specialist Reports 32:335-360.

Dr Stefan Howorka [top]

Not yet available

Professor David Jones

Jones, D.T., & Ward, J.J. (2003) Prediction of disordered regions in proteins from position specific score matrices. Proteins. S6, 573-578.

Jones, D.T., & McGuffin, L.J. (2003) Assembling novel protein folds from super-secondary structural fragments. Proteins. S6, 480-485.

McGuffin, L.J., Jones, D.T. (2003) Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics. 19, 874-881.

McGuffin, L.J., Jones, D.T. (2003) Benchmarking secondary structure prediction for fold recognition. Proteins. 52, 166-175.

Pellegrini-Calace, M., Carotti, A. & Jones, D.T. (2003) Folding in lipid membranes(FILM): a novel method for the prediction of small membrane protein 3-D structures. Proteins: Structure, Function and Genetics. 50, 537-545.

Robinson, D.M., Jones, D.T., Kishino, H., Goldman, N. & Thorne, J.L. (2003) Protein evolution with dependence among codons due to tertiary structure. Mol. Biol. Evol. 20, 1692-1704.

Tress, M.L., Jones, D.T., Valencia, A. (2003) Predicting reliable regions in protein alignments from sequence profiles. J. Mol. Biol. 18, 705-718.

Ward, J.J., McGuffin, L.J., Buxton, B.F. & Jones, D. T.(2003) Secondary structure prediction using support vector machines. Bioinformatics, 19, 1650-1655.

Professor John Ladbury [top]

Bergqvist, S., Williams, M. A., O’Brien, R., & Ladbury, J. E. (2003) Halophilic adaptation of protein-DNA interactions. Biochemical Society Transactions 31, 677-680.

Cliff, M. J. & Ladbury, J. E. (2003) A survey of recent literature of applications of isothermal titration calorimetry. Journal of Molecular Recognition 16, 383-391.

Kowanetz, K., Szymkiewicz, I., Haglund, K., Kowanetz, M., Husnjak, K., Taylor, J. D., Soubeyran, P., Engstrom, U., Ladbury, J. E. & Dikic, I. (2003) Identification of a novel proline-arginine motif involved in CIN85-dependent clustering of Cbl and downregulation of EGF receptors. Journal of Biological Chemistry 278, 39735-39746.

O’Rourke, L., & Ladbury, J. E. (2003) Specificity is complex and time consuming. Accounts of Chemical Research 36, 410-416.

Williams, M. A., & Ladbury J. E. (2003) Hydrogen bonds in protein-ligand interactions. In “Protein-Ligand Interactions: From Molecular Recognition to Drug Design”. Editors H. –J Böhm & G. Schneider. Methods and Principles in Medicinal Chemistry Series. Wiley-VCH. Weinheim, Germany. ISBN 3-527-30521-1. pp. 137-161

Dr Philip Lowden [top]

Electrochemical, in vitro and cell culture analysis of integrated redox catalysts: implications for cancer therapy. G.I. Giles, N.M. Giles, C.A. Collins, K. Holt, F.H. Fry, P.A.S. Lowden, N.J. Gutowski, C. Jacob, Chem Commun 2003, 2030-2031.

Reply to “Minocycline is protective in a mouse model of Huntington's disease“, E. Hockly, J.-L. Beunard, P.A.S. Lowden, G.P. Bates, Annals of Neurology 2003, 54 , 842-843.

Suberoylanilide hydroxamic acid, a histone deacetylase inhibitor, ameliorates motor deficits in a mouse model of Huntington’s Disease. E. Hockly, V.M. Richon, B. Woodman, D.L. Smith, X. Zhou, E. Rosa, K. Sathasivam, S. Ghazi-Noori, A. Mahal, P.A.S. Lowden, J.S. Steffan, J.L. Marsh, L.M. Thompson, C.M. Lewis, P.A. Marks, G.P. Bates, Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 2041-2046.

Minocycline and doxycycline are not beneficial in a model of Huntington's disease”, D.L. Smith, B. Woodman, A. Mahal, K. Sathasivam, S. Ghazi-Noori, P.A.S. Lowden, G.P. Bates, E. Hockly, Annals of Neurology 2003, 54, 186-196.

Dr Charles Marson

R. A. Decréau, C. M. Marson, K. E. Smith and J. M. Behan, “Generation of Malodorous Steroids from Androsta-5,16-dienes and Androsta-4,16-dienes by Corynebacteria and other Human Axillary Bacteria”, J. Steroid Biochem. & Mol. Biol. 2003, 87, 327-336.

"Histone Deacetylase Inhibitors.”, S. P. Joel, C. M. Marson and P. Savy, UK Patent Cooperation Treaty (PCT) Application No. P34922WO, 2003, 88 pages. Filed 18.11.03.

C. M. Marson, A. S. Rioja, K. E. Smith and J. M. Behan, “The First Syntheses of Multiply Hydroxylated 16,17-Ene-Sterols Possessing the Androst-16-ene-3b,5a-diol Motif.”, Synthesis 2003, 535-538.

C. M. Marson, J. H. Pink, D. Hall, M. B. Hursthouse, A. Malik and C. Smith, “An Asymmetric Synthesis of Aza-Analogues of the Tricyclic Skeleton of Daphnane and the ABC Ring System of Phorbol.”, J. Org. Chem., 2003, 68, 792-798.

C. M. Marson, L. D. Farrand, R. Brettle and D. A. Dunmur, “Highly Efficient Syntheses of 3-Aryl-2-cycloalken-1-ones and an Evaluation of their Liquid Crystalline Properties.”, Tetrahedron 2003, 59, 4377-4381.

C. M. Marson, J. H. Pink and C. Smith, “Synthesis of the First Monoaromatic B-Ring 13-Azasteroid Ring System by Sequential Angular Annulation.”, Tetrahedron 2003, 59, 10019-10023.

C. M. Marson, N. Serradji, A. S. Rioja, S. P. Gastaud, J. P. Alao, R. C. Coombes and D. M. Vigushin, “Stereodefined and Polyunsaturated Inhibitors of Histone Deacetylase based on (2E,4E)-5-Arylpenta-2,4-dienoic Acid Hydroxyamides”, Bioorg. Med. Chem. Lett. 2004, 14, accepted.

Dr Andrew Martin [top]

Collis, A.V.J., Brouwer, A.R., Martin, A.C.R. (2003). Analysis of the Antigen Combining Site - Correlations Between Length and Sequence Composition of the Hypervariable Loops and the Nature of the Antigen. Journal of Molecular Biology 325(2), 337-354

Krauss, J., Arndt, M.A.E., Martin, A.C.R., Liu, H., Rybak, S.M. (2003). Specificity grafting of human antibody frameworks selected from a phage display library: generation of a highly stable humanized anti-CD22 single chain Fv fragment. Protein Engineering 16, 753-759

Dr Nigel Martin [top]

The CATH database: an extended protein family resource for structural and functional genomics, F. M. G. Pearl, C. F. Bennett, J. E. Bray, A. P. Harrison, N. Martin, A. Shepherd, I. Sillitoe, J. Thornton, C. A. Orengo, Nucleic Acids Res, 31(1), 452-455, (2003).

Dr Neil McDonald [top]

Movahedzadeh, F., Smith, D.A., Norman, R.A., Dinadayala, P., Murray-Rust, J. Russell, D.G., Kendall,S.L., Rison,S.A.G., McAlister, M.S.B., Bancroft, B.J., McDonald, N.Q., Daffe, M., Av-Gay, Y. a+A72nd Stoker. N. The Mycobacterium tuberculosis ino1 gene is essential for growth and virulence. Molecular Microbiology (2004) Feb;51(4):1003-14.

Tilley, S.J., Skippend, A., Murray-Rust, J., Swigart, P.M., Stewart, A., Morgan, C.P., Cockcroft, S. & McDonald, N.Q. Structure-function analysis of human phosphatidylinositol transfer protein alpha bound to phosphatidylinositol. Structure (2004) 12, 317-326.

Professor Boris Mirkin [top]

B. Mirkin, T. Fenner, M. Galperin and E. Koonin (2003) Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes, BMC Evolutionary Biology 2003, 3:2.

B. Mirkin and E. Koonin (2003) A top-down method for building genome classification trees with linear binary hierarchies, in M. Janowitz, J.-F. Lapointe, F. McMorris, B. Mirkin, and F. Roberts (Eds.) Bioconsensus, DIMACS Series, V. 61, Providence: AMS, 97-112.

S. Nascimento, B. Mirkin, and F. Moura-Pires (2003) Modeling proportional membership in fuzzy clustering, IEEE Transactions on Fuzzy Systems, 11, no. 2, 173-186.

Dr Carolyn Moores [top]

Regulation of KinI kinesin ATPase activity by binding to the microtubule lattice. Moores CA, Hekmat-Nejad M, Sakowicz R, Milligan RA. J Cell Biol 2003 Dec 8;163(5):963-71

A double-take on MAPS. Moores CA, Francis F, Perderiset M, Houdusse A. Nat Strucy Biol 2003 May;10(5):314-6

An atomic model for actin binding by the CH domains and spectrin-repeat modules of utrophin and dystrophin. Sutherland-Smith AJ, Moores CA, Norwood FL, Hatch V, Craig R, Kendrick-Jones J, Lehman, W. J Mol Biol 2003 May 23;329(1):15-33

Professor David Moss [top]

Clostridium absonum α-toxin: New insights into Clostridial phospholipase C substrate binding and specificity, Clark, G C, Briggs, D C, Karasawa, T, Wang, X, Cole, A R, Maegawa, T, Jayasekara, P N, Naylor, C E , Miller, J, Moss, D S, Nakamura, S, Basak, A K. and Titball, R W, J. Mol. Biol. (2003), 333, 759-769.

Estimation of weights and validation: a marginal likelihood approach, Lebedev, A A, Tickle, I J, Laskowski, R A and Moss, D S, Acta Cryst., (2003), D59, 1557-1566.

Dr Sylvia Nagl [top]

Giles I., J. Haley, D. A. Isenberg, D. S. Latchman, S. B. Nagl, A. Rahman (2003). Systematic review of sequences of human antiphospholipid and anti-beta 2 glycoprotein I antibodies (aPL). Seminars in Arthritis and Rheumatism, 32, 246-265.

Giles I. P., J. Haley, S. Nagl, D. S. Latchman, P. P. Chen, R. U. Chukwuocha, D. A. Isenberg DA, A. Rahman (2003). Relative importance of different human aPL derived heavy and light chains in the binding of aPL to cardiolipin. Molecular Immunology 40:49-60.

Kumar, S., S. Nagl, J. K. Kalsi, C. T. Ravirajan, D. Athwal, D. S. Latchman, L. H. Pearl, D. A. Isenberg (2003). Anti-cardiolipin/beta-2 glycoportein activities co-exist on human anti-DNA antibody light chains. Molecular Immunology 40: 517-530.

Nagl, S. B. (2003). Molecular evolution in Orengo, C., Jones, D. and Thornton, J. Bioinformatics: Sequence, Structure, Function. BIOS Publishing.

Nagl, S. B. (2003). Function prediction from protein sequence in Orengo, C., Jones, D. and Thornton, J. (eds.), Bioinformatics: Sequence, Structure, Function. BIOS Publishing.

Talmud, P. J., S. Martin, George Steiner et al. (2003). Progression of atherosclerosis is associated with variation in the a1-antitrypsin gene. Arterioscler Thromb Vasc Biol 23:644-649.

Professor Christine Orengo [top]

"Buchan DW, Rison SC, Bray JE, Lee D, Pearl F, Thornton JM, Orengo CA. Gene3D: structural assignments for the biologist and bioinformaticist alike. Nucleic Acids Res. (2003) 31:469-73.

Harrison, A, Mott, R., Sillitoe, I, Slidel, T., Thornton, J. and Orengo, C. Recognising the fold of a protein structure. Bioinformatics (2003) Vol 19, 1748.

Lee D, Grant A, Buchan D, Orengo C. A structural perspective on genome evolution. Curr Opin Struct Biol. 2003 Jun;13(3):359-69.

Orengo, CA. Sequence Comparison Methods In: Orengo CA, Jones DT, Thornton JM, editors. Bioinformatics: Sequence, Structure, Function. BIOS Publishing, 2003

Orengo, CA. Protein Structure Comparison. In: Orengo CA, Jones DT, Thornton JM, editors. Bioinformatics: Sequence, Structure, Function. BIOS Publishing, 2003.

Orengo, CA. Protein Strcture Classification. In: Orengo CA, Jones DT, Thornton JM, editors. Bioinformatics: Sequence, Structure, Function. BIOS Publishing, 2003.

Orengo CA, Pearl. F. The CATH Database in Bourne P. editor. Structural Bioinformatics. Wiley Publishing, 2003.

Orengo CA, Pearl FM, Thornton JM. The CATH domain structure database. Methods Biochem Anal. 2003;44:249-71.

Pearl FM, Bennett CF, Bray JE, Harrison AP, Martin N, Shepherd A, Sillitoe I, Thornton J, Orengo CA. The CATH database: an extended protein family resource for structural and functional genomics. Nucleic Acids Res. 2003 Jan 1;31(1):452-5.

Ranea, J, Buchan D., Thornton, J., Orengo, C. Distribution of Protein Superfamilies and Bacterial Genome Size:Evolutionary and Functional Analysis. J. Mol. Biol. (2003).

Watson JD, Todd AE, Bray J, Laskowski RA, Edwards A, Joachimiak A, Orengo CA, Thornton JM. Target selection and determination of function in structural genomics. IUMB Life. 2003 Apr-May;55(4-5):249-55.

Dr Elena Orlova [top]

Klaholz BP, Pape T, Zavialov AV, Myasnikov AG, Orlova EV, Vestergaard B, Ehrenberg M, van Heel M. Structure of the Escherichia coli ribosomal termination complex with release factor 2. (2003) Nature 421(6918):90-4.

Meissner U, Stohr M, Kusche K, Burmester T, Stark H, Harris JR, Orlova EV, Markl J. Quaternary structure of the European spiny lobster (Palinurus elephas) 1x6-mer hemocyanin from cryoEM and amino acid sequence data. (2003) J Mol Biol. 325(1):99-109.

Orlova EV, Gowen B, Droge A, Stiege A, Weise F, Lurz R, Van Heel M, Tavares P. Structure of a viral DNA gatekeeper at 10 A resolution by cryo-electron microscopy. (2003) EMBO J., 22(6):1255-1262.

Orlova EV, Papakosta M, Booy FP, van Heel M, Dolly JO. Voltage-gated K(+) Channel from Mammalian Brain: 3D Structure at 18A of the Complete (alpha)4(beta)4 Complex. (2003) J Mol Biol. 326(4):1005-12.

Professor Steve Perkins [top]

Aslam, M., Guthridge, J. M., Hack, B. K., Quigg, R. J., Holers, V. M. & Perkins, S. J. (2003) J. Mol. Biol., 329, 525 - 550. The extended multidomain solution structures of the complement protein Crry and its chimaeric conjugate Crry-Ig by scattering, analytical ultracentrifugation and constrained modelling: implications for function and therapy.

Deam, S., Uprichard, J. Eaton, J. T., Perkins, S. J. & Dolan, G. (2003) Factor X Leicester: Ile411Phe associated with a low antigen level and a disproportionately low functional activity of Factor X. Journal of Thrombosis & Haemostasis, 1, 603-605.

Idowu, S. M., Gautel, M, Perkins, S. J. & Pfuhl, M. (2003) J. Mol. Biol., 329, 745-761. Structure, stability and dynamics of the central domain of cardiac myosin binding protein C: Implications for multidomain assembly and cardiomyopathy related mutations.

Lee, Y.-C., Flora, R., McCafferty, J., Gor, J., Tsaneva, I. R. & Perkins, S. J. (2003) J. Mol. Biol. 333, 677-682. A tetramer-octamer equilibrium in Mycobacterium leprae and Escherichia coli RuvA by analytical ultracentrifugation.

Professor Peter Rich [top]

Iwaki,M.,Giotta,L.,Akinsiku,A.O.,Schägger,H.,Fisher,N.,Breton,J.,Rich,P.R. (2003). Redox transitions in bovine cytochrome bc1 complex studied by perfusion-induced ATR-FTIR spectroscopy. Biochemistry 42, 11109-11119

Iwaki,M.,Puustinen,A.,Wikström,M.,Rich,P.R. (2003). ATR-FTIR spectroscopy of the PM and F intermediates of bovine and Paracoccus denitrificans cytochrome c oxidase. Biochemistry 42, 8809-8817

Rich,P.R. (2003). The cost of living. Nature 421, 583

Rich, P.R. (2003) The molecular machinery of Keilin’s respiratory chain. Biochem. Soc. Trans., 31, 1095-1105.16:39

Professor David Saggerson [top]

Broadway, N.M., Pease, R.J., Birdsey, G., Shayeghi, M., Turner, N.A., Saggerson, E.D. (2003). The liver isoform of carnitine palmitoyltransferase 1 is not targeted to the endoplasmic reticulum. Biochemical Journal 370, 223-231

Professor Helen Saibil [top]

Farr GW, Fenton WA, Chaudhuri TK, Clare DK, Saibil HR, Horwich AL 'Folding with and without encapsulation by cis- and trans-only GroEL-GroES complexes' (2003) EMBO J. 22, 3220-3230.

Saibil, H, Cone,R & Chabre, M. 'Biophysics: is rhodopsin dimeric in native retinal rods?' (2003) Nature 426, 30-31.

Dr Renos Savva

Crystal structure of the Escherichia coli dcm very-short-patch DNA repair endonuclease bound to its reaction product-site in a DNA superhelix. Bunting KA, Roe SM, Headley A, Brown T, Savva R, Pearl LH Nucleic Acids Research 31 (6): 1633-1639 MAR 15 2003

Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome dos Reis M, Wernisch L, Savva R Nucleic Acids Research 31 (23): 6976-6985 DEC 1 2003

Dr David Selwood

Not yet available

Professor Elizabeth Shephard [top]

Bolsover, S.R., Hyams, J.S., Shephard, E.A., White, H., A.Weidemann, C.G. (2003), Cell Biology: A Short Course. Second edition., USA: Wiley-Liss

Bolsover,S.,R.,Hyams,J.S.,Shephard,E.A.,White,H.A.,Wiedemann,G.C. (2003), Cell Biology, A Short Course, New York: Wiley, 531pp.

Hernandez, D., Addou, S., Lee, D., Orengo, C., Shephard, E.A., Phillips, I.R. (2003). Trimethylaminuria and a human FMO3 mutation database. Human Mutation 22(3), 209-213

Dr Adrian Shepherd

Pearl F M G, Bennett C F, Bray J E, Harrison A P, Martin N, Shepherd A, Sillitoe I, Thornton J, Orengo C A (2003): "The CATH database: an extended protein family resource for structural and functional genomics", Nucleic Acids Research 31(1), 452-455

Shepherd A J, Gorse D, Thornton J M (2003): "A novel approach to the recognition of protein architecture from sequence using Fourier analysis and neural networks", Proteins 50(2), 290-302

Dr Christine Slingsby [top]

Aquilina, J.A., Benesch, J.L.P., Bateman, O.A., Slingsby, C. & Robinson, C.V. Polydispersity of a mammalian chaperone: mass spectrometry reveals the population of oligomers in alphaB-crystallin. (2003) Proc. Natl. Acad. Sci. 100, 10611-10616.

Basak, A., Bateman, O., Slingsby, C., Pande, A., Asherie, N., Ogun, O., Benedek, G.B. & Pande, J. High-resolution x-ray crystal structures of human gammaD crystallin (1.25A) and the R58H mutant (1.15A) associated with aculeiform cataract. (2003) J. Mol. Biol. 328, 1137 - 1147.

Bateman, O.A.,* Purkiss, A.G.,* van Montfort, R., Slingsby, C., Graham,C. & Wistow, G. The crystal structure of eta-crystallin: adaptation of a class 1 aldehyde dehydrogenase for a new role in the eye lens. (2003) Biochemistry 42, 4349-4356. (* equal first authors).

Bateman, O.A., Sarra, R., van Genesen, S.T., G. Kapp, G., Lubsen, N.H. and Slingsby, C. The stability of human acidic beta-crystallin oligomers and hetero-oligomers. (2003) Exp. Eye Res. 77, 409-422.

Nandrot, E., Slingsby, C., Basak, A., Cherif-Chefchaouni, M., Benazzouz B., Hajaji, Y., Boutayeb, S., Gribouval, O., Arbogast, L., Berraho, A., Abitbol M. & Hilal, L. Gamma-D Crystallin gene (CRYGD) mutation causes autosomal dominant congenital cerulean cataracts. (2003) J. Med. Genet. 40, 262-267.

van Montfort, R.L.M., Bateman, O.A., Lubsen, N.H. and Slingsby, C. Crystal structure of truncated human betaB1-crystallin. (2003) Protein Science, 12, 2606-2612.

Dr Alethia Tabor [top]

J. H. Dawe, C. T. Porter, J. M. Thornton, A. B. Tabor, A template search reveals mechanistic similarities and differences in b-ketoacyl synthases (KAS) and related enzymes. PROTEINS, Structure, Function and Genetics, 52, 427-435 (2003).

M. F. Mohd Mustapa, R. Harris, D. Esposito, N. A. L. Chubb, J. Mould, D. Schultz, P. C. Driscoll and A. B. Tabor, Synthesis of a cyclic peptide containing nor-lanthionine: effect of the thioether bridge on peptide conformation. J. Org. Chem., 68, 8193-8198 (2003).

M. F. Mohd Mustapa, R. Harris, N. Bulic-Subanovic, S. L. Elliott, M. F. A. Groussier, S. Bregant, J. Mould, N. A. L. Chubb, D. Schultz, P. R. J. Gaffney, P. C. Driscoll, A. B. Tabor, Synthesis of orthogonally protected lanthionines. J. Org. Chem., 68, 8185-8192 (2003).

M. A. Pilkington-Miksa, A. B. Tabor, H. C. Hailes, S. L. Hart, M. Writer, P. A. Shamlou, S. Sarkar, Synthesis of unusual integrin-binding peptides for inclusion into LID transfection complexes. Molecular Therapy, 7, 558 (2003).

S. Sarkar, H. Zhang, S. L. Hart, H. C. Hailes, A. B. Tabor, P. Ayazi Shamlou, Prediction of size distribution of lipid-peptide-DNA vector particles using Monte Carlo simulation techniques. Biotechnology and Applied Biochemistry, 38, 95-102 (2003).

S. Sarkar, H. Zhang, S. L. Hart, H. C. Hailes, A. B. Tabor, P. Ayazi Shamlou, M. S. Levy. Impact of Biophysical and Chemical Properties of Non-viral Vector, AICHE Topical Conference Proceedings paper (2003)

M. J. Writer, C. Hsu, J. Devitt, A. B. Tabor, C. Kinnon, D. Von Seggern, S. L. Hart, Increased efficiency of gene transfer into dendritic cells using phage display-derived peptides Molecular Therapy, 7, 1213 (2003).

Professor Gabriel Waksman [top]

S. Kumaran, R.A. Grucza, and G. Waksman (2003). The tandem SH2 domain of the Syk kinase: A Molecular Device that Adapts to Inter-phosphotyrosine Distances. Proceedings of the National Academy of Sciences (USA) .100:14828-14833.

O.Y. Lubman and G.Waksman (2003). Structural and Thermodynamic Basis for the Interaction of the Src SH2 Domain with the Activated Form of the PDGF b -Receptor. Journal of Molecular Biology . 328:655-668.

S.N. Savvides, H-J. Yeo, M.R. Beck, F. Blaesing, R. Lurz, E. Lanka, R. Buhrdorf, W. Fischer, R. Haas and G. Waksman (2003). VirB11 ATPases are dynamic hexameric assemblies: New insights into bacterial type IV secretion. EMBO Journal . 22:1969-1980.

H-J Yeo, Q. Yuan, M.R. Beck, C. Baron, and G. Waksman (2003). Structural and functional characterization of the VirB5 protein from the type IV secretion system encoded by the conjugative plasmid pKM101. Proceedings of the National Academy of Sciences (USA) . 100:15947-15952.

Professor Bonnie Wallace [top]

Cronin, N., O'Reilly, A., Duclohier, H., and Wallace, B.A. (2003) Binding of the anticonvulsant drug lamotrigine and the neurotoxin batrachotoxin to voltage-gated sodium channels induces conformational changes associated with block and steady-state activation. J. Biol. Chem. 278:10675-10682.

Galbraith, T.P., Harris, R., Driscoll, P.C., and Wallace, B.A. (2003) Solution NMR studies of antiamoebin, a membrane channel-forming polypeptide. Biophysical J. 84:185-194.

Miles, A.J., Wien, F., Lees, J.G., Rodger, A., Janes, R.W., and Wallace, B.A. (2003) Calibration and Standardisation of Synchrotron Radiation Circular Dichroism (SRCD) Amplitudes and Conventional Circular Dichroism (CD) Spectrophotometers. Spectroscopy 17:653-661.

O'Boyle, F. and Wallace, B.A. (2003) The Temperature Dependence of Gramicidin Conformational States in Octanol. Protein and Peptide Letters 10:9-17.

O'Reilly, A.O. and Wallace, B.A. (2003) The Peptaibol Antiamoebin as a Model Ion Channel: Similarities to Bacterial Potassium Channels. J. Pept. Sci., 9:769-775.

Richards, M.W., Eaton, J.T., Butcher, A.J., Berrow, N.S., Dolphin, A.C., Perkins, S.J., and Wallace, B.A. (2003) Solution structure of a calcium channel b subunit by molecular hydrodynamic methods. Biophysical J. 84:403a.

Wallace, B.A. and Janes, R.W. (2003) Circular Dichroism and Synchrotron Radiation Circular Dichroism Spectroscopy: Tools for Drug Discovery. Biochemical Transactions 31:631-633.

Wallace, B.A. Lees, J.G., Orry, A., Wien, F., Whitmore, L., Lobley, A., and Janes, R.J. (2003) Circular Dichroism Analyses of Membrane Proteins. Biophysical Journal 84:136a.

Wallace, B.A., Lees, J., Orry, A.J.W., Lobley, A., and Janes, R.W. (2003) Analyses of Circular Dichroism Spectra of Membrane Proteins. Protein Science 12:875-884.

Whitmore, L., Chugh, J.K., Snook, C.F. and Wallace, B.A. (2003) The Peptaibol Database A Sequence and Structure Resource. J. Pept. Sci. 9:663-665.

Dr Lorenz Wernisch

Not yet available



Institute of Structural Molecular Biology, University of London
Last modifi
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