Astbury Centre for Structural Molecular Biology

The Astbury Centre for Structural Molecular Biology

Astbury Centre Publications 2004-2007

Publications by Astbury Centre Members 2007

Allen, L. R. & Paci, E. (2007). Transition states for protein folding using molecular dynamics and experimental restraints. J. Phys.: Condens. Matter 19, Jul 18.
Ansell, R. J., Barrett, S. A., Meegan, J. E. & Warriner, S. L. (2007). On the interactions of alkyl 2-hydroxycarboxylic acids with alkoxysilanes: Selective esterification of simple 2-hydroxycarboxylic acids. Chem. Eur. J. 13, 4654-4664.
Baldwin, S. A., McConkey, G. A., Cass, C. E. & Young, J. D. (2007). Nucleoside transport as a potential target for chemotherapy in malaria. Curr. Pharm. Des. 13, 569-580.
Borysik, A. J., Morten, I. J., Radford, S. E. & Hewitt, E. W. (2007). Specific glycosaminoglycans promote unseeded amyloid formation from beta(2)-microglobulin under physiological conditions. Kidney Int. 72, 174-181.
Bracey, K. & Wray, D. (2007). Effect of tubulin binding on the heag2 potassium channel. Biophys. J., 126A-127A.
Brockwell, D. J. (2007). Force denaturation of proteins - an unfolding story. Current Nanoscience 3, 3-15.
Brockwell, D. J. (2007). Probing the mechanical stability of proteins using the atomic force microscope. Biochem. Soc. Trans. 35, 1564-1568.
Brockwell, D. J. & Radford, S. E. (2007). Intermediates: ubiquitous species on folding energy landscapes? Curr. Opin. Struct. Biol. 17, 30-37.
Bunka, D. H. J., Mantle, B. J., Morten, I. J., Tennent, G. A., Radford, S. E. & Stockley, P. G. (2007). Production and characterization of RNA aptamers specific for amyloid fibril epitopes. J. Biol. Chem. 282, 34500-34509.
Burgess, S. A., Yu, S. Z., Walker, M. L., Hawkins, R. J., Chalovich, J. M. & Knight, P. J. (2007). Structures of smooth muscle myosin and heavy meromyosin in the folded, shutdown state. J. Mol. Biol. 372, 1165-1178.
Burnley, B. T., Kalverda, A. P., Paisey, S. J., Berry, A. & Homans, S. W. (2007). Hadamard NMR spectroscopy for relaxation measurements of large (> 35 kDa) proteins. J. Biomol. NMR 39, 239-245.
Campbell, F., Plante, J., Carruthers, C., Hardie, M. J., Prior, T. J. & Wilson, A. J. (2007). Macrocyclic scaffolds derived from p-aminobenzoic acid. Chemical Communications, 2240-2242.
Care, M. A., Needham, C. J., Bulpitt, A. J. & Westhead, D. R. (2007). Deleterious SNP prediction: be mindful of your training data! Bioinformatics 23, 664-672.
Carr, S. B., Makris, G., Phillips, S. E. V. & Thomas, C. D. (2007). Crystallization and preliminary X-ray diffraction analysis of two N-terminal fragments of the DNA-cleavage domain of topoisomerase IV from Staphylococcus aureus. Acta Cryst F -Struct Biol & Crystal Commun 63, 59-59.
Caryl, J. A. & Thomas, C. D. (2007). The pC221 relaxosome: essential interactions for nicking and mobilization. Plasmid 57, 195-195.
Casey, T. M., Meade, J. L. & Hewitt, E. W. (2007). Organelle proteomics. Molecular & Cellular Proteomics 6, 767-780.
Cawood, R., Harrison, S. M., Dove, B. K., Reed, M. L. & Hiscox, J. A. (2007). Cell cycle dependent nucleolar localization of the coronavirus nucleocapsid protein. Cell Cycle 6, 863-867.
Cockell, S. J., Oliva, B. & Jackson, R. M. (2007). Structure-based evaluation of in silico predictions of protein-protein interactions using comparative docking. Bioinformatics 23, 573-581.
Craven, C. J., Al-Owais, M. & Parker, M. J. (2007). A systematic analysis of backbone amide assignments achieved via combinatorial selective labelling of amino acids. J. Biomol. NMR 38, 151-159.
Dalton, J. A. R. & Jackson, R. M. (2007). An evaluation of automated homology modelling methods at low target-template sequence similarity. Bioinformatics 23, 1901-1908.
Damaraju, V. L., Elwi, A. N., Hunter, C., Carpenter, P., Santos, C., Barron, G. M., Sun, X. J., Baldwin, S. A., Young, J. D., Mackey, J. R., Sawyer, M. B. & Cass, C. E. (2007). Localization of broadly selective equilibrative and concentrative nucleoside transporters, hENT1 and hCNT3, in human kidney. Am. J. Physiol. - Renal Physiol. 293, F200-F211.
Damiano, T., Morton, D. & Nelson, A. (2007). Photochemical transformations of pyridinium salts: mechanistic studies and applications in synthesis. Organic & Biomolecular Chemistry 5, 2735-2752.
Davies, J. R., Jackson, R. M., Mardia, K. V. & Taylor, C. C. (2007). The Poisson Index: a new probabilistic model for protein ligand binding site similarity. Bioinformatics 23, 3001-3008.
Dodd, K., Morton, D., Worden, S., Narquizian, R. & Nelson, A. (2007). Desymmetrisation of a centrosymmetric molecule by carbon-carbon bond formation: Asymmetric aldol reactions of a centrosymmetric dialdehyde. Chem. Eur. J. 13, 5857-5861.
Duarte, A. M. S., Wolfs, C., van Nuland, N. A. J., Harrison, M. A., Findlay, J. B. C., van Mierlo, C. P. M. & Hemminga, M. A. (2007). Structure and localization of an essential transmembrane segment of the proton translocation channel of yeast H+-VATPase. Biochimica Et Biophysica Acta-Biomembranes 1768, 218-227.
Embery, J., Graham, R. S., Duckett, R. A., Groves, D., Collis, M., Mackley, M. R. & McLeish, T. C. B. (2007). Tearing energy study of "oriented and relaxed" polystyrene in the glassy state. Journal Of Polymer Science Part B-Polymer Physics 45, 377-394.
Erbe, A., Bushby, R. J., Evans, S. D. & Jeuken, L. J. C. (2007). Tethered bilayer lipid membranes studied by simultaneous attenuated total reflectance infrared spectroscopy and electrochemical impedance spectroscopy. Journal Of Physical Chemistry B 111, 3515-3524.
Espinosa, M. & Thomas, C. D. (2007). Replication - Summary. Plasmid 57, 183-185.
Garner, A. E., Smith, D. A. & Hooper, N. M. (2007). Sphingomyelin chain length influences the distribution of GPI-anchored proteins in rafts in supported lipid bilayers. Mol. Membr. Biol. 24, 233-242.
Garnett, J. A., Baumberg, S., Stockley, P. G. & Phillips, S. E. V. (2007). A high-resolution structure of the DNA-binding domain of AhrC, the arginine repressor/activator protein from Bacillus subtilis. Acta Cryst F -Struct Biol & Crystal Commun 63, 914-917.
Garnett, J. A., Baumberg, S., Stockley, P. G. & Phillips, S. E. V. (2007). Structure of the C-terminal effector-binding domain of AhrC bound to its corepressor L-arginine. Acta Cryst F -Struct Biol & Crystal Commun 63, 918-921.
Garrow, A. G. & Westhead, D. R. (2007). A consensus algorithm to screen genomes for novel families of transmembrane beta barrel proteins. Proteins-Structure Function And Bioinformatics 69, 8-18.
Gold, N. D., Deville, K. & Jackson, R. M. (2007). New opportunities for protease ligand-binding site comparisons using SitesBase. Biochem. Soc. Trans. 35, 561-565.
Griffiths, R. & Whitehouse, A. (2007). Herpesvirus saimiri episomal persistence is maintained via interaction between open reading frame 73 and the cellular chromosome-associated protein MeCP2. J. Virol. 81, 4021-4032.
Gunn, S. J., Baker, A., Bertrarn, R. D. & Warriner, S. L. (2007). A novel approach to the solid-phase synthesis of peptides with a tetrazole at the C-terminus. Synlett, 2643-2646.
Gutmann, D. A. P., Mizohata, E., Newstead, S., Ferrandon, S., Henderson, P. J. F., Van Veen, H. W. & Byrne, B. (2007). A high-throughput method for membrane protein solubility screening: The ultracentrifugation dispersity sedimentation assay. Protein Sci. 16, 1422-1428.
Hadden, J. M., Declais, A. C., Carr, S. B., Lilley, D. M. J. & Phillips, S. E. V. (2007). The structural basis of Holliday junction resolution by T7 endonuclease. Nature 449, 621-U615.
Hamming, I., Cooper, M. E., Haagmans, B. L., Hooper, N. M., Korstanje, R., Osterhaus, A., Timens, W., Turner, A. J., Navis, G. & van Goor, H. (2007). The emerging role of ACE2 in physiology and disease. J. Pathol. 212, 1-11.
Hann, E., Kirkpatrick, N., Kleanthous, C., Smith, D. A., Radford, S. E. & Brockwell, D. J. (2007). The effect of protein complexation on the mechanical stability of Im9. Biophys. J. 92, L79-L81.
Harrison, S. M., Dove, B. K., Rothwell, L., Kaiser, P., Tarpey, I., Brooks, G. & Hiscox, J. A. (2007). Characterisation of cyclin D1 down-regulation in coronavirus infected cells. FEBS Lett. 581, 1275-1286.
Harrison, S. M., Tarpey, I., Rothwell, L., Kaiser, P. & Hiscox, J. A. (2007). Lithium chloride inhibits the coronavirus infectious bronchitis virus in cell culture. Avian Pathology 36, 109-114.
Heikkila, T., Ramsey, C., Davies, M., Galtier, C., Stead, A. M. W., Johnson, A. P., Fishwick, C. W. G., Boa, A. N. & McConkey, G. A. (2007). Design and synthesis of potent inhibitors of the malaria parasite dihydroorotate dehydrogenase. J. Med. Chem. 50, 186-191.
Henderson, P., Szakonyi, G., Leng, D., Ma, P., Blessie, H. Y. V. & Phillips-Jones, M. (2007). Bacterial membrane drug efflux and receptor proteins. Drugs Of The Future 32, 6-6.
Hiscox, J. A. (2007). RNA viruses: hijacking the dynamic nucleolus. Nature Reviews Microbiology 5, 119-127.
Hodgson, R., Kennedy, A., Nelson, A. & Perry, A. (2007). Synthesis of 3-sulfonyloxypyridines: Oxidative ring expansion of alpha-furylsulfonamides and N -> O sulfonyl transfer. Synlett, 1043-1046.
Homans, S. W. (2007). Dynamics and thermodynamics of ligand-protein interactions in Bioactive Conformation I. Top. Curr. Chem. 272, 51-82.
Homans, S. W. (2007). Water, water everywhere - except where it matters? Drug Discovery Today 12, 534-539.
Hong, B., Phornphisutthimas, S., Tilley, E., Baumberg, S. & McDowall, K. J. (2007). Streptomycin production by Streptomyces griseus can be modulated by a mechanism not associated with change in the adpA component of the A-factor cascade. Biotechnol. Lett. 29, 57-64.
Huysmans, G. H. M., Radford, S. E., Brockwell, D. J. & Baldwin, S. A. (2007). The N-terminal helix is a post-assembly clamp in the bacterial outer membrane protein PagP. J. Mol. Biol. 373, 529-540.
Ironmonger, A., Whittaker, B., Baron, A. J., Clique, B., Adams, C. J., Ashcroft, A. E., Stockley, P. G. & Nelson, A. (2007). Scanning conformational space with a library of stereo- and regiochemically diverse aminoglycoside derivatives: the discovery of new ligands for RNA hairpin sequences. Organic & Biomolecular Chemistry 5, 1081-1086.
Isguder, S. Z., Hooper, N. M. & Naim, H. Y. (2007). GPI-Anchor dictates trafficking of membrane dipeptidase. FASEB J. 21, A610-A610.
Jeuken, L. J. C., Bushby, R. J. & Evans, S. D. (2007). Proton transport into a tethered bilayer lipid membrane. Electrochemistry Communications 9, 610-614.
Jeuken, L. J. C., Daskalakis, N. N., Han, X. J., Sheikh, K., Erbe, A., Bushby, R. J. & Evans, S. D. (2007). Phase separation in mixed self-assembled monolayers and its effect on biomimetic membranes. Sensors And Actuators B-Chemical 124, 501-509.
Khatri, B. S., Kawakami, M., Byrne, K., Smith, D. A. & McLeish, T. C. B. (2007). Entropy and barrier-controlled fluctuations determine conformational viscoelasticity of single biomolecules. Biophys. J. 92, 1825-1835.
Khatri, B. S. & McLeish, T. C. B. (2007). Rouse model with internal friction: A coarse grained framework for single biopolymer dynamics. Macromolecules 40, 6770-6777.
Kotani, N., Sakakibara, H., Burgess, S. A., Kojima, H. & Oiwa, K. (2007). Mechanical properties of inner-arm dynein-F (dynein I1) studied with in vitro motility assays. Biophys. J. 93, 886-894.
Legrand, B., Ashcroft, A. E., Buchaillot, L. & Arscott, S. (2007). SOI-based nanoelectrospray emitter tips for mass spectrometry: a coupled MEMS and microfluidic design. Journal Of Micromechanics And Microengineering 17, 509-514.
Linse, S., Cabaleiro-Lago, C., Xue, W. F., Lynch, I., Lindman, S., Thulin, E., Radford, S. E. & Dawson, K. A. (2007). Nucleation of protein fibrillation by nanoparticles. Proc. Natl. Acad. Sci. U. S. A. 104, 8691-8696.
Liu, B. B., Westhead, D. R., Boyett, M. R. & Warwicker, J. (2007). Modelling the pH-dependent properties of Kv1 potassium channels. J. Mol. Biol. 368, 328-335.
MacRaild, C. A., Daranas, A. H., Bronowska, A. & Homans, S. W. (2007). Global changes in local protein dynamics reduce the entropic cost of carbohydrate binding in the arabinose-binding protein. J. Mol. Biol. 368, 822-832.
Manfield, I. W., Devlin, P. F., Jen, C. H., Westhead, D. R. & Gilmartin, P. M. (2007). Conservation, convergence, and divergence of light-responsive, circadian-regulated, and tissue-specific expression patterns during evolution of the Arabidopsis GATA gene family. Plant Physiol. 143, 941-958.
Mardia, K. V., Nyirongo, V. B., Green, P. J., Gold, N. D. & Westhead, D. R. (2007). Bayesian refinement of protein functional site matching. Bmc Bioinformatics 8.
Maruta, F., Akita, N., Nakayama, J., Miyagawa, S., Ismail, T., Rowlands, D. C., Kerr, D. J., Fisher, K. D., Seymour, L. W. & Parker, A. L. (2007). Bacteriophage biopanning in human tumour biopsies to identify cancer-specific targeting ligands. J. Drug Target. 15, 311-319.
Mathai, M., Radford, S. E. & Holland, P. (2007). Progressive glycosylation of albumin and its effect on the binding of homocysteine may be a key step in the pathogenesis of vascular damage in diabetes mellitus. Med. Hypotheses 69, 166-172.
McLeish, T. C. B. (2007). A theory for heterogeneous states of polymer melts produced by single chain crystal melting. Soft Matter 3, 83-87.
Morten, I. J., Gosal, W. S., Radford, S. E. & Hewitt, E. W. (2007). Investigation into the role of macrophages in the formation and degradation of beta(2)-microglobulin amyloid fibrils. J. Biol. Chem. 282, 29691-29700.
Morton, V. L., Friel, C. T., Allen, L. R., Paci, E. & Radford, S. E. (2007). The effect of increasing the stability of non-native interactions on the folding landscape of the bacterial immunity protein Im9. J. Mol. Biol. 371, 554-568.
Nagalingam, A. C., Radford, S. E. & Warriner, S. L. (2007). Avoidance of epimerization in the synthesis of peptide thioesters using Fmoc protection. Synlett, 2517-2520.
Needham, C. J., Bradford, J. R., Bulpitt, A. J. & Westhead, D. R. (2007). A primer on learning in Bayesian networks for computational biology. Plos Computational Biology 3, 1409-1416.
Noronha, M., Lima, J. C., Paci, E., Santos, H. & Macanita, A. L. (2007). Tracking local conformational changes of ribonuclease A using picosecond time-resolved fluorescence of the six tyrosine residues. Biophys. J. 92, 4401-4414.
Numata, N., Roberts, A., Burgess, S. A., Kon, T., Okura, R., Knight, P. & Sutoh, K. (2007). Are six AAA modules sufficient to form the AAA ring of dynein? Biophys. J., 496A-496A.
Parkin, E. T., Watt, N. T., Hussain, I., Eckman, E. A., Eckman, C. B., Manson, J. C., Baybutt, H. N., Turner, A. J. & Hooper, N. M. (2007). Cellular prion protein regulates beta-secretase cleavage of the Alzheimer's amyloid precursor protein. Proc. Natl. Acad. Sci. U. S. A. 104, 11062-11067.
Perazzolo, C., Verde, M., Homans, S. W. & Bodenhausen, G. (2007). Evidence of chemical exchange in recombinant Major Urinary Protein and quenching thereof upon pheromone binding. J. Biomol. NMR 38, 3-9.
Pinney, J. W., Papp, B., Hyland, C., Warnbua, L., Westhead, D. R. & McConkey, G. A. (2007). Metabolic reconstruction and analysis for parasite genomes. Trends In Parasitology 23, 548-554.
Rahman, M., Ismat, F., McPherson, M. J. & Baldwin, S. A. (2007). Topology-informed strategies for the overexpression and purification of membrane proteins. Mol. Membr. Biol. 24, 407-U416.
Reed, M. L., Howell, G., Harrison, S. M., Spencer, K. A. & Hiscox, J. A. (2007). Characterization of the nuclear export signal in the coronavirus infectious bronchitis virus nucleocapsid protein. J. Virol. 81, 4298-4304.
Reig, N., del Rio, C., Casagrande, F., Ratera, M., Gelpi, J. L., Torrents, D., Henderson, P. J. F., Xie, H., Baldwin, S. A., Zorzano, A., Fotiadis, D. & Palacin, M. (2007). Functional and structural characterization of the first prokaryotic member of the L-amino acid transporter (LAT) family - A model for APC transporters. J. Biol. Chem. 282, 13270-13281.
Rella, M., Elliot, J. L., Revett, T. J., Lanfear, J., Phelan, A., Jackson, R. M., Turner, A. J. & Hooper, N. M. (2007). Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE. Bmc Genomics 8.
Rogers, M. S., Tyler, E. M., Akyumani, N., Kurtis, C. R., Spooner, R. K., Deacon, S. E., Tamber, S., Firbank, S. J., Mahmoud, K., Knowles, P. F., Phillips, S. E. V., McPherson, M. J. & Dooley, D. M. (2007). The stacking tryptophan of galactose oxidase: A second-coordination sphere residue that has profound effects on tyrosyl radical behavior and enzyme catalysis. Biochemistry 46, 4606-4618.
Sader, K., Reedy, M., Popp, D., Lucaveche, C. & Trinick, J. (2007). Measuring the resolution of uncompressed plastic sections cut using an oscillating knife ultramicrotome. J. Struct. Biol. 159, 29-35.
Say, Y. H. & Hooper, N. M. (2007). Contamination of nuclear fractions with plasma membrane lipid rafts. Proteomics 7, 1059-1064.
Shibayama, K., Wachino, J., Arakawa, Y., Saidijam, M., Rutherford, N. G. & Henderson, P. J. F. (2007). Metabolism of glutamine and glutathione via gamma-glutamyltranspeptidase and glutamate transport in Helicobacter pylori: possible significance in the pathophysiology of the organism. Mol. Microbiol. 64, 396-406.
Slugoski, M. D., Loewen, S. K., Ng, A. M. L., Smith, K. M., Yao, S. Y. M., Karpinski, E., Cass, C. E., Baldwin, S. A. & Young, J. D. (2007). Specific mutations in transmembrane helix 8 of human concentrative Na+/nucleoside cotransporter hCNT1 affect permeant selectivity and cation coupling. Biochemistry 46, 1684-1693.
Smith, D. P., Giles, K., Bateman, R. H., Radford, S. E. & Ashcroft, A. E. (2007). Monitoring copopulated conformational states during protein folding events using Electrospray ionization-ion mobility spectrometry-mass spectrometry. J. Am. Soc. Mass Spectrom. 18, 2180-2190.
Smith, F. M., Slugosic, M. D., Cass, C. E., Baldwin, S. A., Karpinsi, E. & Young, J. D. (2007). Cation coupling properties of human concentrative nucleoside transporters hCNT1, hCNT2 and hCNT3. Mol. Membr. Biol. 24, 53-64.
Song, C. F., Kendrick-Jones, J. & Trinick, J. (2007). Electron microscopy of negatively stained myosin VI molecules. Biophys. J., 494A-494A.
Spencer, K. A., Dee, M., Britton, P. & Hiscox, J. A. (2007). Role of phosphorylation clusters in the biology of the coronavirus infectious bronchitis virus nucleocapsid protein. Virology 370, 373-381.
Spencer, K. A., Osori, F. A. & Hiscox, J. A. (2007). Recombinant viral proteins for use in diagnostic ELISAs to detect virus infection. Vaccine 25, 5653-5659.
Stead, J. A. & McDowall, K. J. (2007). Two-dimensional gel electrophoresis for identifying proteins that bind DNA or RNA. Nature Protocols 2, 1839-1848.
Stead, M. A., Trinh, C. H., Garnett, J. A., Carr, S. B., Baron, A. J., Edwards, T. A. & Wright, S. C. (2007). A beta-sheet interaction interface directs the tetramerisation of the Miz-1 POZ domain. J. Mol. Biol. 373, 820-826.
StGelais, C., Tuthill, T. J., Clarke, D. S., Rowlands, D. J., Harris, M. & Griffin, S. (2007). Inhibition of hepatitis C virus p7 membrane channels in a liposome-based assay system. Antiviral Res. 76, 48-58.
Stockley, P. G., Rolfsson, O., Thompson, G. S., Basnak, G., Francese, S., Stonehouse, N. J., Homans, S. W. & Ashcroft, A. E. (2007). A simple, RNA-mediated allosteric switch controls the pathway to formation of a T=3 viral capsid. J. Mol. Biol. 369, 541-552.
Syme, N. R., Dennis, C., Phillips, S. E. V. & Homans, S. W. (2007). Origin of heat capacity changes in a "Nonclassical" hydrophobic interaction. Chembiochem 8, 1509-1511.
Szakonyi, G., Leng, D., Ma, P., Bettaney, K. E., Saidijam, M., Ward, A., Zibaei, S., Gardiner, A. T., Cogdell, R. J., Butaye, P., Kolsto, A. B., O'Reilly, J., Hope, R. J., Rutherford, N. G., Hoyle, C. J. & Henderson, P. J. F. (2007). A genomic strategy for cloning, expressing and purifying efflux proteins of the major facilitator superfamily. J. Antimicrob. Chemother. 59, 1265-1270.
Taylor, D. R. & Hooper, N. M. (2007). The low-density lipoprotein receptor-related protein 1 (LRP1) mediates the endocytosis of the cellular prion protein. Biochem. J. 402, 17-23.
Taylor, D. R. & Hooper, N. M. (2007). Role of lipid rafts in the processing of the pathogenic prion and Alzheimer's amyloid-beta proteins. Semin. Cell Dev. Biol. 18, 638-648.
Tedbury, P. R. & Harris, M. (2007). Characterisation of the role of zinc in the hepatitis C virus NS2/3 auto-cleavage and NS3 protease activities. J. Mol. Biol. 366, 1652-1660.
Teixeira, P. I. C., Read, D. J. & McLeish, T. C. B. (2007). Demixing instability in coil-rod blends undergoing polycondensation reactions. J. Chem. Phys. 126.
Thomas, C. D. & Joce, C. M. (2007). The inverted complementary repeat is a consequence of, not a requirement for, the action of a replication initiator protein at a replication origin. Plasmid 57, 186-186.
Thomson, N. H., Crampton, N., Bonass, W. A., Kirkham, J. & Rivetti, C. (2007). RNA polymerase collisions in the atomic force microscope. Biophys. J., 411A-411A.
Trinh, C. H., Liu, Y., Phillips, S. E. V. & Phillips-Jones, M. K. (2007). Structure of the response regulator VicR DNA-binding domain. Acta Crystallographica Section D-Biological Crystallography 63, 266-269.
Tuthill, T. J., Rowlands, D. J. & Killington, R. A. (2007). Picornavirus entry. Future Virology 2, 343-351.
Vardy, E., Rice, P. J., Bowie, P. C. W., Holmes, J. D., Grant, P. J. & Hooper, N. M. (2007). Increased circulating insulin-like growth factor-1 in late-onset Alzheimer's disease. Journal Of Alzheimers Disease 12, 285-290.
Visser, F., Sun, L. J., Damaraju, V., Tackaberry, T., Peng, Y. S., Robins, M. J., Baldwin, S. A., Young, J. D. & Cass, C. E. (2007). Residues 334 and 338 in transmembrane segment 8 of human equilibrative nucleoside transporter 1 are important determinants of inhibitor sensitivity, protein folding, and catalytic turnover. J. Biol. Chem. 282, 14148-14157.
Vohra, R. S., Murphy, J., Walker, J. H., Homer-Vanniasinkam, S. & Ponnambalam, S. (2007). Refolding and functional characterization of the lectin-like oxidized low-density lipoprotein scavenger receptor (LOX-1). FASEB J. 21, A852-A852.
Vohra, R. S., Murphy, J. E., Walker, J. H., Homer-Vanniasinkam, S. & Ponnambalam, S. (2007). Functional refolding of a recombinant C-type lectin-like domain containing intramolecular disulfide bonds. Protein Expr. Purif. 52, 415-421.
Watt, N. T., Routledge, M. N., Wild, C. P. & Hooper, N. M. (2007). Cellular prion protein protects against reactive-oxygen-species-induced DNA damage. Free Radic. Biol. Med. 43, 959-967.
White, H. D. & Ashcroft, A. E. (2007). Real-time measurement of myosin-nucleotide noncovalent complexes by electrospray ionization mass spectrometry. Biophys. J. 93, 914-919.
Whittaker, S. B. M., Spence, G. R., Grossmann, J. G., Radford, S. E. & Moore, G. R. (2007). NMR analysis of the conformational properties of the trapped on-pathway folding intermediate of the bacterial immunity protein Im7. J. Mol. Biol. 366, 1001-1015.
Wijma, H. J., Jeuken, L. J. C., Verbeet, M. P., Armstrong, F. A. & Canters, G. W. (2007). Protein film voltammetry of copper-containing nitrite reductase reveals reversible inactivation. J. Am. Chem. Soc. 129, 8557-8565.
Wilson, A. J. (2007). Non-covalent polymer assembly using arrays of hydrogen-bonds. Soft Matter 3, 409-425.
Wilson, S. J., Tsao, E. H., Webb, B. L. J., Ye, H. T., Dalton-Griffin, L., Tsantoulas, C., Gale, C. V., Du, M. Q., Whitehouse, A. & Kellam, P. (2007). X box binding protein XBP-1s transactivates the Kaposi's sarcoma-associated herpesvirus (KSHV) ORF50 promoter, linking plasma cell differentiation to KSHV reactivation from latency. J. Virol. 81, 13578-13586.
Wozniak, A. L., Griffin, S., Rowlands, D., Harris, M. & Weinman, S. A. (2007). Hepatitis CP 7 protein alters the proton conductance of intracellular membrane vesicles. Hepatology 46, 452A-452A.
Yao, S. Y. M., Ng, A. M. L., Slugoski, M. D., Smith, K. M., Mulinta, R., Karpinski, E., Cass, C. E., Baldwin, S. A. & Young, J. D. (2007). Conserved glutamate residues are critically involved in Na+/Nucleoside cotransport by human concentrative nucleoside transporter 1 (hCNT1). J. Biol. Chem. 282, 30607-30617.
Yoon, H. J., Park, S. W., Lee, H. B., Im, S. Y., Hooper, N. M. & Park, H. S. (2007). Release of renal dipeptidase from glycosylphosphatidylinositol anchor by insulin-triggered phospholipase C/intracellular Ca2+. Arch. Pharm. Res. 30, 608-615.
You, J. H., Reed, M. L. & Hiscox, J. A. (2007). Trafficking motifs in the SARS-coronavirus nucleocapsid protein. Biochem. Biophys. Res. Commun. 358, 1015-1020.
Zhang, J., Visser, F., King, K. M., Baldwin, S. A., Young, J. D. & Cass, C. E. (2007). The role of nucleoside transporters in cancer chemotherapy with nucleoside drugs. Cancer Metastasis Rev. 26, 85-110.
Zhang, W. K., Dillingham, M. S., Thomas, C. D., Allen, S., Roberts, C. J. & Soultanas, P. (2007). Directional loading and stimulation of PcrA helicase by the replication initiator protein RepD. J. Mol. Biol. 371, 336-348.

Publications by Astbury Centre Members 2006

Anstiss, M. & Nelson, A. (2006). Catalytic and stoichiometric approaches to the desymmetrisation of centrosymmetric piperazines by enantioselective acylation: a total synthesis of Dragmacidin A. Org. Biomol. Chem. 4, 4135-4143.
Arscott, S., Gaudet, M., Brinkmann, M., Ashcroft, A. E. & Blossey, R. (2006). Capillary filling of miniaturized sources for electrospray mass spectrometry. J. Phys.-Condes. Matter 18, S677-S690.
Barnes, K., Dobrzynski, H., Foppolo, S., Beal, P. R., Ismat, F., Scullion, E. R., Sun, L. J., Tellez, J., Ritzel, M. W. L., Claycomb, W. C., Cass, C. E., Young, J. D., Billeter-Clark, R., Boyett, M. R. & Baldwin, S. A. (2006). Distribution and functional characterization of equilibrative nucleoside transporter-4, a novel cardiac adenosine transporter activated at acidic pH. Circulation Research 99, 510-519.
Barratt, E., Bronowska, A., Vondrasek, J., Cerny, J., Bingham, R., Phillips, S. & Homans, S. W. (2006). Thermodynamic penalty arising from burial of a ligand polar group within a hydrophobic pocket of a protein receptor. J. Mol. Biol. 362, 994-1003.
Bentham, M., Mazaleyrat, S. & Harris, M. (2006). A cluster of arginine residues near the N-terminus of the HIV-1 Nef protein is required both for membrane association and CD4 down-modulation. J. Gen. Virol. 87, 563-571.
Bentham, M., Mazaleyrat, S. & Harris, M. (2006). Role of myristoylation and N-terminal basic residues in membrane association of the human immunodeficiency virus type 1 Nef protein. J. Gen. Virol. 87, 563-571.
Besong, G., Jarowicki, K., Kocienski, P. J., Sliwinski, E. & Boyle, F. T. (2006). Synthesis of (S)-(-)-N-acetylcolchinol using intramolecular biaryl oxidative coupling. Org. Biomol. Chem. 4, 2193-2207.
Bingham, R. J., Dive, V., Phillips, S. E. V., Shirras, A. D. & Isaac, R. E. (2006). Structural diversity of angiotensin-converting enzyme - Insights from structure-activity comparisons of two Drosophila enzymes. Febs J. 273, 362-373.
Boda, K. & Johnson, A. P. (2006). Molecular complexity analysis of de novo designed ligands. Journal of Medicinal Chemistry 49, 5869-5879.
Boyne, J. R. & Whitehouse, A. (2006). gamma-2 Herpes virus post-transcriptional gene regulation. Clin. Microbiol. Infect. 12, 110-117.
Boyne, J. R. & Whitehouse, A. (2006). Nucleolar trafficking is essential for nuclear export of intronless herpesvirus mRNA. Proc. Natl. Acad. Sci. U. S. A. 103, 15190-15195.
Bracey, K. & Wray, D. (2006). Tubulin as a possible binding partner of the heag2 potassium channel. Acta Pharmacologica Sinica 27, 186-186.
Bradford, J. R., Needham, C. J., Bulpitt, A. J. & Westhead, D. R. (2006). Insights into protein-protein interfaces using a Bayesian network prediction method. J. Mol. Biol. 362, 365-386.
Bunka, D. H. J. & Stockley, P. G. (2006). Aptamers come of age - at last. Nature Reviews Microbiology 4, 588-596.
Burgoyne, N. J. & Jackson, R. M. (2006). Predicting protein interaction sites: binding hot-spots in protein-protein and protein-ligand interfaces. Bioinformatics 22, 1335-1342.
Carr, S. B., Makris, G., Phillips, S. E. V. & Thomas, C. D. (2006). Crystallization and preliminary X-ray diffraction analysis of two N-terminal fragments of the DNA-cleavage domain of topoisomerase IV from Staphylococcus aureus. Acta Crystallographica Section F-Structural Biology and Crystallization Communications 62, 1164-1167.
Caryl, J. A. & Thomas, C. D. (2006). Investigating the basis of substrate recognition in the pC221 relaxosome. Molecular Microbiology 60, 1302-1318.
Clare, D. K., Orlova, E. V., Finbow, M. A., Harrison, M. A., Findlay, J. B. C. & Saibil, H. R. (2006). An expanded and flexible form of the vacuolar ATPase membrane sector. Structure 14, 1149-1156.
Clarke, D., Griffin, S., Beales, L., Gelais, C. S., Burgess, S., Harris, M. & Rowlands, D. (2006). Evidence for the formation of a heptameric ion channel complex by the hepatitis C virus p7 protein in vitro. J. Biol. Chem. 281, 37057-37068.
Cobos, E. S. & Radford, S. E. (2006). Sulfate-induced effects in the on-pathway intermediate of the bacterial immunity protein Im7. Biochemistry 45, 2274-2282.
Connell, S. D. & Smith, D. A. (2006). The atomic force microscope as a tool for studying phase separation in lipid membranes. Mol. Membr. Biol. 23, 17-28.
Cooksey, J. P., Kocienski, P. J., Li, Y. F., Schunk, S. & Snaddon, T. N. (2006). Synthesis of the C1-C16 fragment of ionomycin using a neutral (eta(3)-allyl)iron complex. Org. Biomol. Chem. 4, 3325-3336.
Cordy, J. M., Hooper, N. M. & Turner, A. J. (2006). The involvement of lipid rafts in Alzheimer's disease. Mol. Membr. Biol. 23, 111-122.
Crampton, N., Bonass, W. A., Kirkham, J., Rivetti, C. & Thomson, N. H. (2006). Collision events between RNA polymerases in convergent transcription studied by atomic force microscopy. Nucleic Acids Res. 34, 5416-5425.
Crampton, N., Bonass, W. A., Kirkham, J. & Thomson, N. H. (2006). Studying silane mobility on hydrated mica using ambient AFM. Ultramicroscopy 106, 765-770.
Crampton, N., Thomson, N. H., Kirkham, J., Gibson, C. W. & Bonass, W. A. (2006). Imaging RNA polymerase-amelogenin gene complexes with single molecule resolution using atomic force microscopy. European Journal of Oral Sciences 114, 133-138.
Crawford, C., Nelson, A. & Patel, I. (2006). Development of an approach to the synthesis of the ABC ring system of Hemibrevetoxin B. Organic Letters 8, 4231-4234.
Das, C., Inkson, N. J., Read, D. J., Kelmanson, M. A. & McLeish, T. C. B. (2006). Computational linear rheology of general branch-on-branch polymers. Journal of Rheology 50, 207-235.
Das, C., Read, D. J., Kelmanson, M. A. & McLeish, T. C. B. (2006). Dynamic scaling in entangled mean-field gelation polymers. Phys. Rev. E 74.
Davies, R. P. W., Aggeli, A., Beevers, A. J., Boden, N., Carrick, L. M., Fishwick, C. W. G., McLeish, T. C. B., Nyrkova, I. & Semenov, A. N. (2006). Self-assembling beta-sheet tape forming peptides. Supramolecular Chemistry 18, 435-443.
Dobrzynski, H., Tellez, J. O., Barnes, K., Chandler, N. J., Qureshi, M. A., Imrit, N., Greener, I. D., Baldwin, S. A., Billeter, R., Boyett, M. R. & Howarth, F. C. (2006). Effects of streptozotocin-induced diabetes on connexin43 mRNA and protein expression in ventricular muscle. Journal of Molecular and Cellular Cardiology 40, 1008-1008.
Dove, B., Brooks, G., Bicknell, K., Wurm, T. & Hiscox, J. A. (2006). Cell cycle perturbations induced by infection with the coronavirus infectious bronchitis virus and their effect on virus replication. J. Virol. 80, 4147-4156.
Dove, B. K., Bicknell, K., Brooks, G., Harrison, S. & Hiscox, J. A. (2006). Infectious bronchitis coronavirus induces cell-cycle perturbations. In Nidoviruses: Toward Control of Sars and Other Nidovirus Diseases, Vol. 581, pp. 357-362.
Dove, B. K., You, J. H., Reed, M. L., Emmett, S. R., Brooks, G. & Hiscox, J. A. (2006). Changes in nucleolar morphology and proteins during infection with the coronavirus infectious bronchitis virus. Cellular Microbiology 8, 1147-1157.
Dubuis, E., Rockliffe, N., Hussain, M., Boyett, M., Wray, D. & Gawler, D. (2006). Evidence for multiple Src binding sites on the alpha 1c L-type Ca2+ channel and their roles in activity regulation. Cardiovascular Research 69, 391-401.
Edwards, T. A., Butterwick, J. A., Zeng, L., Gupta, Y. K., Wang, X., Wharton, R. P., Palmer, A. G. & Aggarwal, A. K. (2006). Solution structure of the Vts1 SAM domain in the presence of RNA. J. Mol. Biol. 356, 1065-1072.
Ellingham, M., Bunka, D. H. J., Rowlands, D. J. & Stonehouse, N. J. (2006). Selection and characterization of RNA aptamers to the RNA-dependent RNA polymerase from foot-and-mouth disease virus. RNA 12, 1970-1979.
Ewan, L. C., Jopling, H. M., Jia, H. Y., Mittar, S., Bagherzadeh, A., Howell, G. J., Walker, J. H., Zachary, I. C. & Ponnambalam, S. (2006). Intrinsic tyrosine kinase activity is required for vascular endothelial growth factor receptor 2 ubiquitination, sorting and degradation in endothelial cells. Traffic 7, 1270-1282.
Geierhaas, C. D., Best, R. B., Paci, E., Vendruscolo, M. & Clarke, J. (2006). Structural comparison of the two alternative transition states for folding of TI I27. Biophys. J. 91, 263-275.
Gillings, A. S., Yang, J., Marley, A. E., Holman, G. D., Peckham, M., Kilgour, E. & Baldwin, S. A. (2006). Investigation of the role of Kv1.3 as a potential regulator of peripheral insulin sensitivity. Diabetologia 49, 366-366.
Gold, N. D. & Jackson, R. M. (2006). Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships. J. Mol. Biol. 355, 1112-1124.
Gold, N. D. & Jackson, R. M. (2006). A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships. Journal of Chemical Information and Modeling 46, 736-742.
Gold, N. D. & Jackson, R. M. (2006). SitesBase: a database for structure-based protein-ligand binding site comparisons. Nucleic Acids Res. 34, D231-D234.
Gosal, W. S., Myers, S. L., Radford, S. E. & Thomson, N. H. (2006). Amyloid under the atomic force microscope. Protein Pept. Lett. 13, 261-270.
Graham, R. S., Bent, J., Hutchings, L. R., Richards, R. W., Groves, D. J., Embery, J., Nicholson, T. M., McLeish, T. C. B., Likhtman, A. E., Harlen, O. G., Read, D. J., Gough, T., Spares, R., Coates, P. D. & Grillo, I. (2006). Measuring and predicting the dynamics of linear monodisperse entangled polymers in rapid flow through an abrupt contraction. A small angle neutron scattering study. Macromolecules 39, 2700-2709.
Griffiths, R. A., Boyne, J. A. & Whitehouse, A. (2006). Herpesvirus saimiri-based gene delivery vectors. Current Gene Therapy 6, 1-15.
Gsponer, J., Hopearuoho, H., Whittaker, S. B. M., Spence, G. R., Moore, G. R., Paci, E., Radford, S. E. & Vendruscolo, M. (2006). Determination of an ensemble of structures representing the intermediate state of the bacterial immunity protein Im7. Proc. Natl. Acad. Sci. U. S. A. 103, 99-104.
Hawkins, R. J. & McLeish, T. C. B. (2006). Coupling of global and local vibrational modes in dynamic allostery of proteins. Biophys. J. 91, 2055-2062.
Hawkins, R. J. & McLeish, T. C. B. (2006). Dynamic allostery of protein alpha helical coiled-coils. Journal of the Royal Society Interface 3, 125-138.
Heeley, E. L., Fernyhough, C. M., Graham, R. S., Olmsted, P. D., Inkson, N. J., Embery, J., Groves, D. J., McLeish, T. C. B., Morgovan, A. C., Meneau, F., Bras, W. & Ryan, A. J. (2006). Shear-induced crystallization in blends of model linear and long-chain branched hydrogenated polybutadienes. Macromolecules 39, 5058-5071.
Heikkila, T., Thirumalairajan, S., Davies, M., Parsons, M. R., McConkey, A. G., Fishwick, C. W. G. & Johnson, A. P. (2006). The first de novo designed inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase. Bioorg. Med. Chem. Lett. 16, 88-92.
Holyoake, J., Caulfeild, V., Baldwin, S. A. & Sansom, M. S. P. (2006). Modeling, docking, and simulation of the major facilitator superfamily. Biophys. J. 91, L84-L86.
Hooper, N. M. (2006). Foreword: lipid rafts/biophysics, cell signalling, trafficking and processing. Mol. Membr. Biol. 23, 1-3.
Horn, W. T., Tars, K., Grahn, E., Heigstrand, C., Baron, A. J., Lago, H., Adams, C. J., Peabody, D. S., Phillips, S. E. V., Stonehouse, N. J., Liljas, L. & Stockley, P. G. (2006). Structural basis of RNA binding discrimination between bacteriophages Q beta and MS2. Structure 14, 487-495.
Hyland, C., Pinney, J. W., McConkey, G. A. & Westhead, D. R. (2006). metaSHARK: a WWW
platform for interactive exploration of metabolic networks. Nucleic Acids Res. 34, W725-
W728.
Inkson, N. J., Graham, R. S., McLeish, T. C. B., Groves, D. J. & Fernyhough, C. M. (2006). Viscoelasticity of monodisperse comb polymer melts. Macromolecules 39, 4217-4227.
Jack, E., Newsome, M., Stockley, P. G., Radford, S. E. & Middleton, D. A. (2006). The organization of aromatic side groups in an amyloid fibril probed by solid-state H-2 and F-19 NMR spectroscopy. J. Am. Chem. Soc. 128, 8098-8099.
Jahn, T. R., Parker, M. J., Homans, S. W. & Radford, S. E. (2006). Amyloid formation under physiological conditions proceeds via a native-like folding intermediate. Nat. Struct. Mol. Biol. 13, 195-201.
Jen, C. H., Manfield, I. W., Michalopoulos, I., Pinney, J. W., Willats, W. G. T., Gilmartin, P. M. & Westhead, D. R. (2006). The Arabidopsis co-expression tool ((ACT)): a WWW-based tool and database for microarray-based gene expression analysis. Plant Journal 46, 336-348.
Jeuken, L. J. C., Connell, S. D., Henderson, P. J. F., Gennis, R. B., Evans, S. D. & Bushby, R. J. (2006). Redox enzymes in tethered membranes. J. Am. Chem. Soc. 128, 1711-1716.
Johnson, A. P., Boda, K., Weaver, S., Valko, A. & Valko, V. (2006). De novo design tools for the generation of synthetically accessible ligands. Abstr. Pap. Am. Chem. Soc. 231.
Johnson, R., Gamblin, R. J., Ooi, L., Bruce, A. W., Donaldson, I. J., Westhead, D. R., Wood, I. C., Jackson, R. M. & Buckley, N. J. (2006). Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication. Nucleic Acids Res. 34, 3862-3877.
Ju, M. & Wray, D. (2006). Molecular regions responsible for differences in activation between heag channels. Biochem. Biophys. Res. Commun. 342, 1088-1097.
Kawakami, M., Byrne, K., Brockwell, D. J., Radford, S. E. & Smith, D. A. (2006). Viscoelastic study of the mechanical unfolding of a protein by AFM. Biophys. J. 91, L16-L18.
Kawakami, M., Byrne, K., Khatri, B. S., McLeish, T. C. B. & Smith, D. A. (2006). Viscoelastic properties of single poly(ethylene glycol) molecules. Chemphyschem 7, 1710-1716.
King, A. E., Ackley, M. A., Cass, C. E., Young, J. D. & Baldwin, S. A. (2006). Nucleoside transporters: from scavengers to novel therapeutic targets. Trends Pharmacol. Sci. 27, 416-425.
Kirkham, J., Andreev, I., Robinson, C., Brookes, S. J., Shore, R. C. & Smith, D. A. (2006). Evidence for direct amelogenin-target cell interactions using dynamic force spectroscopy. European Journal of Oral Sciences 114, 219-224.
Kobrinsky, E., Stevens, L., Kazmi, Y., Wray, D. & Soldatov, N. M. (2006). Molecular rearrangements of the K(v)2.1 potassium channel termini associated with voltage gating. J. Biol. Chem. 281, 19233-19240.
Laguri, C., Stenzel, R. A., Donohue, T. J., Phillips-Jones, M. K. & Williamson, M. P. (2006). Activation of the global gene regulator PrrA (RegA) from Rhodobacter sphaeroides. Biochemistry 45, 7872-7881.
Laurie, A. T. R. & Jackson, R. M. (2006). Methods for the prediction of protein-ligand binding sites for Structure-Based Drug Design and virtual ligand screening. Current Protein & Peptide Science 7, 395-406.
Le Duff, C. S., Whittaker, S. B. M., Radford, S. E. & Moore, G. R. (2006). Characterisation of the conformational properties of urea-unfolded Im7: Implications for the early stages of protein folding. J. Mol. Biol. 364, 824-835.
Leach, R. N., Gell, C., Wigneshweraraj, S., Buck, M., Smith, A. & Stockley, P. G. (2006). Mapping ATP-dependent activation at sigma(54) promoter. J. Biol. Chem. 281, 33717-33726.
Mankouri, J., Taneja, T. K., Smith, A. J., Ponnambalam, S. & Sivaprasadarao, A. (2006). Kir6.2 mutations causing neonatal diabetes prevent endocytosis of ATP-sensitive potassium channels. Embo J. 25, 4142-4151.
Marincs, F., Manfield, I. W., Stead, J. A., McDowall, K. J. & Stockley, P. G. (2006). Transcript analysis reveals an extended regulon and the importance of protein-protein co-operativity for the Escherichia coli methionine repressor. Biochem. J. 396, 227-234.
Masca, S. I., Rodriguez-Mendieta, I. R., Friel, C. T., Radford, S. E. & Smith, D. A. (2006). Detailed evaluation of the performance of microfluidic T mixers using fluorescence and ultraviolet resonance Raman spectroscopy. Review of Scientific Instruments 77.
McCormick, C. J., Brown, D., Griffin, S., Challinor, L., Rowlands, D. J. & Harris, M. (2006). A link between translation of the hepatitis C virus polyprotein and polymerase function; possible consequences for hyperphosphorylation of NS5A. J. Gen. Virol. 87, 93-102.
McCormick, C. J., Maucourant, S., Griffin, S., Rowlands, D. J. & Harris, M. (2006). Tagging of NS5A expressed from a functional hepatitis C virus replicon. J. Gen. Virol. 87, 635-640.
McLeish, T. C. B. (2006). Diffusive searches in high-dimensional spaces and apparent 'two-state' behaviour in protein folding. J. Phys.-Condes. Matter 18, 1861-1868.
Murphy, J. E., Tacon, D., Tedbury, P. R., Hadden, J. M., Knowling, S., Sawamura, T., Peckham, M., Phillips, S. E. V., Walker, J. H. & Ponnambalam, S. (2006). LOX-1 scavenger receptor mediates calcium-dependent recognition of phosphatidylserine and apoptotic cells. Biochem. J. 393, 107-115.
Myers, S. L., Jones, S., Jahn, T. R., Morten, I. J., Tennent, G. A., Hewitt, E. W. & Radford, S. E. (2006). A systematic study of the effect of physiological factors on beta 2-microglobulin amyloid formation at neutral pH. Biochemistry 45, 2311-2321.
Myers, S. L., Thomson, N. H., Radford, S. E. & Ashcroft, A. E. (2006). Investigating the structural properties of amyloid-like fibrils formed in vitro from beta 2-microglobulin using limited proteolysis and electrospray ionisation mass spectrometry. Rapid Commun. Mass Spectrom. 20, 1628-1636.
Needham, C. J., Bradford, J. R., Bulpitt, A. J., Care, M. A. & Westhead, D. R. (2006). Predicting the effect of missense mutations on protein function: analysis with Bayesian networks. BMC Bioinformatics 7.
Needham, C. J., Bradford, J. R., Bulpitt, A. J. & Westhead, D. R. (2006). Inference in Bayesian networks. Nature Biotechnology 24, 51-53.
Neelov, I. M., Adolf, D. B., McLeish, T. C. B. & Paci, E. (2006). Molecular dynamics simulation of dextran extension by constant force in single molecule AFM. Biophys. J. 91, 3579-3588.
Netherton, C. L., McCrossan, M. C., Denyer, M., Ponnambalam, S., Armstrong, J., Takamatsu, H. H. & Wileman, T. E. (2006). African swine fever virus causes microtubule-dependent dispersal of the trans-golgi network and slows delivery of membrane protein to the plasma membrane. J. Virol. 80, 11385-11392.
Omaetxebarria, M. J., Hagglund, P., Elortza, F., Hooper, N. M., Arizmendi, J. M. & Jensen, O. N. (2006). Isolation and characterization of glycosylphosphatidylinositol-anchored peptides by hydrophilic interaction chromatography and MALDI tandem mass spectrometry. Analytical Chemistry 78, 3335-3341.
Phillips, S. E. V. (2006). Turning up the HEAT on translation. Structure 14, 806-807.
Potter, C. A., Jeong, E. L., Williamson, M. P., Henderson, P. J. F. & Phillips-Jones, M. K. (2006). Redox-responsive in vitro modulation of the signalling state of the isolated PrrB sensor kinase of Rhodobacter sphaeroides NCIB 8253. FEBS Lett. 580, 3206-3210.
Protopapa, E., Aggeli, A., Boden, N., Knowles, P. F., Salay, L. C. & Nelson, A. (2006). Electrochemical screening of self-assembling beta-sheet peptides using supported phospholipid monolayers. Medical Engineering & Physics 28, 944-955.
Radford, S. E. (2006). GroEL: More than just a folding cage. Cell 125, 831-833.
Ranson, N., Stromer, T., Bousset, L., Melki, R. & Serpell, L. C. (2006). Insights into the architecture of the Ure2p yeast protein assemblies from helical twisted fibrils. Protein Sci. 15, 2481-2487.
Ranson, N. A., Clare, D. K., Farr, G. W., Houldershaw, D., Horwich, A. L. & Saibil, H. R. (2006). Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes. Nat. Struct. Mol. Biol. 13, 147-152.
Redondo, C., Burke, B. J. & Findlay, J. B. C. (2006). The retinol-binding protein system: A potential paradigm for steroid-binding globulins? Hormone and Metabolic Research 38, 269-278.
Reed, M. L., Dove, B. K., Jackson, R. M., Collins, R., Brooks, G. & Hiscox, J. A. (2006). Delineation and modelling of a nucleolar retention signal in the coronavirus nucleocapsid protein. Traffic 7, 833-848.
Rella, M. & Jackson, R. M. (2006). Identification of novel ACE2 inhibitors by structure-based pharmacophore modeling and virtual screening. Abstr. Pap. Am. Chem. Soc. 231.
Rella, M., Rushworth, C. A., Guy, J. L., Turner, A. J., Langer, T. & Jackson, R. M. (2006). Structure-based pharmacophore design and virtual screening for novel angiotensin converting enzyme 2 inhibitors. Journal of Chemical Information and Modeling 46, 708-716.
Remaut, H., Rose, R. J., Hannan, T. J., Hultgren, S. J., Radford, S. E., Ashcroft, A. E. & Waksman, G. (2006). Donor-strand exchange in chaperone-assisted pilus assembly proceeds through a concerted beta strand displacement mechanism. Mol. Cell 22, 831-842.
Robinson, M. A., Wood, J. P. A., Capaldi, S. A., Baron, A. J., Gell, C., Smith, D. A. & Stonehouse, N. J. (2006). Affinity of molecular interactions in the bacteriophage phi 29 DNA packaging motor. Nucleic Acids Res. 34, 2698-2709.
Saidijam, M., Benedetti, G., Ren, Q. H., Xu, Z. Q., Hoyle, C. J., Palmer, S. L., Ward, A., Bettaney, K. E., Szakonyi, G., Meuller, J., Morrison, S., Pos, M. K., Butaye, P., Walravens, K., Langton, K., Herbert, R. B., Skurray, R. A., Paulsen, I. T., O'Reilly, J., Rutherford, N. G., Brown, M. H., Bill, R. M. & Henderson, P. J. F. (2006). Microbial drug efflux proteins of the major facilitator superfamily. Current Drug Targets 7, 793-811.
Seeber, M., Fanelli, F., Paci, E. & Caflisch, A. (2006). Sequential unfolding of individual helices of bacterioopsin observed in molecular dynamics simulations of extraction from the purple membrane. Biophys. J. 91, 3276-3284.
Shimokhina, N., Bronowska, A. & Homans, S. W. (2006). Contribution of ligand desolvation to binding thermodynamics in a ligand-protein interaction. Angew. Chem.-Int. Edit. 45, 6374-6376.
Smith, A. M., Jahn, T. R., Ashcroft, A. E. & Radford, S. E. (2006). Direct observation of oligomeric species formed in the early stages of amyloid fibril formation using electrospray ionisation mass spectrometry. J. Mol. Biol. 364, 9-19.
Spencer, K. A. & Hiscox, J. A. (2006). Characterisation of the RNA binding properties of the coronavirus infectious bronchitis virus nucleocapsid protein amino-terminal region. FEBS Lett. 580, 5993-5998.
Spencer, K. A. & Hiscox, J. A. (2006). Expression and structural analysis of infectious bronchitis virus nucleoprotein. In Nidoviruses: Toward Control of Sars and Other Nidovirus Diseases, Vol. 581, pp. 133-138.
Stead, J. A., Keen, J. N. & McDowall, K. J. (2006). The identification of nucleic acid-interacting proteins using a simple proteomics-based approach that directly incorporates the electrophoretic mobility shift assay. Molecular & Cellular Proteomics 5, 1697-1702.
Suzuki, S. & Henderson, P. J. F. (2006). The hydantoin transport protein from Microbacterium liquefaciens. J. Bacteriol. 188, 3329-3336.
Taylor, D. R. & Hooper, N. M. (2006). The prion protein and lipid rafts. Mol. Membr. Biol. 23, 89-99.
Tezuka-Kawakami, T., Gell, C., Brockwell, D. J., Radford, S. E. & Smith, D. A. (2006). Urea-induced unfolding of the immunity protein Im9 monitored by spFRET. Biophys. J. 91, L42-L44.
Thirumurugan, K., Sakamoto, T., Hammer, J. A., Sellers, J. R. & Knight, P. (2006). The cargo-binding domain regulates structure and activity of myosin 5. Nature 442, 212-215.
Thomas, D. A., Francis, P., Smith, C., Ratcliffe, S., Ede, N. J., Kay, C., Wayne, G., Martin, S. L., Moore, K., Amour, A. & Hooper, N. M. (2006). A broad-spectrum fluorescence-based peptide library for the rapid identification of protease substrates. Proteomics 6, 2112-2120.
Tuthill, T. J., Bubeck, D., Rowlands, D. J. & Hogle, J. M. (2006). Characterization of early steps in the poliovirus infection process: Receptor-decorated liposomes induce conversion of the virus to membrane-anchored entry-intermediate particles. J. Virol. 80, 172-180.
Unwin, R. D., Smith, D. L., Blinco, D., Wilson, C. L., Miller, C. J., Evans, C. A., Jaworska, E., Baldwin, S. A., Barnes, K., Pierce, A., Spooncer, E. & Whetton, A. D. (2006). Quantitative proteomics reveals posttranslational control as a regulatory factor in primary hematopoietic stem cells. Blood 107, 4687-4694.
Vohra, R. S., Murphy, J. E., Walker, J. H., Ponnambalam, S. & Homer-Vanniasinkam, S. (2006). Atherosclerosis and the lectin-like oxidized low-density lipoprotein scavenger receptor. Trends in Cardiovascular Medicine 16, 60-64.
Wallace, E. J., Hooper, N. M. & Olmstedz, P. D. (2006). Effect of hydrophobic mismatch on phase behavior of lipid membranes. Biophys. J. 90, 4104-4118.
West, D. K., Brockwell, D. J., Olmsted, P. D., Radford, S. E. & Paci, E. (2006). Mechanical resistance of proteins explained using simple molecular models. Biophys. J. 90, 287-297.
West, D. K., Brockwell, D. J. & Paci, E. (2006). Prediction of the translocation kinetics of a protein from its mechanical properties. Biophys. J. 91, L51-L53.
West, D. K., Olmsted, P. D. & Paci, E. (2006). Free energy for protein folding from nonequilibrium simulations using the Jarzynski equality. Journal of Chemical Physics 125.
West, D. K., Olmsted, P. D. & Paci, E. (2006). Mechanical unfolding revisited through a simple but realistic model. Journal of Chemical Physics 124.
West, D. K., Paci, E. & Olmsted, P. D. (2006). Internal protein dynamics shifts the distance to the mechanical transition state. Phys. Rev. E 74.
Wijma, H. J., Jeuken, L. J. C., Verbeet, M. P., Armstrong, F. A. & Canters, G. W. (2006). A random-sequential mechanism for nitrite binding and active site reduction in copper-containing nitrite reductase. J. Biol. Chem. 281, 16340-16346.
Williams, G. J., Woodhall, T., Farnsworth, L. M., Nelson, A. & Berry, A. (2006). Creation of a pair of stereochemically complementary biocatalysts. J. Am. Chem. Soc. 128, 16238-16247.
Wilson, A. J., van Gestel, J., Sijbesma, R. P. & Meijer, E. W. (2006). Amplification of chirality in benzene tricarboxamide helical supramolecular polymers. Chem. Commun., 4404-4406.
You, J. H., Reed, M. L., Dove, B. K. & Hiscox, J. A. (2006). Three-dimensional reconstruction of the nucleolus using meta-confocal microscopy in cells expressing the coronavirus nucleoprotein. In Nidoviruses: Toward Control of Sars and Other Nidovirus Diseases, Vol. 581, pp. 313-318.
Zhang, J., Smith, K. M., Tackaberry, T., Sun, X. J., Carpenter, P., Slugoski, M. D., Robins, M. J., Nielsen, L. P. C., Nowak, I., Baldwin, S. A., Young, J. D. & Cass, C. E. (2006). Characterization of the transport mechanism and permeant binding profile of the uridine permease Fui1p of Saccharomyces cerevisiae. J. Biol. Chem. 281, 28210-28221.
Zhang, J., Sun, X. J., Smith, K. M., Visser, F., Carpenter, P., Barron, G., Peng, Y. S., Robins, M. J., Baldwin, S. A., Young, J. D. & Cass, C. E. (2006). Studies of nucleoside transporters using novel autofluorescent nucleoside probes. Biochemistry 45, 1087-1098.
Zhang, J., Tackaberry, T., Ritzel, M. W. L., Raborn, T., Barron, G., Baldwin, S. A., Young, J. D. & Cass, C. E. (2006). Cysteine-accessibility analysis of transmembrane domains 11-13 of human concentrative nucleoside transporter 3. Biochem. J. 394, 389-398.
Zsoldos, Z., Reid, D., Simon, A., Sadjad, B. S. & Johnson, A. P. (2006). eHITS: An innovative approach to the docking and scoring function problems. Current Protein & Peptide Science 7, 421-435.

Publications by Astbury Centre Members 2005

Ackley, M.A., Baldwin, S.A. and King, A.E. (2005). "Adenosine contributes to mu-opioid synaptic inhibition in rat substantia gelatinosa in vitro." Neuroscience Letters 376, 102-106.
Ali, M.A., Bhogal, N., Findlay, J.B.C. and Fishwick, C.W.G. (2005). "The first de novo-designed antagonists of the human NK2 receptor." Journal of Medicinal Chemistry 48, 5655-5658.
Ashcroft, A.E. (2005). "Recent developments in electrospray ionisation mass spectrometry: noncovalently bound protein complexes." Natural Product Reports 22, 452-464.
Ashcroft, A.E., Lago, H., Macedo, J.M.B., Horn, W.T., Stonehouse, N.J. and Stockley, P.G. (2005). "Engineering thermal stability in RNA phage capsids via disulphide bonds." Journal of Nanoscience and Nanotechnology 5, 2034-2041.
Badjic, J.D., Nelson, A., Cantrill, S.J., Turnbull, W.B. and Stoddart, J.F. (2005). "Multivalency and cooperativity in supramolecular chemistry." Accounts of Chemical Research 38, 723-732.
Bakhetia, M., Charlton, W., Atkinson, H.J. and McPherson, M.J. (2005). "RNA interference of dual oxidase in the plant nematode Meloidogyne incognita." Molecular Plant-Microbe Interactions 18, 1099-1106.
Bakhetia, M., Charlton, W.L., Urwin, P.E., McPherson, M.J. and Atkinson, H.J. (2005). "RNA interference and plant parasitic nematodes." Trends in Plant Science 10, 362-367.
Baldwin, S.A., Yao, S.Y.M., Hyde, R.J., Ng, A.M.L., Foppolo, S., Barnes, K., Ritzel, M.W.L., Cass, C.E. and Young, J.D. (2005). "Functional characterization of novel human and mouse equilibrative nucleoside transporters (hENT3 and mENT3) located in intracellular membranes." Journal of Biological Chemistry 280, 15880-15887.
Barnes, K., McIntosh, E., Whetton, A.D., Daley, G.Q., Bentley, J. and Baldwin, S.A. (2005). "Chronic myeloid leukaemia: an investigation into the role of Bcr-Abl-induced abnormalities in glucose transport regulation." Oncogene 24, 3257-3267.
Barratt, E., Bingham, R.J., Warner, D.J., Laughton, C.A., Phillips, S.E.V. and Homans, S.W. (2005). "Van der waals interactions dominate ligand-protein association in a protein binding site occluded from solvent water." Journal of the American Chemical Society 127, 11827-11834.
Barrett, S., Bartlett, S., Bolt, A., Ironmonger, A., Joce, C., Nelson, A. and Woodhall, T. (2005). "Configurational stability of bisindolylmaleimide cyclophanes: From conformers to the first configurationally stable, atropisomeric bisindolylmaleimides." Chemistry-a European Journal 11, 6277-6285.
Bartlett, S., Beddard, G.S., Jackson, R.M., Kayser, V., Kilner, C., Leach, A., Nelson, A., Oledzki, P.R., Parker, P., Reid, G.D. and Warriner, S.L. (2005). "Comparison of the ATP binding sites of protein kinases using conformationally diverse bisindolylmaleimides." Journal of the American Chemical Society 127, 11699-11708.
Beccaluva, L., Bianchini, G., Bonadiman, C., Nowell, G.M., Pearson, D.G., Siena, F. and Wilson, A. (2005). "The metasomatic history of the lithospheric mantle beneath NE Spain." Geochimica Et Cosmochimica Acta 69, A787-A787.
Besong, G.E., Bostock, J.M., Stubbings, W., Chopra, I., Roper, D.I., Lloyd, A.J., Fishwick, C.W.G. and Johnson, A.P. (2005). "A de novo designed inhibitor of D-Ala-D-Ala ligase from E. coli." Angewandte Chemie-International Edition 44, 6403-6406.
Bicknell, K., Brooks, G., Kaiser, P., Chen, H.Y., Dove, B.K. and Hiscox, J.A. (2005). "Nucleolin is regulated both at the level of transcription and translation." Biochemical and Biophysical Research Communications 332, 817-822.
Blades, M.J., Ison, J.C., Ranasinghe, R. and Findlay, J.B.C. (2005). "Automatic generation and evaluation of sparse protein signatures for families of protein structural domains." Protein Science 14, 13-23.
Blanchard, A., Graham, R.S., Heinrich, M., Pyckhout-Hintzen, W., Richter, D., Likhtman, A.E., McLeish, T.C.B., Read, D.J., Straube, E. and Kohlbrecher, J. (2005). "Small angle neutron scattering observation of chain retraction after a large step deformation." Physical Review Letters 95.
Bourque, E., Kocienski, P.J., Stocks, M. and Yuen, J. (2005). "Synthesis of the C14-C28 fragment of tetronasin." Synthesis-Stuttgart, 3219-3224.
Bracey, K., Stevens, L. and Wray, D. (2005). "Comparison of the extent of movement of S4 in voltage-gated potassium and calcium channels." Biophysical Journal 88, 200A-200A.
Bradford, J.R. and Westhead, D.R. (2005). "Improved prediction of protein-protein binding sites using a support vector machines approach." Bioinformatics 21, 1487-1494.
Brockwell, D.J., Beddard, G.S., Paci, E., West, D.K., Olmsted, P.D., Smith, D.A. and Radford, S.E. (2005). "Mechanically unfolding the small, topologically simple protein L." Biophysical Journal 89, 506-519.
Bullock, A.N., Debreczeni, J.E., Fedorov, O.Y., Nelson, A., Marsden, B.D. and Knapp, S. (2005). "Structural basis of inhibitor specificity of the human protooncogene proviral insertion site in Moloney murine leukemia virus (PIM-1) kinase." Journal of Medicinal Chemistry 48, 7604-7614.
Calderwood, M., White, R.E., Griffiths, R.A. and Whitehouse, A. (2005). "Open reading frame 73 is required for herpesvirus saimiri A11-S4 episomal persistence." Journal of General Virology 86, 2703-2708.
Callaghan, A.J., Marcaida, M.J., Stead, J.A., McDowall, K.J., Scott, W.G. and Luisi, B.F. (2005). "Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover." Nature 437, 1187-1191.
Callaghan, A.J., Redko, Y., Murphy, L.M., Grossmann, J.G., Yates, D., Garman, E., Ilag, L.L., Robinson, C.V., Symmons, M.F., McDowall, K.J. and Luisi, B.F. (2005). ""Zn-Link": A metal-sharing interface that organizes the quaternary structure and catalytic site of the endoribonuclease, RNase E." Biochemistry 44, 4667-4675.
Caryl, J.A. and Thomas, C.D. (2005). "Initial events in small staphylococcal plasmid transfer in Thomas, C.M. et al (eds) Plasmid Biology 2004: International symposium on molecular biology of bacterial plasmids and other mobile genetic elements." Plasmid 53, 47-48.
Cavalli, A., Vendruscolo, M. and Paci, E. (2005). "Comparison of sequence-based and structure-based energy functions for the reversible folding of a peptide." Biophysical Journal 88, 3158-3166.
Chen, H.Y., Gill, A., Dove, B.K., Emmett, S.R., Kemp, C.F., Ritchie, M.A., Dee, M. and Hiscox, J.A. (2005). "Mass spectroscopic characterization of the coronavirus infectious bronchitis virus nucleoprotein and elucidation of the role of phosphorylation in RNA binding by using surface plasmon resonance." Journal of Virology 79, 1164-1179.
Clique, B., Ironmonger, A., Whittaker, B., Colley, J., Titchmarsh, J., Stockley, P. and Nelson, A. (2005). "Synthesis of a library of stereo- and regiochemically diverse aminoglycoside derivatives." Organic & Biomolecular Chemistry 3, 2776-2785.
Collis, M.W., Lele, A.K., Mackley, M.R., Graham, R.S., Groves, D.J., Likhtman, A.E., Nicholson, T.M., Harlen, O.G., McLeish, T.C.B., Hutchings, L.R., Fernyhough, C.M. and Young, R.N. (2005). "Constriction flows of monodisperse linear entangled polymers: Multiscale modeling and flow visualization." Journal of Rheology 49, 501-522.
Cooksey, J., Kocienski, P. and Li, Y.F. (2005). "A synthesis of the C1-C9 fragment of ionomycin using cationic eta(3)-allylicmolybdenum and -iron complexes." Collection of Czechoslovak Chemical Communications 70, 1653-1668.
Cordier, C. and Nelson, A. (2005). "Reaching the target: Small molecules aim to probe barrier quality." Chembiochem 6, 1953-1955.
Cox, A., Donnelly, D., Kaur, M., Cheetham, S.C., Cockcroft, V.B. and Findlay, J.B.C. (2005). "MTSEA prevents ligand binding to the human melanocortin-4 receptor by modification of cysteine 130 in transmembrane helix 3." FEBS Letters 579, 285-291.
Crampton, N., Bonass, W.A., Kirkham, J. and Thomson, N.H. (2005). "Formation of aminosilane-functionalized mica for atomic force microscopy imaging of DNA." Langmuir 21, 7884-7891.
Cranz-Mileva, S., Friel, C.T. and Radford, S.E. (2005). "Helix stability and hydrophobicity in the folding mechanism of the bacterial immunity protein Im9." Protein Engineering Design & Selection 18, 41-50.
Curcio, R., Caflisch, A. and Paci, E. (2005). "Change of the unbinding mechanism upon a mutation: A molecular dynamics study of an antibody-hapten complex." Protein Science 14, 2499-2514.
Dennis, C.A., Baron, A., Grossmann, J.G., Mazaleyrat, S., Harris, M. and Jaeger, J. (2005). "Co-translational myristoylation alters the quaternary structure of HIV-1 Nef in solution." Proteins-Structure Function and Bioinformatics 60, 658-669.
Di Cola, E., Waigh, T.A., Trinick, J., Tskhovrebova, L., Houmeida, A., Pyckhout-Hintzen, W. and Dewhurst, C. (2005). "Persistence length of titin from rabbit skeletal muscles measured with scattering and microrheology techniques." Biophysical Journal 88, 4095-4106.
Dugan, G.E. and Hewitt, E.W. (2005). "Functional dissection of the human cytomegalovirus immune evasion protein US6." Immunology 116, 68-68.
Espadaler, J., Romero-Isart, O., Jackson, R.M. and Oliva, B. (2005). "Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships." Bioinformatics 21, 3360-3368.
Fielding, A.B., Schonteich, E., Matheson, J., Wilson, G., Yu, X.Z., Hickson, G.R.X., Srivastava, S., Baldwin, S.A., Prekeris, R. and Gould, G.W. (2005). "Rab11-FIP3 and FIP4 interact with Arf6 and the Exocyst to control membrane traffic in cytokinesis." EMBO Journal 24, 3389-3399.
Forman, J.R., Qamar, S., Paci, E., Sandford, R.N. and Clarke, J. (2005). "The remarkable mechanical strength of polycystin-1 supports a direct role in mechanotransduction." Journal of Molecular Biology 349, 861-871.
Fry, E.E., Stuart, D.I. and Rowlands, D.J. (2005). The structure of foot-and-mouth disease virus. Foot and Mouth Disease Virus. 288: 71-101.
Garrow, A.G., Agnew, A. and Westhead, D.R. (2005). "TMB-Hunt: a web server to screen sequence sets for transmembrane beta-barrel proteins." Nucleic Acids Research 33, W188-W192.
Garrow, A.G., Agnew, A. and Westhead, D.R. (2005). "TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins." Bmc Bioinformatics 6.
Gibson, C.T., Smith, D.A. and Roberts, C.J. (2005). "Calibration of silicon atomic force microscope cantilevers." Nanotechnology 16, 234-238.
Gibson, C.W., Thomson, N.H., Abrams, W.R. and Kirkham, J. (2005). "Nested genes: Biological implications and use of AFM for analysis." Gene 350, 15-23.
Gilbert, R.J.C., Beales, L., Blond, D., Simon, M.N., Lin, B.Y., Chisari, F.V., Stuart, D.I. and Rowlands, D.J. (2005). "Hepatitis B small surface antigen particles are octahedral." Proceedings of the National Academy of Sciences of the United States of America 102, 14783-14788.
Gosal, W.S., Morten, I.J., Hewitt, E.W., Smith, D.A., Thomson, N.H. and Radford, S.E. (2005). "Competing pathways determine fibril morphology in the self-assembly of beta(2)-microglobulin into amyloid." Journal of Molecular Biology 351, 850-864.
Governo, R.J.M., Deuchars, J., Baldwin, S.A. and King, A.E. (2005). "Localization of the NBMPR-sensitive equilibrative nucleoside transporter, ENT1, in the rat dorsal root ganglion and lumbar spinal cord." Brain Research 1059, 129-138.
Grewal, S., Herbert, S.P., Ponnambalam, S. and Walker, J.H. (2005). "Cytosolic phospholipase A(2)-alpha and cyclooxygenase-2 localize to intracellular membranes of EA.hy.926 endothelial cells that are distinct from the endoplasmic reticulum and the Golgi apparatus." Febs Journal 272, 1278-1290.
Griffin, S., Clarke, D., McCormick, C., Rowlands, D. and Harris, M. (2005). "Signal peptide cleavage and internal targeting signals direct the hepatitis C virus p7 protein to distinct intracellular membranes." Journal of Virology 79, 15525-15536.
Griffin, S.D.C., McCormick, C.J., Rowlands, D.J. and Harris, M. (2005). "Sub-cellular localisation of native p7 protein in cells expressing the full-length hepatitis C virus polyprotein." Journal of Virology 79, 15525-15536.
Guy, J.L., Jackson, R.M., Jensen, H.A., Hooper, N.M. and Turner, A.J. (2005). "Identification of critical active-site residues in angiotensin-converting enzyme-2 (ACE2) by site-directed mutagenesis." FEBS Journal 272, 3512-3520.
Guy, J.L., Lambert, D.W., Wamer, F.J., Hooper, N.M. and Turner, A.J. (2005). "Membrane-associated zinc peptidase families: comparing ACE and ACE2." Biochimica et Biophysica Acta-Proteins and Proteomics 1751, 2-8.
Hackenberger, C.P.R., Friel, C.T., Radford, S.E. and Imperiali, B. (2005). "Semisynthesis of a glycosylated lm7 analogue for protein folding studies." Journal of the American Chemical Society 127, 12882-12889.
Hawkins, R.J. and McLeish, T.C.B. (2005). "Dynamic allostery of protein alpha helical coiled-colis." J. Roy. Soc. Interface 100, 3143-3148.
Herbert, S.P., Ponnambalam, S. and Walker, J.H. (2005). "Cytosolic phospholipase A(2)-alpha mediates endothelial cell proliferation and is inactivated by association with the Golgi apparatus." Molecular Biology of the Cell 16, 3800-3809.
Homans, S.W. (2005). "Probing the binding entropy of ligand-protein interactions by NMR." Chembiochem 6, 1585-.
Ironmonger, A., Stockley, P. and Nelson, A. (2005). "Asymmetric double ring-opening of a C-2h-symmetric bis-epoxide: improved enantiomeric excess of the product through enantioselective desymmetrisation and 'proof-reading' steps." Organic & Biomolecular Chemistry 3, 2350-2353.
Jahn, T.R. and Radford, S.E. (2005). "The Yin and Yang of protein folding." FEBS Journal 272, 5962-5970.
Jarowicki, K. and Kocienski, P.J. (2005). "1,2-metallate rearrangements of alpha-alkoxyalkyl cuprates." Synlett, 167-169.
Jen, C.H., Michalopoulos, I., Westhead, D.R. and Meyer, P. (2005). "Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation." Genome Biology 6.
Jeuken, L.J.C., Connell, S.D., Nurnabi, M., O'Reilly, J., Henderson, P.J.F., Evans, S.D. and Bushby, R.J. (2005). "Direct electrochemical interaction between a modified gold electrode and a bacterial membrane extract." Langmuir 21, 1481-1488.
Jones, R.P.O., Durose, L.J., Findlay, J.B.C. and Harrison, M.A. (2005). "Defined sites of interaction between subunits E (Vma4p), C (Vma5p), and G (Vma10p) within the stator structure of the vacuolar H+-ATPase." Biochemistry 44, 3933-3941.
Kalverda, A., Thompson, G.S. and Turnbull, W.B. (2005). The importance of protein structural dynamics and the contribution of NMR spectroscopy. The encyclopedia of genetics, genomics, proteomics and bioinformatics. M. J. D. e. al, Wiley Intescience.
Kawakami, M., Byrne, K., Khatri, B.S., McLeish, T.C.B., Radford, S.E. and Smith, D.A. (2005). "Viscoelastic measurements of single molecules on a millisecond time scale by magnetically driven oscillation of an atomic force microscope cantilever." Langmuir 21, 4765-4772.
Kennedy, A., Nelson, A. and Perry, A. (2005). "A general, two-directional approach to aza-C-(1 -> 1)-linked disaccharide mimetics." Chemical Communications, 1646-1648.
Kennedy, A., Perry, A. and Nelson, A. (2005). "Methods for the synthesis of polyhydroxylated piperidines by diastereoselective dihydroxylation: Exploitation in the two-directional synthesis of aza-C-linked disaccharide derivatives." Beilstein J. Org. Chem. 1, 2-.
Khan, A., Ashcroft, A.E., Higenell, V., Korchazhkina, O.V. and Exley, C. (2005). "Metals accelerate the formation and direct the structure of amyloid fibrils of NAC." Journal of Inorganic Biochemistry 99, 1920-1927.
Knight, P.J., Thirumurugan, K., Xu, Y.H., Wang, F., Kalverda, A.P., Stafford, W.F., Sellers, J.R. and Peckham, M. (2005). "The predicted coiled-coil domain of myosin 10 forms a novel elongated domain that lengthens the head." Journal of Biological Chemistry 280, 34702-34708.
Kocienski, P.J., Christopher, J.A., Bell, R. and Otto, B. (2005). "Nucleophilic addition of alpha-metallated carbamates to planar chiral cationic eta(3)-allylmolybdenum complexes: A stereochemical study." Synthesis-Stuttgart, 75-84.
Lambert, D.W., Yarski, M., Warner, F.J., Thornhill, P., Parkin, E.T., Smith, A.I., Hooper, N.M. and Turner, A.J. (2005). "Tumor necrosis factor-alpha convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2)." Journal of Biological Chemistry 280, 30113-30119.
Langton, K.P., Henderson, P.J.F. and Herbert, R.B. (2005). "Antibiotic resistance: multidrug efflux proteins, a common transport mechanism?" Natural Product Reports 22, 439-451.
Laurie, A.T.R. and Jackson, R.M. (2005). "Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites." Bioinformatics 21, 1908-1916.
Leisle, L., Parkin, E.T., Turner, A.J. and Hooper, N.M. (2005). "Angiotensin-converting enzyme as a GPIase: a critical reevaluation." Nature Medicine 11, 1139-1140.
Li, J.Y., Stevens, L. and Wray, D. (2005). "Molecular regions underlying the activation of low- and high-voltage activating calcium channels." European Biophysics Journal with Biophysics Letters 34, 1017-1029.
Liang, W.J., Wilson, K.J., Xie, H., Knol, J., Suzuki, S., Rutherford, N.G., Henderson, P.J.F. and Jefferson, R.A. (2005). "The gusBC genes of Escherichia coli encode a glucuronide transport system." Journal of Bacteriology 187, 2377-2385.
Lindorff-Larsen, K., Rogen, P., Paci, E., Vendruscolo, M. and Dobson, C.M. (2005). "Protein folding and the organization of the protein topology universe." Trends in Biochemical Sciences 30, 13-19.
Macdonald, A., Chan, J.K.Y. and Harris, M. (2005). "Perturbation of epidermal growth factor receptor complex formation and Ras signalling in cells harbouring the hepatitis C virus subgenomic replicon." Journal of General Virology 86, 1027-1033.
Macdonald, A., Mazaleyrat, S., McCormick, C., Street, A., Burgoyne, N.J., Jackson, R.M., Cazeaux, V., Shelton, H., Saksela, K. and Harris, M. (2005). "Further studies on hepatitis C virus NS5A-SH3 domain interactions: identification of residues critical for binding and implications for viral RNA replication and modulation of cell signalling." Journal of General Virology 86, 1035-1044.
Malham, R., Johnstone, S., Bingham, R.J., Barratt, E., Phillips, S.E.V., Laughton, C.A. and Homans, S.W. (2005). "Strong solute-solute dispersive interactions in a protein-ligand complex." Journal of the American Chemical Society 127, 17061-17067.
Mann, J., Patrick, C.N., Cragg, M.S., Honeychurch, J., Mann, D.A. and Harris, M. (2005). "Functional analysis of HIV type 1 Nef reveals a role for PAK2 as a regulator of cell phenotype and function in the murine dendritic cell line, DC2.4." Journal of Immunology 175, 6560-6569.
Maxwell, K.L., Wildes, D., Zarrine-Afsar, A., de los Rios, M.A., Brown, A.G., Friel, C.T., Hedberg, L., Horng, J.C., Bona, D., Miller, E.J., Vallee-Belisle, A., Main, E.R.G., Bemporad, F., Qiu, L.L., Teilum, K., Vu, N.D., Edwards, A.M., Ruczinski, I., Poulsen, F.M., Kragelund, B.B., Michnick, S.W., Chiti, F., Bai, Y.W., Hagen, S.J., Serrano, L., Oliveberg, M., Raleigh, D.P., Wittung-Stafshede, P., Radford, S.E., Jackson, S.E., Sosnick, T.R., Marqusee, S., Davidson, A.R. and Plaxco, K.W. (2005). "Protein folding: Defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins." Protein Science 14, 602-616.
McLeish, T.C.B. (2005). "Protein folding in high-dimensional spaces: Hypergutters and the role of nonnative interactions." Biophysical Journal 88, 172-183.
Morten, I.J., Radford, S.E. and Hewitt, E.W. (2005). "Investigation into the role of lysosomes in dialysis related amyloidosis." Immunology 116, 63-63.
Mure, M., Brown, D.E., Saysell, C., Rogers, M.S., Wilmot, C.M., Kurtis, C.R., McPherson, M.J., Phillips, S.E.V., Knowles, P.F. and Dooley, D.M. (2005). "Role of the interactions between the active site base and the substrate Schiff base in amine oxidase catalysis. Evidence from structural and spectroscopic studies of the 2-hydrazinopyridine adduct of Escherichia coli amine oxidase." Biochemistry 44, 1568-1582.
Mure, M., Kurtis, C.R., Brown, D.E., Rogers, M.S., Tambyrajah, W.S., Saysell, C., Wilmot, C.M., Phillips, S.E.V., Knowles, P.F., Dooley, D.M. and McPherson, M.J. (2005). "Active site rearrangement of the 2-hydrazinopyridine adduct in Escherichia coli amine oxidase to an azo copper(II) chelate form: A key role for tyrosine 369 in controlling the mobility of the TPQ-2HP adduct." Biochemistry 44, 1583-1594.
Murphy, J.E., Tedbury, P.R., Homer-Vanniasinkam, S., Walker, J.H. and Ponnambalam, S. (2005). "Biochemistry and cell biology of mammalian scavenger receptors." Atherosclerosis 182, 1-15.
Ng, S.P., Rounsevell, R.W.S., Steward, A., Geierhaas, C.D., Williams, P.M., Paci, E. and Clarke, J. (2005). "Mechanical unfolding of TNfn3: The unfolding pathway of a fnIII domain probed by protein engineering, AFM and MD simulation." Journal of Molecular Biology 350, 776-789.
Paci, E., Greene, L.H., Jones, R.M. and Smith, L.J. (2005). "Characterization of the molten globule state of retinol-binding protein using a molecular dynamics simulation approach." FEBS Journal 272, 4826-4838.
Paci, E., Lindorff-Larsen, K., Dobson, C.M., Karplus, M. and Vendruscolo, M. (2005). "Transition state contact orders correlate with protein folding rates." Journal of Molecular Biology 352, 495-500.
Paci, E. and Vendruscolo, M. (2005). "Detection of non-native hydrophobic interactions in the denatured state of lysozyme by molecular dynamics simulations." Journal of Physics-Condensed Matter 17, S1617-S1626.
Patching, S.G., Baldwin, S.A., Baldwin, A.D., Young, J.D., Gallagher, M.P., Henderson, P.J.F. and Herbert, R.B. (2005). "The nucleoside transport proteins, NupC and NupG, from Escherichia coli: specific structural motifs necessary for the binding of ligands." Organic & Biomolecular Chemistry 3, 462-470.
Perrazzollo, C., Wist, J., Poggi, L., Homans, S.W. and Bodenhausen, G. (2005). "Effects of protein-pheromone complexation on correlated chemical shift modulations." J. Biomol. NMR 33, 233-242.
Pinney, J.W., Shirley, M.W., McConkey, G.A. and Westhead, D.R. (2005). "metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella." Nucleic Acids Research 33, 1399-1409.
Plattt, G.W., McParland, V.J., Kalverda, A.P., Homans, S.W. and Radford, S.E. (2005). "Dynamics in the unfolded state of beta(2)-microglobulin studied by NMR." Journal of Molecular Biology 346, 279-294.
Radford, S.E., Gosal, W.S. and Platt, G.W. (2005). "Towards an understanding of the structural molecular mechanism of beta(2)-microglobulin amyloid formation in vitro." Biochimica et Biophysica Acta-Proteins and Proteomics 1753, 51-63.
Redzic, Z.B., Biringer, J., Barnes, K., Baldwin, S.A., Al-Sarraf, H., Nicola, P.A., Young, J.D., Cass, C.E., Barrand, M.A. and Hladky, S.B. (2005). "Polarized distribution of nucleoside transporters in rat brain endothelial and choroid plexus epithelial cells." Journal of Neurochemistry 94, 1420-1426.
Robinson, C., Connell, S., Brookes, S.J., Kirkham, J., Shore, R.C. and Smith, D.A.M. (2005). "Surface chemistry of enamel apatite during maturation in relation to pH: implications for protein removal and crystal growth." Archives of Oral Biology 50, 267-270.
Robinson, C., Connell, S.D., Kirkham, J. and Smith, D.A.M. (2005). "Regular nano-domains in apatite crystals from developing enamel: Implications for crystal assembly from subunits and protein binding sites for growth modulation." Geochimica et Cosmochimica Acta 69, A66-A66.
Rodriguez-Mendieta, I.R., Spence, G.R., Gell, C., Radford, S.E. and Smith, D.A. (2005). "Ultraviolet resonance Raman studies reveal the environment of tryptophan and tyrosine residues in the native and partially folded states of the E colicin-binding immunity protein Im7." Biochemistry 44, 3306-3315.
Sadowski, M.I., Parish, J.H. and Westhead, D.R. (2005). "Automated derivation and refinement of sequence length patterns for protein sequences using evolutionary computation." Biosystems 81, 247-254.
Sanderson, J.A., Findlay, J.B.C. and Fishwick, C.W.G. (2005). "Preparation of novel 3H-trifluoromethyldiazirine-based photoactivatable potassium channel antagonists." Tetrahedron 61, 11244-11252.
Sharma-Oates, A., Quirke, P. and Westhead, D.R. (2005). "TmaDB: a repository for tissue microarray data." Bmc Bioinformatics 6.
Smith, K.M., Slugoski, M.D., Loewen, S.K., Ng, A.M.L., Yao, S.Y.M., Chen, X.Z., Karpinski, E., Cass, C.E., Baldwin, S.A. and Young, J.D. (2005). "The broadly selective human Na+/nucleoside cotransporter (hCNT3) exhibits novel cation-coupled nucleoside transport characteristics." Journal of Biological Chemistry 280, 25436-25449.
Smith, P.G., Burchill, S.A., Brooke, D., Coletta, P.L. and Whitehouse, A. (2005). "Efficient infection and persistence of a herpesvirus saimiri-based gene delivery vector into human tumor xenografts and multicellular spheroid cultures." Cancer Gene Therapy 12, 248-256.
Smith, P.G., Oakley, F., Fernandez, M., Mann, D.A., Lemoine, N.R. and Whitehouse, A. (2005). "Herpesvirus saimiri-based vector biodistribution using noninvasive optical imaging." Gene Therapy 12, 1465-1476.
Stafford, W.F., Walker, M.L., Trinick, J.A. and Coluccio, L.M. (2005). "Mammalian class I myosin, Myo1b, is monomeric and cross-links actin filaments as determined by hydrodynamic studies and electron microscopy." Biophysical Journal 88, 384-391.
Stockley, P.G., Ashcroft, A.E., Francese, S., Thompson, G.S., Ranson, N.A., Smith, D.A.M., Homans, S.W. and Stonehouse, N.J. (2005). "Dissecting the fine details of assembly of a T=3 capsid." Journal of Theoretical Medicine 6, 119-125.
Street, A., Macdonald, A., McCormick, C. and Harris, M. (2005). "Hepatitis C virus NS5A-mediated activation of phosphoinositide 3-kinase results in stabilization of cellular beta-catenin and stimulation of beta-catenin-responsive transcription." Journal of Virology 79, 5006-5016.
Taib, M., Pinney, J.W., Westhead, D.R., McDowall, K.J. and Adams, D.J. (2005). "Differential expression and extent of fungal/plant and fungal/bacterial chitinases of Aspergillus fumigatus." Archives of Microbiology 184, 78-81.
Taylor, D.R., Watt, N.T., Perera, W.S.S. and Hooper, N.M. (2005). "Assigning functions to distinct regions of the N-terminus of the prion protein that are involved in its copper-stimulated, clathrin-dependent endocytosis." Journal of Cell Science 118, 5141-5153.
Tezel, A.K., Leal, L.G. and McLeish, T.C.B. (2005). "Rheo-optical evidence of CCR in an entangled four-arm star." Macromolecules 38, 1451-1455.
Thomas, G.L., Sessions, R.B. and Parker, M.J. (2005). "Density guided importance sampling: application to a reduced model of protein folding." Bioinformatics 21, 2839-2843.
Thomson, N.H. (2005). "Imaging the substructure of antibodies with tapping-mode AFM in air: the importance of a water layer on mica." Journal of Microscopy 217, 193-199.
Thomson, N.H. (2005). "The substructure of immunoglobulin G resolved to 25 kDa using amplitude modulation AFM in air." Ultramicroscopy 105, 103-110.
Torrance, G.M., Gilbert, D.R., Michalopoulos, I. and Westhead, D.W. (2005). "Protein structure topological comparison, discovery and matching service." Bioinformatics 21, 2537-2538.
Tskhovrebova, L. and Trinick, J. (2005). "Muscle disease: a giant feels the strain." Nature Medicine 11, 478-479.
Tsuboi, T., Ravier, M.A., Xie, H., Ewart, M.A., Gould, G.W., Baldwin, S.A. and Rutter, G.A. (2005). "Mammalian exocyst complex is required for the docking step of insulin vesicle exocytosis." Journal of Biological Chemistry 280, 25565-25570.
Uguru, G.C., Stephens, K.E., Stead, J.A., Towle, J.E., Baumberg, S. and McDowall, K.J. (2005). "Transcriptional activation of the pathway-specific regulator of the actinorhodin biosynthetic genes in Streptomyces coelicolor." Molecular Microbiology 58, 131-150.
Urquhart, P., Pang, S. and Hooper, N.M. (2005). N-glycans as apical targeting signals in polarized epithelial cells. Lipids, Rafts and Traffic. 72: 39-45.
Vardy, E., Catto, A.J. and Hooper, N.M. (2005). "Proteolytic mechanisms in amyloid-beta metabolism: therapeutic implications for Alzheimer's disease." Trends in Molecular Medicine 11, 464-472.
Visser, F., Baldwin, S.A., Isaac, R.E., Young, J.D. and Cass, C.E. (2005). "Identification and mutational analysis of amino acid residues involved in dipyridamole interactions with human and Caenorhabditis elegans equilibrative nucleoside transporters." Journal of Biological Chemistry 280, 11025-11034.
Visser, F., Zhang, J., Raborn, R.T., Baldwin, S.A., Young, J.D. and Cass, C.E. (2005). "Residue 33 of human equilibrative nucleoside transporter 2 is a functionally important component of both the dipyridamole and nucleoside binding sites." Molecular Pharmacology 67, 1291-1298.
Wakenshaw, L., Walters, M.S. and Whitehouse, A. (2005). "The herpesvirus saimiri replication and transcription activator acts synergistically with CCAAT enhancer binding protein alpha to activate the DNA polymerase promoter." Journal of Virology 79, 13548-13560.
Wallace, E.J., Hooper, N.M. and Olmsted, P.D. (2005). "The kinetics of phase separation in asymmetric membranes." Biophysical Journal 88, 4072-4083.
Walters, M.S., Hall, K.T. and Whitehouse, A. (2005). "The herpesvirus saimiri Rta gene autostimulates via binding to a non-consensus response element." Journal of General Virology 86, 581-587.
Wang, J.J., Saito, Y., Batchelder, D.N., Kirkham, J., Robinson, C. and Smith, D.A. (2005). "Controllable method for the preparation of metalized probes for efficient scanning near-field optical Raman microscopy." Applied Physics Letters 86.
Warner, F.J., Lew, R.A., Smith, I.A., Lambert, D.W., Hooper, N.M. and Turner, A.J. (2005). "Angiotensin-converting enzyme 2 (ACE2), but not ACE, is preferentially localized to the apical surface of polarized kidney cells." Journal of Biological Chemistry 280, 39353-39362.
Weiss, J.L., Evans, N.A., Ahmed, T., Wrigley, J.D.J., Khan, S., Wright, C., Keen, J.N., Holzenburg, A. and Findlay, J.B.C. (2005). "Methionine-rich repeat proteins: a family of membrane- associated proteins which contain unusual repeat regions." Biochimica et Biophysica Acta-Biomembranes 1668, 164-174.
Whitehouse, C., Fang, J.Y., Aggeli, A., Bell, M., Brydson, R., Fishwick, C.W.G., Henderson, J.R., Knobler, C.M., Owens, R.W., Thomson, N.H., Smith, D.A. and Boden, N. (2005). "Adsorption and self-assembly of peptides on mica substrates." Angewandte Chemie-International Edition 44, 1965-1968.
Whyteside, G., Meek, P.J., Ball, S.K., Dixon, N., Finbow, M.E., Kee, T.P., Findlay, J.B.C. and Harrison, M.A. (2005). "Concanamycin and indolyl pentadieneamide inhibitors of the vacuolar H+-ATPase bind with high affinity to the purified proteolipid subunit of the membrane domain." Biochemistry 44, 15024-15031.
Williams, B.J.L., Boyne, J.R., Goodwin, D.J., Roaden, L., Hautbergue, G.M., Wilson, S.A. and Whitehouse, A. (2005). "The prototype gamma-2 herpesvirus nucleocytoplasmic shuttling protein, ORF 57, transports viral RNA through the cellular mRNA export pathway." Biochemical Journal 387, 295-308.
Williams, G.J., Woodhall, T., Nelson, A. and Berry, A. (2005). "Structure-guided saturation mutagenesis of N-acetylneuraminic acid lyase for the synthesis of sialic acid mimetics." Protein Engineering Design & Selection 18, 239-246.
Wood, J.P.A., Capaldi, S.A., Robinson, M.A., Baron, A.J. and Stonehouse, N.J. (2005). "RNA multimerisation in the DNA packaging motor of bacteriophage phi29." Journal of Theoretical Medicine 6, 127-134.
Woodhall, T., Williams, G., Berry, A. and Nelson, A. (2005). "Creation of a tailored aldolase for the parallel synthesis of sialic acid mimetics." Angewandte Chemie-International Edition 44, 2109-2112.
Woodhall, T., Williams, G., Berry, A. and Nelson, A. (2005). "Synthesis of screening substrates for the directed evolution of sialic acid aldolase: towards tailored enzymes for the preparation of influenza A sialidase inhibitor analogues." Organic & Biomolecular Chemistry 3, 1795-1800.
Woodhall, T., Williams, G.J., Berry, A. and Nelson, A. (2005). "Directed evolution of an aldolase for the parallel synthesis of sialic acid mimetics." Angewandte Chemie-International Edition 44, 2109-2112.
You, J.W., Dove, B.K., Enjuanes, L., DeDiego, M.L., Alvarez, E., Howell, G., Heinen, P., Zambon, M. and Hiscox, J.A. (2005). "Subcellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein." Journal of General Virology 86, 3303-3310.
Zhang, J., Smith, K.M., Tackaberry, T., Visser, F., Robins, M.J., Nielsen, L.P.C., Nowak, I., Karpinski, E., Baldwin, S.A., Young, J.D. and Cass, C.E. (2005). "Uridine binding and transportability determinants of human concentrative nucleoside transporters." Molecular Pharmacology 68, 830-839.

Publications by Astbury Centre Members 2004

Appleford, P.J., Griffiths, M., Yao, S.Y.M., Ng, A.M.L., Chomey, E.G., Isaac, R.E., Coates, D., Hope, I.A., Cass, C.E., Young, J.D. and Baldwin, S.A. (2004). "Functional redundancy of two nucleoside transporters of the ENT family (CeENT1, CeENT2) required for development of Caenorhabditis elegans." Molecular Membrane Biology 21, 247-259.
Baldwin, S.A., Beal, P.R., Yao, S.Y.M., King, A.E., Cass, C.E. and Young, J.D. (2004). "The equilibrative nucleoside transporter family, SLC29." European Journal of Physiology 447, 735-743.
Baldwin, S.A. and Lucy, J.A. (2004). "The structural biology of membrane proteins." Molecular Membrane Biology 21, 127-128.
Barnes, K., Ingram, J.C., Bennett, M.D.M., Stewart, G.W. and Baldwin, S.A. (2004). "Methyl-beta-cyclodextrin stimulates glucose uptake in Clone 9 cells: a possible role for lipid rafts." Biochemical Journal 378, 343-351.
Bartlett, S. and Nelson, A. (2004). "Evaluation of alternative approaches for the synthesis of macrocyclic bisindolylmaleimides." Organic & Biomolecular Chemistry 2, 2874-2883.
Bartlett, S. and Nelson, A. (2004). "Towards configurationally stable bisindolylmaleimide cyclophanes: potential tools for investigating protein kinase function." Chemical Communications, 1112-1113.
Bhogal, N., Blaney, F.E., Ingley, P.M., Rees, J. and Findlay, J.B.C. (2004). "Evidence for the proximity of the extreme N-terminus of the neurokinin-2 (NK2) tachykinin receptor to Cys(167) in the putative fourth transmembrane helix." Biochemistry 43, 3027-3038.
Billington, N., Burgess, S.A., Patel, H., Chantler, P.D., White, H.D., Trinick, J. and Knight, P.J. (2004). "Conformational changes in myosin heads during ATPase." Biophysical Journal 86, 403A-404A.
Bingham, R.J., Findlay, J.B.C., Hsieh, S.Y., Kalverda, A.P., Kjeliberg, A., Perazzolo, C., Phillips, S.E.V., Seshadri, K., Trinh, C.H., Turnbull, W.B., Bodenhausen, G. and Homans, S.W. (2004). "Thermodynamics of binding of 2-methoxy-3-isopropylpyrazine and 2-methoxy-3-isobutylpyrazine to the major urinary protein." Journal of the American Chemical Society 126, 1675-1681.
Borysik, A.J.H., Radford, S.E. and Ashcroft, A.E. (2004). "Co-populated conformational ensembles of beta(2)-microglobulin uncovered quantitatively by electrospray ionization mass spectrometry." Journal of Biological Chemistry 279, 27069-27077.
Borysik, A.J.H., Read, P., Little, D.R., Bateman, R.H., Radford, S.E. and Ashcroft, A.E. (2004). "Separation of beta(2)-microglobulin conformers by high-field asymmetric waveform ion mobility spectrometry (FAIMS) coupled to electrospray ionisation mass spectrometry." Rapid Communications in Mass Spectrometry 18, 2229-2234.
Brakoulias, A. and Jackson, R.M. (2004). "Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: An automated all-against-all structural comparison using geometric matching." Proteins-Structure Function and Bioinformatics 56, 250-260.
Burgess, S., Walker, M., Knight, P.J., Sparrow, J., Schmitz, S., Offer, G., Bullard, B., Leonard, K., Holt, J. and Trinick, J. (2004). "Structural studies of arthrin: Monoubiquitinated actin." Journal of Molecular Biology 341, 1161-1173.
Burgess, S.A. and Knight, P.J. (2004). "Is the dynein motor a winch?" Current Opinion in Structural Biology 14, 138-146.
Burgess, S.A., Walker, M.L., Sakakibara, H., Oiwa, K. and Knight, P.J. (2004). "The structure of dynein-c by negative stain electron microscopy." Journal of Structural Biology 146, 205-216.
Burgess, S.A., Walker, M.L., Thirumurugan, K., Trinick, J. and Knight, P.J. (2004). "Use of negative stain and single-particle image processing to explore dynamic properties of flexible macromolecules." Journal of Structural Biology 147, 247-258.
Burt, J., Dean, T. and Warriner, S. (2004). "The parallel synthesis of a disaccharide library using a solid phase, peptide-templated strategy." Chemical Communications, 454-455.
Calderwood, M.A., Hall, K.T., Matthews, D.A. and Whitehouse, A. (2004). "The herpesvirus saimiri ORF73 gene product interacts with host- cell mitotic chromosomes and self-associates via its C terminus." Journal of General Virology 85, 147-153.
Calderwood, N.A., White, R.E. and Whitehouse, A. (2004). "Development of herpesvirus-based episomally maintained gene delivery vectors." Expert Opinion on Biological Therapy 4, 493-505.
Caryl, J.A., Smith, M.C.A. and Thomas, C.D. (2004). "Reconstitution of a staphylococcal plasmid-protein relaxation complex in vitro." Journal of Bacteriology 186, 3374-3383.
Cobbold, C., Coventry, J., Ponnambalam, S. and Monaco, A.P. (2004). "Actin and microtubule regulation of trans-Golgi network architecture, and copper-dependent protein transport to the cell surface." Mol Membr Biol 21, 59-66.
Cooksey, J., Gunn, A., Kocienski, P.J., Kuhl, A., Uppal, S., Christopher, J.A. and Bell, R. (2004). "The nucleophilic addition of alpha-metallated 1,3-dioxanes to planar chiral cationic eta(3)-allylmolybdenum complexes. Synthesis of (2E,5S,6R,7E)-6-methyl-8-phenylocta-2,7-dienoic acid methyl ester, a key component of the Cryptophycins." Organic & Biomolecular Chemistry 2, 1719-1731.
Daranas, A.H., Kalverda, A.P., Chiovitti, A. and Homans, S.W. (2004). "Backbone resonance assignment of the L- arabinose binding protein in complex with D-galactose." Journal of Biomolecular NMR 28, 191-192.
Daranas, A.H., Shimizu, H. and Homans, S.W. (2004). "Thermodynamics of binding of D-galactose and deoxy derivatives thereof to the L-arabinose-binding protein." Journal of the American Chemical Society 126, 11870-11876.
de Maturana, R.L., Treece-Birch, J., Abidi, F., Findlay, J.B.C. and Donnelly, D. (2004). "Met-204 and Tyr-205 are together important for binding GLP-1 receptor agonists but not their N-terminally truncated analogues." Protein and Peptide Letters 11, 15-22.
Deacon, S.E., Mahmoud, K., Spooner, R.K., Firbank, S.J., Knowles, P.F., Phillips, S.E.V. and McPherson, M.J. (2004). "Enhanced fructose oxidase activity in a galactose oxidase variant." Chembiochem 5, 972-979.
Dimitriadis, G., Drysdale, A., Myers, J.K., Arora, P., Radford, S.E., Oas, T.G. and Smith, D.A. (2004). "Microsecond folding dynamics of the F13W G29A mutant of the B domain of staphylococcal protein A by laser-induced temperature jump." Proceedings of the National Academy of Sciences of the United States of America 101, 3809-3814.
Emmett, S.R., Dove, B.K., Mahoney, L., Wurm, T. and Hiscox, J.A. (2004). "The cell cycle and virus infection." Methods in Molecular Biology. 296, 197-218.
Fadouloglou, V.E., Tampakaki, A.P., Glykos, N.M., Bastaki, M.N., Hadden, J.M., Phillips, S.E., Panopoulos, N.J. and Kokkinidis, M. (2004). "Structure of HrcQ(B)-C, a conserved component of the bacterial type III secretion systems." Proceedings of the National Academy of Sciences of the United States of America 101, 70-75.
Firbank, S., Rogers, M., Guerrero, R.H., Dooley, D.M., Halcrow, M.A., Phillips, S.E., Knowles, P.F. and McPherson, M.J. (2004). Cofactor processing galactose oxidase. Free Radicals: Enzymology, Signalling and Disease: 15-25.
Fournier, L., Kocienski, P. and Pons, J.M. (2004). "The beta-lactone route to alpha,beta-unsaturated delta- lactones. Total syntheses of (+/-)-goniothalamin and (-)- massoialactone." Tetrahedron 60, 1659-1663.
Friel, C.T., Beddard, G.S. and Radford, S.E. (2004). "Switching two-state to three-state kinetics in the helical protein Im9 via the optimisation of stabilising non-native interactions by design." Journal of Molecular Biology 342, 261-273.
Gorski, S.A., Le Duff, C.S., Capaldi, A.P., Kalverda, A.P., Beddard, G.S., Moore, G.R. and Radford, S.E. (2004). "Equilibrium hydrogen exchange reveals extensive hydrogen bonded secondary structure in the on-pathway intermediate of Im7." Journal of Molecular Biology 337, 183-193.
Grewal, S., Smith, J., Ponnambalam, S. and Walker, J. (2004). "Stimulation-dependent recruitment of cytosolic phospholipase A(2)-alpha to EA.hy.926 endothelial cell membranes leads to calcium-independent association." European Journal of Biochemistry 271, 69-77.
Griffin, S.D.C., Harvey, R., Clarke, D.S., Barclay, W.S., Harris, M. and Rowlands, D.J. (2004). "A conserved basic loop in hepatitis C virus p7 protein is required for amantadine-sensitive ion channel activity in mammalian cells but is dispensable for localization to mitochondria." Journal of General Virology 85, 451-461.
Hao, J. and Berry, A. (2004). "A thermostable variant of fructose bisphosphate aldolase constructed by directed evolution also shows increased stability in organic solvents." Protein Eng. Des. Sel. 17, 689-697.
Hawkins, R.J. and McLeish, T.C.B. (2004). "Coarse-grained model of entropic allostery." Physical Review Letters 93, art. no.-098104.
Heddle, J.G., Mitelheiser, S., Maxwell, A. and Thomson, N.H. (2004). "Nucleotide binding to DNA gyrase causes loss of DNA wrap." Journal of Molecular Biology 337, 597-610.
Heinrich, M., Pyckhout-Hintzen, W., Allgaier, J., Richter, D., Straube, E., McLeish, T.C.B., Wiedenmann, A., Blackwell, R.J. and Read, D.J. (2004). "Small-angle neutron scattering study of the relaxation of a melt of polybutadiene H-polymers following a large step strain." Macromolecules 37, 5054-5064.
Hernández-Daranas, A., Kalverda, A.P., Chiovitti, A. and Homans, S.W. (2004). "Backbone resonance assignment of the L-arabinose binding protein in complex with D-galactose." J. Biomol. NMR 28, 191-192.
Hernández-Daranas, A., Shimizu, H. and Homans, S.W. (2004). "Thermodynamics of binding of D-galactose and deoxy-derivatives thereof to the L-arabinose-binding protein." J. Am. Chem. Soc. 128, 11870-11876.
Hodgson, R. and Nelson, A. (2004). "A two-directional synthesis of the C-58-C-71 fragment of palytoxin." Organic & Biomolecular Chemistry 2, 373-386.
Homans, S.W. (2004). "NMR spectroscopy tools for structure-aided drug design." Angewandte Chemie-International Edition 43, 290-300.
Horn, W.T., Convery, M.A., Stonehouse, N.J., Adams, C.J., Liljas, L., Phillips, S.E.V. and Stockley, P.G. (2004). "The crystal structure of a high affinity RNA stem-loop complexed with the bacteriophage MS2 capsid: Further challenges in the modeling of ligand-RNA interactions." RNA 10, 1776-1782.
Houmeida, A., Thompson, B., Tskhovrebova, L., Knight, P.J., Thirumurugan, K., Stafford, W.F. and Trinick, J. (2004). "Characterisation of the region of titin that forms end- filaments in the I-band of muscle sarcomeres." Biophysical Journal 86, 212A-212A.
Howell, G.J., Herbert, S.P., Smith, J.M., Mittar, S., Ewan, L.C., Mohammed, M., Hunter, A.R., Simpson, N., Turner, A.J., Zachary, I., Walker, J.H. and Ponnambalam, S. (2004). "Endothelial cell confluence regulates Weibel-Palade body formation." Molecular Membrane Biology 21, 413-421.
Jung, H.S., Burgess, S.A., Colegrave, M., Patel, H., Chantler, P.D., Chalovich, J.M., Trinick, J. and Knight, P.J. (2004). "Comparative studies of the folded structures of scallop striated and vertebrate smooth muscle myosins." Biophysical Journal 86, 403A-403A.
Jung, H.S., Park, H.H., Mendieta, I.R. and Smith, D.A. (2004). "Determination of bonding structure of Si, Ge, and N incorporated amorphous carbon films by near-edge X-ray absorption fine structure and ultraviolet Raman spectroscopy." Journal of Applied Physics 96, 1013-1018.
Kawakami, M., Byrne, K., Khatri, B., McLeish, T.C.B., Radford, S.E. and Smith, D.A. (2004). "Viscoelastic properties of single polysaccharide molecules determined by analysis of thermally driven oscillations of an atomic force microscope cantilever." Langmuir 20, 9299-9303.
Kennedy, A., Nelson, A. and Perry, A. (2004). "Highly diastereoselective addition of ketone enolates to N- sulfinyl imines: Asymmetric synthesis of syn- and anti-1,3- amino alcohol derivatives." Synlett, 967-970.
Khan, A., Ashcroft, A.E., Korchazhkina, O.V. and Exley, C. (2004). "Metal-mediated formation of fibrillar ABri amyloid." J. Inorg. Biochem. 98, 2006 - 2010.
Kocienski, P., Bell, R., Bourque, E., Christopher, J.A., Cooksley, J., Gunn, A., Kuhl, A., Li, Y.F., Uppal, S. and Yuen, J. (2004). "Synthetic applications of planar chiral cationic eta(3)- allylmolybdenum complexes." Pure and Applied Chemistry 76, 477-494.
Lawrenson, I.D. and Stockley, P.G. (2004). "Kinetic analysis of operator binding by the E. coli methionine repressor highlights the role(s) of electrostatic interactions." Febs Letters 564, 136-142.
Lister, I., Roberts, R., Schmitz, S., Walker, M., Trinick, J., Veigel, C., Buss, F. and Kendrick-Jones, J. (2004). "Myosin VI: a multifunctional motor." Biochemical Society Transactions 32, 685-688.
Lister, I., Schmitz, S., Walker, M., Trinick, J., Buss, F., Veigel, C. and Kendrick-Jones, J. (2004). "A monomeric myosin VI with a large working stroke." Embo Journal 23, 1729-1738.
Macdonald, A., Crowder, K., Street, A., McCormick, C. and Harris, M. (2004). "The hepatitis C virus NS5A protein binds to members of the Src family of tyrosine kinases and regulates kinase activity." Journal of General Virology 85, 721-729.
Macdonald, A. and Harris, M. (2004). "Hepatitis C virus NS5A: tales of a promiscuous protein." Journal of General Virology 85, 2485-2502.
McConkey, G.A., Pinney, J.W., Westhead, D.R., Plueckhahn, K., Fitzpatrick, T.B., Macheroux, P. and Kappes, B. (2004). "Annotating the Plasmodium genome and the enigma of the shikimate pathway." Trends in Parasitology 20, 60-65.
McCormick, C.J., Challinor, L., Macdonald, A., Rowlands, D.J. and Harris, M. (2004). "Introduction of replication-competent hepatitis C virus transcripts using a tetracycline-regulable baculovirus delivery system." Journal of General Virology 85, 429-439.
Michalopoulos, I., Torrance, G.M., Gilbert, D.R. and Westhead, D.R. (2004). "TOPS: an enhanced database of protein structural topology." Nucleic Acids Research 32, D251-D254.
Mocquet, C.M. and Warriner, S.L. (2004). "Metal-free bifunctional catalysis of the asymmetric Baylis- Hillman reaction." Synlett, 356-358.
Morten, I.J., Hewitt, E.W. and Radford, S.E. (2004). Beta-2-microglobulin and dialysis-related amyloidosis. Protein Misfolding, Aggregation and Conformational Diseases. V. N. a. F. Uversky, A.L, Kluwer Academic/Plenum Publishers.
Murtagh, M.S., Burgess, S., Sparrow, J., Knight, P.J. and Trinick, J. (2004). "Single particle image processing of muscle thin filaments." Biophysical Journal 86, 212A-212A.
Nelson, A. (2004). "The development of strategies and methods for the synthesis of biologically active compounds." New Journal of Chemistry 28, 771-776.
Paci, E., Friel, C.T., Lindorff-Larsen, K., Radford, S.E., Karplus, M. and Vendruscolo, M. (2004). "Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints." Proteins-Structure Function and Genetics 54, 513-525.
Pali, T., Whyteside, G., Dixon, N., Kee, T.P., Ball, S., Harrison, M.A., Findlay, J.B.C., Finbow, M.E. and Marsh, D. (2004). "Interaction of inhibitors of the vacuolar H+-ATPase with the transmembrane V-o-sector." Biochemistry 43, 12297-12305.
Parkinson, N.M., Conyers, C., Keen, J., MacNicoll, A., Smith, I., Audsley, N. and Weaver, R. (2004). "Towards a comprehensive view of the primary structure of venom proteins from the parasitoid wasp Pimpla hypochondriaca." Insect Biochemistry and Molecular Biology 34, 565-571.
Patching, S.G., Brough, A.R., Herbert, R.B., Rajakarier, J.A., Henderson, P.J.F. and Middleton, D.A. (2004). "Substrate affinities for membrane transport proteins determined by C-13 cross-polarization magic-angle spinning nuclear magnetic resonance spectroscopy." Journal of the American Chemical Society 126, 3072-3080.
Patching, S.G., Herbert, R.B., O'Reilly, J., Brough, A.R. and Henderson, P.J.F. (2004). "Low C-13-background for NMR-based studies of ligand binding using C-13-depleted glucose as carbon source for microbial growth: C-13-labeled glucose and C-13-forskolin binding to the galactose-H+ symport protein GaIP in Escherichia coli." Journal of the American Chemical Society 126, 86-87.
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Rodgers-Gray, T.P., Smith, J.E., Ashcroft, A.E., Isaac, R.E. and Dunn, A.M. (2004). "Mechanisms of parasite-induced sex reversal in Gammarus duebeni." International Journal for Parasitology 34, 747-753.
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Sessions, R.B., Thomas, G.L. and Parker, M.J. (2004). "Water as a conformational editor in protein folding." Journal of Molecular Biology 343, 1125-1133.
Sharma-Oates, A., Quirke, P. and Westhead, D.R. (2004). "TmaDB: A tissue microarray database." Journal of Pathology 204, 51A-51A.
Smith, A.J., Mair, L.A., Ponnambalam, S. and Sivaprasadarao, A. (2004). "Trafficking and functional defects associated with genetic mutations in the Kir6.2 subunit of K-ATP channels." Biophysical Journal 86, 580A-580A.
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Tskhovrebova, L. and Trinick, J. (2004). "Properties of titin immunoglobulin and fibronectin-3 domains." Journal of Biological Chemistry 279, 46351-46354.
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Yegutkin, G.G., Salminen, T., Koskinen, K., Kurtis, C.R.P., McPherson, M.J., Jalkanen, S. and Salmi, M. (2004). "A peptide inhibitor of vascular adhesion protein-1 (VAP-1) blocks leukocyte-endothelial interactions under shear stress." European Journal of Immunology 34, 2276-2285.

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