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Research Papers

Research papers held by members of the Prozomix Research and Development Team:

[1]        Zhang M, McDonald FM, Sturrock SS, Charnock SJ, Humphery-Smith I, Black GW (2007) Group A streptococcus cell-associated pathogenic proteins as revealed by growth in hyaluronic acid-enriched media. Proteomics 7, 1379-90.

[2]        Humphrey D, Andrews M, Santos SR, James EK, Vinogradova LV, Perin L, Reis VM, Cummings SP (2007) Phylogenetic assignment and mechanism of action of a crop growth promoting Rhizobium radiobacter strain used as a biofertiliser on graminaceous crops in Russia. Antonie Van Leeuwenhoek 91, 105-113.

[3]   buySheldon WL, MacAuley MS, Taylor EJ, Robinson CE, Charnock SJ, Davies GJ, Vocadlo DJ, Black GW (2006) Functional analysis of a group A streptococcal glycoside hydrolase Spy1600 from family 84 reveals it is a beta-N-acetylglucosaminidase and not a hyaluronidase. Biochem. J. 399, 241-247.

[4]        Cummings SP, Humphry DR, Santos SR, Andrews M, James EK (2006). The potential and pitfalls of exploiting nitrogen fixing bacteria in agricultural soils as a substitute for inorganic fertiliser. Environ. Biotech. 2, 1-10.

[5]        McCleary, BV, Charnock, SJ, Rossiter, PC, O'Shea, MF, Power, AM, Lloyd, RM (2006) Measurement of carbohydrates in grain, feed and food. Journal of the Science of Food and Agriculture 86, 1648-1661.

[6]        van den Broek LAM, Lloyd RM, Beldman G, Verdoes JC, McCleary BV, Voragen AGJ (2005) Cloning and characterization of arabinoxylan arabinofuranohydrolase-D3 (AXHd3) from Bifidobacterium adolescentis DSM20083. Appl. Microbiol. Biotechnol. 67, 641-647.

[7]   buySmith NL, Taylor EJ, Lindsay AM, Charnock SJ, Turkenburg JP, Dodson EJ, Davies, GJ, Black GW (2005) Structure of a group A streptococcal phage-encoded virulence factor reveals a catalytically active triple-stranded beta-helix. Proc. Natl. Acad. Sci. USA 102,17652-17657.

[8]        Proctor MR, Taylor EJ, Nurizzo D, Turkenburg JP, Lloyd RM, Vardakou M, Davies GJ, Gilbert HJ (2005) Tailored catalysts for plant cell-wall degradation: Redesigning the exo/endo preference of Cellvibrio japonicus arabinanase 43A. Proc. Natl. Acad. Sci. USA 102, 2697-2702.

[9]        Taylor EJ, Smith NL, Colby J, Charnock SJ, Black GW (2004) The gene encoding the ribulose monophosphate pathway enzyme, 3-hexulose-6-phosphate synthase, from Aminomonas aminovorus C2A1 is adjacent to coding sequences that exhibit similarity to histidine biosynthesis enzymes. Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology 86,167-172.

[10]      Pell G, Szabo L, Charnock SJ, Xie HF, Gloster TM, Davies GJ, Gilbert HJ (2004) Structural and biochemical analysis of Cellvibrio japonicus xylanase 10C - How variation in substrate-binding cleft influences the catalytic profile of family GH-10 xylanases. J. Biol. Chem. 279, 11777-11788.

[11]       Vincent F, Charnock SJ, Verschueren KHG, Turkenburg JP, Scott DJ, Offen WA, Roberts S, Pell G, Gilbert HJ, Davies, GJ, Brannigan JA (2003) Multifunctional xylooligosaccharide/cephalosporin C deacetylase revealed by the hexameric structure of the Bacillus subtilis enzyme at 1.9 angstrom resolution. J. Mol. Biol. 330, 593-606.

[12]       Humphrey D, Black GW, Cummings SP (2003) Reclassification of 'Pseudomonas fluorescens subsp cellulosa' NCIMB 10462 (Ueda et al. 1952) as Cellvibrio japonicus sp nov and revival of Cellvibrio vulgaris sp nov., nom. rev. and Cellvibrio fulvus sp nov., nom. rev. International Journal of Systematic and Evolutionary Microbiology 53, 393-400.

[13]       Nurizzo D, Turkenburg JP, Charnock SJ, Roberts SM, Dodson EJ, McKie VA, Tailor EJ, Gilbert HJ, Davies GJ (2002) Cellvibrio japonicus alpha-L-arabinanase 43A has a novel five-blade beta-propeller fold. Nature Struct. Biol. 9, 665-668.

[14]       Moroz OV, Antson AA, Dodson EJ, Burrell HJ, Grist SJ, Lloyd RM, Maitland NJ, Dodson GG, Wilson KS, Lukanidin E, Bronstein IB (2002) The structure of S100A12 in a hexameric form and its proposed role in receptor signalling. Acta Crystallogr., Sect. D: Biol. Crystallogr. 58, 407-413.

[15]       Gibson RP, Turkenburg JP, Charnock SJ, Lloyd RM, Davies GJ (2002) Insights into trehalose synthesis provided by the structure of the retaining glucosyltransferase OtsA. Chem. Biol. 9, 1337-1346.

[16]       Gibson RP, Lloyd RM, Charnock SJ, Davies GJ (2002) Characterization of Escherichia coli OtsA, a trehalose-6-phosphate synthase from glycosyltransferase family 20. Acta Crystallogr., Sect. D: Biol. Crystallogr. 58, 349-351.

[17] buyCharnock SJ, Brown IE, Turkenburg JP, Black GW, Davies GJ (2002) Convergent evolution sheds light on the anti-beta-elimination mechanism common to family 1 and 10 polysaccharide lyases. Proc. Natl. Acad. Sci. USA 99, 12067-12072.

[18]       Charnock SJ, Bolam DN, Nurizzo D, Szabo L, McKie VA, Gilbert HJ, Davies GJ (2002) Promiscuity in ligand-binding: The three-dimensional structure of a Piromyces carbohydrate-binding module, CBM29-2, in complex with cello-and mannohexaose. Proc. Natl. Acad. Sci. USA 99, 14077-14082.

[19]       Nagy T, Emami K, Fontes CM, Ferreira LM, Humphry DR, Gilbert HJ (2002) The membrane-bound alpha-glucuronidase from Pseudomonas cellulosa hydrolyzes 4-O-methyl-D-glucuronoxylooligosaccharides but not 4-O-methyl-D-glucuronoxylan. J. Bacteriol. 184, 4925-4929.

[20]       Xie HF, Gilbert HJ, Charnock SJ, Davies GJ, Williamson MP, Simpson PJ, Raghothama S, Fontes CM, Dias FM, Ferreira LM, Bolam DN (2001) Clostridium thermocellum Xyn10B carbohydrate-binding module 22-2: The role of conserved amino acids in ligand binding. Biochemistry 40, 9167-9176.

[21]       Taylor EJ, Charnock SJ, Colby J, Davies GJ, Black GW (2001) Cloning, purification and characterization of the 6-phospho-3-hexulose isomerase YckF from Bacillus subtilis. Acta Crystallogr., Sect. D: Biol. Crystallogr. 57, 1138-1140.

[22]       Tarbouriech N, Charnock SJ, Davies GJ (2001) Three-dimensional structures of the Mn and Mg dTDP complexes of the family GT-2 glycosyltransferase SpsA: A comparison with related NDP-sugar glycosyltransferases. J. Mol. Biol. 314, 655-661.

[23]       Szabo U, Jamal S, Xie HF, Charnock SJ, Bolam DN, Gilbert HJ, Davies GJ (2001) Structure of a family 15 carbohydrate-binding module in complex with xylopentaose - Evidence that xylan binds in an approximate 3-fold helical conformation. J. Biol. Chem. 276, 49061-49065.

[24]       Prates JAM, Tarbouriech N, Charnock SJ, Fontes C, Ferreira LMA, Davies GJ (2001) The structure of the feruloyl esterase module of xylanase 10B from Clostridium thermocellum provides insights into substrate recognition. Structure 9, 1183-1190.

[25]       Humphrey D, George A, Black GW, Cummings SP (2001) Flavobacterium frigidarium sp nov., an aerobic, psychrophilic, xylanolytic and laminarinolytic bacterium from Antarctica. International Journal of Systematic and Evolutionary Microbiology 51, 1235-1243.

[26]       Davies GJ, Charnock SJ, Henrissat B (2001) The enzymatic synthesis of glycosidic bonds: "Glycosynthases" and glycosyltransferases. Trends in Glycoscience and Glycotechnology 13, 105-120.

[27]       Charnock SJ, Henrissat B, Davies GJ (2001) Three-dimensional structures of UDP-sugar glycosyltransferases illuminate the biosynthesis of plant polysaccharides. Plant Physiol. 125, 527-531.

[28] buyCharnock SJ, Brown IE, Turkenburg JP, Black GW, Davies GJ (2001) Characterization of a novel pectate lyase, Pel10A, from Pseudomonas cellulosa. Acta Crystallogr., Sect. D: Biol. Crystallogr. 57, 1141-1143.

[29] buyBrown IE, Mallen MH, Charnock SJ, Davies GJ, Black GW. Pectate lyase 10A from Pseudomonas cellulosa is a modular enzyme containing a family 2a carbohydrate-binding module. Biochem. J. 355, 155-65.

[30]       Armand S, Andrews SR, Charnock SJ, Gilbert HJ (2001) Influence of the aglycone region of the substrate binding cleft of Pseudomonas xylanase 10A on catalysis. Biochemistry 40, 7404-7409.

[31]       Ducros V, Charnock SJ, Derewenda U, Derewenda ZS, Dauter Z, Dupont C, Shareck F, Morosoli R, Kluepfel D, Davies GJ (2000) Substrate specificity in glycoside hydrolase family 10 - Structural and kinetic analysis of the streptomyces lividans xylanase 10A. J. Biol. Chem. 275, 23020-32026.

[32] buyCharnock SJ, Bolam DN, Turkenburg JP, Gilbert HJ, Ferreira LMA, Davies GJ, Fontes CM (2000) The X6 "thermostabilizing" domains of xylanases are carbohydrate-binding modules: Structure and biochemistry of the Clostridium thermocellum X6b domain. Biochemistry 39, 5013-5021.

[33]       Andrews SR, Charnock SJ, Lakey JH, Davies GJ, Claeyssens M, Nerinckx W, Underwood M, Sinnott ML, Warren RA, Gilbert HJ (2000) Substrate specificity in glycoside hydrolase family 10 - Tyrosine 87 and Leucine 314 play a pivotal, role in discriminating between glucose and xylose binding in the proximal active site of pseudomonas cellulosa xylanase 10A. J. Biol. Chem. 275, 23027-23033.

[34]       Charnock SJ, Davies GJ (1999) Cloning, crystallization and preliminary X-ray analysis of a nucleotide-diphospho-sugar transferase spsA from Bacillus subtilis. Acta Crystallogr., Sect. D: Biol. Crystallogr. 55, 677-678.

[35]       Charnock SJ, Davies GJ (1999) Structure of the nucleotide-diphospho-sugar transferase, SpsA from Bacillus subtilis, in native and nucleotide-complexed forms. Biochemistry 38, 6380-6385.

[36]       Charnock SJ, Spurway TD, Xie HF, Beylot MH, Virden R, Warren RAJ, Hazelwood GP, Gilbert HJ (1998) The topology of the substrate binding clefts of glycosyl hydrolase family 10 xylanases are not conserved. J. Biol. Chem. 273, 32187-32199.

[37]       Bolam DN, Charnock SJ, Gilbert HJ, Hughes NA (1998) Synthesis of 2,4-dinitrophenyl glycosides of D-xylobiose and D-mannobiose. Carbohydr. Res. 312, 85-89.

[38]       Charnock SJ, Lakey JH, Virden R, Hughes N, Sinnott ML, Hazlewood GP, Pickersgill R, Gilbert HJ (1997) Key residues in subsite F play a critical role in the activity of Pseudomonas fluorescens subspecies cellulosa xylanase A against xylooligosaccharides but not against highly polymeric substrates such as xylan. J. Biol. Chem. 272, 2942-2951.

[39] buyBraithwaite KL, Barna T, Spurway TD, Charnock SJ, Black GW, Hughes N, Lakey JH, Virden R, Hazlewood GP, Henrissat B, Gilbert HJ (1997) Evidence that galactanase A from Pseudomonas fluorescens subspecies cellulosa is a retaining family 53 glycosyl hydrolase in which E161 and E270 are the catalytic residues. Biochemistry 36, 15489-15500.



Patents, reviews, book chapters, abstracts, proceedings, etc, held by members of the Prozomix Research and Development Team:


[1]        Charnock SJ, McCleary BV (2006) Assay for determination of free D-galactase and/or L-arabinose. WO/2006/064487, June.

[2]        McCleary BV, Charnock SJ (2006) A kit for colorimetric assays of food and beverage analytes. WO/2006/064488, June.

[3]        Charnock SJ, McCleary BV (2006) Megazyme advanced test kits for wine – general characteristics and validation. Revue des Enology 120, 33-37.

[4]        Charnock SJ and McCleary BV (2005) Grape and wine analysis: Oenologists to exploit advanced test kits. Revue des Enology 117, 42-47.

[5]        Charnock, SJ and McCleary BV (2005) Enzymes: industrial and analytical applications. Review des Enology 116, 11-15.

[6]        Vinogradova LV, Humphry DR, Andrews M, Cummings SP, James EK, Gyaneshewar P, Perin L, Reis VM, Zavalin AA (2003) Taxonomic review and mechanistic analysis of the crop growth promoting effect of Agrobacterium radiobacter strain 204: used as a biofertiliser on graminaceous crops in Russia. Aspects Appl. Biol. 70, 175-181.

[7]        Humphry DR, Cummings SP, Andrews M (2001) Comparison and tentative identification of Rhizobiaceae isolated from nodules of lentil grown in New Zealand and the United Kingdom. Aspects Appl. Biol. 63, 101-110.

[8]        Haswell M, Humphry DR, Cummings SP, Andrews M (2001) Nodule structure and development in lentil (Lens culinaris): a light and electron microscopy study. Aspects Appl. Biol. 63, 83-85.

[9]        Cummings SP, Humphry DR. Andrews M (2001) A review of the current taxonomy and diversity of symbiotic rhizosphere and bulk soil nitrogen-fixing bacteria, which are beneficial to plants. Aspects Appl. Biol. 63, 5-18.

[10]       Andrews M, Humphry DR, Haswell M, Cummings SP (2001) The current taxonomy of Rhizobia which infect grain legumes focusing on genotypic characterisation IN: Proceedings of the 4th European Conference on Grain Legumes, Paris: L' Association Européene de Recherché sur les Protéageneuse (AEP) 322-323.

[11]       Davies GJ, Charnock SJ, Varrot A, Schulein M (2000) Structural enzymology of enzymatic glycosyl transfer: Glycoside hydrolases, polysaccharide lyases, and glycosyltransferases. Biochemistry 39, 1542-1582.

[12]       Davies GJ, Charnock SJ, Varrot A, Schulein M. (2000) Structural enzymology of enzymatic glycosyl transfer: Glycoside hydrolases, polysaccharide lyases, and glycosyltransferases. Abstracts of Papers of the American Chemical Society 219, U125-U.

[13]       Davies GJ, Charnock SJ, Varrot A, Schulein M (2000) Structures and mechanisms of cellulases. Abstracts of Papers of the American Chemical Society 219, U524-U.

[14]       Humphry DR, Cummings SP, Black GW (1999) Carbohydrases as  tools for understanding how cold enzymes are adapted to function at low temperatures. In Recent Advances in Carbohydrate Bioengineering (Eds. Gilbert HJ, Davies G, Henrissat B and Svensson B), pp. 82-88, Royal Society of Chemistry, Cambridge UK.