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  • 1
    Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL ( 2008) GenBank. Nucleic Acids Res 36: D25D30.
  • 2
    Burley SK, Joachimiak A, Montelione GT, Wilson IA ( 2008) Contributions to the NIH-NIGMS protein structure initiative from the PSI production centers. Structure 16: 511.
  • 3
    Mirkovic N, Li Z, Parnassa A, Murray D ( 2007) Strategies for high-throughput comparative modeling: applications to leverage analysis in structural genomics and protein family organization. Proteins 66: 766777.
  • 4
    Cort JR, Koonin EV, Bash PA, Kennedy MA ( 1999) A phylogenetic approach to target selection for structural genomics: solution structure of YciH. Nucleic Acids Res 27: 40184027.
  • 5
    Levitt M ( 2007) Growth of novel protein structural data. Proc Natl Acad Sci USA 104: 31833188.
  • 6
    Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE ( 2000) The protein data bank. Nucleic Acids Res 28: 235242.
  • 7
    Powers R, Copeland J, Mercier K ( 2008) Application of FAST-NMR in drug discovery. Drug Discov Today 13: 172179.
  • 8
    Lee D, Redfern O, Orengo C ( 2007) Predicting protein function from sequence and structure. Nat Rev Mol Cell Biol 8: 9951005.
  • 9
    Plewczynski D, Pas J, Von Grotthuss M, Rychlewski L ( 2002) 3D-Hit: fast structural comparison of proteins. Appl Bioinformatics 1: 223225.
  • 10
    Sousa SF, Fernandes PA, Ramos MJ ( 2006) Protein-ligand docking: current status and future challenges. Proteins: Struct Funct Bioinformatics 65: 1526.
  • 11
    Mercier KA, Baran M, Ramanathan V, Revesz P, Xiao R, Montelione GT, Powers R ( 2006) FAST-NMR: functional annotation screening technology using nmr spectroscopy. J Am Chem Soc 128: 1529215299.
  • 12
    Mercier KA, Germer K, Powers R ( 2006) Design and characterization of a functional library for NMR screening against novel protein targets. Comb Chem High Throughput Screen 9: 515534.
  • 13
    Stark J, Powers R ( 2008) Rapid protein-ligand costructures using chemical shift perturbations. J Am Chem Soc 130: 535545.
  • 14
    Powers R, Copeland JC, Germer K, Mercier KA, Ramanathan V, Revesz P ( 2006) Comparison of protein active site structures for functional annotation of proteins and drug design. Proteins: Struct Funct Bioinformatics 65: 124135.
  • 15
    Stover C, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, Hickey MJ, Brinkman FS, Hufnagle WO, Kowalik DJ, Lagrou M, Garber RL, Goltry L, Tolentino E, Westbrock-Wadman S, Yuan Y, Brody LL, Coulter SN, Folger KR, Kas A, Larbig K, Lim R, Smith K, Spencer D, Wong GK, Wu Z, Paulsen IT, Reizer J, Saier MH, Hancock RE, Lory S, Olson MV ( 2000) Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 406: 959964.
  • 16
    Poole K ( 2005) Pseudomonas aeruginosa. Front Antimicrob Res 355366.
  • 17
    Kirisits MJ, Parsek MR ( 2006) Does Pseudomonas aeruginosa use intercellular signalling to build biofilm communities? Cell Microbiol 8: 18411849.
  • 18
    Rejman J, Di Gioia S, Bragonzi A, Conese M ( 2007) Pseudomonas aeruginosa infection destroys the barrier function of lung epithelium and enhances polyplex-mediated transfection. Hum Gene Ther 18: 642652.
  • 19
    Hsueh PR, Chen WH, Luh KT ( 2005) Relationships between antimicrobial use and antimicrobial resistance in Gram-negative bacteria causing nosocomial infections from 1991-2003 at a university hospital in Taiwan. Int J Antimicrob Agents 26: 463472.
  • 20
    Landman D, Bratu S, Kochar S, Panwar M, Trehan M, Doymaz M, Quale J ( 2007) Evolution of antimicrobial resistance among Pseudomonas aeruginosa, Acinetobacter baumannii and Klebsiella pneumoniae in Brooklyn, NY. J Antimicrob Chemother 60: 7882.
  • 21
    Hall-Stoodley L, Costerton JW, Stoodley P ( 2004) Bacterial biofilms: from the natural environment to infectious diseases. Nat Rev Microbiol 2: 95108.
  • 22
    Boroumand MA, Esfahanifard P, Saadat S, Sheihkvatan M, Hekmatyazdi S, Saremi M, Nazemi L ( 2007) A report of Pseudomonas aeruginosa antibiotic resistance from a multicenter study in Iran. Ind J Med Microbiol 25: 435436.
  • 23
    Southey-Pillig CJ, Davies DG, Sauer K ( 2005) Characterization of temporal protein production in Pseudomonas aeruginosa biofilms. J Bacteriol 187: 81148126.
  • 24
    Chen J, Li LF, Guan XD, Chen DM, Chen MY, Ouyang B, Huang SW, Wu JF ( 2006) The drug resistance of pathogenic bacteria of nosocomial infections in surgical intensive care unit. Zhonghua Wai Ke Za Zhi 44: 11891192.
  • 25
    Hentzer M, Wu H, Andersen JB, Riedel K, Rasmussen TB, Bagge N, Kumar N, Schembri MA, Song Z, Kristoffersen P, Manefield M, Costerton JW, Molin S, Eberl L, Steinberg P, Kjelleberg S, Hoiby N, Givskov M ( 2003) Attenuation of Pseudomonas aeruginosa virulence by quorum sensing inhibitors. EMBO J 22: 38033815.
  • 26
    Schuster M, Lostroh CP, Ogi T, Greenberg EP ( 2003) Identification, timing, and signal specificity of Pseudomonas aeruginosa quorum-controlled genes: a transcriptome analysis. J Bacteriol 185: 20662079.
  • 27
    Waite RD, Paccanaro A, Papakonstantinopoulou A, Hurst JM, Saqi M, Littler E, Curtis MA ( 2006) Clustering of Pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles. BMC Genomics 7.
  • 28
    Kuchma SL, Connolly JP, O'Toole GA ( 2005) A three-component regulatory system regulates biofilm maturation and type III secretion in Pseudomonas aeruginosa. J Bacteriol 187: 14411454.
  • 29
    Liu J, Hegyi H, Acton TB, Montelione GT, Rost B ( 2004) Automatic target selection for structural genomics on eukaryotes. Proteins: Struct Funct Bioinformatics 56: 188200.
  • 30
    Wunderlich Z, Acton TB, Liu J, Kornhaber G, Everett J, Carter P, Lan N, Echols N, Gerstein M, Rost B, Montelione GT ( 2004) The protein target list of the Northeast Structural Genomics Consortium. Proteins 56: 181187.
  • 31
    Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y ( 2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36: D480D484.
  • 32
    Peterson JD, Umayam LA, Dickinson T, Hickey EK, White O ( 2001) The comprehensive microbial resource. Nucleic Acids Res 29: 123125.
  • 33
    Hirokawa T, Boon-Chieng S, Mitaku S ( 1998) SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics 14: 378379.
  • 34
    Bhattacharya A, Tejero R, Montelione GT ( 2007) Evaluating protein structures determined by structural genomics consortia. Proteins 66: 778795.
  • 35
    Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM ( 1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8: 477486.
  • 36
    Lovell SC, Davis IW, Arendall WBIII,de Bakker PI, Word JM, Prisant MG, Richardson JS, Richardson DC ( 2003) Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins 50: 437450.
  • 37
    Huang YJ, Tejero R, Powers R, Montelione GT ( 2006) AutoStructure: A topology-constrained distance network algorithm for protein structure determination from NOESY data. Proteins: Struct Funct Bioinformatics 62: 587603.
  • 38
    Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G ( 2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 2529.
  • 39
    Heger A, Korpelainen E, Hupponen T, Mattila K, Ollikainen V, Holm L ( 2008) PairsDB atlas of protein sequence space. Nucleic Acids Res 36: D276D280.
  • 40
    Petrey D, Honig B ( 2003) GRASP 2: visualization, surface properties, and electrostatics of macromolecular structures and sequences. Methods Enzymol 374: 492509.
  • 41
    Brown TA, Yang TM, Zaitsevskaia T, Xia Y, Dunn CA, Sigle RO, Knudsen B, Carter WG ( 2004) Adhesion or plasmin regulates tyrosine phosphorylation of a novel membrane glycoprotein p80/gp140/CUB domain-containing protein 1 in epithelia. J Biol Chem 279: 1477214783.
  • 42
    Botta M, Manetti F, Corelli F ( 2000) Fibroblast growth factors and their inhibitors. Curr Pharm Des 6: 18971924.
  • 43
    Capila I, Linhardt RJ ( 2002) Heparin-protein interactions. Angew Chem Int Ed Engl 41: 391412.
  • 44
    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: 655661.
  • 45
    Lyczak JB, Cannon CL, Pier GB ( 2002) Lung infections associated with cystic fibrosis. Clin Microbiol Rev 15: 194222.
  • 46
    Overhage J, Schemionek M, Webb JS, Rehm BHA ( 2005) Expression of the psl Operon in Pseudomonas aeruginosa PAO1 Biofilms: PslA performs an essential function in biofilm formation. Appl Environ Microbiol 71: 44074413.
  • 47
    Vuong C, Gerke C, Somerville GA, Fischer ER, Otto M ( 2003) Quorum-sensing control of biofilm factors in Staphylococcus epidermidis. J Infect Dis 188: 706718.
  • 48
    Yarwood JM, Bartels DJ, Volper EM, Greenberg EP ( 2004) Quorum sensing in Staphylococcus aureus biofilms. J Bacteriol 186: 18381850.
  • 49
    Kong KF, Vuong C, Otto M ( 2006) Staphylococcus quorum sensing in biofilm formation and infection. Int J Med Microbiol 296: 133139.
  • 50
    De Kievit TR, Iglewski BH ( 1999) Quorum sensing, gene expression, and Pseudomonas biofilms. Methods Enzymol 310: 117128.
  • 51
    Schuster M, Lostroh P, Ogi T, Greenberg EP ( 2003) Identification, Timing, and Signal Specificity of Pseudomonas aeruginosa Quorum-Controlled Genes: a Transcriptome Analysis. J Bacteriol 185.
  • 52
    Gotz F ( 2002) Staphylococcus and biofilms. Mol Microbiol 43: 13671378.
  • 53
    Stanley NR, Lazazzera BA ( 2004) Environmental signals and regulatory pathways that influence biofilm formation. Mol Microbiol 52: 917924.
  • 54
    Cramton SE, Ulrich M, Gotz F, Doring G ( 2001) Anaerobic conditions induce expression of polysaccharide intercellular adhesin in Staphylococcus aureus and Staphylococcus epidermidis. Infect Immun 69: 40794085.
  • 55
    Deighton M, Borland R ( 1993) Regulation of slime production in Staphylococcus epidermidis by iron limitation. Infect Immun 61: 44734479.
  • 56
    Evans E, Brown MRW, Gilbert P ( 1994) Iron chelator, exopolysaccharide and protease production in Staphylococcus epidermidis: a comparative study of the effects of specific growth rate in biofilm and planktonic culture. Microbiology 140: 153157.
  • 57
    Elci S, Atmaca S, Guel K ( 1995) Effect of iron limitation on the amount of slime produced by strains of Staphylococcus epidermidis. Cytobios 84: 141146.
  • 58
    Rachid S, Ohlsen K, Wallner U, Hacker J, Hecker M, Ziebuhr W ( 2000) Alternative transcription factor sB is involved in regulation of biofilm expression in a Staphylococcus aureus mucosal isolate. J Bacteriol 182: 68246826.
  • 59
    Rachid S, Ohlsen K, Witte W, Hacker J, Ziebuhr W ( 2000) Effect of subinhibitory antibiotic concentrations on polysaccharide intercellular adhesin expression in biofilm-forming Staphylococcus epidermidis. Antimicrob Agents Chemother 44: 33573363.
  • 60
    Knobloch JKM, Bartscht K, Sabottke A, Rohde H, Feucht HH, Mack D ( 2001) Biofilm formation by Staphylococcus epidermidis depends on functional RsbU, an activator of the sigB operon: differential activation mechanisms due to ethanol and salt stress. J Bacteriol 183: 26242633.
  • 61
    Campbell IM, Crozier DN, Pawagi AB, Buivids IA ( 1983) In vitro response of Staphylococcus aureus from cystic fibrosis patients to combinations of linoleic and oleic acids added to nutrient medium. J Clin Microbiol 18: 408415.
  • 62
    Mack D, Siemssen N, Laufs R ( 1992) Parallel induction by glucose of adherence and a polysaccharide antigen specific for plastic-adherent Staphylococcus epidermidis: evidence for functional relation to intercellular adhesion. Infect Immun 60: 20482057.
  • 63
    Gerke C, Kraft A, Sussmuth R, Schweitzer O, Gotz F ( 1998) Characterization of the N-acetylglucosaminyltransferase activity involved in the biosynthesis of the Staphylococcus epidermidis polysaccharide intercellular adhesin. J Biol Chem 273: 1858618593.
  • 64
    Cramton SE, Gerke C, Schnell NF, Nichols WW, Gotz F ( 1999) The intercellular adhesion (ica) locus is present in Staphylococcus aureus and is required for biofilm formation. Infect Immun 67: 54275433.
  • 65
    Mack D, Fischer W, Krokotsch A, Leopold K, Hartmann R, Egge H, Laufs R ( 1996) The intercellular adhesin involved in biofilm accumulation of Staphylococcus epidermidis is a linear beta-1,6-linked glucosaminoglycan: purification and structural analysis. J Bacteriol 178: 175183.
  • 66
    Maira-Litran T, Kropec A, Abeygunawardana C, Joyce J, Mark GIII,Goldmann DA, Pier GB ( 2002) Immunochemical properties of the Staphylococcal poly-N-acetylglucosamine surface polysaccharide. Infect Immun 70: 44334440.
  • 67
    Dobinsky S, Kiel K, Rohde H, Bartscht K, Knobloch JKM, Horstkotte MA, Mack D ( 2003) Glucose-related dissociation between icaADBC transcription and biofilm expression by Staphylococcus epidermidis: evidence for an additional factor required for polysaccharide intercellular adhesin synthesis. J Bacteriol 185: 28792886.
  • 68
    Shanks RMQ, Donegan NP, Graber ML, Buckingham SE, Zegans ME, Cheung AL, O'Toole GA ( 2005) Heparin stimulates Staphylococcus aureus Biofilm Formation. Infect Immun 73: 45964606.
  • 69
    Plotkowski MC, Costa AO, Morandi V, Barbosa HS, Nader HB, De Benizmann S, Puchelle E ( 2001) Role of heparan sulphate proteoglycans as potential receptors for non-piliated Pseudomonas aeruginosa adherence to non-polarised airway epithelial cells. J Med Microbiol 50: 183190.
  • 70
    Zhu-Salzman K, Shade RE, Koiwa H, Salzman RA, Narasimhan M, Bressan RA, Hasegawa PM, Murdock LL ( 1998) Carbohydrate binding and resistance to proteolysis control insecticidal activity of Griffonia simplicifolia lectin II. Proc Natl Acad Sci USA 95: 1512315128.
  • 71
    Simpson HD, Barras F ( 1999) Functional analysis of the carbohydrate-binding domains of Erwinia chrysanthemi Cel5 (endoglucanase Z) and an Escherichia coli putative chitinase. J Bacteriol 181: 46114616.
  • 72
    Chavez CA, Bohnsack RN, Kudo M, Gotschall RR, Canfield WM, Dahms NM ( 2007) Domain 5 of the cation-independent mannose 6-phosphate receptor preferentially binds phosphodiesters (Mannose 6-Phosphate N-Acetylglucosamine Ester). Biochemistry 46: 1260412617.
  • 73
    Kumar J, Ethayathulla AS, Srivastava DB, Singh N, Sharma S, Kaur P, Srinivasan A, Singh TP ( 2007) Carbohydrate-binding properties of goat secretory glycoprotein (SPG-40) and its functional implications: structures of the native glycoprotein and its four complexes with chitin-like oligosaccharides. Acta Crystallogr D Biol Crystallogr D63: 437446.
  • 74
    Bae B, Ohene-Adjei S, Kocherginskaya S, Mackie RI, Spies MA, Cann IKO, Nair SK ( 2008) Molecular basis for the selectivity and specificity of ligand recognition by the family 16 carbohydrate-binding modules from Thermoanaerobacterium polysaccharolyticum ManA. J Biol Chem 283: 1241512425.
  • 75
    Nagae M, Nishi N, Nakamura-Tsuruta S, Hirabayashi J, Wakatsuki S, Kato R ( 2008) Structural analysis of the human galectin-9 N-terminal carbohydrate recognition domain reveals unexpected properties that differ from the mouse orthologue. J Mol Biol 375: 119135.
  • 76
    Hachem MA, Karlsson EN, Bartonek-Roxa E, Raghothama S, Simpson PJ, Gilbert HJ, Williamson MP, Holst O ( 2000) Carbohydrate-binding modules from a thermostable Rhodothermus marinus xylanase: cloning, expression and binding studies. Biochem J 345: 5360.
  • 77
    Wandall HH, Irazoqui F, Tarp MA, Bennett EP, Mandel U, Takeuchi H, Kato K, Irimura T, Suryanarayanan G, Hollingsworth MA, Clausen H ( 2007) The lectin domains of polypeptide GalNAc-transferases exhibit carbohydrate-binding specificity for GalNAc: lectin binding to GalNAc-glycopeptide substrates is required for high density GalNAc-O-glycosylation. Glycobiology 17: 374387.
  • 78
    Matei E, Furey W, Gronenborn AM ( 2008) Solution and crystal structures of a sugar binding site mutant of cyanovirin-N: no evidence of domain swapping. Structure 16: 11831194.
  • 79
    Koebnik R ( 2005) TonB-dependent trans-envelope signaling: the exception or the rule? Trends Microbiol 13: 343347.
  • 80
    Abbas A, Adams C, Scully N, Glennon J, O'Gara F ( 2007) A role for TonB1 in biofilm formation and quorum sensing in Pseudomonas aeruginosa. FEMS Microbiol Lett 274: 269278.
  • 81
    Blanvillain S, Meyer D, Boulanger A, Lautier M, Guynet C, Denance N, Vasse J, Lauber E, Arlat M ( 2007) Plant carbohydrate scavenging through TonB-dependent receptors: a feature shared by phytopathogenic and aquatic bacteria. PLoS One 2.
  • 82
    Neugebauer H, Herrmann C, Kammer W, Schwarz G, Nordheim A, Braun V ( 2005) ExbBD-dependent transport of maltodextrins through the novel MalA protein across the outer membrane of Caulobacter crescentus. J Bacteriol 187: 83008311.
  • 83
    Schauer K, Rodionov DA, de Reuse H ( 2008) New substrates for TonB-dependent transport: do we only see the tip of the iceberg'? Trends Biochem Sci 33: 330338.
  • 84
    Kall L, Krogh A, Sonnhammer Erik LL ( 2007) Advantages of combined transmembrane topology and signal peptide prediction—the Phobius web server. Nucleic Acids Res 35: W429W432.
  • 85
    Braun M, Endriss F, Killmann H, Braun V ( 2003) In vivo reconstitution of the FhuA transport protein of Escherichia coli K-12. J Bacteriol 185: 55085518.
  • 86
    Wandersman C, Delepelaire P ( 2004) Bacterial iron sources: from siderophores to hemophores. Ann Rev Microbiol 58: 611647.
  • 87
    Usher KC, Ozkan E, Gardner KH, Deisenhofer J ( 2001) The plug domain of FepA, a TonB-dependent transport protein from Escherichia coli, binds its siderophore in the absence of the transmembrane barrel domain. Proc Natl Acad Sci USA 98: 1067610681.
  • 88
    Neri D, Szyperski T, Otting G, Senn H, Wuthrich K ( 1989) Stereospecific nuclear magnetic resonance assignments of the methyl groups of valine and leucine in the DNA-binding domain of the 434 repressor by biosynthetically directed fractional 13C labeling. Biochemistry 28: 75107516.
  • 89
    Cavanaugh J ( 1996) Protein NMR spectroscopy: principles and practice. Academic Press, San Diego.
  • 90
    Ferentz AE, Wagner G ( 2000) NMR spectroscopy: a multifaceted approach to macromolecular structure. Q Rev Biophys 33: 2965.
  • 91
    Linge JP, Nilges M ( 1999) Influence of non-bonded parameters on the quality of NMR structures: a new force field for NMR structure calculation. J Biomol NMR 13: 5159.
  • 92
    Cornilescu G, Delaglio F, Bax A ( 1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13: 289302.
  • 93
    Vuister GW, Bax A ( 1992) Measurement of two-bond JCOH alpha coupling constants in proteins uniformly enriched with 13C. J Biomol NMR 2: 401405.
  • 94
    Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A ( 1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6: 277293.
  • 95
    Schwieters CD, Clore GM ( 2001) The VMD-XPLOR visualization package for NMR structure refinement. J Magn Reson 149: 239244.
  • 96
    Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ ( 1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19: 16391662.