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Volumn 9783709108703, Issue , 2012, Pages 361-383

Computational techniques applied to defining carbohydrate antigenicity

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EID: 84930584759     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-7091-0870-3_15     Document Type: Chapter
Times cited : (6)

References (51)
  • 1
    • 0017443443 scopus 로고
    • The emergence of Group B streptococci in infections of the newborn infant
    • Anthony BF, Okada DM. (1977). The emergence of Group B streptococci in infections of the newborn infant. Ann Rev Med 28: 355-369
    • (1977) Ann Rev Med , vol.28 , pp. 355-369
    • Anthony, B.F.1    Okada, D.M.2
  • 3
    • 0034859343 scopus 로고    scopus 로고
    • Carbohydrate-protein recognition: Molecular dynamics simulations and free energy analysis of oligosaccharide binding to concanavalin A
    • Bryce RA, Hillier IH, Naismith JH. (2001). Carbohydrate-protein recognition: molecular dynamics simulations and free energy analysis of oligosaccharide binding to concanavalin A. Biophys J 81: 1373-1388
    • (2001) Biophys J , vol.81 , pp. 1373-1388
    • Bryce, R.A.1    Hillier, I.H.2    Naismith, J.H.3
  • 4
    • 0028300617 scopus 로고
    • Solution structure of a trisaccharide-antibody complex: Comparison of NMR measurements with a crystal structure
    • Bundle DR, Baumann H, Brisson JR, Gagne SM, Zdanov A, Cygler M. (1994). Solution structure of a trisaccharide-antibody complex: comparison of NMR measurements with a crystal structure. Biochemistry 33: 5183-5192
    • (1994) Biochemistry , vol.33 , pp. 5183-5192
    • Bundle, D.R.1    Baumann, H.2    Brisson, J.R.3    Gagne, S.M.4    Zdanov, A.5    Cygler, M.6
  • 6
    • 0025866369 scopus 로고
    • Antibodies to poly[ (28) -a-N-acetylneuraminic acid and poly[ (29) -a-N-acetylneuraminic acid] are elicited by immunization of mice with Escherichia coli K92 conjugates: Potential vaccines for groups B and C meningococci and E. coli K1
    • Devi SJN, Robbins JB, Schneerson R. (1991). Antibodies to poly[ (28) -a-N-acetylneuraminic acid] and poly[ (29) -a-N-acetylneuraminic acid] are elicited by immunization of mice with Escherichia coli K92 conjugates: Potential vaccines for groups B and C meningococci and E. coli K1. Proc Natl Acad Sci USA 88: 7175-7179
    • (1991) Proc Natl Acad Sci USA , vol.88 , pp. 7175-7179
    • Devi, S.J.N.1    Robbins, J.B.2    Schneerson, R.3
  • 7
    • 0023200962 scopus 로고
    • Group B streptococcal carriage and disease: A 6 year prospective study
    • Dillon HC, Khare S, Gray BM. (1987). Group B streptococcal carriage and disease: a 6 year prospective study. J Pediatr 110: 31-36
    • (1987) J Pediatr , vol.110 , pp. 31-36
    • Dillon, H.C.1    Khare, S.2    Gray, B.M.3
  • 8
    • 0001094662 scopus 로고    scopus 로고
    • Glycobiology: Toward understanding the function of sugars
    • Dwek RA. (1996). Glycobiology: toward understanding the function of sugars. Chem Rev 96: 683-720
    • (1996) Chem Rev , vol.96 , pp. 683-720
    • Dwek, R.A.1
  • 9
    • 84930578219 scopus 로고    scopus 로고
    • Predicting the 3D structures of anti-carbohydrate antibodies: Combining comparative modeling and MD simulations
    • Vliegenthart JFG, Woods RJ (eds) American Chemical Society, Washington, D.C
    • Dyekjaer JD, Woods RJ. (2006). Predicting the 3D structures of anti-carbohydrate antibodies: combining comparative modeling and MD simulations. In: Vliegenthart JFG, Woods RJ (eds) NMR spectroscopy and computer modeling of carbohydrates: recent advances, vol 930. American Chemical Society, Washington, D.C, p 18
    • (2006) NMR Spectroscopy and Computer Modeling of Carbohydrates: Recent Advances , vol.930 , pp. 18
    • Dyekjaer, J.D.1    Woods, R.J.2
  • 10
    • 0020556178 scopus 로고
    • Protection of mice from experimental infection with type iii group b streptococcus using monoclonal antibodies
    • Egan ML, Pritchard DG, Dillon HC Jr, Gray MB. (1983). Protection of mice from experimental infection with Type III Group B Streptococcus using monoclonal antibodies. J Exp Med 158: 1006-1011
    • (1983) J Exp Med , vol.158 , pp. 1006-1011
    • Egan, M.L.1    Pritchard, D.G.2    Dillon, H.C.3    Gray, M.B.4
  • 11
    • 0029043808 scopus 로고
    • Evidence for the extended helical nature of polysaccharide epitopes the 2.8 åresolution structure and thermodynamics of ligand binding of an antigen binding fragment specific for a- (2-8) -polysialic acid
    • Evans SV, Sigurskjold BW, Jennings HJ, Brisson JR, To R, Altman E, Frosch M, Weisgerber C, Kratzin H. (1995). Evidence for the extended helical nature of polysaccharide epitopes. The 2.8 Åresolution structure and thermodynamics of ligand binding of an antigen binding fragment specific for a- (2-8) -Polysialic acid. Biochemistry 34: 6737-6744
    • (1995) Biochemistry , vol.34 , pp. 6737-6744
    • Evans, S.V.1    Sigurskjold, B.W.2    Jennings, H.J.3    Brisson, J.R.4    To, R.5    Altman, E.6    Frosch, M.7    Weisgerber, C.8    Kratzin, H.9
  • 12
    • 77955476492 scopus 로고    scopus 로고
    • Molecular simulations of carbohydrates and protein-carbohydrate interactions: Motivation, issues and prospects
    • Fadda E, Woods RJ. (2010). Molecular simulations of carbohydrates and protein-carbohydrate interactions: motivation, issues and prospects. Drug Discov Today 15: 596
    • (2010) Drug Discov Today , vol.15 , pp. 596
    • Fadda, E.1    Woods, R.J.2
  • 13
    • 0020518256 scopus 로고
    • Antigenic similarities between brain components and bacteria causing meningitis - Implications for vaccine development and pathogenesis
    • Finne J, Leinonen M, Mäkelä HP. (1983). Antigenic similarities between brain components and bacteria causing meningitis - implications for vaccine development and pathogenesis. Lancet 2: 355-357
    • (1983) Lancet , vol.2 , pp. 355-357
    • Finne, J.1    Leinonen, M.2    Mäkelä, H.P.3
  • 14
    • 0021933175 scopus 로고
    • Cleavage of the polysialosyl units of brain glycoproteins by a bacteriophage endosialidase - Involvement of a long oligosaccharide segment in molecularinteractions of polysialic acid
    • Finne J, Mäkelä PH. (1985). Cleavage of the polysialosyl units of brain glycoproteins by a bacteriophage endosialidase - involvement of a long oligosaccharide segment in molecularinteractions of polysialic acid. J Biol Chem 260: 1265-1270
    • (1985) J Biol Chem , vol.260 , pp. 1265-1270
    • Finne, J.1    Mäkelä, P.H.2
  • 15
    • 0141704154 scopus 로고    scopus 로고
    • Molecular dynamics simulations of galectin-1- oligosaccharide complexes reveal the molecular basis for ligand diversity
    • Ford MG, Weimar T, Köhli T, Woods RJ. (2003). Molecular dynamics simulations of Galectin-1- oligosaccharide complexes reveal the molecular basis for ligand diversity. PROTEINS: Struct Funct Genet 53: 229-240
    • (2003) Proteins: Struct Funct Genet , vol.53 , pp. 229-240
    • Ford, M.G.1    Weimar, T.2    Köhli, T.3    Woods, R.J.4
  • 16
    • 15044357698 scopus 로고    scopus 로고
    • Structural elucidation of type III group B Streptococcus capsular polysaccharide using molecular dynamics simulations: The role of sialic acid
    • Gonzalez-Outeriño J, Kadirvelraj R, Woods RJ. (2005). Structural elucidation of type III group B Streptococcus capsular polysaccharide using molecular dynamics simulations: the role of sialic acid. Carbohydr Res 340: 1007-1018
    • (2005) Carbohydr Res , vol.340 , pp. 1007-1018
    • Gonzalez-Outeriño, J.1    Kadirvelraj, R.2    Woods, R.J.3
  • 17
    • 33746024043 scopus 로고    scopus 로고
    • Reconciling solvent effects on rotamer populations in carbohydrates: A joint MD and NMR analysis
    • Gonzalez-Outeiriño J, Kirschner KN, Thobhani S, Woods RJ. (2006). Reconciling solvent effects on rotamer populations in carbohydrates: a joint MD and NMR analysis. Can J Chem 84: 569-579
    • (2006) Can J Chem , vol.84 , pp. 569-579
    • Gonzalez-Outeiriño, J.1    Kirschner, K.N.2    Thobhani, S.3    Woods, R.J.4
  • 18
    • 0037234043 scopus 로고    scopus 로고
    • Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods
    • Gouda H, Kuntz ID, Case DA, Kollmann PA. (2003). Free energy calculations for theophylline binding to an RNA aptamer: comparison of MM-PBSA and thermodynamic integration methods. Biopolymers 68: 16-34
    • (2003) Biopolymers , vol.68 , pp. 16-34
    • Gouda, H.1    Kuntz, I.D.2    Case, D.A.3    Kollmann, P.A.4
  • 19
    • 0037433595 scopus 로고    scopus 로고
    • Conformational flexibility of the group B meningococcal polysaccharide in solution
    • Henderson TJ, Venable R, Egan W. (2003). Conformational flexibility of the group B meningococcal polysaccharide in solution. J Am Chem Soc 125: 2930-2939
    • (2003) J Am Chem Soc , vol.125 , pp. 2930-2939
    • Henderson, T.J.1    Venable, R.2    Egan, W.3
  • 20
    • 0022519159 scopus 로고
    • Induction of meningococcal group-B polysaccharidespecific IgG antibodies in mice by using an N-propionylated-B polysaccharide-tetanus toxoid conjugate vaccine
    • Jennings HJ, Roy R, Gamian A. (1986). Induction of meningococcal group-B polysaccharidespecific IgG antibodies in mice by using an N-propionylated-B polysaccharide-tetanus toxoid conjugate vaccine. J Immunol 137: 1708-1713
    • (1986) J Immunol , vol.137 , pp. 1708-1713
    • Jennings, H.J.1    Roy, R.2    Gamian, A.3
  • 21
    • 0026623499 scopus 로고
    • Further approaches for optimizing polysaccharide-protein conjugate vaccines for prevention of invasive bacterial disease
    • Jennings H. (1992). Further approaches for optimizing polysaccharide-protein conjugate vaccines for prevention of invasive bacterial disease. J Infect Dis 165: 156-159
    • (1992) J Infect Dis , vol.165 , pp. 156-159
    • Jennings, H.1
  • 22
    • 0001236963 scopus 로고    scopus 로고
    • Capsular polysaccharides from Neisseria meningitidis and Streptococcus pneumoniae
    • Jones C. (1998). Capsular polysaccharides from Neisseria meningitidis and Streptococcus pneumoniae. Carbohydr Eur 21: 10-16
    • (1998) Carbohydr Eur , vol.21 , pp. 10-16
    • Jones, C.1
  • 23
    • 0023810773 scopus 로고
    • The epitope associated with the binding of the capsular polysaccharide of the group-b meningococcus and of escherichia coli k1 to a human monoclonal macroglobulin, IgM nov
    • Kabat EA, Liao J, Osserman EF, Gamian A, Michon F, Jennings HJ. (1988). The epitope associated with the binding of the capsular polysaccharide of the Group-B meningococcus and of Escherichia coli K1 to a human monoclonal macroglobulin, IgM nov. J Exp Med 168: 699-711
    • (1988) J Exp Med , vol.168 , pp. 699-711
    • Kabat, E.A.1    Liao, J.2    Osserman, E.F.3    Gamian, A.4    Michon, F.5    Jennings, H.J.6
  • 25
    • 58049202316 scopus 로고    scopus 로고
    • Involvement of water in carbohydrateprotein binding: Concanavalin A revisited
    • Kadirvelraj R, Foley BL, Dyekjaer JD, Woods RJ. (2008). Involvement of water in carbohydrateprotein binding: Concanavalin A revisited. J Am Chem Soc 130: 16933-16942
    • (2008) J Am Chem Soc , vol.130 , pp. 16933-16942
    • Kadirvelraj, R.1    Foley, B.L.2    Dyekjaer, J.D.3    Woods, R.J.4
  • 26
    • 0035845496 scopus 로고    scopus 로고
    • Solvent interactions determine carbohydrate conformation
    • Kirschner KN, Woods RJ. (2001). Solvent interactions determine carbohydrate conformation. Proc Natl Acad Sci USA 98: 10541-10545
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 10541-10545
    • Kirschner, K.N.1    Woods, R.J.2
  • 29
    • 0141990820 scopus 로고    scopus 로고
    • Specific empirical free energy function for automated docking of carbohydrates to proteins
    • Laederach A, Reilly PJ. (2002). Specific empirical free energy function for automated docking of carbohydrates to proteins. J Comp Chem 24: 1748-1757
    • (2002) J Comp Chem , vol.24 , pp. 1748-1757
    • Laederach, A.1    Reilly, P.J.2
  • 30
    • 0034693137 scopus 로고    scopus 로고
    • Biochemical engineering of surface a2-8 polysialic acid for immunotargeting tumor cells
    • Liu T, Guo Z, Yang Q, Subash S, Jennings HJ. (2000). Biochemical engineering of surface a2-8 polysialic acid for immunotargeting tumor cells. J Biol Chem 275: 32832-32836
    • (2000) J Biol Chem , vol.275 , pp. 32832-32836
    • Liu, T.1    Guo, Z.2    Yang, Q.3    Subash, S.4    Jennings, H.J.5
  • 31
    • 0023657067 scopus 로고
    • Conformational differences between linear a (2-8) -linked homosialooligosaccharides and the epitope of the group B meningococcal polysaccharide
    • Michon F, Brisson J-R, Jennings HJ. (1987). Conformational differences between linear a (2-8) -linked homosialooligosaccharides and the epitope of the group B meningococcal polysaccharide. Biochemistry 26: 8399-8405
    • (1987) Biochemistry , vol.26 , pp. 8399-8405
    • Michon, F.1    Brisson, J.-R.2    Jennings, H.J.3
  • 33
    • 0033972258 scopus 로고    scopus 로고
    • Relative energies of binding for antibody-carbohydrate-antigen complexes computed from free-energy simulations
    • Pathiaseril A, Woods RJ. (2000). Relative energies of binding for antibody-carbohydrate-antigen complexes computed from free-energy simulations. J Am Chem Soc 122: 331-338
    • (2000) J Am Chem Soc , vol.122 , pp. 331-338
    • Pathiaseril, A.1    Woods, R.J.2
  • 34
    • 23044467529 scopus 로고    scopus 로고
    • Molecular modeling of cardiac glycoside binding by the human sequence monoclonal antibody 1B3
    • Paula S, Monson N, Ball WJ Jr. (2005). Molecular modeling of cardiac glycoside binding by the human sequence monoclonal antibody 1B3. Proteins 60: 382-391
    • (2005) Proteins , vol.60 , pp. 382-391
    • Paula, S.1    Monson, N.2    Ball, W.J.3
  • 35
    • 0000106306 scopus 로고
    • Nuclear magnetic resonance of hydroxyl and amido protons of oligosaccharides in aqueous solution: Evidence for a strong intramolecular hydrogen bond in sialic acid residues
    • Poppe L, van Halbeek H. (1991). Nuclear magnetic resonance of hydroxyl and amido protons of oligosaccharides in aqueous solution: evidence for a strong intramolecular hydrogen bond in sialic acid residues. J Am Chem Soc 113: 363-365
    • (1991) J Am Chem Soc , vol.113 , pp. 363-365
    • Poppe, L.1    Van Halbeek, H.2
  • 36
    • 85193165214 scopus 로고    scopus 로고
    • Conformation of carbohydrates harwood academic, amsterdam regenmortel mhv 1989) the concept and operational definition of protein epitopes
    • Rao VSR, Qasba PK et al. (1998). Conformation of carbohydrates. Harwood Academic, Amsterdam Regenmortel MHV. (1989). The concept and operational definition of protein epitopes. Phil Trans R Soc Lond B 323: 461-466
    • (1998) Phil Trans R Soc Lond B , vol.323 , pp. 461-466
    • Rao, V.S.R.1    Qasba, P.K.2
  • 37
    • 0027339137 scopus 로고
    • Carbohydrates in cell recognition
    • Sharon N, Lis H. (1993). Carbohydrates in cell recognition. Sci Am 268: 82-89
    • (1993) Sci Am , vol.268 , pp. 82-89
    • Sharon, N.1    Lis, H.2
  • 38
    • 77950138792 scopus 로고    scopus 로고
    • Conformational analysis of arabinofuranosides: Prediction of 3JH, H using MD simulations with DFT-derived spin-spin coupling profiles
    • Taha HA, Castillo N, Sears DN, Wasylishen RE, Lowary TL, Roy PN. (2010). Conformational analysis of arabinofuranosides: prediction of 3JH, H using MD simulations with DFT-derived spin-spin coupling profiles. J Chem Theory Comput 6: 212-222
    • (2010) J Chem Theory Comput , vol.6 , pp. 212-222
    • Taha, H.A.1    Castillo, N.2    Sears, D.N.3    Wasylishen, R.E.4    Lowary, T.L.5    Roy, P.N.6
  • 39
    • 0033555542 scopus 로고    scopus 로고
    • Bactericidal antibody recognition of meningococcal pora by induced fit comparison of liganded and unliganded fab structures
    • van Den Elsen J, Vandeputte-Rutten L, Kroon J, Gros P. (1999). Bactericidal antibody recognition of meningococcal PorA by induced fit. Comparison of liganded and unliganded Fab structures. J Biol Chem 274: 1495-1501
    • (1999) J Biol Chem , vol.274 , pp. 1495-1501
    • Van Den Elsen, J.1    Vandeputte-Rutten, L.2    Kroon, J.3    Gros, P.4
  • 40
    • 0027318961 scopus 로고
    • Biological roles of oligosaccharides: All of the theories are correct
    • Varki A. (1993). Biological roles of oligosaccharides: all of the theories are correct. Glycobiology 3: 97-130
    • (1993) Glycobiology , vol.3 , pp. 97-130
    • Varki, A.1
  • 42
    • 0037137222 scopus 로고    scopus 로고
    • Molecular recognition of oligosaccharide epitopes by a monoclonal Fab specific for Shigella flexneri y Lipopolysaccharide: X-ray structures and thernodynamics
    • Vyas NK, Vyas MN, Chervenak MC, Johnson MA, Pinto BM, Bundle DR, Quiocho FA. (2002). Molecular recognition of oligosaccharide epitopes by a monoclonal Fab specific for Shigella flexneri Y Lipopolysaccharide: x-ray structures and thernodynamics. Biochemistry 41: 13575-13586
    • (2002) Biochemistry , vol.41 , pp. 13575-13586
    • Vyas, N.K.1    Vyas, M.N.2    Chervenak, M.C.3    Johnson, M.A.4    Pinto, B.M.5    Bundle, D.R.6    Quiocho, F.A.7
  • 43
    • 4544388758 scopus 로고    scopus 로고
    • Combining NMR and simulation methods in oligosaccharide conformational analysis
    • Jiménez-Barbero J (ed) Wiley, Weinheim
    • Weimar T, Woods RJ. (2002). Combining NMR and simulation methods in oligosaccharide conformational analysis. In: Jiménez-Barbero J (ed) NMR of glycoconjugates. Wiley, Weinheim, pp 111-144
    • (2002) NMR of Glycoconjugates , pp. 111-144
    • Weimar, T.1    Woods, R.J.2
  • 44
    • 0023655148 scopus 로고
    • Structure and immunochemistry of an oligosaccharide repeating unit of the capsular polysaccharide of type III group B Streptococcus
    • Wessels MR, Pozsgay V, Kasper DL, Jennings HJ. (1987). Structure and immunochemistry of an oligosaccharide repeating unit of the capsular polysaccharide of type III group B Streptococcus. J Biol Chem 262: 8262-8267
    • (1987) J Biol Chem , vol.262 , pp. 8262-8267
    • Wessels, M.R.1    Pozsgay, V.2    Kasper, D.L.3    Jennings, H.J.4
  • 45
    • 0001825704 scopus 로고
    • On the magnitudes and origins of the anomeric effects, exoanomeric effects, reverse anomeric effects, and C-X and C-Y bond lengths in XCH2YH molecules
    • Wolfe S, Whangbo M-H, Mitchell DJ. (1979). On the magnitudes and origins of the anomeric effects, exoanomeric effects, reverse anomeric effects, and C-X and C-Y bond lengths in XCH2YH molecules. Carbohydr Res 69: 1-26
    • (1979) Carbohydr Res , vol.69 , pp. 1-26
    • Wolfe, S.1    Whangbo, M.-H.2    Mitchell, D.J.3
  • 46
    • 78049424266 scopus 로고    scopus 로고
    • Computational glycoscience: Characterizing the spatial and temporal properties of glycans and glycan-protein complexes
    • Woods RJ, Tessier MB. (2010). Computational glycoscience: characterizing the spatial and temporal properties of glycans and glycan-protein complexes. Curr Opin Struct Biol 20: 575-583
    • (2010) Curr Opin Struct Biol , vol.20 , pp. 575-583
    • Woods, R.J.1    Tessier, M.B.2
  • 47
    • 0034625308 scopus 로고    scopus 로고
    • Crystal structure of the 64 M-2 antibody Fab fragment in complex with a DNA dT (6-4) T photoproduct formed by ultraviolet radiation
    • Yokoyama H, Mizutani R, Satow Y, Komatsu Y, Ohtsuka E, Nikaido O. (2000). Crystal structure of the 64 M-2 antibody Fab fragment in complex with a DNA dT (6-4) T photoproduct formed by ultraviolet radiation. J Mol Biol 299 (3): 711-723
    • (2000) J Mol Biol , vol.299 , Issue.3 , pp. 711-723
    • Yokoyama, H.1    Mizutani, R.2    Satow, Y.3    Komatsu, Y.4    Ohtsuka, E.5    Nikaido, O.6
  • 48
    • 41649092368 scopus 로고    scopus 로고
    • On achieving experimental accuracy from molecular dynamics simulations of flexible molecules: Aqueous glycerol
    • Yongye AB, Foley BL, Woods RJ (2008a) On achieving experimental accuracy from molecular dynamics simulations of flexible molecules: aqueous glycerol. J Phys Chem A 112 (12): 2634-2639
    • (2008) J Phys Chem A , vol.112 , Issue.12 , pp. 2634-2639
    • Yongye, A.B.1    Foley, B.L.2    Woods, R.J.3
  • 49
    • 56749148321 scopus 로고    scopus 로고
    • The conformational properties of methyl a- 2 8) -di/trisialosides and their N-acyl analogs: Implications for Anti-Neisseria meningitidis B vaccine design
    • Yongye AB, Gonzales Outeriño J, Glushka J, Schultheis V, Woods RJ (2008b) The conformational properties of methyl a- (2, 8) -di/trisialosides and their N-acyl analogs: implications for Anti-Neisseria meningitidis B vaccine design. Biochemistry 47 (47): 12493-12514
    • (2008) Biochemistry , vol.47 , Issue.47 , pp. 12493-12514
    • Yongye, A.B.1    Gonzales Outeriño, J.2    Glushka, J.3    Schultheis, V.4    Woods, R.J.5


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