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Volumn 17, Issue 6, 2012, Pages 6658-6671

Application of paramagnetic NMR-validated molecular dynamics simulation to the analysis of a conformational ensemble of a branched Oligosaccharide

Author keywords

Ganglioside; Lanthanide; Molecular dynamics; NMR spectroscopy; Oligosaccharide; Pseudocontact shift

Indexed keywords

CARBOHYDRATE; OLIGOSACCHARIDE;

EID: 85053142053     PISSN: None     EISSN: 14203049     Source Type: Journal    
DOI: 10.3390/molecules17066658     Document Type: Article
Times cited : (37)

References (29)
  • 1
    • 0027318961 scopus 로고
    • Biological roles of oligosaccharides: All of the theories are correct
    • Varki, A. Biological roles of oligosaccharides: All of the theories are correct. Glycobiology 1993, 3, 97-130. (Pubitemid 23132602)
    • (1993) Glycobiology , vol.3 , Issue.2 , pp. 97-130
    • Varki, A.1
  • 2
    • 34047255890 scopus 로고    scopus 로고
    • Lectins: Carbohydrate-specific reagents and biological recognition molecules
    • Sharon, N. Lectins: Carbohydrate-specific reagents and biological recognition molecules. J. Biol. Chem. 2007, 282, 2753-2764.
    • (2007) J. Biol. Chem. , vol.282 , pp. 2753-2764
    • Sharon, N.1
  • 3
    • 35048842895 scopus 로고    scopus 로고
    • Structural views of glycoprotein-fate determination in cells
    • DOI 10.1093/glycob/cwm046
    • Kato, K.; Kamiya, Y. Structural views of glycoprotein-fate determination in cells. Glycobiology 2007, 17, 1031-1044. (Pubitemid 47553527)
    • (2007) Glycobiology , vol.17 , Issue.10 , pp. 1031-1044
    • Kato, K.1    Kamiya, Y.2
  • 4
    • 0036462598 scopus 로고    scopus 로고
    • Conformational studies of oligosaccharides and glycopeptides: Complementarity of NMR, X-ray crystallography, and molecular modelling
    • DOI 10.1021/cr990368i
    • Wormald, M. R.; Petrescu, A. J.; Pao, Y. L.; Glithero, A.; Elliott, T.; Dwek, R. A. Conformational studies of oligosaccharides and glycopeptides: Complementarity of NMR, X-ray crystallography, and molecular modelling. Chem. Rev. 2002, 102, 371-386. (Pubitemid 35377620)
    • (2002) Chemical Reviews , vol.102 , Issue.2 , pp. 371-386
    • Wormald, M.R.1    Petrescu, A.J.2    Pao, Y.-L.3    Glithero, A.4    Elliott, T.5    Dwek, R.A.6
  • 5
    • 79960324099 scopus 로고    scopus 로고
    • Structural and molecular basis of carbohydrate-protein interaction systems as potential therapeutic targets
    • Kamiya, Y.; Yagi-Utsumi, M.; Yagi, H.; Kato, K. Structural and molecular basis of carbohydrate-protein interaction systems as potential therapeutic targets. Curr. Pharm. Des. 2011, 17, 1672-1684.
    • (2011) Curr. Pharm. Des. , vol.17 , pp. 1672-1684
    • Kamiya, Y.1    Yagi-Utsumi, M.2    Yagi, H.3    Kato, K.4
  • 6
    • 85123307912 scopus 로고    scopus 로고
    • Glycoproteins and Antibodies: Solution NMR Studies
    • Harris, R. K., Wasylishen, R. K., Eds.;, John Wiley: Chichester, UK;, doi:10.1002/9780470034590.emrstm1233
    • Kato, K.; Yamaguchi, Y. Glycoproteins and Antibodies: Solution NMR Studies. In Encyclopedia of Magnetic Resonance; Harris, R. K., Wasylishen, R. K., Eds.; John Wiley: Chichester, UK; 2011, pp. 1-12; doi:10.1002/9780470034590. emrstm1233.
    • (2011) Encyclopedia of Magnetic Resonance , pp. 1-12
    • Kato, K.1    Yamaguchi, Y.2
  • 8
    • 0027717805 scopus 로고
    • Conformation and dynamics of oligosaccharides in solution
    • Homans, S. W. Conformation and dynamics of oligosaccharides in solution. Glycobiology 1993, 3, 551-555. (Pubitemid 24028860)
    • (1993) Glycobiology , vol.3 , Issue.6 , pp. 551-555
    • Homans, S.W.1
  • 9
    • 79955018520 scopus 로고    scopus 로고
    • Carbohydrate-protein interactions: A 3D view by NMR
    • Roldos, V.; Canada, E. J.; Jiménez-Barbero, J. Carbohydrate-protein interactions: A 3D view by NMR. Chembiochem 2011, 12, 990-1005.
    • (2011) Chembiochem , vol.12 , pp. 990-1005
    • Roldos, V.1    Canada, E.J.2    Jiménez-Barbero, J.3
  • 10
    • 80051521890 scopus 로고    scopus 로고
    • Paramagnetic lanthanide tagging for NMR conformational analyses of N-Linked oligosaccharides
    • Yamamoto, S.; Yamaguchi, T.; Erdélyi, M.; Griesinger, C.; Kato, K. Paramagnetic lanthanide tagging for NMR conformational analyses of N-Linked oligosaccharides. Chem. Eur. J. 2011, 17, 9280-9282.
    • (2011) Chem. Eur. J. , vol.17 , pp. 9280-9282
    • Yamamoto, S.1    Yamaguchi, T.2    Erdélyi, M.3    Griesinger, C.4    Kato, K.5
  • 12
    • 75749138064 scopus 로고    scopus 로고
    • Presentation of membrane-anchored glycosphingolipids determined from molecular dynamics simulations and NMR paramagnetic relaxation rate enhancement
    • DeMarco, M. L.; Woods, R. J.; Prestegard, J. H.; Tian, F. Presentation of membrane-anchored glycosphingolipids determined from molecular dynamics simulations and NMR paramagnetic relaxation rate enhancement. J. Am. Chem. Soc. 2010, 132, 1334-1338.
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 1334-1338
    • DeMarco, M.L.1    Woods, R.J.2    Prestegard, J.H.3    Tian, F.4
  • 13
    • 84859941651 scopus 로고    scopus 로고
    • Lanthanide-assisted NMR evaluation of a dynamic ensemble of oligosaccharide conformations
    • Yamamoto, S.; Zhang, Y.; Yamaguchi, T.; Kameda, T.; Kato, K. Lanthanide-assisted NMR evaluation of a dynamic ensemble of oligosaccharide conformations. Chem. Commun. 2012, 48, 4752-4754.
    • (2012) Chem. Commun. , vol.48 , pp. 4752-4754
    • Yamamoto, S.1    Zhang, Y.2    Yamaguchi, T.3    Kameda, T.4    Kato, K.5
  • 16
    • 0006209003 scopus 로고
    • Theoretical studies on the conformation of monosialogangliosides and disialogangliosides
    • Veluraja, K.; Rao, V. S. R. Theoretical studies on the conformation of monosialogangliosides and disialogangliosides. Carbohydr. Polym. 1983, 3, 175-192.
    • (1983) Carbohydr. Polym. , vol.3 , pp. 175-192
    • Veluraja, K.1    Rao, V.S.R.2
  • 17
    • 0001634270 scopus 로고
    • The conformational properties of the ganglioside GM2 and GM1 based on 1H and 13C nuclear magnetic resonance studies
    • Sabesan, S.; Bock, K.; Lemieux, U. The conformational properties of the ganglioside GM2 and GM1 based on 1H and 13C nuclear magnetic resonance studies. Can. J. Chem. 1984, 62, 1034-1045.
    • (1984) Can. J. Chem. , vol.62 , pp. 1034-1045
    • Sabesan, S.1    Bock, K.2    Lemieux, U.3
  • 18
    • 0034465091 scopus 로고    scopus 로고
    • Modeling ganglioside headgroups by conformational analysis and molecular dynamics
    • DOI 10.1023/A:1007161319700
    • Brocca, P.; Bernardi, A.; Raimondi, L.; Sonnino, S. Modeling ganglioside headgroups by conformational analysis and molecular dynamics. Glycoconjugate J. 2000, 17, 283-299. (Pubitemid 32204704)
    • (2000) Glycoconjugate Journal , vol.17 , Issue.5 , pp. 283-299
    • Brocca, P.1    Bernardi, A.2    Raimondi, L.3    Sonnino, S.4
  • 19
    • 77956416072 scopus 로고    scopus 로고
    • 3DSDSCAR-A three dimensional structural database for sialic acid-containing carbohydrates through molecular dynamics simulation
    • Veluraja, K.; Selvin, J. F. A.; Venkateshwari, S.; Priyadarzini, T. R. K. 3DSDSCAR-a three dimensional structural database for sialic acid-containing carbohydrates through molecular dynamics simulation. Carbohydr. Res. 2010, 345, 2030-2037.
    • (2010) Carbohydr. Res. , vol.345 , pp. 2030-2037
    • Veluraja, K.1    Selvin, J.F.A.2    Venkateshwari, S.3    Priyadarzini, T.R.K.4
  • 20
    • 0026357863 scopus 로고
    • 1H-NMR study of GM2 ganglioside: Evidence that an interresidue amide-carboxyl hydrogen bond contributes to stabilization of a preferred conformation
    • 1H-NMR study of GM2 ganglioside: Evidence that an interresidue amide-carboxyl hydrogen bond contributes to stabilization of a preferred conformation. Glycoconjugate J. 1991, 8, 484-92.
    • (1991) Glycoconjugate J. , vol.8 , pp. 484-492
    • Levery, S.B.1
  • 21
    • 0021111040 scopus 로고
    • High-resolution proton NMR studies of gangliosides. 1. Use of homonuclear two-dimensional spin-echo J-correlated spectroscopy for determination of residue composition and anomeric configurations
    • Koerner, T. A. W., Jr.; Prestegard, J. H.; Demou, P. C.; Yu, R. K. High-resolution proton NMR studies of gangliosides. 1. Use of homonuclear two-dimensional spin-echo J-correlated spectroscopy for determination of residue composition and anomeric configurations. Biochemistry 1983, 22, 2676-2687.
    • (1983) Biochemistry , vol.22 , pp. 2676-2687
    • Koerner Jr., T.A.W.1    Prestegard, J.H.2    Demou, P.C.3    Yu, R.K.4
  • 24
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comput. Phys. 1977, 23, 327-341.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 25
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N·log (N) method for Ewald sums in large systems
    • Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An N·log (N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98, 10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 27
  • 28
    • 0004040543 scopus 로고    scopus 로고
    • University of California, San Francisco, CA, USA
    • Goddard, T. D.; Kneller, D. G. SPARKY 3; University of California, San Francisco, CA, USA, 2008.
    • (2008) SPARKY 3
    • Goddard, T.D.1    Kneller, D.G.2
  • 29
    • 64349102959 scopus 로고    scopus 로고
    • Residual dipolar couplings of freely rotating groups in small molecules. Stereochemical assignment and side-chain conformation of 8-phenylmenthol
    • Sánchez-Pedregal, V. M.; Santamaría-Fernández, R.; Navarro-Vázquez, A. Residual dipolar couplings of freely rotating groups in small molecules. stereochemical assignment and side-chain conformation of 8-phenylmenthol. Org. Lett. 2009, 11, 1471-1474.
    • (2009) Org. Lett. , vol.11 , pp. 1471-1474
    • Sánchez-Pedregal, V.M.1    Santamaría-Fernández, R.2    Navarro-Vázquez, A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.