메뉴 건너뛰기




Volumn 258, Issue 2, 1998, Pages 372-386

The high degree of internal flexibility observed for an oligomannose oligosaccharide does not alter the overall topology of the molecule

Author keywords

AMBER; GLYCAM; Molecular dynamics; NMR; NOE; Oligosaccharide; Simulations

Indexed keywords

GLYCAN; GLYCOPROTEIN; GLYCOSIDE; MANNOSE; OLIGOSACCHARIDE;

EID: 0032403790     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1432-1327.1998.2580372.x     Document Type: Article
Times cited : (130)

References (49)
  • 1
    • 0023661070 scopus 로고
    • Virtual and solution conformations of oligosaccharides
    • Cumming, D. A. & Carver, J. P. (1987) Virtual and solution conformations of oligosaccharides, Biochemistry 26, 6664-6676.
    • (1987) Biochemistry , vol.26 , pp. 6664-6676
    • Cumming, D.A.1    Carver, J.P.2
  • 2
    • 0025469640 scopus 로고
    • Uncertainties in structural determinations of oligosaccharide conformation, using measurements of nuclear Overhauser effects
    • Wooten, E. W., Edge, C. J., Bazzo, R., Dwek, R. A. & Rademacher, T. W. (1990) Uncertainties in structural determinations of oligosaccharide conformation, using measurements of nuclear Overhauser effects, Carbohydr. Res. 203, 13-17.
    • (1990) Carbohydr. Res. , vol.203 , pp. 13-17
    • Wooten, E.W.1    Edge, C.J.2    Bazzo, R.3    Dwek, R.A.4    Rademacher, T.W.5
  • 3
    • 7844235205 scopus 로고    scopus 로고
    • Carbohydrate force fields
    • (Kollman, P. A., v. Schleyer, P. R., Allinger, N. L. & Schaefer, H. F. III, eds), John Wiley and Sons, New York
    • Woods, R. J. (1997) Carbohydrate force fields, in Encyclopedia of computational chemistry (Kollman, P. A., v. Schleyer, P. R., Allinger, N. L. & Schaefer, H. F. III, eds), John Wiley and Sons, New York.
    • (1997) Encyclopedia of Computational Chemistry
    • Woods, R.J.1
  • 4
    • 0031424426 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the N-linked oligosaccharide of the lectin from Erythrina corallodendron
    • Naidoo, K. J., Denysyk, D. & Brady, J. W. (1997) Molecular dynamics simulations of the N-linked oligosaccharide of the lectin from Erythrina corallodendron, Protein Eng. 10, 1249-1261.
    • (1997) Protein Eng. , vol.10 , pp. 1249-1261
    • Naidoo, K.J.1    Denysyk, D.2    Brady, J.W.3
  • 5
    • 0030953911 scopus 로고    scopus 로고
    • NMR and molecular dynamics studies of the conformational epitope of the type III group B Streptococcus type III capsular polysaccharide
    • Brisson, J.-R., Uhrínova, S., Woods, R. J., van der Zwan, M., Jarrell, H. C., Paoletti, L. C., Kasper, D. L. & Jennings, H. J. (1997) NMR and molecular dynamics studies of the conformational epitope of the type III group B Streptococcus type III capsular polysaccharide, Biochemistry 36, 3278-3292.
    • (1997) Biochemistry , vol.36 , pp. 3278-3292
    • Brisson, J.-R.1    Uhrínova, S.2    Woods, R.J.3    Van Der Zwan, M.4    Jarrell, H.C.5    Paoletti, L.C.6    Kasper, D.L.7    Jennings, H.J.8
  • 6
    • 33751155339 scopus 로고
    • Molecular mechanical and molecular dynamical simulations of glycoproteins and oligosaccharides. 1. GLYCAM_93 parameter development
    • Woods, R. J., Dwek, R. A., Edge, C. J. & Fraser-Reid, B. (1995) Molecular mechanical and molecular dynamical simulations of glycoproteins and oligosaccharides. 1. GLYCAM_93 parameter development, J. Phys. Chem. 99, 3832-3846.
    • (1995) J. Phys. Chem. , vol.99 , pp. 3832-3846
    • Woods, R.J.1    Dwek, R.A.2    Edge, C.J.3    Fraser-Reid, B.4
  • 7
    • 0028041189 scopus 로고
    • Molecular dynamics simulations of high-mannose oligosaccharides
    • Balaji, P. V., Qasha, P. K. & Rao, V. S. R. (1994) Molecular dynamics simulations of high-mannose oligosaccharides, Glycobiology 4, 497-515.
    • (1994) Glycobiology , vol.4 , pp. 497-515
    • Balaji, P.V.1    Qasha, P.K.2    Rao, V.S.R.3
  • 8
    • 0027978318 scopus 로고
    • Restrained vs free dynamics simulations of oligosaccharides: Application to solution dynamics of biantennary and bisected N-linked glycans
    • Rutherford, T. J. & Homans, S. W. (1994) Restrained vs free dynamics simulations of oligosaccharides: application to solution dynamics of biantennary and bisected N-linked glycans, Biochemistry 33, 9606-9614.
    • (1994) Biochemistry , vol.33 , pp. 9606-9614
    • Rutherford, T.J.1    Homans, S.W.2
  • 9
    • 0028921674 scopus 로고
    • The effects of variable glycosylation on the functional activities of ribonuclease, plasminogen and tissue plasminogen activator
    • Rudd, P. M., Woods, R. J., Wormald, M. R., Opdenakker, G., Downing, K. A., Campbell, I. D. & Dwek, R. A. (1994) The effects of variable glycosylation on the functional activities of ribonuclease, plasminogen and tissue plasminogen activator, Biochem. Biophys. Acta 1248, 1-10.
    • (1994) Biochem. Biophys. Acta , vol.1248 , pp. 1-10
    • Rudd, P.M.1    Woods, R.J.2    Wormald, M.R.3    Opdenakker, G.4    Downing, K.A.5    Campbell, I.D.6    Dwek, R.A.7
  • 12
    • 0027526639 scopus 로고
    • Flexibility in a tetrasaccharide fragment from the high mannose type of N-linked oligosaccharides
    • Imberty, A., Pérez, S., Hricovíni, M., Shah, R. N. & Carver, J. P. (1993) Flexibility in a tetrasaccharide fragment from the high mannose type of N-linked oligosaccharides, Int. J. Biol. Macromol. 15, 17-23.
    • (1993) Int. J. Biol. Macromol. , vol.15 , pp. 17-23
    • Imberty, A.1    Pérez, S.2    Hricovíni, M.3    Shah, R.N.4    Carver, J.P.5
  • 14
    • 0023660995 scopus 로고
    • Structure and dynamics in oligomannose-type oligosaccharides
    • Homans, S. W., Pastore, A., Dwek, R. A. & Rademacher, T. W. (1987) Structure and dynamics in oligomannose-type oligosaccharides, Biochemistry 26, 6649-6655.
    • (1987) Biochemistry , vol.26 , pp. 6649-6655
    • Homans, S.W.1    Pastore, A.2    Dwek, R.A.3    Rademacher, T.W.4
  • 15
    • 0023661004 scopus 로고
    • Solution conformations of N-linked oligosaccharides
    • Homans, S. W., Dwek, R. A. & Rademacher, T. W. (1987) Solution conformations of N-linked oligosaccharides, Biochemistry 26, 6571-6578.
    • (1987) Biochemistry , vol.26 , pp. 6571-6578
    • Homans, S.W.1    Dwek, R.A.2    Rademacher, T.W.3
  • 16
    • 0028824692 scopus 로고
    • Three-dimensional structures of oligosaccharides
    • Woods, R. J. (1995) Three-dimensional structures of oligosaccharides, Curr. Opin. Struct. Biol. 5, 591-598.
    • (1995) Curr. Opin. Struct. Biol. , vol.5 , pp. 591-598
    • Woods, R.J.1
  • 17
    • 0030839727 scopus 로고    scopus 로고
    • The solution NMR structure of glucosylated N-glycans involved in early stages of glycoprotein biosynthesis and folding
    • Petrescu, A. J., Butters, T. D., Reinkensmeier, G., Petrescu, S., Platt, F. M., Dwek, R. A. & Wormald, M. R. (1997) The solution NMR structure of glucosylated N-glycans involved in early stages of glycoprotein biosynthesis and folding, EMBO J. 16, 4302-4310.
    • (1997) EMBO J. , vol.16 , pp. 4302-4310
    • Petrescu, A.J.1    Butters, T.D.2    Reinkensmeier, G.3    Petrescu, S.4    Platt, F.M.5    Dwek, R.A.6    Wormald, M.R.7
  • 19
    • 0023646675 scopus 로고
    • Tertiary structure in N-linked oligosaccharides
    • Homans, S. W., Dwek, R. A. & Rademacher, T. W. (1987) Tertiary structure in N-linked oligosaccharides, Biochemistry 26, 6553-6560.
    • (1987) Biochemistry , vol.26 , pp. 6553-6560
    • Homans, S.W.1    Dwek, R.A.2    Rademacher, T.W.3
  • 20
    • 0027641048 scopus 로고
    • The systematic use of negative nuclear Overhauser constraints in the determination of oligosaccharide conformations: Application to sialyl-Lewis X
    • Wormald, M. R. & Edge, C. J. (1993) The systematic use of negative nuclear Overhauser constraints in the determination of oligosaccharide conformations: application to sialyl-Lewis X, Carbohydr. Res. 246, 337-344.
    • (1993) Carbohydr. Res. , vol.246 , pp. 337-344
    • Wormald, M.R.1    Edge, C.J.2
  • 21
    • 7844250911 scopus 로고
    • The role of non-bonded interactions in determining the solution conformations of oligosaccharides
    • (Smith, D., ed.) American Chemical Society, Washington. D.C.
    • Woods, R. J., Edge, C. J. & Dwek, R. A. (1994) The role of non-bonded interactions in determining the solution conformations of oligosaccharides, In Modelling the hydrogen bond (Smith, D., ed.) vol. 569, pp. 252-268, American Chemical Society, Washington. D.C.
    • (1994) Modelling the Hydrogen Bond , vol.569 , pp. 252-268
    • Woods, R.J.1    Edge, C.J.2    Dwek, R.A.3
  • 22
    • 4143084743 scopus 로고
    • GLYCAM_93: A generalized parameter set for molecular dynamics simulations of glycoproteins and oligosaccharides. Application to the structure and dynamics of a disaccharide related to oligomannose
    • (Bock, K., Clausen, H., Krogsgaard-Larsen, P. & Kofod, H., eds) Munksgaard, Copenhagen, Denmark
    • Woods, R. J., Edge, C. J., Wormald, M. R. & Dwek, R. A. (1993) GLYCAM_93: A generalized parameter set for molecular dynamics simulations of glycoproteins and oligosaccharides. Application to the structure and dynamics of a disaccharide related to oligomannose, in Complex carbohydrates in drug research. (Bock, K., Clausen, H., Krogsgaard-Larsen, P. & Kofod, H., eds) vol. 36, pp. 15-36, Munksgaard, Copenhagen, Denmark.
    • (1993) Complex Carbohydrates in Drug Research , vol.36 , pp. 15-36
    • Woods, R.J.1    Edge, C.J.2    Wormald, M.R.3    Dwek, R.A.4
  • 25
    • 0029339153 scopus 로고
    • Conformations and internal mobility of a glycopeptide derived from bromelain using molecular dynamics simulations and NOESY analysis
    • Lommerse, J. P. M., Kroon-Batenburg, L. M. J., Kroon, J., Kamerling, J. P. & Vliegenthart, J. F. G. (1995) Conformations and internal mobility of a glycopeptide derived from bromelain using molecular dynamics simulations and NOESY analysis, J. Biomol. NMR 5, 79-94.
    • (1995) J. Biomol. NMR , vol.5 , pp. 79-94
    • Lommerse, J.P.M.1    Kroon-Batenburg, L.M.J.2    Kroon, J.3    Kamerling, J.P.4    Vliegenthart, J.F.G.5
  • 26
    • 0026867034 scopus 로고
    • A Conformational Study of α-L-Rhap-(1-2)-α-L-Rhap-(1-OMe) by NMR nuclear Overhauser effect spectroscopy (NOESY) and molecular dynamics calculations
    • Widmalm, G., Byrd, A. R. & Egan, W. (1992) A Conformational Study of α-L-Rhap-(1-2)-α-L-Rhap-(1-OMe) by NMR nuclear Overhauser effect spectroscopy (NOESY) and molecular dynamics calculations, Carbohydr. Res. 229, 195-211.
    • (1992) Carbohydr. Res. , vol.229 , pp. 195-211
    • Widmalm, G.1    Byrd, A.R.2    Egan, W.3
  • 27
    • 0002365919 scopus 로고
    • The exo-anomeric effect
    • (Szarek, W. A. & Horton, D., eds) American Chemical Society, Washington, D.C.
    • Lemieux, R. U., Koto, S. & Voisin, D. (1979) The exo-anomeric effect, in Anomeric effect. Origin and consequences (Szarek, W. A. & Horton, D., eds) vol. 87, pp. 17-29, American Chemical Society, Washington, D.C.
    • (1979) Anomeric Effect. Origin and Consequences , vol.87 , pp. 17-29
    • Lemieux, R.U.1    Koto, S.2    Voisin, D.3
  • 28
    • 0000195076 scopus 로고
    • 13C-N.M.R.-spectral study of synthetic methyl D-manno-oligosaccharides
    • 13C-N.M.R.-spectral study of synthetic methyl D-manno-oligosaccharides. Carbohydr. Res. 97, 205-227.
    • (1981) Carbohydr. Res. , vol.97 , pp. 205-227
    • Ogawa, T.1    Sasajima, K.2
  • 29
    • 0001620546 scopus 로고
    • Molecular mechanics modeling of α-(1-2)-, α-(1-3)-, and a-(1-6)-linked mannosyl disaccharides with MM3(92)
    • Dowd, M. K., French, A. D. & Reilly, P. J. (1995) Molecular mechanics modeling of α-(1-2)-, α-(1-3)-, and a-(1-6)-linked mannosyl disaccharides with MM3(92), J. Carbohydr. Chem. 14, 589-600.
    • (1995) J. Carbohydr. Chem. , vol.14 , pp. 589-600
    • Dowd, M.K.1    French, A.D.2    Reilly, P.J.3
  • 30
    • 0025366497 scopus 로고
    • Data Bank of three-dimensional structures of disaccharides, a tool to build 3-D structures of oligosaccharides
    • Imberty, A., Gerber, S., Tran, V. & Pérez, S. (1990) Data Bank of three-dimensional structures of disaccharides, a tool to build 3-D structures of oligosaccharides, Glycoconjugate J. 7, 27-54.
    • (1990) Glycoconjugate J. , vol.7 , pp. 27-54
    • Imberty, A.1    Gerber, S.2    Tran, V.3    Pérez, S.4
  • 31
    • 84986642261 scopus 로고
    • Synthesis and conformational analysis of methyl 2-O-(α-D-mannopyranosyl)-α-D-mannopyranoside
    • Peters, T. (1991) Synthesis and conformational analysis of methyl 2-O-(α-D-mannopyranosyl)-α-D-mannopyranoside. Liebigs Ann. Chem., 135-141.
    • (1991) Liebigs Ann. Chem. , pp. 135-141
    • Peters, T.1
  • 32
    • 0026464832 scopus 로고
    • Structure of a C-type mannose-binding protein complexed with an oligosaccharide
    • Weis, W. I., Drickamer, K. & Hendrickson, W. A. (1992) Structure of a C-type mannose-binding protein complexed with an oligosaccharide, Nature 360, 127-134.
    • (1992) Nature , vol.360 , pp. 127-134
    • Weis, W.I.1    Drickamer, K.2    Hendrickson, W.A.3
  • 33
    • 0004210285 scopus 로고
    • Biosym/MSI, San Diego
    • Biosym/MSI (1995) Insight II. Biosym/MSI, San Diego.
    • (1995) Insight II
  • 34
    • 0001844723 scopus 로고
    • The crystal and molecular structure of O-α-D-mannopyranosyl-(1-3)-O-β-D-mannopyranosyl-(1-4)-2-acetamido-2- deoxy-α-D-glucopyranose
    • Warin, V., Baert, F., Fouret, R., Strecker, G., Spik, G., Fournet, B. & Montreuil, J. (1979) The crystal and molecular structure of O-α-D-mannopyranosyl-(1-3)-O-β-D-mannopyranosyl-(1-4)-2-acetamido-2- deoxy-α-D-glucopyranose, Carbohydr. Res. 76, 11-22.
    • (1979) Carbohydr. Res. , vol.76 , pp. 11-22
    • Warin, V.1    Baert, F.2    Fouret, R.3    Strecker, G.4    Spik, G.5    Fournet, B.6    Montreuil, J.7
  • 35
    • 0025050372 scopus 로고
    • A molecular mechanical force field for the conformational analysis of oligosaccharides: Comparison of theoretical and crystal structures of Manα1-3Manβ1-4GlcNAc
    • Homans, S. W. (1990) A molecular mechanical force field for the conformational analysis of oligosaccharides: comparison of theoretical and crystal structures of Manα1-3Manβ1-4GlcNAc, Biochemistry 29, 9110-9118.
    • (1990) Biochemistry , vol.29 , pp. 9110-9118
    • Homans, S.W.1
  • 36
    • 0028518483 scopus 로고
    • The potential energy surface of methyl 3-O-(α-D-mannopyranosyl)-α-D-mannopyranoside in aqueous solution: Conclusions derived from optical rotation
    • Stevens, E. S. (1994) The potential energy surface of methyl 3-O-(α-D-mannopyranosyl)-α-D-mannopyranoside in aqueous solution: conclusions derived from optical rotation, Biopolymers 34, 1395-1401.
    • (1994) Biopolymers , vol.34 , pp. 1395-1401
    • Stevens, E.S.1
  • 38
    • 0025345646 scopus 로고
    • Solvent effect on the conformation of the hydroxymethyl group established by molecular dynamics simulations of methyl-β-D-glucoside in water
    • Kroon-Batenburg, L. M. J. & Kroon, J. (1990) Solvent effect on the conformation of the hydroxymethyl group established by molecular dynamics simulations of methyl-β-D-glucoside in water, Biopolymers 29, 1243-1248.
    • (1990) Biopolymers , vol.29 , pp. 1243-1248
    • Kroon-Batenburg, L.M.J.1    Kroon, J.2
  • 39
    • 84985666143 scopus 로고
    • Conformations of the hydroxymethyl group in crystalline aldohexopyranoses
    • Marchessault, R. H. & Perez, S. (1979) Conformations of the hydroxymethyl group in crystalline aldohexopyranoses, Biopolymers 18, 2369-2374.
    • (1979) Biopolymers , vol.18 , pp. 2369-2374
    • Marchessault, R.H.1    Perez, S.2
  • 40
    • 0001092761 scopus 로고
    • On the conformational variability of the N-acetylglucosamin β-(1-4) linked dimer. Crystal and molecular structure of β-N,N′-diacetylchitobiose trihydrate
    • Mo, F. (1979) On the conformational variability of the N-acetylglucosamin β-(1-4) linked dimer. Crystal and molecular structure of β-N,N′-diacetylchitobiose trihydrate, Acta Chem. Scand. A33, 207-218.
    • (1979) Acta Chem. Scand. , vol.A33 , pp. 207-218
    • Mo, F.1
  • 41
    • 0000479294 scopus 로고
    • The crystal structure of a B-(1-4) linked disaccharide, β-N,N′-diacetylchitobiose monohydrate
    • Mo, F. & Jensen, L. H. (1978) The crystal structure of a B-(1-4) linked disaccharide, β-N,N′-diacetylchitobiose monohydrate, Acta Crystallogr. B34, 1562-1569.
    • (1978) Acta Crystallogr. , vol.B34 , pp. 1562-1569
    • Mo, F.1    Jensen, L.H.2
  • 42
    • 0030520310 scopus 로고    scopus 로고
    • The application of molecular modeling techniques to the determination of oligosaccharide solution conformations
    • (Lipkowitz, K. B. & Boyd, D. B., eds) Chapter 3, VCH Publishers, Inc., New York
    • Woods, R. J. (1996) The application of molecular modeling techniques to the determination of oligosaccharide solution conformations. In Reviews in computational chemistry (Lipkowitz, K. B. & Boyd, D. B., eds) Chapter 3, VCH Publishers, Inc., New York.
    • (1996) Reviews in Computational Chemistry
    • Woods, R.J.1
  • 43
    • 0025131921 scopus 로고
    • Isolation, characterization, and expression of cDNA encoding a rat liver endoplasmic reticulum α-mannosidase
    • Bischoff, J., Moremen, K. & Lodish, H. F. (1990) Isolation, characterization, and expression of cDNA encoding a rat liver endoplasmic reticulum α-mannosidase, J. Biol. Chem. 265, 17110-17117.
    • (1990) J. Biol. Chem. , vol.265 , pp. 17110-17117
    • Bischoff, J.1    Moremen, K.2    Lodish, H.F.3
  • 45
    • 0021099732 scopus 로고
    • Evidence for an α-mannosidase in endoplasmic reticulum of rat liver
    • Bischoff, J. & Kornfeld, R. (1983) Evidence for an α-mannosidase in endoplasmic reticulum of rat liver, J. Biol. Chem. 258, 7907-7910.
    • (1983) J. Biol. Chem. , vol.258 , pp. 7907-7910
    • Bischoff, J.1    Kornfeld, R.2
  • 47
    • 0026337737 scopus 로고
    • Structure of a legume lectin with an ordered N-linked carbohydrate in complex with lactose
    • Shaanan, B., Lis, H. & Sharon, N. (1991) Structure of a legume lectin with an ordered N-linked carbohydrate in complex with lactose, Science 254, 862-866.
    • (1991) Science , vol.254 , pp. 862-866
    • Shaanan, B.1    Lis, H.2    Sharon, N.3
  • 48
    • 0024571818 scopus 로고
    • Human leukocyte and porcine pancreatic elastase: X-ray crystal structures, mechanism, substrate specificity, and mechanism-based inhibitors
    • Bode, W., Meyer, E. Jr & Powers, J. C. (1989) Human leukocyte and porcine pancreatic elastase: X-ray crystal structures, mechanism, substrate specificity, and mechanism-based inhibitors, Biochemistry 28, 1951-1963.
    • (1989) Biochemistry , vol.28 , pp. 1951-1963
    • Bode, W.1    Meyer Jr., E.2    Powers, J.C.3
  • 49
    • 0025194450 scopus 로고
    • 2.9 Å resolution structure of the N-terminal domain of a variant surface glycoprotein from Trypanosoma brucei
    • Freymann, D., Down, J., Carrington, M., Roditi, I., Turner, M. & Wiley, D. (1990) 2.9 Å resolution structure of the N-terminal domain of a variant surface glycoprotein from Trypanosoma brucei, J. Mol. Biol. 216, 141-160.
    • (1990) J. Mol. Biol. , vol.216 , pp. 141-160
    • Freymann, D.1    Down, J.2    Carrington, M.3    Roditi, I.4    Turner, M.5    Wiley, D.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.