Conformational insights on the molecular recognition processes of carbohydrate molecules by proteins and enzymes: A 3D view by using NMR

References

• Andrews CW, Fraser-Reid B, Bowen JP. An Ab initio Study (6-31g-Star) Of Transition-States In Glycoside Hydrolysis Based On Axial And Equatorial 2-Methoxytetrahydropyrans. J Am Chem Soc 1991; 113: 8293–8298
   Google Scholar
• Arepalli S, Rao R, Glaudemans CPJ, Daves G, Doyle Jr G, Kovac P, Bax A. Identification of protein-mediated indirect NOE effects in a disaccharide-Fab' complex by transferred ROESY. J Magn Reson B 1995; 106: 195–198
   PubMedGoogle Scholar
• Asensio JL, Cañada FJ, Jimenez-Barbero J. Studies of the bound conformations of methyl alpha-lactoside and methyl beta-allolactoside to ricin B chain using transferred NOE experiments in the laboratory and rotating frames, assisted by molecular mechanics and dynamics calculations. Eur J Biochem 1995; 233: 618–630
   PubMedGoogle Scholar
• Asensio JL, Martin-Pastor M, Jimenez-Barbero J. The use of the MM3* and ESFF force fields in conformational analysis of carbohydrate molecules in solution: The methyl alpha-lactoside case. J Mol Struct Theochem 1997; 395: 245–270
   Google Scholar
• Asensio JL, Cañada FJ, Bruix M, Gonzalez C, Khiar N, Rodriguez-Romero A, Jiménez-Barbero J. NMR investigations of protein-carbohydrate interactions: refined three-dimensional structure of the complex between hevein and methyl beta-chitobioside. Glycobiology 1998; 8: 569–577
   PubMedGoogle Scholar
• Asensio JL, Espinosa JF, Dietrich H, Cañada J, Schmidt RR, MartínLomas M, André S, Gabius H.-J., Jiménez-Barbero J. Bovine Heart Galectin-1 selects an unique (syn) conformation of C-lactose, a lactose analogue. J Am Chem Soc 1999a; 121: 8995–9000
   Google Scholar
• Asensio JL, García-Herrero A, Murillo MT, Fernández-Mayoralas A, Cañada FJ, Johnson CR, Jiménez-Barbero J. Conformational behavior of aza-C-glycosides: Experimental demonstration of the relative role of the exo-anomeric effect and 13-type interactions in controlling the conformation of regular glycosides. J Am Chem Soc 1999b; 121: 11318–11327
   Web of Science ®Google Scholar
• Asensio JL, Cañada FJ, Siebert HC, Laynez J, Poveda A, Nieto PM, Soedjanaatmadja UM, Gabius HJ, Jiménez-Barbero J. Structural basis for chitin recognition by defense proteins: GlcNAc residues are bound in a multivalent fashion by extended binding sites in hevein domains. Chem Biol 2000; 7: 529–543
   PubMedGoogle Scholar
• Bader, RFW. 1998. Atoms in Molecules. In: Encyclopedia of computational Chemistry. Schleyer PvR. Editor. John Wiley & Sons. p 64
   Google Scholar
• Benie AJ, Moser R, Bäuml E, Blaas D, Peters T. Virus-ligand interactions: identification and characterization of ligand binding by NMR spectroscopy. J Am Chem Soc 2003; 125: 14–15
   PubMedGoogle Scholar
• Bewley CA. Solution structure of a cyanovirin-N:Man alpha 1-2Man alpha complex:structural basis for high-affinity carbohydrate-mediated binding to gp120. Structure 2001; 9: 931–940
   PubMedGoogle Scholar
• Biegler-Koing FW, Bader RFW, Tang TH. Calculation of the average properties of atoms in molecules. J Comput Chem 1982; 3: 317–328
   Google Scholar
• Bevilacqua VL, Thomson DS, Prestegard JH. Conformation of methyl beta-lactoside bound to the ricin B-chain: interpretation of transferred nuclear Overhauser effects facilitated by spin simulation and selective deuteration. Biochemistry 1990; 29: 5529–5534
   PubMed Web of Science ®Google Scholar
• Bevilacqua VL, Kim Y, Prestegard JH. Conformation of beta-methylmelibiose bound to the ricin B-chain as determined from transferred nuclear Overhauser effects. Biochemistry 1992; 31: 9339–9346
   PubMed Web of Science ®Google Scholar
• Bothner-By AA, Gassend R. Binding of small molecules to proteins. Ann N Y Acad Sci 1973; 222: 608–614
   Google Scholar
• Bothner-By AA, Noggle JH. Time development of nuclear Overhauser effects in multispin systems. J Am Chem Soc 1979; 101: 5152–5157
   Web of Science ®Google Scholar
• Boys SF, Bernardi F. Calculation of small molecular interactions by differences of separate total energies-some procedures with reduced errors. Mol Phys 1970; 19: 553
   Web of Science ®Google Scholar
• Bundle DR, Young NM. Carbohydrate-protein interactions in antibodies and lectins. Curr Opin Struct Biol 1992; 2: 666–673
   Google Scholar
• Carlomagno T, Felli IC, Czech M, Fischer R, Sprinzl M, Griesinger C. Transferred cross-correlated relaxation: Application to the determination of sugar pucker in an aminoacylated tRNA-mimetic weakly bound to EF-Tu. J Am Chem Soc 1999; 121: 1945–1948
   Web of Science ®Google Scholar
• Chavez, MI, Vidal, P, Aboitiz, N, Freire, F, Groves, P, Andreu, C, Asensio, G, Muraki, M, Asensio, JL, Cañada, FJ, Jiménez-Barbero, J. On the Importance of Carbohydrate-Aromatic Interactions for the Molecular Recognition of Oligosaccharides by Proteins. NMR Studies of the Structure and Binding Affinity of AcAMP2-Like Peptides with non Natural Napthyl and Fluoroaromatic Residues. Chem Eur J, 11:7060–7074
   PubMedGoogle Scholar
• Drickamer K. C-type lectin-like domains. Curr Opin Struct Biol 1999; 9: 585–590
   PubMed Web of Science ®Google Scholar
• Dougherty DA. Cation-pi interactions in chemistry and biology: a new view of benzene, Phe, Tyr, and Trp. Science 1996; 271: 163–166
   PubMed Web of Science ®Google Scholar
• Dwek RA. Glycobiology: Toward Understanding the Function of Sugars. Chem Rev 1996; 96: 683–720
   PubMed Web of Science ®Google Scholar
• Espinosa JF, Asensio JL, Cañada J, Dietrich H, Martin-Lomas M, Schmidt RR, Jimenez-Barbero J. Conformational differences of O/C-glycosides in the protein-bound-state: different conformations of C-lactose and its O-analogue are recognized by ricin, a galactose-binding protein Angew. Chem Int Edit Engl. 1996; 35: 303–306
   Google Scholar
• Espinosa JF, Montero E, Vian A, Garcia JL, Dietrich H, Schmidt RR, Martin-Lomas M, Imberty A, Cañada FJ, Jimenez-Barbero J. Escherichia coli beta-galactosidase recognizes a high-energy conformation of C-lactose, a nonhydrolizable substrate analogue. NMR and modeling studies of the molecular complex. J Am Chem Soc 1998; 120: 1309–1314
   Google Scholar
• Fernández Alonso MC, Asensio JL, Cañada FJ, Jiménez-Barbero J, Cuevas G. G2 and DFT rigorous description of the inversion process of oxane and thiane used as simple ring systems to model sugar components. Chem Phys Chem 2003; 4: 748–753
   Google Scholar
• Fernández Alonso MC, Cañada FJ, Jiménez-Barbero J, Cuevas G. Theoretical Study of Inversion and Topomerization Processes of Substituted Cyclohexanes: The Relevance of the Energy 3D Hypersurface. Chem Phys Chem 2005a; 6: 671–680
   Google Scholar
• Fernández Alonso MC, Cañada FJ, Jiménez-Barbero J, Cuevas G. Molecular recognition of saccharides by proteins. Insights on the origin of carbohydrate-aromatic interactions. J Am Chem Soc 2005b; 127: 7379–7386
   PubMedGoogle Scholar
• Fielding L. NMR methods for the determination of protein-ligand dissociation constants. Curr Topics Med Chem 2003; 3: 39–53
   PubMedGoogle Scholar
• Gabius, HJ, Gabius, S. 1997. eds. Glycosciences: Status and Perspectives. London: Chapman & Hall.
   Google Scholar
• Gabius HJ, Siebert HC, André S, Jiménez-Barbero J, Rüdiger H. Chemical biology of the sugar code. Chem Bio Chem 2004; 5: 740–764
   Google Scholar
• García-Herrero A, Montero E, Muñoz JL, Espinosa JF, Vián A, García JL, Asensio JL, Cañada J, Jiménez-Barbero J. Conformational selection of glycomimetics at enzyme catalytic sites: experimental demonstration of the binding of distinct high-energy distorted conformations of C-, S-, and O-glycosides by E. Coli beta-galactosidases. J Am Chem Soc 2002; 124: 4804–4810
   PubMedGoogle Scholar
• Glaudemans CPJ, Lerner L, Daves G, Kovac P, Venable R, Bax A. Significant conformational changes in an antigenic carbohydrate epitope upon binding to a monoclonal antibody. Biochemistry 1990; 29: 10906–10911
   PubMed Web of Science ®Google Scholar
• Haselhorst T, Espinosa JF, Jiménez-Barbero J, Sokolowski T, Kosma P, Brade H, Brade L, Peters T. NMR experiments reveal distinct antibody-bound conformations of a synthetic disaccharide representing a general structural element of bacterial lipopolysaccharide epitopes. Biochemistry 1999; 38: 6449–6459
   PubMedGoogle Scholar
• Heightam TD, Vasella AT. Recent insights into inhibition, structure, and mechanism of configuration-retaining glycosidases. Angew Chem Int Ed 1999; 38: 750–770
   PubMedGoogle Scholar
• Hunter CA. Quantifying intermolecular interactions: guidelines for the molecular recognition toolbox. Angew Chem Int Ed Engl 2004; 43: 5310–5324
   PubMed Web of Science ®Google Scholar
• Hricovini M, Shah RN, Carver JP. Detection of internal motions in oligosaccharides by 1H relaxation measurements at different magnetic fields. Biochemistry 1992; 31: 10018–10023
   PubMed Web of Science ®Google Scholar
• Imberty A. Oligosaccharide structures: theory versus experiment. Curr Opin Struct Biol 1997; 7: 617–623
   PubMedGoogle Scholar
• Imberty A, Pérez S. Structure, conformation, and dynamics of bioactive oligosaccharides: theoretical approaches and experimental validations. Chem Rev 2000; 100: 4567–4588
   PubMed Web of Science ®Google Scholar
• Jain NU, Venot A, Umemoto K, Leffler H, Prestegard JH. Distance mapping of protein-binding sites using spin-labeled oligosaccharide ligands. Protein Sci 2001; 10: 2393–2400
   PubMedGoogle Scholar
• Jiménez-Barbero, J, Peters, T. 2002. In: NMR Spectroscopy of Glycoconjugates. Weinheim: Wiley-VCH.
   Google Scholar
• Krishna, NR, Moseley, HNB. 1999. In: Biological Magnetic Resonance 17:223–307. New York: Kluwer Academic/Plenum Publishers.
   Google Scholar
• Lambert JB, Mixon CE, Johnson DH. Conformational-analysis of selenanes and telluranes. J Am Chem Soc 1973; 95: 4634–4639
   Google Scholar
• Legler G. Glycoside hydrolases: mechanistic information from studies with reversible and irreversible inhibitors. Adv Carbohydr Chem Biochem 1990; 48: 319
   PubMed Web of Science ®Google Scholar
• Lemieux RU. How water provides the impetus for molecular recognition in aqueous solution. Acc Chem Res 1996; 29: 373–380
   Web of Science ®Google Scholar
• Lippens G, Wieruzeski JM, Talaga P, Bohin JP, Desvaux H. Correlation between the chemical shift values and precise interglycosidic distance measurements in the cyclic glucan of Burkholderia solanacearum. J Am Chem Soc 1996; 118: 7227–7228
   Google Scholar
• Lis H, Sharon N. Lectins: Carbohydrate-Specific Proteins That Mediate Cellular Recognition. Chem Rev 1998; 98: 637–674
   PubMed Web of Science ®Google Scholar
• Loris R, Hamelryck T, Bouckaert J, Wyns L. Legume lectin structure. Biochim Biophys Acta 1998; 1383: 9–36
   PubMed Web of Science ®Google Scholar
• Mari S, Serrano-Gomez D, Cañada J, Corbi A, Jiménez-Barbero J. 1D saturation transfer difference NMR experiments on living cells: the DC-SIGN/oligomannose interaction. Angew Chem Int Ed. 2005; 44: 296–298
   Web of Science ®Google Scholar
• Martin-Pastor M, Canales A, Corzana F, Asensio JL, Jiménez-Barbero J. Limited flexibility of lactose detected from residual dipolar couplings using molecular dynamics simulations and steric alignment methods. J Am Chem Soc 2005; 127: 3589–3595
   PubMedGoogle Scholar
• Massefsky M, Redfield AG. Elimination of multiple-step spin diffusion effects in two-dimensional noe spectroscopy of nucleic-acids. J Magn Reson 1988; 78: 150–155
   Google Scholar
• Mayer M, Meyer B. Characterization of ligand binding by Saturation Transfer Difference NMR spectroscopy. Angew Chem Int Ed 1999; 38: 1784–1788
   PubMed Web of Science ®Google Scholar
• Mayer M, Meyer B. Group epitope mapping by saturation transfer difference NMR to identify segments of a ligand in direct contact with a protein receptor. J Am Chem Soc 2001; 123: 6108–6117
   PubMed Web of Science ®Google Scholar
• Montero E, Querol A, Perez Pons J, Jimenez-Barbero J, Cañada J. Studies on the bound conformation of thiocellobiose bound to Streptomyces Sp. Glucosidase. Febs Lett 1998; 421: 243–248
   PubMedGoogle Scholar
• Moore JM. NMR screening in drug discovery. Curr Opin Biotechnol 1999; 10: 54–58
   PubMedGoogle Scholar
• Neufeld EF. Lysosomal storage diseases. Annu Rev Biochem 1991; 60: 257
   PubMed Web of Science ®Google Scholar
• Neuhaus, D, MP Williamson. 2000. In: The Nuclear Overhauser Effect in Structural Conformational Analysis. New York: John Wiley & Sons.
   Google Scholar
• Notenboom V, Williams SJ, Hoos R, Withers SG, Rose DR. Detailed structural analysis of glycosidase/inhibitor interactions: complexes of Cex from Cellulomonas fimi with xylobiose-derived aza-sugars. Biochemistry. 2000; 39: 11553–11563
   PubMedGoogle Scholar
• Pellecchia M, Sem DS, Wüthrich K. NMR in drug discovery. Nat Rev Drug Discov 2002; 1: 211–219
   PubMed Web of Science ®Google Scholar
• Perez S, Imberty A, Engelsen SB, Gruza J, Mazeau K, Jimenez-Barbero J, Poveda A, Espinosa JF, van Eick JBP, Johnson G, French AD, Kouwijzer MLCE, Grootenhuis PDJ, Bernardi A, Raimondi L, Senderowitz H, Durier V, Vergoten G, Rasmussen KJ. A comparison and chemometric analysis of several molecular mechanics force fields and parameter sets applied to carbohydrates. Carbohydr Res 1998; 314: 141–155
   Google Scholar
• Peters T, Pinto BM. Structure and dynamics of oligosaccharides: NMR and modeling studies. Curr Opin Struct Biol 1996; 6: 710–720
   PubMed Web of Science ®Google Scholar
• Poveda A, Asensio JL, Martin-Pastor M, Jiménez-Barbero J. Solution conformation and dynamics of a tetrasaccharide related to the Lewis(x) antigen deduced by NMR relaxation measurements. J Biomol NMR 1997; 10: 29–43
   PubMedGoogle Scholar
• Poveda A, Jiménez-Barbero J. NMR studies of carbohydrate-protein interactions in solution. Chem Soc Rev 1998; 27: 133–143
   Google Scholar
• Rini JM, Lobsanov YD. New animal lectin structures. Curr Opin Struct Biol 1999; 9: 578–584
   PubMed Web of Science ®Google Scholar
• Roy R. Syntheses and some applications of chemically defined multivalent glycoconjugates. Curr Opin Struct Biol. 1996; 6: 692–792
   PubMed Web of Science ®Google Scholar
• Rüdiger H, Siebert HC, Solís D, Jiménez-Barbero J, Romero A, von der Lieth CW, Díaz-Mauriño T, Gabius HJ. Medicinal chemistry based on the sugar code: fundamentals of lectinology and experimental strategies with lectins as targets. Curr Med Chem 2000; 7: 389–416
   PubMed Web of Science ®Google Scholar
• Scherf T, Anglister J. A T1 rho-filtered two-dimensional transferred NOE spectrum for studying antibody interactions with peptide antigens. Biophys J 1993; 64: 754–761
   PubMedGoogle Scholar
• Sujatha MS, Sasidhar YU, Balaji PV. Insights into the role of the aromatic residue in galactose-binding sites: MP2/6-311G + +** study on galactose- and glucose-aromatic residue analogue complexes. Biochemistry 2005; 44: 8554–8562
   PubMedGoogle Scholar
• Thompson GS, Shimizu H, Homans SW, Donohue-Rolfe A. Localization of the binding site for the oligosaccharide moiety of Gb3 on verotoxin 1 using NMR residual dipolar coupling measurements. Biochemistry 2000; 39: 13153–13156
   PubMedGoogle Scholar
• Shidu G, Withers SG, Nguyen NT, McIntosh LP, Ziser L, Brayer GD. Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase. Biochemistry 1999; 38: 5346–5354
   PubMedGoogle Scholar
• Sinnott ML. Catalytic mechanisms of enzymatic glycosyl transfer. Chem Rev 1990; 90: 1171
   Web of Science ®Google Scholar
• Solis D, Jimenez-Barbero J, Kaltner H, Romero A, Siebert HC, von der Lieth CW, Gabius HJ. Towards defining the role of glycans as hardware in information storage and transfer: basic principles, experimental approaches and recent progress. Cells Tissues Organs 2001; 168: 5–23
   PubMedGoogle Scholar
• Solis D, Kogelberg H, Jiménez-Barbero J. New structural insights into carbohydrate-protein interactions from NMR spectroscopy. Curr Opin Struct Biol 2003; 13: 646–653
   PubMedGoogle Scholar
• Stockman BJ, Dalvit C. NMR screening techniques in drug discovery and drug design. Prog Nucl Magn Reson 2002; 41: 187–231
   Web of Science ®Google Scholar
• Toone E. Structure and energetics of protein-carbohydrate complexes. Curr Opin Struct Biol 1994; 4: 719–728
   Web of Science ®Google Scholar
• Tvaroska I, Carver JP. Ab initio molecular orbital calculation of carbohydrate model compounds .5. Anomeric, exo-anomeric, and reverse anomeric effects in C-, N-, and S-glycosyl compounds. J Phys Chem 1996; 100: 11305
   Web of Science ®Google Scholar
• Vincent SFJ, Zwahlen C, Post CB, Burgner JW, Bodenhausen G. The conformation of NAD+ bound to lactate dehydrogenase determined by nuclear magnetic resonance with suppression of spin diffusion. Proc Nat Acad Sci USA 1997; 94: 4383–4388
   PubMedGoogle Scholar
• Lütteke, T, von der Lieth, CW. 2005. GlyVicinity: Analysis of Protein-Carbohydrate interactions contained in the protein data bank. Sixth Carbohydrate Bioengineering meeting (CBM6) held at CosmoCaixa. April, 3–6, Barcelona, P75.
   Google Scholar
• von Itzstein, M, Wu Wy, Kok, GB, Pegg, MS, Dyanson, JC, Jin, BPTV, Smythe, ML, White, HF, Oliver, SW,Colman, PM,Varghese, JN,Ryan, DM, Woods, JM,Bethell, RC,Hotham, VJ,Cameron, JM,Penn, CR. 1993.Rational design of potent sialidase-based inhibitors of influenza virus replication. Nature, 363:1332
   Google Scholar
• Weimar T, Peters T. Aleuria-Aurantia Agglutinin Recognizes Multiple Conformations Of Alpha-L-Fuc-(1-6)-Beta-D-Glcnac-Ome. Angew Chem Int Ed 1994; 33: 88–91
   Google Scholar
• Wormald MR, Petrescu AJ, Pao YL, Glithero A, Elliott T, Dwek RA. Conformational studies of oligosaccharides glycopeptides:complementarity of NMR X-ray crystallography molecular modelling. Chem Rev 2002; 102: 371–386
   PubMed Web of Science ®Google Scholar
• Xantheas SS. On the importance of the fragment relaxation energy terms in the estimation of the basis set superposition error correction to the intermolecular interaction energy. J Chem Phys 1996; 104: 8821–8824
   Web of Science ®Google Scholar
• Zou J, Kleywegt GJ, Stahlberg J, Driguez H, Nerinckx W, Claeyssens M, Koivula A, Teeri TT, Jones TA. Crystallographic evidence for substrate ring distortion and protein conformational changes during catalysis in cellobiohydrolase Ce16A from Trichoderma reesei. Structure Fold Des 1999; 7: 1035
   Google Scholar