Depiction of the forces participating in the 2-O-sulfo-α-l-iduronic acid conformational preference in heparin sequences in aqueous solutions

Carbohydrate Research

Volumn 343, Issue 9, 2008, Pages 1435-1445

  Pol Fachin, Laercio ^a   Verli, Hugo ^a  

^a FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

Author keywords

Heparin; IdoA; Iduronic acid; Molecular dynamics; Polysaccharide

Indexed keywords

COMPUTER SIMULATION; CONFORMATIONS; HYDROGEN BONDS; MOLECULAR DYNAMICS; POLYSACCHARIDES;

ANTICOAGULANT; ANTITHROMBOTIC POLYSACCHARIDE; BIOLOGICAL SOLUTIONS;

CARBOXYLIC ACIDS;

2 2 SULFO ALPHA LEVO IDURONIC ACID; HEPARIN; IDURONIC ACID; MONOSACCHARIDE; OLIGOSACCHARIDE; POLYSACCHARIDE; SERINE PROTEINASE;

AQUEOUS SOLUTION; ARTICLE; CRYSTALLOGRAPHY; HYDROGEN BOND; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; X RAY ANALYSIS;

CARBOHYDRATE CONFORMATION; CARBOHYDRATE SEQUENCE; COMPUTER SIMULATION; HEPARIN; IDURONIC ACID; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; POLYSACCHARIDES;

EID: 44249097241     PISSN: 00086215     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.carres.2008.04.016     Document Type: Article

References (39)

1. Nader H.B., Pinhal M.A.S., Baú E.C., Castro R.A.B., Medeiros G.F., Chavante S.F., Leite E.L., Trindade E.S., Shinjo S.K., Rocha H.A., Tersariol I.L.S., Mendes A., and Dietrich C.P. Braz. J. Med. Biol. Res. 34 (2001) 699-709
2. Silva M.E., and Dietrich C.P. J. Biol. Chem. 250 (1975) 6841-6846
3. Gettins P.G.W. Chem. Rev. 102 (2002) 4751-4803
4. Ferro D.R., Provasoli A., Ragazzi M., Torri G., Casu B., Gatti G., Jacquinet J.C., Sinay P., Petitou M., and Choay J. J. Am. Chem. Soc. 108 (1986) 6773-6778
5. Mulloy B., and Forster M. J. Glycobiol. 10 (2000) 1147-1156
6. Casu B., Choay J., Ferro D.R., Gatti G., Jacquinet J.C., Petitou M., Provasoli A., Ragazzi M., Sinay P., and Torri G. Nature 322 (1986) 215-216
7. Hricovíni M. Carbohydr. Res. 341 (2006) 2575-2580
8. Remko M., and von der Lieth C.-W. J. Chem. Inf. Model. 46 (2006) 1194-1200
9. Verli H., and Guimarães J.A. J. Mol. Graph. Model. 24 (2005) 203-212
10. Jin L., Abrahams J.P., Skinner R., Petitou M., Pike R.N., and Carrell R.W. Proc. Natl. Acad. Sci. U.S.A. 94 (1997) 14683-14688
11. van Boeckel C.A.A., Beetz T., and van Aelst S.F. Tetrahedron Lett. 29 (1988) 803-806
12. Canales A., Angulo J., Ojeda R., Bruix M., Fayos R., Lozano R., Giménez-Gallego G., Martín-Lomas M., Nieto P.M., and Jiménez-Barbero J. J. Am. Chem. Soc. 127 (2005) 5578-5779
13. Canales A., Lozano R., López-Méndez B., Angulo J., Ojeda R., Nieto P.M., Martín-Lomas M., Giménez-Gallego G., and Jiménez-Barbero J. FEBS J. 273 (2006) 4716-4727
14. Mulloy B., Forster M.J., Jones C., and Davies D.B. Biochem. J. 293 (1993) 849-858
15. Verli H., and Guimarães J.A. Carbohydr. Res. 339 (2004) 281-290
16. IUPAC-IUB Commission on Biochemical Nomenclature, Pure Appl. Chem. 1996, 68, 1919-2008.
17. Schuettelkopf A.W., and van Aalten D.M.F. Acta Crystallogr., Sect. D 60 (2004) 1355-1363
18. Schaftenaar, G. MOLDEN. CAOS/CAMM Center, University of Nijmegen, Toernooiveld 1, 6525 ED NIJMEGEN, The Netherlands, 1997.
19. van der. Spoel D., Lindahl E., Hess B., Groenhof G., Mark A.E., and Berendsen H.J.C. J. Comput. Chem. 26 (2005) 1701-1718
20. Becker C.F., Guimarães J.A., and Verli H. Carbohydr. Res. 340 (2005) 1499-1507
21. van Boeckel C.A.A., Aelst S.F., Wagenaars G.N., Mellema J.-R., Paulsen H., Peters T., Pollex A., and Sinwell V. Recl. Trav. Chim. Pays-Bas 106 (1987) 19-29
22. de Groot B.L., and Grubmüller H. Science 294 (2001) 2353-2357
23. Hess B., Bekker H., Berendsen H.J.C., and Fraaije J.G.E.M. J. Comput. Chem. 18 (1997) 1463-1472
24. Darden T., York D., and Pedersen L. J. Chem. Phys. 98 (1992) 10089-10092
25. Luzar A., and Chandler D. Nature 379 (1996) 55-57
26. DiGabriele A.D., Lax I., Chen D.I., Svahn C.M., Jaye M., Schlessinger J., and Hendrickson W.A. Nature 393 (1998) 812-817
27. Schlessinger J., Plotnikov A.N., Ibrahimi O.A., Eliseenkova A.V., Yeh B.K., Yayon A., Linhardt R.J., and Mohammadi M. Mol Cell. 6 (2000) 743-750
28. Swaminathan G.J., Myszka D.G., Katsamba P.S., Ohnuki L.E., Gleich G.J., and Acharya K.R. Biochemistry 44 (2005) 14152-14158
29. Capila I., Hernaiz M.J., Mo Y.D., Mealy T.R., Campos B., Dedman J.R., Linhardt R.J., and Seaton B.A. Structure 9 (2001) 57-64
30. Lietha D., Chirgadze D.Y., Mulloy B., Blundell T.L., and Gherardi E. Embo J. 20 (2001) 5543-5555
31. Pellegrini L., Burke D.F., von Delft F., Mulloy B., and Blundell T.L. Nature 407 (2000) 1029-1034
32. Guerrini M., Guglieri S., Beccati D., Torri G., Viskov C., and Mourrier P. Biochem. J. 399 (2006) 191-198
33. Ganesh V.K., Smith S.A., Kotwal G.J., and Murthy K.H.M. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 8924-8929
34. Verli H., and Guimarães J.A. Molecular Modeling in the Assessment of Glycosaminoglycans Structure and Function. In: Verli H. (Ed). Insights into Carbohydrate Structure and Biological Function (2006), Transworld Research Network, Kerala 108
35. Ferro D.R., Provasoli A., Ragazzi M., Casu B., Torri G., Bossennec V., Perly B., Sinay P., Petitou M., and Choay J. Carbohydr. Res. 195 (1990) 157-167
36. Engelsen S.B., Monteiro C., de Penhoat C.H., and Pérez S. Biophys. Chem. 93 (2001) 103-127
37. Ernst S., Venkataraman G., Sasisekharan V., Langer R., Cooney C.L., and Sasisekharan R. J. Am. Chem. Soc. 120 (1997) 2099-2107
38. Angulo J., Nieto P.M., and Martín-Lomas M. Chem. Commun. 13 (2003) 1512-1513
39. Hricovíni M., Scholtzová E., and Bízik F. Carbohydr. Res. 342 (2007) 1350-1356