Binding diversity of the two binding sites of ricin B lectin

Biopolymers

Volumn 83, Issue 1, 2006, Pages 83-94

  Ganguly, Debabani ^a   Mukhopadhyay, Chaitali ^a  

^a UNIVERSITY OF CALCUTTA   (India)

Author keywords

Binding site; Free energy perturbation; Linear interaction energy; MD simulation; Ricin B chain

Indexed keywords

BINDING ENERGY; HYDROGEN BONDS; MOLECULAR STRUCTURE; PERTURBATION TECHNIQUES; POLYSACCHARIDES;

BINDING SITE; FREE ENERGY PERTURBATION; LINEAR INTERACTION ENERGY; MD SIMULATION; RICIN B CHAIN;

PROTEINS;

DISACCHARIDE; LECTIN; MONOSACCHARIDE; RICIN; RICIN B; UNCLASSIFIED DRUG;

ARTICLE; BINDING KINETICS; BINDING SITE; HYDROGEN BOND; LECTIN BINDING; LECTIN BINDING SITE; THERMODYNAMICS;

BINDING SITES; BIOPOLYMERS; DISACCHARIDES; LIGANDS; MODELS, MOLECULAR; MONOSACCHARIDES; RICIN; THERMODYNAMICS;

EID: 33748359338     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.20530     Document Type: Article

References (45)

1. Liang, G.; Schmidt, R. K.; Yu, H. A.; Cumming, D. A.; Brady, J. W. J Phys Chem 1996, 100, 2528-2534.
2. Imberty, A.; Pérez, S. Glycobiology 1994, 4, 351-366.
3. Zacharias, M.; Straatsma, T. P.; McCammon, J. A.; Quiocho, F. A. Biochemistry 1993, 32, 7428-7434.
4. Pathiaseril, A.; Woods, R. J. J Am Chem Soc 2000, 122, 331-338.
5. Ford, M. G.; Weimar, T.; Kohli, T.; Woods, R. J. Proteins Struct Funct Genet 2003, 53, 229-240.
6. Lis, H.; Sharon, N. Curr Opin Struct Biol 1991, 1, 741-749.
7. Hazes, B.; Read, R. J. Biochemistry 1997, 36, 11051-11054.
8. Wales, R.; Roberts, L. M.; Lord, J. M. J Biol Chem 1993, 268, 23986-23990.
9. Nicolson, G. L.; Blaustein, J. Biochim Biophys Acta 1972, 266, 543-547.
10. Rutenber, E.; Robertus, J. D. Proteins Struct Funct Genet 1991, 10, 260-269.
11. Houston, L. L.; Dooley, T. P. J Biol Chem 1982, 257, 4147-4151.
12. Wales, R.; Richardson, P. T.; Roberts, L. M.; Woodland, H. R.; Lord, J. M. J Biol Chem 1991, 266, 19172-19179.
13. Yamasaki, N.; Hatakeyama, T.; Funatsu, G. J Biochem 1985, 98, 1555-1560.
14. Hatakeyama, T.; Yamasaki, N.; Funatsu, G. J Biochem 1986, 100, 781-788.
15. Sujatha, M. S.; Sasidhar, Y. U.; Balaji, P. V. Protein Sci 2004, 13, 2502-2514.
16. Sujatha, M. S.; Sasidhar, Y. U.; Balaji, P. V. Biochemistry 2005, 44, 8554-8562.
17. Beveridge, D. L.; DiCapua, F. M. Ann Rev Biophys Biophys Chem 1989, 18, 431-492.
18. Åqvist, J.; Medina, C.; Samuelsson, J. E. Protein Eng 1994, 7, 385-391.
19. Åqvist, J.; Luzhkov, V. B.; Brandsdal, B. O. Acc Chem Res 2002, 35, 358-365.
20. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J Comput Chem 1983, 4, 187-217.
21. Beck, A. C.; Armen, R. S.; Daggett, V. Biochemistry 2005, 44, 609-616.
22. Stocker, U.; Juchli, D.; van Gunsteren, W. F. Mol Simul 2003, 29, 123-138.
23. Ha, S.; Gao, J.; Tidor, B.; Brady, J. W.; Karplus, M. J Am Chem Soc 1991, 113, 1553-1557.
24. Schmidt, R. K.; Karplus, M.; Brady, J. W. J Am Chem Soc 1996, 118, 541-546.
25. Rao, B. G.; Tilton, R. F.; Singh, U. C. J Am Chem Soc 1992, 114, 4447-4452.
26. Daggett, V.; Brown, F.; Kollman, P. J Am Chem Soc 1989, 111, 8247-8256.
27. Pitera, J. W.; van Gunsteren, W. F. Mol Simul 2002, 28, 45-65.
28. Calson, H. A.; Jorgensen, W. L. J Phys Chem 1995, 99, 10667-10673.
29. Jones-Hertzog, D. K.; Jorgensen, W. L. J Med Chem 1997, 40, 1539-1549.
30. Hansson, T.; Marelius, J.; Aqvist, J. J Comput-Aided Mol Design 1998, 12, 27-35.
31. Huang, D.; Caflisch, A. J Med Chem 2004, 47, 5791-5797.
32. Montfort, W.; Villafranca, J. E.; Monzingo, A. F.; Ernst, S. R.; Katzin, B.; Rutenber, E.; Xuong, N. H.; Hamlin, R.; Robertus, J. D. J Biol Chem 1987, 262, 5398-5403.
33. Miranker, A.; Karplus, M. Proteins 1991, 11, 29-34.
34. Caflisch, A.; Miranker, A.; Karplus, M. J Med Chem 1993, 36, 2142-2167.
35. Bernard, D.; Coop, A.; Mackerell, A. D., Jr. J Med Chem 2005, 48, 7773-7780.
36. Elgavish, S.; Shaanan, B. TIBS 1997, 22, 462-467.
37. Mandal, T. K.; Mukhopadhyay, C. Ind J Biochem Biophys 2001, 38, 96-103.
38. Olsnes, S.; Saltvedt, E.; Pihl, A. J Biol Chem 1974, 249, 803-810.
39. Paulsen, M. D.; Ornstein, R. L. Protein Eng 1996, 9, 567-571.
40. Wang, W.; Wang, J.; Kollman, P. A. Proteins Struct Funct Genet 1999, 34, 395-402.
41. Mandal, T. K.; Mukhopadhyay, C. Protein Eng 2002, 15, 979-986.
42. Wang, J.; Dixon, R.; Kollman, P. A. Proteins Struct Funct Genet 1999, 34, 69-81.
43. Hou, T.; Guo, S.; Xu, X. J Phys Chem B 2002, 106, 5527-5535.
44. Almlöf, M.; Brandsdal, B. O.; Åqvist, J. J Comp Chem 2004, 25, 1242-1254. .
45. Zentz, C.; Frenoy, J. P.; Bourrillon, R. Biochim Biophys Acta 1978, 536, 18-26.