Extended binding site of ricin B lectin for oligosaccharide recognition

Biopolymers

Volumn 86, Issue 4, 2007, Pages 311-320

  Ganguly, Debabani ^a   Mukhopadhyay, Chaitali ^a  

^a UNIVERSITY OF CALCUTTA   (India)

Author keywords

Binding free energy; MD simulation; MM GB SA; Oligosaccharide; Ricin B chain

Indexed keywords

GALACTOSE; GAS PHASE; PLANT LECTIN RICIN B CHAIN; SOLVATION ENERGIES;

BINDING ENERGY; COMPUTER SIMULATION; CRYSTALLOGRAPHY; LIGANDS; OLIGOSACCHARIDES; PLANTS (BOTANY);

BINDING SITES;

OLIGOSACCHARIDE; RICIN; RICIN B; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; ENTHALPY; ENTROPY;

BINDING SITES; CARBOHYDRATE CONFORMATION; HYDROGEN BONDING; OLIGOSACCHARIDES; PROTEIN BINDING; RICIN; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY; THERMODYNAMICS;

EID: 34447568526     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.20746     Document Type: Article

References (45)

1. Hughes, R. C. In Glycoproteins; Brammar, W. J.; Edidin, M., Eds.; Chapman and Hall: New York, 1983; p 58.
2. Lis, H.; Sharon, N. Chem Rev 1998, 98, 637-674.
3. Garcia-Hernandez, E.; Hernandez-Arana, A. Protein Sci 1999, 8, 1075-1086.
4. Lasky, L. A. Science 1992, 258, 964-969.
5. Sharon, N. Trends Biochem Sci 1993, 18, 221-226.
6. Rini, J. M. Annu Rev Biophys Biomol Struct 1995, 24, 551-577.
7. Weis, W. I.; Drickamer, K. Annu Rev Biochem 1996, 65, 441-473.
8. Sharon, N.; Lis, H. Lectine; Chapman and Hall: London, 1989; p 127.
9. Goldstein, I. J.; Poretz R. D. Lectins: Properties, Functions and Applications in Biology and Medicine; Liener, I. E.; Sharon, N.; Goldstein, I. J. Eds.; Academic Press: Orlando, 1986; p 35.
10. Baxa, U.; Cooper, A.; Weintraub, A.; Pfeil, W; Seckler, R. Biochemistry 2001, 40, 5144-5150.
11. Imberty, A.; Perez, S. Chem Rev 2000, 100, 4567-4588.
12. Toone, E. J. Curr Opin Struct Biol 1994, 4, 719-728.
13. Bundle, D. R.; Young, N. M. Curr Opin Struct Biol 1992, 2, 666-673.
14. Baenziger, J. U.; Fiete, D. J Biol Chem 1979, 254, 9795-9799.
15. Rutenber, E.; Robertus, J. D. Proteins 1991, 10, 260-269.
16. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J Comput Chem 1983, 4, 187-217.
17. Mukhopadhyay, C. Biopolymers 1998, 45, 177-190.
18. Qiu, D.; Shenkin, P. S.; Hollinger, F. P.; Still, W. C. J Phys Chem 1997, 101, 3005-3014.
19. Feig, M.; Onufriev, A.; Lee, M. S.; Im, W.; Case, D. A.; Brooks C. L.,JII.J Comput Chem 2004, 25, 265-284.
20. Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., III. Acc Chem Res 2000, 33, 889-897.
21. Srinivasan, J.; Cheatham, T. E., III; Cieplak, P.; Kollman, P. A; Case, D. A. J Am Chem Soc 1998, 120, 9401-9409.
22. Im, W.; Lee, M. S.; Brooks, C. L., III. J Comput Chem 2003, 24, 1691-1702.
23. Chen, J.; Im, W.; Brooks, C. L., III. J Am Chem Soc 2006, 28, 3728-3736.
24. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J Am Chem Soc 1990, 112, 6127-6129.
25. Dominy, B. N.; Brooks, C. L., III. J Phys Chem B 1999, 103, 3765-3773.
26. Bryce, R. A.; Hiller, I. H.; Naismith, J. H. Biophys J 2001, 81, 1373-1388.
27. Bonnet, P.; Bryce, R. A. Protein Sci 2004, 13, 946-957.
28. Massova, I.; Kollman, P. A. J Am Chem Soc 1999, 121, 8133-8143.
29. Constanciel, R.; Contreras, R. Theo Chim Acta 1984, 65, 1-11.
30. Janežič, D.; Brooks, B. R. J Comput Chem 1995, 16, 1543-1553.
31. McQuarrie, D. A. Statistical Mechanics; Harper Row: New York, 1976.
32. Mandal, T. K.; Mukhopadhyay, C. Biopolymers 2001, 59, 11-23.
33. Balaji, P. V.; Qasba, P. K.; Rao, V. S. R. Biochemistry 1993, 32, 12599-12611.
34. Rutherford, T. J.; Partridge, J.; Weller, C. T.; Homans, S. W. Biochemistry 1993, 32, 12715-12724.
35. Rivera-Sagredo, A.; Solis, D.; Diaz-Maurino, T.; Jimenez-Barbero, J.; Martin-Lomas, M. Eur J Biochem 1991, 197, 217-228.
36. Solis, D.; Fernandez, P.; Diaz-Maurino, T.; Jimenez-Barbero, J.; Martin-Lomas, M. Eur J Biochem 1993, 214, 677-683.
37. Ganguly, D.; Mukhopadhyay, C. Biopolymers 2006, 83, 83-94.
38. Fernandez-Alonso, M. C.; Canada, F. J.; Jimenez-Barbero, J.; Cuevas, G. J Am Chem Soc 2005, 127, 7379-7386.
39. Ford, M. G.; Weimar, T.; Kohli, T.; Woods, R. J. Proteins: Struct Funct Genet 2003, 53, 229-240.
40. Mukhopadhyay C.; Bush, C. A. Biopolymers 1994, 34, 11-20.
41. Houston, L. L.; Dooley, T. P. J Biol Chem 1982, 257, 4147-4151.
42. Zentz, C.; Frenoy, J. P.; Bourrillon, R. Biochim Biophys Acta 1978, 536, 18-26.
43. Steeves, R. M.; Denton, M. E.; Barnard, F. C.; Henry, A.; Lambert, J. M. Biochemistry 1999, 38, 11677-11685.
44. Venkatesh, Y. P.; Bottomley, S.; Lambert, J. M. Lectins: Biology, Biochemistry, Clinical Biochemistry; Van Druessche, E.; Fischer, J.; Boghansen, T. C. Eds.; Textop: Hellerup, Denmark, 1994; Vol. 10, pp 194-202.
45. Brewer, C. F. Chemtracts Biochem Mol Biol 1996, 6, 165.