Retardation of the unfolding process by single N-glycosylation of ribonuclease A based on molecular dynamics simulations

Biopolymers

Volumn 89, Issue 2, 2008, Pages 114-123

  Choi, Youngjin ^a   Jong, Hyun Lee ^a   Hwang, Suntae ^b   Kim, Joong Kwon ^c   Jeong, Karpjoo ^a   Jung, Seunho ^a  

^a Konkuk University   (South Korea)

^b Kookmin University   (South Korea)

^c Korea Institute of Science and Technology Information (KISTI)   (South Korea)

Author keywords

Conformational analysis; Denatured conformation; N glycosylation; Nonlocal interaction; Unfolding MD simulations

Indexed keywords

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

CONFORMATIONAL ANALYSIS; DENATURED CONFORMATION; N-GLYCOSYLATION; NONLOCAL INTERACTION;

PROTEIN FOLDING;

RIBONUCLEASE A;

ARTICLE; CONFORMATION; DENATURATION; ENZYME GLYCOSYLATION; MOLECULAR DYNAMICS; PROTEIN INTERACTION; PROTEIN STRUCTURE;

ANIMALS; CATTLE; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; GLYCOSYLATION; HEAT; HYDROGEN BONDING; HYDROGEN-ION CONCENTRATION; MOLECULAR CONFORMATION; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; RIBONUCLEASE, PANCREATIC; SOFTWARE;

BOVINAE;

EID: 38949140514     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.20867     Document Type: Article

References (34)

1. Sinclair, A. M.; Elliott, S. J Pharm Sci 2005, 94, 1626-1635.
2. Wang, C.; Eufemi, M.; Turano, C.; Giartosio, A. Biochemisty 1996, 35, 7299-7307.
3. Parodi, A. J. Annu Rev Biochem 2000, 69, 69-93.
4. Lins, R. D.; Pereira, C. S.; Hunenberger, P. H. Proteins 2004, 55, 177-186.
5. Xie, G.; Timasheff, S. N. Protein Sci 1997, 6, 211-221.
6. Swanwick, R. S.; Daines, A. M.; Tey, L. H.; Flitsch, S. L.; Allemann, R. K. ChemBioChem 2005, 6, 1338-1340.
7. Plummer, T. H.; Tarentino, A.; Maley, F. J Biol Chem 1968, 243, 5158-5164.
8. Williams, R. G.; Greene, S. M.; McPherson, A. J Biol Chem 1987, 262, 16020-16031.
9. Arnold, U.; Schierhorn, A.; Ulbrich-Hofmann, R. Biochemistry 1997, 36, 2166-2172.
10. Arnold, U.; Schierhorn, A.; Ulbrich-Hofmann, R. Eur J Biochem 1999, 259, 470-475.
11. Gotte, G.; Libonati, M.; Laurents, D. V. J Biol Chem 2003, 278, 46241-46251.
12. Merlino, A.; Vitagliano, L.; Ceruso, M. A.; Mazzarella, L. Biophys J 2004, 86, 2383-2391.
13. Gu, W.; Wang, T.; Zhu, J.; Shi, Y.; Liu, H. Biophys Chem 2003, 104, 79-94.
14. Neelan, J. M.; Jackson, S. E. Biophys Chem 2004, 111, 159-171.
15. Day, R.; Bennion, B. J.; Ham, S.; Daggett, V. J Mol Biol 2002, 322, 189-203.
16. Raines, R. T. Chem Rev 1998, 98, 1045-1066.
17. Esposito, L.; Daggett, V. Biochemistry 2005, 44, 3358-3368.
18. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J Comput Chem 1983, 4, 187-217.
19. Berisio, R.; Sica, F.; Lamzin, V. S.; Wilson, K. S.; Zagari, A.; Mazzarella, L. Acta Crystallogr D 2002, 58, 441-450.
20. Naidoo, K. J.; Kuttel, M. J Comput Chem 2001, 22, 445-456.
21. Jorgensen, W. L. J Chem Phys 1983, 79, 926-935.
22. Darden, T.; York, D.; Pedersen, L. J Chem Phys 1993, 98, 10089-10092.
23. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J Comput Phys 1977, 23, 327-341.
24. Feller, S. E.; Zhang, Y.; Pastor, R. W.; Brooks, B. R. J Chem Phys 1995, 103, 4613-4621.
25. Dill, K. A.; Shortle, D. Annu Rev Biochem 1991, 60, 795-825.
26. Phillips, C. M.; Mizutani, Y.; Hochstrasser, R. M. Proc Natl Acad Sci USA 1995, 92, 7292-7296.
27. Sosnick, T. R.; Trewhella, J. Biochemistry 1992, 31, 8329-8335.
28. Miller, W. G.; Goebel, C. V. Biochemistry 1968, 7, 3925-3935.
29. Xu, G.; Narayan, M.; Scheraga, H. A. Biochemistry 2005, 44, 9817-9823.
30. Sherman, E.; Haran, G. Proc Natl Acad Sci USA 2006, 103, 11539-11543.
31. Onufriev, A.; Case, D. A.; Bashford, D. J Mol Biol 2003, 325, 555-567.
32. Yamaguchi, H. Trend Glycosci Glycotechnol 2002, 14, 139-151.
33. Sola, R. J.; Rodriguez-Martinez, J. A.; Griebenow, K. Cell Mol Life Sci 2007, 64, 2133-2152.
34. Broersen, K.; Voragen, A. G.; Hamer, R. J.; De Jongh, H. H. Biotechnol Bioeng 2004, 86, 78-87.