Ionic peptide aggregation: Exploration of conformational dynamics in aqueous solution by computational techniques

Journal of Physical Chemistry B

Volumn 111, Issue 5, 2007, Pages 1165-1175

  Duce, Celia ^a   Monti, Susanna ^b   Solaro, Roberto ^a   Tiné, Maria Rosaria ^a  

^a UNIVERSITY OF PISA   (Italy)

^b AREA DELLA RICERCA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

AGGLOMERATION; COMPUTATIONAL METHODS; COMPUTER SIMULATION; IONS; MOLECULAR DYNAMICS; SELF ASSEMBLY; SOLUTIONS; SUPRAMOLECULAR CHEMISTRY; WATER;

CONFORMATIONAL DYNAMICS; INTERCHAIN INTERACTIONS; INTERMOLECULAR INTERACTIONS; TERMINAL REGIONS;

POLYPEPTIDES;

EID: 33847012180     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp066307n     Document Type: Article

References (45)

1. Zhang, S.; Holmes, T. A.; Lockshin, C.; Rich, A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 3334-3338.
2. Zhang, S.; Lockshin, C.; Cook, R.; Rich, A. Biopolymers 1994, 34, 663-672.
3. Zhang, S.; Holmes, T. A.; DiPersio, C. M.; Hynes, R. O.; Su, X.; Rich, A. Biomaterials 1995, 16, 1385-1393.
4. Zhang, S.; Rich, A. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 23-28.
5. León, E.; Verma, N.; Zhang, S.; Lauffenburger, D. A.; Kamm, R. M. J. Biomater. Sci., Polym. Ed. 1998, 9, 297-312.
6. Thirumalai, D.; Klimov, D. K.; Dina, R. I. Curr. Opin. Struct. Biol. 2003, 13, 146-159.
7. Caplan, M. R.; Lauffenburger, D. A. Ind. Eng. Chem. Res. 2002, 41, 403-412.
8. Fernandez-López, S.; Kim, H. S.; Choi, E. C.; Delgado, M.; Granja, J. R.; Khasanov, A.; Kraehenbuehl, K.; Long, G.; Weinberger, D. A.; Wilcoxen, K. M.; Ghadiri, M. R. Nature 2001, 412, 452-455.
9. Zhang, S.; Marini, D. M.; Hwang, W.; Santoso, S. Curr. Opin. Chem. Biol. 2002, 6, 865-871.
10. Yokoi, H.; Kinoshita, T.; Zhang, S. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 8414-8419.
11. Nowak, A. P.; Breedveld, V.; Pakstis, L.; Ozbas, B.; Iine, D. J.; Pochan, D.; Deming, T. J. Nature 2002, 417, 424-428.
12. Hartgerink, D. J.; Beniash, E.; Stupp, S. I. Science 2001, 294, 1684-1687.
13. Vanthey, S.; Santos, S.; Gong, H.; Watson, N.; Zhang, S. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 5355-5360.
14. Ellis-Behnke, R. G.; Liang, Y.-X.; You, S.-W.; Tay, D. K. C.; Zhang, S.; So, K.-F. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 5054-5059.
15. Keye-Baig, C.; Fung, J. D. S. Y.; Bezaire, J.; Chen, P. J. Am. Chem. Soc. 2004, 126, 7522-7532.
16. Duce, C. Physical chemical methods in the rational design of new materials: QSAR and calorimetric approaches', Ph.D. thesis: University of Pisa, 2005.
17. Bianucci, A. M.; Massarelli, I.; Chiellini, F.; Eidelman, C.; Chiellini, E. J. Biomater. Sci., Polym. Ed. 2004, 15, 1203-1222.
18. Fung, S. Y.; Keyes, C.; Duhamel, J.; Chen, P. Biophys. J. 2003, 85, 537-548.
19. Hong, Y.; Legge, R.; Zhang, S.; Chen, P. Biomacromolecules 2003, 4, 1433-1442.
20. Jun, S.; Hong, Y.; Imamura, H.; Ha, B.-Y.; Bechhoefer, J.; Chen, P. Biophys. J. 2004, 87, 1249-1259.
21. Hwang, W.; Marini, D. M.; Kamm, R. D.; Zhang, S. J. Chem. Phys. 2003, 118, 389-397.
22. Bitan, G.; Kirkitadze, M. D.; Lomakin, A.; Vollers, S. S.; Benedek, G. B.; Teplow, D. B. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 330-335.
23. Kayed, R.; Head, E.; Thompson, J. L.; McIntire, T. M.; Milton, S. C.; Cotman, C. W.; Glabe, C. G. Proc. Natl. Acad. Sci. U.S.A. 2003, 300, 486-489.
24. Ding, F.; Dokholyan, N. V. Trends Biotechnol. 2005, 23, 450-455.
25. Dokholyan, N. V.; Borreguero, J. M.; Buldyrev, S. V.; Ding, F.; Stanley, H. E.; Shakhnovich, E. I. Methods Enzymol. 2003, 374, 616-638.
26. Dokholyan, N. V.; Buldyrev, S. V.; Stanley, H. E.; Shakhnovich, E. I. Folding Des. 1998, 3, 577-587.
27. Peng, S.; Ding, F.; Urbane, B.; Buldyrev, S. V.; Cruz, L.; Stanley, H. E.; Dokholyan, N. V. Phys. Rev. E 2004, 69, 41908-1914.
28. Urbane, B.; Cruz, L.; Ding, F.; Sammond, D.; Khare, S.; Buldyrev, S. V.; Stanley, H. E.; Dokholyan, N. V. Biophys. J. 2004, 87, 2310-2321.
29. Dokholyan, N. V. Curr. Opin. Struct. Biol. 2006, 16, 79-85.
30. Smith, A. V.; Hall, C. K. Proteins: Struct., Funct., Genet. 2001, 44, 376-391.
31. Case, D. A. et al. AMBER 8; University of California: San Francisco, 2002.
32. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M. J.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
33. Wang, J.; Cieplak, P.; Kollman, P. A. J. Comput. Chem. 2000, 21, 1049-1074.
34. Carravetta, V.; Monti, S. J. Phys. Chem. B 2006, 110, 6160-6169.
35. Polzonetti, G.; Battocchio, C.; Dettin, M.; Gambaretto, R.; Bello, C. D.; Carravetta, V.; Monti, S.; lucci, G. Submitted for publication.
36. Blanco, M. J. Comp. Chem. 1991, 12, 237-247.
37. SYBYL Molecular Modelling Software, Version 7.2; TRIPOS Associates: St. Louis, MO, 2005.
38. Jorgensen, W. L. J. Am. Chem. Soc. 1981, 103, 335-350.
39. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comp. Phys. 1977, 23, 327-341.
40. Jeffrey, G. A.; Saenger, W. Hydrogen Bonding in Biological Structures; Springer-Verlag: Berlin Heidelberg, 1991.
41. Sugita, S.; Okamoto, Y. Biophys. J. 2005, 88, 3180-3190.
42. Lee, B.; Richards, F. M. J. Mol. Biol. 1971, 55, 379-400.
43. Takano, K.; Yamagata, Y.; Yutani, K. Proteins: Struct., Funct., Genet. 2001, 45, 274-280.
44. Takano, K.; Yamagata, Y.; Yutani, K. Proteins 2001, 44, 233-243.
45. Komeiji, Y.; Uebayasi, M.; Someya, J.; Yamato, I. Proteins: Struct., Funct., Genet. 1993, 16, 268-277.