Collective dynamics of large proteins from mixed coarse-grained elastic network model

QSAR and Combinatorial Science

Volumn 24, Issue 4, 2005, Pages 443-448

  Kurkcuoglu, Ozge ^a,b   Jernigan, Robert L ^a,b   Doruker, Pemra ^a,b  

^a BOGAZICI UNIVERSITY   (Turkey)

^b IOWA STATE UNIVERSITY   (United States)

Author keywords

Binding; Collective dynamics; Domain motion; Low resolution models; Triosephosphate isomerase

Indexed keywords

PROTEIN; TRIOSEPHOSPHATE ISOMERASE;

ALGORITHM; COMPLEX FORMATION; CONFERENCE PAPER; CONFORMATIONAL TRANSITION; DRUG DESIGN; MATHEMATICAL ANALYSIS; METHODOLOGY; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SUPRAMOLECULAR CHEMISTRY;

EID: 20544467352     PISSN: 1611020X     EISSN: None     Source Type: Journal    
DOI: 10.1002/qsar.200430922     Document Type: Conference Paper

References (18)

1. J. S. Mincer, S. D. Schwartz, J. Chem. Phys. 2004, 120, 7755-7760.
2. A. McCammon, S. C. Harvey, Dynamics of Proteins and Nucleic Acids, Cambridge University Press, Cambridge, 1987.
3. A. Kitao, N. Go, Curr. Opin. Struct. Biol. 1999, 9, 164-169.
4. H. J. C. Berendsen, S. Hayward, Curr. Opin. Struct. Biol. 2000, 10, 165-169.
5. I. Bahar, A. R, Atilgan, B. Erman, Fold. Des. 1997, 2, 173-181.
6. A. R. Atilgan, S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin, I. Bahar, Biophys. J. 2001, 80, 505-515.
7. I. Bahar, R. L. Jernigan, J. Mol. Biol. 1998, 281, 871-884.
8. B. Isin, P. Doruker, I. Bahar, Biophys. J. 2002, 82, 569-581.
9. Y. Wang, A. J. Rader, I. Bahar, R. L. Jernigan, J. Struct. Biol. 2004, 147, 302-314.
10. O. Kurkcuoglu, R. L. Jernigan, P. Doruker, Polymer 2004, 45, 649-657.
11. J. R. Knowles, Nature 1991, 350, 121-124.
12. Z. Zhang, S Sugio, E. A. Komives, K. D. Liu, J. R. Knowles, G. A. Petsko, D. Ringe, Biochemistry 1994, 33, 2830-2837.
13. R. Desamero, S. Rozovsky, N. Zhadin, A. McDermott, R. Callender, Biochemistry 2003, 42, 2941-2951.
14. J. Xiang, J. Jung, N. S. Sampson, Biochemistry 2004, 43, 11436-11445.
15. V. Guallar, M. Jacobson, A, McDermott, R. A. Friesner, J. Mol. Biol. 2004, 337, 227-239.
16. S. G. Waley, J. C. Miller, I. A. Rose, E. L. O'Connell, Nature 1970, 227, 181.
17. N. S. Sampson, J. R. Knowles, Biochemistry 1992, 31, 8482-8487.
18. T. C. Alber, D. W. Banner, A. C. Bloomer, G. A. Petsko, Sir D. C. Phillips, P. S. River, I. A. Wilson, Phil. Trans. R. Soc. 1981, B293, 159-171.