Analysis of correlations between energy and residue fluctuations in native proteins and determination of specific sites for binding

Physical Review Letters

Volumn 102, Issue 8, 2009, Pages

  Haliloglu, Turkan ^a   Erman, Burak ^b  

^a BOGAZICI UNIVERSITY   (Turkey)

^b KOÇ UNIVERSITY   (Turkey)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; PROTEINS; STATISTICAL TESTS;

DATA SETS; DRUG BINDINGS; ENERGY FLUCTUATIONS; GAUSSIAN NETWORK MODELS; HIV PROTEASE; NATIVE PROTEINS; SPECIFIC SITES; UNBOUND STATE;

BINDING ENERGY;

EID: 61849151934     PISSN: 00319007     EISSN: 10797114     Source Type: Journal    
DOI: 10.1103/PhysRevLett.102.088103     Document Type: Article

References (23)

1. I. Bahar, A.R. Atilgan, and B. Erman, Folding Des. FODEFH 1359-0278 2, 173 (1997). 10.1016/S1359-0278(97)00024-2
2. T. Haliloglu, I. Bahar, and B. Erman, Phys. Rev. Lett. 79, 3090 (1997). PRLTAO 0031-9007 10.1103/PhysRevLett.79.3090
3. M.M. Tirion, Phys. Rev. Lett. 77, 1905 (1996). PRLTAO 0031-9007 10.1103/PhysRevLett.77.1905
4. Q. Cui and I. Bahar, Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems (Chapman and Hall, London, 2006).
5. I. Bahar, Phys. Rev. Lett. 80, 2733 (1998). PRLTAO 0031-9007 10.1103/PhysRevLett.80.2733
6. M.C. Demirel, Protein Sci. 7, 2522 (1998). PRCIEI 0961-8368 10.1002/pro.5560071205
7. A.T.R. Laurie and R.M. Jackson, Bioinformatics BOINFP 1367-4803 21, 1908 (2005). 10.1093/bioinformatics/bti315
8. See EPAPS Document No. E-PRLTAO-102-069910 for (1)fluctuations of residues in the fastest mode versus drug binding sites, (2)the statistical thermodynamics equations of fluctuations, and (3)fluctuations of DHFR. For more information on EPAPS, see http://www.aip.org/pubservs/epaps.html.
9. I.T. Weber and R.W. Harrison, Protein Eng. 12, 469 (1999). PRENE9 0269-2139 10.1093/protein/12.6.469
10. W.L. DeLano, The PyMOL Molecular Graphics System (2002), http://www.pymol.org
11. A. Wlodawer and J. Erickson, Annu. Rev. Biochem. 62, 543 (1993). ARBOAW 0066-4154 10.1146/annurev.bi.62.070193.002551
12. K.C. Chou, Anal. Biochem. 233, 1 (1996). ANBCA2 0003-2697 10.1006/abio.1996.0001
13. L.E. Henderson, J. Virol. 62, 2587 (1998). JOVIAM 1070-6321
14. L.H. Pearl and W.R. Taylor, Nature (London) 329, 351 (1987). NATUAS 0028-0836 10.1038/329351a0
15. I.T. Weber, J. Biol. Chem. 265, 10492 (1990). JBCHA3 0021-9258
16. J.M. Louis, J. Biol. Chem. 278, 6085 (2003). JBCHA3 0021-9258 10.1074/jbc.M209726200
17. J.M. Louis, Biochem. Biophys. Res. Commun. BBRCA9 0006-291X 164, 30 (1989). 10.1016/0006-291X(89)91678-1
18. T. Blundell and L.H. Pearl, Nature (London) 337, 596 (1989). NATUAS 0028-0836 10.1038/337596a0
19. W. Wei Wang and P.A. Kollman, Proc. Natl. Acad. Sci. U.S.A. 98, 14937 (2001). PNASA6 0027-8424 10.1073/pnas.251265598
20. http://www.ebi.ac.uk/pdbsum/.
21. F. Wong, T. Selzer, and S.J. Benkovic, Proc. Natl. Acad. Sci. U.S.A. 102, 6807 (2005). PNASA6 0027-8424 10.1073/pnas.0408343102
22. T. Haliloglu, E. Seyrek, and B. Erman, Phys. Rev. Lett. 100, 228102 (2008). PRLTAO 0031-9007 10.1103/PhysRevLett.100.228102
23. A. Ertekin, R. Nussinov, and T. Haliloglu, Protein Sci. 15, 2265 (2006). PRCIEI 0961-8368 10.1110/ps.051815006