Atomistic view of the conformational activation of Src kinase using the string method with swarms-of-trajectories

Biophysical Journal

Volumn 97, Issue 4, 2009, Pages L8-

  Gan, Wenxun ^a   Yang, Sichun ^a   Roux, Benoît ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN TYROSINE KINASE; PROTEIN TYROSINE KINASE C SRC; UNCLASSIFIED DRUG; CSK PROTEIN, HUMAN; ONCOPROTEIN;

ALPHA HELIX; ARTICLE; ATOM; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; ENERGY; ENZYME ACTIVE SITE; MOLECULAR DYNAMICS; SIMULATION; BINDING SITE; CATALYSIS; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ENZYME ACTIVATION; LETTER; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE; ULTRASTRUCTURE;

BINDING SITES; CATALYSIS; COMPUTER SIMULATION; ENZYME ACTIVATION; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; PROTEIN-TYROSINE KINASES; PROTO-ONCOGENE PROTEINS;

EID: 69349101321     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.06.016     Document Type: Article

References (18)

1. Bolen, J. B. 1993. Nonreceptor tyrosine protein kinases. Oncogene. 8:2025-2031.
2. Parsons, S. J., and J. T. Parsons. 2004. Src family kinases, key regulators of signal transduction. Oncogene. 23:7906-7909.
3. Xu, W., A. Doshi, M. Lei, M. J. Eck, and S. C. Harrison. 1999. Crystal structures of c-Src reveal features of its autoinhibitory mechanism. Mol. Cell. 3:629-638.
4. Cowan-Jacob, S. W., G. Fendrich, P. W. Manley, W. Jahnke, D. Fabbro, et al. 2005. The crystal structure of a c-Src complex in an active conformation suggests possible steps in c-Src activation. Structure. 13:861-871.
5. Young, M. A., S. Gonfloni, G. Superti-Furga, B. Roux, and J. Kuriyan. 2001. Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation. Cell. 105:115-126.
6. Ozkirimli, E., and C. B. Post. 2006. Src kinase activation: A switched electrostatic network. Protein Sci. 15:1051-1062.
7. Ozkirimli, E., S. S. Yadav, W. T. Miller, and C. B. Post. 2008. An electrostatic network and long-range regulation of Src kinases. Protein Sci. 17:1871-1880.
8. Banavali, N. K., and B. Roux. 2007. Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck. Proteins. 67:1096-1112.
9. Yang, S., and B. Roux. 2008. Src kinase conformational activation: thermodynamics, pathways, and mechanisms. PLoS. Comput. Biol. 4:e1000047.
10. Banavali, N. K., and B. Roux. 2005. The N-terminal end of the catalytic domain of SRC kinase Hck is a conformational switch implicated in long-range allosteric regulation. Structure. 11:1715-1723.
11. Banavali, N. K., and B. Roux. 2008. Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases. Proteins. 74:378-389.
12. Yang, S., N. K. Banavali, and B. Roux. 2009. Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories. Proc. Natl. Acad. Sci. USA. 106:3776-3781.
13. Berteotti, A., A. Cavalli, D. Branduardi, F. L. Gervasio, M. Recanatini, et al. 2009. Protein conformational transitions: the closuremechanism of a kinase explored by atomistic simulations. J. Am. Chem. Soc. 131:244-250.
14. Shan, Y., M. A. Seeliger, M. P. Eastwood, F. Frank, H. Xu, et al. 2009. A conserved protonation-dependent switch controls drug binding in the Abl kinase. Proc. Natl. Acad. Sci. USA. 106:139-144.
15. Pan, A. C., D. Sezer, and B. Roux. 2008. Finding transition pathways using the string method with swarms of trajectories. J. Phys. Chem. B. 112:3432-3440.
16. Ren, W., E. Weinan, and E. Vanden-Eijnden. 2002. String method for the study of rare events. Phys. Rev. B. 66:52301-52304.
17. Maragliano, L., A. Fischer, E. Vanden-Eijnden, and G. Ciccotti. 2006. String method in collective variables: minimum free energy paths and isocommittor surfaces. J. Chem. Phys. 125:24106-24120.
18. Miller, T. F., E. Vanden-Eijnden, and D. Chandler. 2007. Solvent coarsegraining and the string method applied to the hydrophobic collapse of a hydrated chain. Proc. Natl. Acad. Sci. USA. 104:14559-14564.