Past Event: Oden Institute Seminar

Multiscale approach to the activation/inactivation of Src kinases

Benoit Roux, Professor, Department of Biochemistry & Molecular Biology, University of Chicago

Abstract

Src kinases are highly conserved signaling proteins involved in the regulation of many key processes in the cell and whose catalytic activity can be modulated in response to specific cellular signals. Members of this family share a common multi-domain architecture, which comprises a catalytic tyrosine kinase domain, preceded by two peptide-binding modules, the Src-homology domains SH2 and SH3. Available X-ray structures reveal that, in its down-regulated form, the catalytic domain and the SH2 and SH3 modules interact to adopt an auto-inhibitory assembled conformation. A multitude of factors, modulated by various intra-molecular conformational switches and inter-molecular binding processes, can lead to an increase in catalytic activity. The two most well known factors are the dephosphorylation of the C-terminal Tyr527 and the phosphorylation of Tyr416 near the catalytic site. Comparison with X-ray structures of the catalytic domain in its active state indicates the conformational changes required for enzyme activation. Yet, the available X-ray structures do not explain how this occurs or how it is controlled at the atomic level. The critical role that the Src-family kinases play in the onset of cancer makes them important targets for therapeutic intervention. Knowing the microscopic factors regulating Src will help understand the action of kinase inhibitors. Understanding the regulation of Src kinases is about (1) intramolecular conformational changes, (2) multi-domain reorganization, and (3) association of signal peptides to binding modules. I will describe the results of recent computational studies and experiment designed to probe the conformational flexibility of Src. M.A. Young, S. Gonfloni, G. Superti-Furga, B. Roux and J. Kuriyan, Dynamic Coupling Between the SH2 and SH3 Domains of c-Rc and Hck Underlies Their Inactivation by C-terminal Tyrosine Phosphorylation, Cell 105, 115-126 (2001). H.J. Woo and B. Roux, Calculation of absolute protein-ligand binding free energy from computer simulations, Proc. Nat. Acad. Sci. USA 102, 6825-6830 (2005). N.K. Banavali and B. Roux, 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 (2005). N.K. Banavali and B. Roux, Anatomy of a structural pathway for activation of the catalytic domain of Src kinase Hck. Proteins 67:1096-112 (2007). J. Faraldo-Gomez and B. Roux, On the importance of a funneled energy landscape for the assembly and regulation of multidomain Src tyrosine kinases. Proc. Natl. Acad. Sci. USA. 104:13643-8 (2007). A. C. Pan, D. Sezer and B. Roux, Finding Transition Pathways Using the String Method with Swarms of Trajectories, J. Phys. Chem. B 112, 3432-3440 (2007). N.K. Banavali and B. Roux, Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases, Proteins 74, 378-89 (2009). S. Yang and B. Roux Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms, Plos Comp. 4, e1000047 (2008). A. C. Pan and B. Roux, Building Markov state models along pathways to determine free energies and rates of transitions, J. Chem. Phys. 129, 064107 (2008). W. Gan and B. Roux, Binding Specificity of SH2 Domains: Insight from Free Energy Simulations, Proteins (2008, Epub ahead of print). S. Yang, N.K. Banavali and B. Roux, "Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories", PNAS (2008, in press). *Refreshments served at 3:00.