Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms

Tyrosine kinases of the Src-family are large allosteric enzymes that play a key role in cellular signaling. Conversion of the kinase from an inactive to an active state is accompanied by substantial structural changes. Here, we construct a coarse-grained model of the catalytic domain incorporating experimental structures for the two stable states, and simulate the dynamics of conformational transitions in kinase activation. We explore the transition energy landscapes by constructing a structural network among clusters of conformations from the simulations. From the structural network, two major ensembles of pathways for the activation are identified. In the first transition pathway, we find a coordinated switching mechanism of interactions among the αC helix, the activation-loop, and the β strands in the N-lobe of the catalytic domain. In a second pathway, the conformational change is coupled to a partial unfolding of the N-lobe region of the catalytic domain. We also characterize the switching mechanism for the αC helix and the activation-loop in detail. Finally, we test the performance of a Markov model and its ability to account for the structural kinetics in the context of Src conformational changes. Taken together, these results provide a broad framework for understanding the main features of the conformational transition taking place upon Src activation.Author Summary: Src tyrosine kinases are large protein molecules that play an important role in the regulation of cellular growth and proliferation. In doing so, Src kinases have the ability to affect the activity of other proteins inside the cell by turning them “on” or “off.” Dysfunctional Src kinase activity has been associated with many human diseases, most importantly cancer, which makes them important targets for therapeutic intervention. To understand how a Src kinase molecule is able to change its shape (conformation) and switch between its active or inactive states, we constructed a computer model. The results from the model provide a broad conceptual framework for interpreting the main features of the change of protein conformation taking place upon Src activation. It is our hope that these results will help design new experiments to refine our understanding of the activation of Src kinases.