Small-Angle X-Ray Scattering and Computational Modeling Reveal the Multi-Domain Assembly States of Hck in Solution

Abstract

The Src tyrosine kinases are large multi-domain enzymes [SH3-SH2-catalytic domain] involved in cellular signaling. Their ability to alternate between catalytically active (high-regulated) and inactive (down-regulated) states in response to specific signals provides a central switching mechanism in cellular transduction pathways. The activity of Src kinases is controlled by the assembly of this multi-domain enzyme. We propose an approach combining small-angle X-ray solution scattering (SAXS) with coarse-grained simulations to characterize quantitatively the multi-domain assembly states of Hck in solution. First, a basis set comprising a small number (∼10) of assembly state “classes” is generated by clustering the configurations obtained from extensive coarse-grained simulations of Hck. Second, the average theoretical SAXS profile for each class of assembly state in the basis set is calculated by using the coarse-grained Fast-SAXS method [Yang et al, Biophys. J. 96:4449 (2009)]. Finally, the relative population of the different classes of assembly states is determined by using a Bayesian-based Monte Carlo procedure seeking to minimize the difference between the theoretical scattering pattern and SAXS data. This novel integrated approach linking experimental SAXS data and simulations is able to resolve the states of assembly of multi-domain Hck in solution under various conditions. The analysis reveals a shift in the equilibrium population of the assembly states upon the binding of various signaling peptides binding to the SH2 or SH3 domains. This integrated approach provides a new way to investigate complex multi-domain assemblies in solution.