The Activation of c‑Src Tyrosine Kinase: Conformational Transition Pathway and Free Energy Landscape

Tyrosine
kinases are important cellular signaling allosteric enzymes
that regulate cell growth, proliferation, metabolism, differentiation,
and migration. Their activity must be tightly controlled, and malfunction
can lead to a variety of diseases, particularly cancer. The nonreceptor
tyrosine kinase c-Src, a prototypical model system and a representative
member of the Src-family, functions as complex multidomain allosteric
molecular switches comprising SH2 and SH3 domains modulating the activity
of the catalytic domain. The broad picture of self-inhibition of c-Src
via the SH2 and SH3 regulatory domains is well characterized from
a structural point of view, but a detailed molecular mechanism understanding
is nonetheless still lacking. Here, we use advanced computational
methods based on all-atom molecular dynamics simulations with explicit
solvent to advance our understanding of kinase activation. To elucidate
the mechanism of regulation and self-inhibition, we have computed
the pathway and the free energy landscapes for the “inactive-to-active”
conformational transition of c-Src for different configurations of
the SH2 and SH3 domains. Using the isolated c-Src catalytic domain
as a baseline for comparison, it is observed that the SH2 and SH3
domains, depending upon their bound orientation, promote either the
inactive or active state of the catalytic domain. The regulatory structural
information from the SH2–SH3 tandem is allosterically transmitted
via the N-terminal linker of the catalytic domain. Analysis of the
conformational transition pathways also illustrates the importance
of the conserved tryptophan 260 in activating c-Src, and reveals a
series of concerted events during the activation process.