Src kinase activation investigated by computational methods
Abstract
The regulatory mechanism of Src tyrosine kinases includes conformational activation by a change in the catalytic domain tertiary structure and in domain-domain contacts. Phosphorylation of Tyr416 on the activation loop and disruption of contacts between the catalytic domain (CD) and the regulatory SH3 and SH2 domains shifts the enzyme population to the activated form. This conformational activation was investigated using non-equilibrium dynamics to investigate the transition pathway between the active and inactive Src CD conformations in the presence or absence of the regulatory domains. Calculations on the isolated CD revealed an electrostatic network of residues that switch between active and inactive conformations, thus guiding the activation transition of the CD. The exchange between interactions couples the three main motions of the CD: rearrangement of the activation loop (A-loop), opening/closing of the two CD lobes and movement of an αhelix (αC). Extension of these calculations to include the regulatory domains showed that this switched electrostatic network, in cooperation with two highly conserved residues at the CD/regulatory domain interface, establish long-range communication between the active site and the regulatory domains. Analysis of the full-length kinase calculations showed that the large-scale motions of the regulatory domains (release from CD contacts) and of the CD (lobe-lobe opening) upon opening are governed by domain-domain contacts. These calculations also give insight into the mechanism of independent regulation by the two regulatory domains.
Degree
Ph.D.
Advisors
Post, Purdue University.
Subject Area
Biochemistry|Biophysics
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