Csk ?C Helix: A Computational Analysis of an Essential Region for Conformational Transitions

Author(s)

Dias, Raphael Vinicius Rodrigues ; Ferreira, Carolina Tatiani Alves ; Jennings, Patricia Ann ; Whitford, Paul Charles ; de Oliveira, Leandro Cristante

• Document type: Journal article
• Source: Journal of Physical Chemistry B; v. 126, n. 50, p. 10-pg., 2022-12-13.

Abstract

Conformational changes are an essential feature for the function of some dynamic proteins. Understanding the mechanism of such motions may allow us to identify important properties, which may be directly related to the regulatory function of a protein. Also, this knowledge may be employed for a rational design of drugs that can shift the balance between active and inactive conformations, as well as affect the kinetics of the activation process. Here, the conformational changes in carboxyl-terminal Src kinase, the major catalytic repressor to the Src family of kinases, was investigated, and it was proposed as a functionally related hypothesis. A C alpha Structure-Based Model (C alpha-SBM) was applied to provide a description of the overall conformational landscape and further analysis complemented by detailed molecular dynamics simulations. As a first approach to C alpha-SBM simulations, reversible transitions between active (closed) and inactive (open) forms were modeled as fluctuations between these two energetic basins. It was found that, in addition to the interdomain Carboxyl-terminal SRC Kinase (Csk) correlated motions, a conformational change in the alpha C helix is required for a complete conformational transition. The result reveals this as an important region of transition control and domain coordination. Restrictions in the alpha C helix region of the Csk protein were performed, and the analyses showed a direct correlation with the global conformational changes, with this location being propitious for future studies of ligands. Also, the Src Homology 3 (SH3) and SH3 plus Src Homology 2 (SH2) domains were excluded for a direct comparison with experimental results previously published. Simulations where the SH3 was deleted presented a reduction of the transitions during the simulations, while the SH3-SH2 deletion vanishes the Csk transitions, corroborating the experimental results mentioned and linking the conformational changes with the catalytic functionality of Csk. The study was complemented by the introduction of a known kinase inhibitor close to the Csk alpha C helix region where its consequences for the kinetic behavior and domain displacement of Csk were verified through detailed molecular dynamics. The findings describe the mechanisms involving the Csk alpha C helix for the transitions and also support the dynamic correlation between SH3 and SH2 domains against the Csk lobes and how local energetic restrictions or interactions in the Csk alpha C helix can play an important role for long-range motions. The results also allow speculation if the Csk activity is restricted to one specific conformation or a consequence of a state transition, this point being a target for future studies. However, the alpha C helix is revealed as a potential region for rational drug design. (AU)

• FAPESP's process: 16/08753-6 - Evaluating kinase mechanisms and related proteins
• Grantee: Raphael Vinicius Rodrigues Dias
• Support Opportunities: Scholarships in Brazil - Master