Transition path theory analysis of c-Src kinase activation

Yilin Meng, Diwakar Shukla, Vijay S. Pande, BenoÎt Roux

Research output: Contribution to journalArticle

Abstract

Nonreceptor tyrosine kinases of the Src family are large multidomain allosteric proteins that are crucial to cellular signaling pathways. In a previous study, we generated a Markov state model (MSM) to simulate the activation of c-Src catalytic domain, used as a prototypical tyrosine kinase. The long- Time kinetics of transition predicted by the MSM was in agreement with experimental observations. In the present study, we apply the framework of transition path theory (TPT) to the previously constructed MSM to characterize the main features of the activation pathway. The analysis indicates that the activating transition, in which the activation loop first opens up followed by an inward rotation of the αC-helix, takes place via a dense set of intermediate microstates distributed within a fairly broad "transition tube" in a multidimensional conformational subspace connecting the two end-point conformations. Multiple microstates with negligible equilibrium probabilities carry a large transition flux associated with the activating transition, which explains why extensive conformational sampling is necessary to accurately determine the kinetics of activation. Our results suggest that the combination of MSM with TPT provides an effective framework to represent conformational transitions in complex biomolecular systems.

Original languageEnglish (US)
Pages (from-to)9193-9198
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume113
Issue number33
DOIs
StatePublished - Aug 16 2016

Keywords

  • Conformational transition
  • Markov state models
  • Transition path theory

ASJC Scopus subject areas

  • General

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