Locking the active conformation of c-Src kinase through the phosphorylation of the activation loop

J Mol Biol. 2014 Jan 23;426(2):423-35. doi: 10.1016/j.jmb.2013.10.001. Epub 2013 Oct 6.

Abstract

Molecular dynamics umbrella sampling simulations are used to compare the relative stability of the active conformation of the catalytic domain of c-Src kinase while the tyrosine 416 in the activation loop (A-loop) is either unphosphorylated or phosphorylated. When the A-loop is unphosphorylated, there is considerable flexibility of the kinase. While the active conformation of the kinase is not forbidden and can be visited transiently, it is not the predominant state. This is consistent with the view that c-Src displays some catalytic activity even when the A-loop is unphosphorylated. In contrast, phosphorylation of the A-loop contributes to stabilize several structural features that are critical for catalysis, such as the hydrophobic regulatory spine, the HRD motif, and the electrostatic switch. In summary, the free-energy landscape calculations demonstrate that phosphorylation of tyrosine 416 in the A-loop essentially "locks" the kinase into its catalytically competent conformation.

Keywords: MD; MFEP; PMF; SFK; SH2; SH3; Src family kinase; Src-homology 2; Src-homology 3; US; activation loop; c-Src kinase; free-energy landscapes; minimum free-energy pathway; molecular dynamics; phosphorylation; potential of mean force; umbrella sampling; wild type; wt.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • CSK Tyrosine-Protein Kinase
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Molecular Sequence Data
  • Phosphorylation
  • Protein Processing, Post-Translational*
  • Tyrosine / metabolism
  • src-Family Kinases / chemistry*
  • src-Family Kinases / metabolism*

Substances

  • Tyrosine
  • CSK Tyrosine-Protein Kinase
  • src-Family Kinases