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Network approach of the conformational change of c-Src, a tyrosine kinase, by molecular dynamics simulation

Hyun Jung Yoon1, Sungmin Lee2,3, Sun Joo Park4

  • 1Department of Physics, Pukyong National University, Busan, 48513, Republic of Korea.

Scientific Reports
|April 6, 2018
PubMed

Insights

The study reveals how the inactive c-Src kinase becomes active through conformational changes, highlighting Lys321

Area of Science:

  • Biochemistry and molecular biology
  • Cellular signaling pathways
  • Protein kinase regulation

Background:

  • Non-receptor tyrosine kinase c-Src is crucial for cellular signaling.
  • Activation involves large conformational changes regulated by Tyr416 and Tyr527 phosphorylation.
  • The precise mechanism of c-Src activation remains unclear.

Purpose of the Study:

  • To investigate the inactive-to-active conformational change of c-Src.
  • To elucidate the dynamical mechanism of c-Src activation.
  • To identify key residues involved in the c-Src activation pathway.

Main Methods:

  • Targeted molecular dynamics (TMD) simulations.
  • Network analysis of conformational transition pathways.
  • Analysis of phosphorylation site dynamics (Tyr416 and Tyr527).

Main Results:

  • A dynamical scenario for c-Src activation was proposed.
  • The study identified a detailed conformational transition pathway.
  • Lysine 321 (Lys321) was identified as a key residue in c-Src activation.

Conclusions:

  • The study provides a novel dynamical mechanism for c-Src activation.
  • Lys321 plays a pivotal role in mediating the conformational changes during c-Src activation.
  • Understanding this mechanism can inform therapeutic strategies targeting c-Src signaling.

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