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Related Experiment Video

Updated: Mar 29, 2026

Co-immunoprecipitation Assay for Studying Functional Interactions Between Receptors and Enzymes
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Visualizing the Induced Binding of SH2-Phosphopeptide.

T Giorgino1,2, I Buch1, G De Fabritiis1

  • 1Computational Biochemistry and Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra , Barcelona Biomedical Research Park, C/Dr. Aiguader 88, 08003 Barcelona, Spain.

Journal of Chemical Theory and Computation
|November 25, 2015
PubMed
Summary

Understanding how SH2 domains bind phosphopeptides is key. High-throughput simulations reveal a two-phase binding mechanism involving SH2 domain loop stabilization for p56 lck and pYEEI peptide interactions.

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Area of Science:

  • Molecular biology
  • Biochemistry
  • Structural biology

Background:

  • Approximately 100 human proteins possess SH2 domains, crucial for recognizing phosphopeptides.
  • Understanding the atomistic details of phosphopeptide binding to SH2 domains is essential for elucidating signaling pathways.

Purpose of the Study:

  • To investigate the binding mechanism and conformational changes of the p56 lck SH2 domain with the pYEEI phosphopeptide.
  • To provide insights into the binding pathways and induced conformations of SH2-phosphopeptide complexes.

Main Methods:

  • High-throughput molecular dynamics simulations were employed to observe spontaneous binding events.
  • Analysis focused on achieving binding within 2 Å RMSD of crystal structures and matching experimental kinetic rates.

Main Results:

  • Spontaneous binding events between p56 lck SH2 domain and pYEEI peptide were successfully simulated.
  • Binding occurs in two distinct phases: initial phospho-tyrosine contacts followed by ligand rearrangement and SH2 domain loop stabilization.
  • Simulated kinetic rates were compatible with experimental findings.

Conclusions:

  • The study elucidates a two-phase binding mechanism for SH2-phosphopeptide interactions.
  • The findings offer insights into induced conformations and binding pathways relevant to other SH2 domain recognition events.
  • This research contributes to a deeper understanding of molecular recognition in cellular signaling.