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LB-PaCS-MD Guided Simulations Reveal Transient Stabilization during TCR-pMHC Dissociation.

Kun Karnchanapandh1, Phichayut Songpipat2, Chonnikan Hanpaibool3

  • 1Program in Bioinformatics and Computational Biology, College of Interdisciplinary and Integrative Studies, Chulalongkorn University, Bangkok 10330, Thailand.

Journal of Chemical Information and Modeling
|June 15, 2026
PubMed
Summary
This summary is machine-generated.

This study introduces Ligand Binding Parallel Cascade Selection Molecular Dynamics (LB-PaCS-MD) to simulate T cell receptor (TCR)-peptide-MHC (pMHC) dissociation. The method reveals key structural events and identifies a critical residue (Y103) influencing interaction stability.

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Area of Science:

  • Immunology
  • Computational Biology
  • Structural Biology

Background:

  • T cell receptor (TCR)-peptide-MHC (pMHC) interactions are crucial for T cell activation.
  • Simulating dissociation-associated structural rearrangements of TCR-pMHC complexes in silico presents significant challenges.

Purpose of the Study:

  • To develop and apply a novel computational method for exploring TCR-pMHC dissociation pathways.
  • To quantitatively analyze the structural dynamics and transient stabilization mechanisms during TCR-pMHC dissociation.

Main Methods:

  • Application of Ligand Binding Parallel Cascade Selection Molecular Dynamics (LB-PaCS-MD), an iterative, force-free path-sampling technique.
  • Generation of diverse and reproducible unbinding trajectories for TCR-pMHC complexes.
  • Computational mutagenesis to investigate the role of specific residues in dissociation dynamics.

Main Results:

  • LB-PaCS-MD successfully generated TCR-pMHC dissociation trajectories, allowing analysis of contact networks and solvent-accessible surface area.
  • Sequential dissociation events were resolved, starting with the alpha-chain and followed by the beta-chain.
  • The CDR3β residue Y103 was identified as a key modulator of transient interaction stability, with mutations altering dissociation behavior.

Conclusions:

  • LB-PaCS-MD provides an atomistic framework for dissecting transient stabilization in immune recognition without external perturbations.
  • The findings offer insights into the structural basis of TCR-pMHC interactions and dissociation.
  • This method serves as a robust platform for guiding the engineering of antibodies and TCRs for therapeutic applications.