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

The persistence of T cell receptor (TCR)-peptide-MHC (pMHC) interactions influences T cell activation, but capturing dissociation-associated structural rearrangements in silico remains challenging. To overcome these limitations, we applied Ligand Binding Parallel Cascade Selection Molecular Dynamics (LB-PaCS-MD), an iterative, force-free path-sampling technique, to explore TCR-pMHC dissociation. LB-PaCS-MD generated diverse and reproducible unbinding trajectories, enabling quantitative analysis of transient contact networks and solvent-accessible surface area fluctuations that underpin transient stabilization during dissociation. The method resolved sequential dissociation events, beginning with α-chain separation followed by β-chain release, and identified CDR3β residue Y103 as a central modulator of transient interaction stability during dissociation. Computational mutagenesis (Y103D, Y103F, Y103L, Y103P, Y103G) further highlighted how side-chain chemistry reshapes dissociation behavior. By directly mapping dissociation pathways without external perturbation, our study demonstrates how LB-PaCS-MD provides an atomistic framework for dissecting transient stabilization in immune recognition and offers a robust platform for guiding antibody and TCR engineering.