Elucidating HER2-directed chimeric antigen receptor (CAR) activation mechanism using homology modeling and all-atom molecular dynamics simulation

TL;DR

This study uses simulations to explore how HER2-directed CAR T cells activate, revealing a dynamic switch in domain movements when the receptor binds to its target.

Contribution

The study introduces a new mechanistic hypothesis called BIDDS, explaining how antigen binding alters CAR domain dynamics to facilitate signaling.

Findings

Antigen binding induces a dynamic reversal in extracellular and intracellular domain movements of the CAR.

The BIDDS mechanism may facilitate kinase engagement and signaling motif accessibility.

The findings differ from static models of T cell receptor activation.

Abstract

HER2-directed chimeric antigen receptor (CAR) T cells have demonstrated robust in vivo cytotoxic activity against HER2-positive tumors. However, the structural basis of CAR activation and signal transduction across the membrane remains poorly defined due to the lack of full-length, high-resolution CAR structures. Here, we used homology modeling and all-atom molecular dynamics simulations totaling 37.7 µs to probe the structural dynamics of a full-length anti-HER2 CAR embedded in an explicit POPC membrane, sampling both apo-form and antigen-bound (holo-form) states across three independent trajectories. The simulations reveal coordinated, antigen-dependent changes in the dynamics of the extracellular antigen-binding domain (AB) and the intracellular signaling domain (SI), coupled through the intrinsic disordered regions including hinge, transmembrane, and costimulatory domains (HI–TM–CS). In the apo state, AB exhibits broad extracellular conformational sampling consistent with antigen search, whereas intracellular SI sampling remains comparatively restricted. Upon antigen engagement, this dynamic coupling is altered in a manner reminiscent of an oscillating coupled pendulum, with reduced AB spatial sampling and increased intracellular SI mobility, consistent with a redistribution of domain dynamics that may facilitate accessibility of signaling motifs and downstream kinase engagement, like LCK phosphorylation. We refer to this antigen-dependent reversal in coupled domain dynamics as a Binding-Induced Domain Dynamics Switch (BIDDS). BIDDS differs from static safety on/off models of T cell receptor activation and is presented as a mechanistic hypothesis to guide future computational and experimental studies of CAR activation and related multi-domain receptor signaling, with potential relevance to other receptor tyrosine kinases including VEGFR, EGFR, and FGFR.

The putative early steps of the HER2-CAR activation that is critical in the immune response of the engineered CAR T-cells. The size of arrow suggests the magnitude of domain oscillation.

The putative early steps of the HER2-CAR activation that is critical in the immune response of the engineered CAR T-cells. The size of arrow suggests the magnitude of domain oscillation.

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