Multi-scale simulations of the T cell receptor reveal its lipid interactions, dynamics and the arrangement of its cytoplasmic region

Abstract

The T cell receptor (TCR-CD3) initiates T cell activation by binding to peptides of Major Histocompatibility Complexes (pMHC). The TCR-CD3 topology is well understood but the arrangement and dynamics of its cytoplasmic tails remains unknown, limiting our grasp of the signalling mechanism. Here, we use molecular dynamics simulations and modelling to investigate the entire TCR-CD3 embedded in a model membrane. Our study demonstrates conformational changes in the extracellular and transmembrane domains, and the arrangement of the TCR-CD3 cytoplasmic tails. The cytoplasmic tails formed highly interlaced structures while some tyrosines within the immunoreceptor tyrosine-based activation motifs (ITAMs) penetrated the hydrophobic core of the membrane. Interactions between the cytoplasmic tails and phosphatidylinositol phosphate lipids in the inner membrane leaflet led to the formation of a distinct anionic lipid fingerprint around the TCR-CD3. These results increase our understanding of the TCR-CD3 dynamics and the importance of membrane lipids in regulating T cell activation.

Molecular dynamics simulations reveal membrane lipid interactions of the full-length lymphocyte specific kinase Lck

“…Experimental studies also suggest that the SH2 domain prefers to interact with PIP3 compared to PI(4,5)P2 (Sheng et al, 2016) . Interestingly, these lipid species were found to also cluster around the TCR-CD3 and interact with its cytoplasmic region as observed in our previous studies of the complete TCR-CD3 complex (Prakaash et al, 2021).…”

“…Interestingly, this anionic patch was identified on the opposite side of its PIP lipid binding surface (R39, R45) indicating its availability to bind to cationic residues of other proteins, especially those of the BRS motifs of CD3ε and ζ subunits of the TCR-CD3 complex as suggested by NMR experiments (Li et al, 2017). whereas it is also observed that the TCR-CD3 cytoplasmic tails maintain an anionic lipid environment (Prakaash et al, 2021). This sheds light on the potential significance of lipids during TCR-Lck association.…”

“…Given the potential of strong electrostatic interactions between Lck and PIP lipids, and also between the TCR-CD3 cytoplasmic tails and PIP lipids of the inner leaflet of the membrane (Prakaash et al, 2021) , it is possible that TCR-Lck association and ITAM phosphorylation occurs proximal to the inner leaflet of the plasma membrane.…”

“…Further, the lipid interactions of the kinase domain implies that it is likely to be situated proximal to the membrane surface. Therefore, given that the TCR-CD3 cytoplasmic region is also closely associated with the membrane surface (Prakaash et al, 2021), it is likely that Lck kinase-mediated phosphorylation of TCR-CD3 ITAMs and of other downstream signalling proteins during the initial phase of T cell activation is carried out proximal to the plasma membrane. Similarly, given the conservation of important PIP binding sites in the SH2 and kinase domains, ITAM phosphorylation mediated by other members of the Src family may also occur close to the surface of plasma membrane.…”

“…SH2 domains in other tyrosine kinases such as Zap70 have also been reported to direct signalling pathways by binding to PIP lipids (Park et al, 2016). Our previous studies suggested that the TCR-CD3 maintains an anionic lipid environment enriched in PIP lipids with the help of its cytoplasmic region (Prakaash, Cook, Acuto, & Kalli, 2021). Since Lck is also shown to possess high affinity for PIP lipids (Sheng et al, 2016) and its clustering is driven by their open conformational state (Rossy et al, 2013), it is important to understand how the open and closed states of Lck interact with the membrane in molecular detail.…”