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

Abstract

The T cell antigen receptor (TCR-CD3) complex initiates T cell activation following recognition of peptides presented by Major Histocompatibility Complex (pMHC)-encoded proteins. The ligation of pMHC to TCRαβ induces Src family kinases activity via the cytoplasmic tails of the CD3δε, CD3γε and ζζ dimers. The TCR-CD3 topology is well understood, but little is known about its conformational dynamics and arrangement of its cytoplasmic tails, limiting our grasp of the signalling mechanism. Here, we investigated the entire TCR-CD3 embedded in an asymmetric lipid bilayer using molecular modelling and multi-scale molecular dynamics simulations. Our study demonstrates conformational changes in the extracellular and transmembrane domains, and the arrangement of the TCR-CD3 cytoplasmic tails. The TCRαβ variable regions were the most flexible in the extracellular domain. The cytoplasmic tails formed highly interlaced structures while some tyrosine sidechains within the immunoreceptor tyrosine-based activation motifs (ITAMs) of the CD3ε and ζ subunits dynamically penetrated the hydrophobic core of the bilayer. Ionic interactions between the cytoplasmic tails and phosphatidylinositol phosphates (PIP2 and PIP3) in the inner leaflet of the lipid bilayer led to the formation of a distinct annular lipid fingerprint around the TCR-CD3 complex. These results combined with available experiential data increase our understanding of the TCR-CD3 activation mechanism and highlight the importance of membrane lipids in regulating T cell activation.Significance statementThe T cell receptor (TCR-CD3) detects antigenic peptides displayed by major histocompatibility complexes (pMHC) to instigate activation of T cell adaptive immunity. Despite significant structural and functional knowledge of TCR-CD3 topology, the membrane interactions and dynamics of its cytoplasmic moieties remain elusive. Interactions of TCR-CD3 cytoplasmic tails with membrane lipids may regulate their phosphorylation by Src-family kinases, the first intracellular event required for T cell activation. Using the static 3D structure of TCR-CD3 resolved by cryo-electron microscopy, we provide novel insights into the protein-lipid interactions of the complete TCR-CD3 embedded in a bilayer closely mimicking its native membrane environment. Our study sheds light on the dynamics of the TCR-CD3 at near-atomic resolution and further aids in deciphering its activation mechanism.

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 PIP 3 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).…”

“…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.…”

“…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.…”

Structural variability and concerted motions of the T cell receptor – CD3 complex

“…In the absence of transversal forces, the tilt-angle distribution of the TCR-MHC EC domain then can be approximated by the distribution of the TCR EC domain tilt angle observed in our simulations of the TCR -CD3 complex. From the energy contribution − ℎ sin[ ] associated with a transversal force on the TCR-MHC EC complex with extension ℎ ≃ 13 nm (Wang et al, 2009) along the tilt axis and tilt angle in units of rad, the maximum of the tilt-angle distribution can be estimated to be shifted from 34°for zero force to 41°for a transversal force In recent modelling based on the cryo-EM structure of the TCR -CD3 complex, the intracellular signaling domains have been included in coarse-grained simulations of the entire complex with a cumulative simulation time of 25 µs (Prakaash et al, 2021), and the conformations of the TM domain in a complex, asymmetric membrane have been explored in atomistic simulations with a cumulative simulation time of about 4 µs (Lanz et al, 2021). Future atomistic simulations of the TCR -CD3 complex bound to the MHC-peptide EC domain may provide insights on the role of binding-induced conformational changes in TCR activation (Hwang et al, 2020;Ayres et al, 2016).…”

“…How these orientational changes are affected by the membrane composition, and whether they can be related to conformational changes in the largely disordered intracellular signaling domains requires further simulations, likely with atomistic resolution because of limitations in modeling secondary structure propensities and disordered protein segments with coarse-grained force fields ( Monticelli et al, 2008 ; Robustelli et al, 2018 ). In recent modeling based on the cryo-EM structure of the TCR – CD3 complex, the intracellular signaling domains have been included in coarse-grained simulations of the entire complex with a cumulative simulation time of 25 μs ( Prakaash et al, 2021 ), and the conformations of the TM domain in a complex, asymmetric membrane have been explored in atomistic simulations with a cumulative simulation time of about 4 μs ( Lanz et al, 2021 ). Future atomistic simulations of the TCR – CD3 complex bound to the MHC-peptide EC domain may provide insights on the role of binding-induced conformational changes in TCR activation ( Hwang et al, 2020 ; Ayres et al, 2016 ).…”