Biology subjects

Weikl, T. R.

Publications and source records attributed to Weikl, T. R..

10 recordsLinked to original sources

bioRxiv2026

Membrane-mediated cooperativity of antigen receptors and CD2 adhesion receptors in CAR-T cell activation

Chimeric antigen receptor (CAR)-T cells exhibit a major defect in antigen recognition, often requiring 100-1000-fold higher antigen densities for activation than the native T cell receptor (TCR). Recent work has traced this defect to the inefficient use of CD2/CD58 adhesion by CAR-T cells and demonstrated that matching the extracellular dimensions of CD2/CD58 and CAR/antigen complexes can dramatically enhance antigen sensitivity. Remarkably, modest nanometre-scale changes in CD2/CD58 dimensions produce orders-of-magnitude changes in antigen sensitivity, while having little effect on T cell activation at high antigen densities. Here, we present a general model for the length-dependent cooperativity of antigen receptors and CD2 adhesion receptors in CAR-T cell activation, combining statistical-physical theory with coarse-grained simulations. The model predicts that the antigen concentration required for activation increases sharply with the length mismatch between antigen-receptor and adhesion-receptor complexes until a critical mismatch is reached, at which the complexes segregate. Beyond this critical mismatch when complexes segregate, antigen sensitivity becomes largely independent of complex length, consistent with experimental observations. For small to moderate mismatches, the antigen concentration required for activation exhibits a Gaussian dependence on length mismatch with a characteristic width of only a few nanometres, explaining how nanometre-scale changes in CD2 length can alter antigen sensitivity by orders of magnitude. Fitting the model to measurements of CD2-length-dependent CAR-T cell activation further enables estimation of characteristic molecular length scales and concentrations of antigen-receptor and adhesion-receptor complexes. These results provide a quantitative physical framework connecting nanometre-scale organization of the cell-cell interface to CAR-T cell antigen sensitivity and highlight molecular dimensions as a design parameter for T cell-based immunotherapies.

immunology↗

bioRxiv2026

Membrane tubulation by adhesion of spherical nanoparticles

Adhesion of spherical nanoparticles or virus-like particles to membranes can lead to membrane tubules in which linear chains of adhering particles are cooperatively wrapped by the membrane. This cooperative wrapping of spherical particles in tubules is energetically favourable compared to the individual wrapping of the particles because of a favourable interplay of bending and adhesion energies in the contact regions in which the membrane detaches from the particles, and because a particle in a tubule has two such contact regions in the membrane necks that connect the particle to the neighbouring particles, whereas an individually wrapped particle has only one contact region to the surrounding membrane. The energetic gain of cooperative wrapping strongly depends on the range of the particle-membrane adhesion potential, which determines the size of the contact regions. At sufficiently large adhesion energies for wrapping, the energy gain {Delta}E per particle is only weakly affected by the membrane tension{tau} as long as the characteristic length [Formula] of the membranes with bending rigidity{kappa} is clearly larger than the contact regions. For large particle adhesion energies at which the particles are fully wrapped, however, {Delta}E can be limited by the minimum possible radius of the membrane necks, depending on the adhesion potential range.

biophysics↗

bioRxiv2026

Conformational dynamics of plasmepsin X during inhibitor binding

The aspartic protease plasmepsin X (PMX) of the parasite Plasmodium is a promising drug target for novel malaria therapies. Two potent inhibitors of PMX are WM382 and WM4, which both include a guanidinium group that is in contact with the two catalytic aspartates of PMX in the bound complexes. In structural representations of the inhibitors, the guanidinium group is typically depicted as uncharged. However, pKa predictions with standard tools presented in this article indicate that the guanidinium groups of WM382 and WM4 are protonated and, thus, positively charged in the bound complexes. This positive charge is counterbalanced by a negatively charged catalytic aspartate D266 in PMX of Plasmodium falciparum, while the second catalytic aspartate D457 is uncharged. To investigate the interplay of the conformational dynamics of PMX and inhibitor (un)binding, we performed Hamiltonian replica exchange molecular dynamics (H-REMD) simulations starting from the predicted protonation state of the PMX-WM382 complex. On eight unbinding pathways enabled by weakened interactions of PMX and WM382 in the H-REMD simulations, we observed a dominant route of exit of the inhibitor from the binding pocket with a coupling to conformational changes in the "flap" of PMX, a {beta}-hairpin located above the binding pocket. In the bound complex, the flap adopts a closed conformation in which it tightly interacts with and covers the inhibitor. On the dominant route observed in our simulations, unbinding involves an open conformation of the flap that allows the inhibitor to exit the binding pocket. After unbinding, the flap adopts an occluded conformation in which the binding site is blocked by a bulky aromatic sidechain.

biophysics↗

bioRxiv2025

The allosteric mechanism of G-protein-coupled receptors is induced fit, not conformational selection

The allosteric mechanism of G-protein-coupled receptors (GPCRs) involves a population shift from inactive to active receptor conformations in response to the binding of ligand agonists. Two possible kinetic mechanisms for this population shift are induced fit and conformational selection. The two mechanisms differ in the temporal sequence of binding events and conformational changes: Ligand bindings occurs prior to the change from the inactive to the active receptor conformation in the induced-fit mechanism, and after the conformational change in the conformational-selection mechanism. In this article, we discuss the current evidence from experiments that probe the binding kinetics of GPCRs to identify the allosteric mechanism. For the peptide-activated neurotensin receptor 1, the modeling of kinetic data from stopped-flow mixing experiments indicates an induced-fit mechanism 1. The conformational exchange rates of the induced-fit mechanism obtained from this modeling agree with rates measured by saturation transfer difference NMR experiments of the peptide-receptor complex, which corroborates the mechanism. For the small-molecule-activated {beta}2-andrenergic receptor, an induced-fit mechanism has been inferred from a comparison of ligand-association rates for the inactive and the active receptor conformation 2. A stabilization of the active receptor conformation by G proteins or nanobodies leads to a decrease of ligand association rates, which indicates that ligand binding occurs in the inactive conformation and, thus, prior to the change from the inactive to the active conformation as in the induced-fit mechanism. A structural explanation for the induced-fit mechanism of the {beta}2-andrenergic receptor is a closed lid over the binding site that blocks ligand entry in the active conformation. Since constriction and closing of the ligand-binding site in the active conformation is rather common for small-molecule-activated and peptide-activated GPCRs, induced fit likely is shared as allosteric mechanism by these GPCRs.

biophysics↗

bioRxiv2025

Optimising CAR-T cell sensitivity by engineering matched extracellular sizes between CAR/antigen and CD2/CD58 adhesion complexes

Chimeric antigen receptor (CAR)-T cells exhibit low antigen sensitivity, which restricts their therapeutic efficacy and leads to patient relapses when cancer cells downregulate antigen expression. Despite the pressing need to overcome this limitation, the underlying mechanisms remain poorly understood. Here, we demonstrate that enhancing CAR sensitivity to match the sensitivity of the T-cell receptor (TCR) can be achieved by engineering matched extracellular sizes of CAR/antigen and CD2/CD58 complexes. We find that different CAR/antigen sizes, which are generated by different CAR architectures and different target antigens, require a different CD2/CD58 size to optimise sensitivity. This extracellular size-matching improves antigen engagement and co-localisation of CAR/antigen and CD2/CD58 complexes. We also find that size-matching controls co-inhibition of CARs by PD-1/PD-L1. These findngs highlight the importance of size-matching for signal integration by surface receptors and offers a new approach to tune CAR-T cell sensitivity by matching or mismatching extracellular sizes. One sentence summaryThe antigen sensitivity of CAR-T cells can be tuned to match the sensitivity of TCR-T cells by varying the relative extracellular size of CAR/antigen and CD2/CD58 complexes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/631424v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@17e6a55org.highwire.dtl.DTLVardef@771b38org.highwire.dtl.DTLVardef@19c3544org.highwire.dtl.DTLVardef@6d1fe1_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2024

Conformational changes, excess area, and elasticity of the Piezo protein-membrane nanodome from coarse-grained and atomistic simulations

The mechanosensitive ion channels Piezo 1 and 2 induce a curved protein-membrane nanodome that flattens with increasing membrane tension{gamma} . The tension-induced flattening of the nanodome is associated with Piezo activation and driven by the energy{gamma}{Delta} A where {Delta}A is the excess area of the curved nanodome relative to its planar projected area. Based on extensive coarse-grained and atomistic simulations of membrane-embedded Piezo 1 and 2 proteins, we report here an excess area {Delta}A for the Piezo protein-membrane nanodome of about 40 nm2 in tensionless membranes, and a half-maximal reduction of {Delta}A at tension values of about 3 to 4 mN/m, which is within the range of experimentally determined values for the half-maximal activation of Piezo 1. In line with recent experimental investigations of Piezo proteins in cell membranes and membrane vesicles, the membrane-embedded Piezo proteins adopt conformations in our simulations that are significantly less curved than the protein conformation in the detergent micelles of cryo-EM structures. An elasticity analysis of the nanodome shapes and protein conformations obtained from our simulations leads to an elastic model for Piezo activation that distinguishes the different energy components of the protein and the membrane in the tension-induced flattening of the nanodome.

molecular biology↗

bioRxiv2024

Role of van der Waals, electrostatic, and hydrogen-bond interactions for the relative stability of cellulose Iβ and II crystals

Naturally occuring cellulose I{beta} with its characteristic parallel orientation of cellulose chains is less stable than cellulose II, in which neighbouring pairs of chains are oriented antiparallel to each other. While the distinct hydrogen-bond patterns of these two cellulose crystal forms are well established, the energetic role of the hydrogen bonds for crystal stability, in comparison to the van der Waals and overall electrostatic interactions in the crystals, is a matter of current debate. In this article, we investigate the relative stability of cellulose I{beta} and II in energy minimizations with classical force fields. We find that the larger stability of cellulose II results from clearly stronger electrostatic interchain energies that are only partially compensated by stronger van der Waals interchain energies in cellulose I{beta}. In addition, we show that a multipole description of hydrogen bonds that includes the whole COH groups of donor and acceptor oxygen atoms leads to consistent interchain hydrogen-bond energies that account for roughly 70% and 75% of the interchain electrostatics in cellulose I{beta} and II, respectively.

biophysics↗

bioRxiv2022

Mechanical forces impair antigen discrimination by reducing differences in T cell receptor off-rates

T cells use their T cell receptors (TCRs) to discriminate between lower-affinity self and higher-affinity foreign peptide major-histocompatibility-complexes (pMHCs) based on the TCR/pMHC off-rate. It is now appreciated that T cells generate mechanical forces during this process but how force impacts the TCR/pMHC off-rate remains unclear. Here, we measured the effect of mechanical force on the off-rate of multiple TCR/pMHC interactions. Unexpectedly, we found that lower-affinity pMHCs with faster solution off-rates were more resistant to mechanical force (weak slip or catch bonds) than higher-affinity interactions (strong slip bonds), and this was confirmed by molecular dynamic simulations. Consistent with these findings, we show that the best characterized catch-bond, involving the OT-I TCR, has a low affinity and an exceptionally fast solution off-rate. Our findings imply that reducing forces on the TCR/pMHC interaction improves antigen discrimination and we suggest this new force-shielding role for the adhesion receptors CD2 and LFA-1. One sentence summaryMechanical forces disproportionately accelerate the off-rates of higher-affinity antigens reducing T cell antigen discrimination

immunology↗

bioRxiv2021

Cooperative Stabilization of Close-Contact Zones Leads to Sensitivity and Selectivity in T-Cell Recognition

T cells are sensitive to 1 to 10 foreign-peptide-MHC complexes among a vast majority of self-peptide-MHC complexes, and discriminate selectively between peptide-MHC complexes that differ not much in their binding affinity to T-cell receptors (TCRs). Quantitative models that aim to explain this sensitivity and selectivity largely focus on single TCR/peptide-MHC complexes, but T cell adhesion involves a multitude of different complexes. In this article, we demonstrate in a three-dimensional computational model of T-cell adhesion that the cooperative stabilization of close-contact zones is sensitive to 1 to 3 foreign-peptide-MHC complexes and occurs at a rather sharp threshold affinity of these complexes, which implies selectivity. In these close-contact zones with lateral extensions of hundred to several hundred nanometers, few TCR/foreign-peptide-MHC complexes and many TCR/self-peptide-MHC complexes are segregated from LFA-1/ICAM-1 complexes that form at larger membrane separations. Previous high-resolution microscopy experiments indicate that the sensitivity and selectivity in the formation of closed-contact zones reported here is relevant for T-cell recognition, because the stabilization of close-contact zones by foreign, agonist peptide-MHC complexes precedes T-cell signaling and activation in the experiments.

immunology↗

bioRxiv2021

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

We investigate the structural and orientational variability of the membrane-embedded T cell receptor (TCR) - CD3 complex in extensive atomistic molecular dynamics simulations based on the recent cryo-EM structure determined by Dong et al. (2019). We find that the TCR extracellular (EC) domain is highly variable in its orientation by attaining tilt angles relative to the membrane normal that range from 15{degrees} to 55{degrees}. The tilt angle of the TCR EC domain is both coupled to a rotation of the domain and to characteristic changes throughout the TCR - CD3 complex, in particular in the EC interactions of the C{beta} FG loop of the TCR, as well as in the orientation of transmembrane helices. The concerted motions of the membrane-embedded TCR - CD3 complex revealed in our simulations provide atomistic insights for force-based models of TCR activation, which involve such structural changes in response to tilt-inducing forces on antigen-bound TCRs.

immunology↗