Regulated unbinding of ZAP70 at the T cell receptor by kinetic avidity

Kutuzov

Bayer

et al. 2020

Preprint

Self Cite

Immune receptor signalling proceeds by the binding of enzymes to their cytoplasmic tails before they catalyse reactions on substrates within reach. Studies of binding and catalysis have led to a binding- induced allosteric activation model for enzymes, such as SHP-1, whose catalytic activity increases upon recruitment to inhibitory receptors, such as PD-1. However, the impact of molecular reach is poorly understood. Here, we use surface plasmon resonance to measure binding, catalysis, and molecular reach for tethered SHP-1 reactions. We find a molecular reach for SHP-1 (13.0 nm) that is smaller than a maximum stretch estimate (20.4 nm) but larger than an estimate from crystal structure of the active conformation (5.3 nm), suggesting that SHP-1 explores a spectrum of active conformations. The molecular reach confines SHP-1 to a small membrane-proximal volume near its substrates leading membrane recruitment to increase its activity by a 1000-fold increase in concentration with a smaller 2-fold activity increase by PD-1 binding-induced allostery. Lastly, we use mathematical modelling to quantify the degree of co-clustering required for PD-1-SHP-1 complexes to reach their substrates.

Section: Discussionmentioning

confidence: 78%

Determination of the molecular reach of the protein tyrosine phosphatase SHP-1

Kutuzov

Bayer

et al. 2020

Preprint

Self Cite

“…We assume that of N = 10 sites, n P are phosphorylated, and n Z are ZAP70-bound. Only phosphorylated sites can be ZAP70-bound, and ZAP70 sites are protected from dephosphorylation (which is a simplification of the tandem ZAP70-ITAM interaction (17)). Therefore, where k K k F k on , and k off are the rate of phosphorylation, dephosphorylation, ZAP70 binding, and ZAP70 unbinding respectively.…”

Section: Resultsmentioning

confidence: 99%

Section: Integrative Model Of Nonlinear Modulesmentioning

confidence: 99%

“…The tyrosines on these tails are organized in pairs called ITAMs (immunoreceptor tyrosine-based activation motifs) and become phosphorylated by a kinase (LCK) upon extracellular ligand binding to the TCR. Phosphorylation of the ITAMs allows a cytosolic signaling molecule, ZAP70, to bind to the phospho-tyrosines (17) and propagate the activation signal (18). Despite lacking structure in the intracellular cytoplasmic tails, the TCR itself endows the signaling pathway with what we term nonlinearities, raising specific questions:…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Intrinsic disorder in the T cell receptor creates cooperativity and controls ZAP70 binding

Dushek

Allard³

2020

Preprint

Self Cite

Many immunoreceptors have cytoplasmic domains that are intrinsically disordered (i.e., have high configurational entropy), have multiple sites of post-translational modification (e.g., tyrosine phosphorylation), and participate in nonlinear signaling pathways (e.g., exhibiting switch-like behavior). Several hypotheses to explain the origin of these nonlinearities fall under the broad hypothesis that modification at one site changes the immunoreceptor's entropy, which in turn changes further modification dynamics. Here we use coarse-grain simulation to study three scenarios, all related to the chains that comprise the T Cell Receptor. We find that, first, if phosphorylation induces local changes in the flexibility of the TCR ζ-chain, this naturally leads to rate enhancements and cooperativity. Second, we find that TCR CD3 can provide a switch by modulating its residence in the plasma membrane. By constraining our model to be consistent with the previous observation that both basic residues and phosphorylation control membrane residence, we find that there is only a moderate rate enhancement of 10% between first and subsequent phosphorylation events. And third, we find that volume constraints do not limit the number of ZAP70s that can bind the TCR, but that entropic penalties lead to a 200-fold decrease in binding rate by the seventh ZAP70, potentially explaining the observation that each TCR has around six ZAP70 molecules bound following receptor triggering. In all three scenarios, our results demonstrate that phenomena that change an immunoreceptor chain's entropy (stiffening, confinement to a membrane, and multiple simultaneous binding) can lead to nonlinearities (rate enhancement, switching, and negative cooperativity) in how the receptor participates in signaling. These polymer-entropy-driven nonlinearities may augment the nonlinearities that arise from, e.g., kinetic proofreading and cluster formation. They also suggest different design strategies for engineered receptors, e.g., whether or not to put signaling modules on one chain or multiple clustered chains. STATEMENT OF SIGNIFICANCEMany of the proteins involved in signal processing are both mechanically flexible and have multiple sites of interaction, leading to a combinatorial complexity making them challenging to study. One example is the T Cell Receptor, a key player in immunological decision making. It consists of 6 flexible chains with 20 interaction sites, and exhibits nonlinear responses to signal inputs, although the mechanisms are elusive. By using polymer physics to simulate the T Cell Receptor's chains, this work demonstrates that several of the nonlinear responses observed experimentally emerge naturally due to constraints on the chains that change their entropy. This work points to new avenues to modulate signaling proteins for therapeutics by modulating their mechanical flexibility and spatial extent.Challenging the tenet that "structure determines function", more than 40% of human proteins contain intrinsically disordered regions longer than...

“…The TCR has eight subunits, six of which contain intrinsically disordered cytoplasmic tails: z (two per TCR), 3 (two per TCR), d, and g. The tyrosines on these tails are organized in pairs called ITAMs (immunoreceptor tyrosine-based activation motifs) and become phosphorylated by a kinase (LCK) upon extracellular ligand binding to the TCR. Phosphorylation of the ITAMs allows a cytosolic signaling molecule, ZAP70, to bind to the phosphotyrosines (17) and propagate the activation signal (18). Despite lacking structure in the intracellular cytoplasmic tails, the TCR itself endows the signaling pathway with what we term nonlinearities, raising specific questions:…”

Section: Introductionmentioning

confidence: 99%

Intrinsic Disorder in the T Cell Receptor Creates Cooperativity and Controls ZAP70 Binding

Dushek

Allard

2021

Biophysical Journal

Self Cite

Many immunoreceptors have cytoplasmic domains that are intrinsically disordered (i.e., have high configurational entropy), have multiple sites of posttranslational modification (e.g., tyrosine phosphorylation), and participate in nonlinear signaling pathways (e.g., exhibiting switch-like behavior). Several hypotheses to explain the origin of these nonlinearities fall under the broad hypothesis that modification at one site changes the immunoreceptor’s entropy, which in turn changes further modification dynamics. Here, we use coarse-grain simulation to study three scenarios, all related to the chains that constitute the T cell receptor (TCR). We find that first, if phosphorylation induces local changes in the flexibility of the TCR ζ -chain, this naturally leads to rate enhancements and cooperativity. Second, we find that TCR CD3 ɛ can provide a switch by modulating its residence in the plasma membrane. By constraining our model to be consistent with the previous observation that both basic residues and phosphorylation control membrane residence, we find that there is only a moderate rate enhancement of 10% between first and subsequent phosphorylation events. Third, we find that volume constraints do not limit the number of ZAP70s that can bind the TCR but that entropic penalties lead to a 200-fold decrease in binding rate by the seventh ZAP70, potentially explaining the observation that each TCR has around six ZAP70 molecules bound after receptor triggering. In all three scenarios, our results demonstrate that phenomena that change an immunoreceptor chain’s entropy (stiffening, confinement to a membrane, and multiple simultaneous binding) can lead to nonlinearities (rate enhancement, switching, and negative cooperativity) in how the receptor participates in signaling. These polymer-entropy-driven nonlinearities may augment the nonlinearities that arise from, e.g., kinetic proofreading and cluster formation. They also suggest different design strategies for engineered receptors, e.g., whether or not to put signaling modules on one chain or multiple clustered chains.