The influence of molecular reach and diffusivity on the efficacy of membrane-confined reactions

Kutuzov

Bayer

et al. 2021

Biophysical Journal

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Immune receptors signal by recruiting (or tethering) enzymes to their cytoplasmic tails to catalyze reactions on substrates within reach. This is the case for the phosphatase SHP-1, which, upon tethering to inhibitory receptors, dephosphorylates diverse substrates to control T cell activation. Precisely how tethering regulates SHP-1 activity is incompletely understood. Here, we measure binding, catalysis, and molecular reach for tethered SHP-1 reactions. We determine the molecular reach of SHP-1 to be 13.0 nm, which is longer than the estimate from the allosterically active structure (5.3 nm), suggesting that SHP-1 can achieve a longer reach by exploring multiple active conformations. Using modeling, we show that when uniformly distributed, receptor-SHP-1 complexes can only reach 15% of substrates, but this increases to 90% when they are coclustered. When within reach, we show that membrane recruitment increases the activity of SHP-1 by a 1000-fold increase in local concentration. The work highlights how molecular reach regulates the activity of membrane-recruited SHP-1 with insights applicable to other membrane-tethered reactions.

Section: Introductionmentioning

confidence: 99%

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

Kutuzov

Bayer

et al. 2021

Biophysical Journal

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“…7). If realized, this would add to a growing body of work demonstrating the importance of the disordered regions of amino acids between catalytically active or posttranslationally modified parts of proteins (10,13).…”

Section: Discussionmentioning

confidence: 97%

“…These regions often include sites for binding and posttranslational modification, suggestions they serve a purpose beyond as passive tethers (3,8,9). Additionally, the length of the domains themselves influences their interactions, affecting binding kinetics and catalytic performance (10)(11)(12)(13).…”

Section: Introductionmentioning

confidence: 99%

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

Dushek

Allard

2021

Biophysical Journal

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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.

“…7). If realized, this would add to a growing body of work demonstrating the importance of the disordered regions of amino acids between catalytically active or post-translationally modified parts of proteins (10, 13).…”

Section: Discussionmentioning

confidence: 99%

“…These regions often include sites for binding and post-translational modification, suggestions they serve a purpose beyond as passive tethers (3, 8, 9). Additionally, the length of the domains themselves influences their interactions, affecting binding kinetics and catalytic performance (10–13).…”

Section: Introductionmentioning

confidence: 99%

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...