bioRxiv Science⌕ Search

bioRxiv · 10.64898/2026.07.17.739274

Kinetic proofreading decouples signal strength and range in paracrine gradient formation

Abstract

Spatial gradients of signaling molecules pattern multicellular tissues with high precision. The canonical synthesis-diffusion-degradation (SDD) framework imposes a tradeoff on these gradients: ligand-receptor interactions that generate downstream signaling activity are also responsible for consuming the ligand. Correspondingly, at a fixed ligand synthesis rate, raising ligand-receptor affinity increases local signal strength at the expense of spatial range, and lowering it extends range at the expense of strength. Recent live-imaging measurements appear to violate this seemingly fundamental tradeoff, with low-affinity ligands of the epidermal growth factor receptor (EGFR) diffusing farther and driving spatially broader signaling activity compared to high-affinity ligands. Here we explain these observations with a model of multi-step ligand processing at the receptor, and show that the activity-range tradeoff is a consequence of receptor architecture rather than a physical necessity. When receptors process ligand through a multi-step phosphorylation cascade with kinetic-proofreading-like resetting, the states that generate activity decouple from those that consume ligand, and signaling activity and range increase together over a finite window of ligand residence time. This lets cells tune how far a signal travels independently of how strongly it acts through tuning signaling parameters. Realistic EGFR parameters place the low-affinity ligands in this window. Because multi-site phosphorylation and preferential degradation of the active receptor recur across multiple receptor families, kinetic proofreading may be a general strategy for controlling signaling range. Significance StatementCells coordinate by releasing molecules that bind receptors on neighboring cells. For a fixed supply, how strongly a signal acts and how far it spreads are locked together: tight binding gives a strong response but the molecule is captured near its source, while weak binding spreads farther but signals feebly. Yet recent imaging of epidermal growth factor receptor ligands shows the opposite: weak binders activate a broader field of cells. We show this limit reflects how receptors read the signal, not physics. A receptor that processes a bound molecule through several steps, and can release it partway, separates the states that signal from those that destroy it. Cells, and engineers, can then set a signals reach independently of its strength.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Dixit, P. D., Jain, A.. 2026-07-22. Kinetic proofreading decouples signal strength and range in paracrine gradient formation. https://doi.org/10.64898/2026.07.17.739274

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

Scaling of structural variability of ecDNA polymer condensates with copy number boosts and stabilises oncogene regulatory contacts

Extrachromosomal DNAs (ecDNAs) form highly heterogeneous condensates in cancer cells that drive oncogene overexpression, yet how structural variability coexists with stable gene regulation remains unclear. Here, we develop a minimal polymer physics model of MYC-harbouring COLO320-DM ecDNAs, where BRD4-like complexes bind and bridge cognate sites along ecDNA rings. Above a critical binder concentration, ecDNAs phase separate into condensates exhibiting diverse conformations because of their thermodynamic folding degeneracy. Despite this variability, condensates retain conserved interaction scaffolds that give rise to reproducible contact patterns, including in-trans associated domains (I-TADs), genomic regions enriched in intermolecular regulatory contacts between distinct ecDNAs. We find that condensate 3D architecture follows universal scaling relations with ecDNA copy number, n, remaining robust to model parameter changes. Regulatory contacts within I TADs increase linearly with n, yet they are one order of magnitude stronger than in size matched control regions outside I TADs, whereas their relative fluctuations are markedly suppressed as n increases. This scaling produces enhanced, low-noise regulatory environments for oncogenes embedded within I-TADs, such as PVT1-MYC fusions, whereas the canonical MYC copy, located outside, is less amplified as experimentally observed. Our findings reveal universal polymer physics principles underlying ecDNA condensate organization, offering a mechanistic basis for selective oncogene amplification and potential advantages in cancer progression.

biophysics↗

High-resolution mapping of RNA structural maturation during Cas9 assembly with ABEL-FRET

The structural flexibility of RNA is essential for forming ribonucleoprotein (RNP) complexes, which regulate diverse biological processes. This intrinsic property permits RNA to act as a dynamic scaffold along the assembly pathway as it folds into a specific structure for initial recognition by protein and undergoes conformational rearrangements for functional maturation as a complex. Yet, RNA flexibility and RNP multicomponent assembly create significant obstacles for traditional structural methods. To overcome these challenges, we applied recently developed ABEL-FRET spectroscopy to measure tether-free single-molecule Forster resonance energy transfer (smFRET) over extended observation times. Furthermore, ABEL-FRET enables the unique ability for simultaneous measurements of ultrahigh resolution smFRET and hydrodynamic size of individual complexes, which offers distinct advantages for studying dynamic RNA molecules that undergo assembly via sequential binding events. Using ABEL-FRET, we explored how the guide RNA (gRNA) of CRISPR genome editing system folds and modulates its structural flexibility to carry out the roles required for each assembly state from its unbound apo form to the functional Cas9 RNP state for target DNA cleavage. Multi-perspective view of gRNA structure gained by probing its two primary functional domains enabled to capture dramatic changes in gRNA flexibility that are highly dependent on its specific structural domains as well as assembly states. Collectively, our work with ABEL-FRET highlights the intrinsic link between the structural flexibility of RNA and its functionality in RNP assembly.

biophysics↗

De novo design of functional RNAs through higher-order interactions

Designing RNA sequences that reliably adopt functional three-dimensional structures remains a central challenge in RNA engineering because folding depends on cooperative interactions beyond canonical base pairing. Here we present DS3dRNA, an interaction-based framework for de novo RNA sequence design that combines a three-body statistical potential with physics-guided sequence sampling and supports design against multiple conformations. Across the evaluated benchmarks, DS3dRNA outperformed representative RNA inverse-design methods in native-sequence recovery and agreement between predicted and target structures. Energy-sequence-quality analyses further showed that lower design energies generally accompanied higher sequence recovery and macro-averaged F1 scores (MacroF1). Experimentally tested Mango II designs retained high-affinity fluorogenic activity, and five twister ribozyme designs yielded mean endpoint cleavage fractions of 37.7-50.6%, compared with 23.5% for the wild type. These results establish explicit higher-order interaction scoring as a complementary approach to emerging data-driven RNA design methods and provide a framework for designing functional RNAs from experimental or predicted structural ensembles.

biophysics↗