Reuse & Permissions

It is not necessary to obtain permission to reuse this article or its components as it is available under the terms of the Creative Commons Attribution 4.0 International license. This license permits unrestricted use, distribution, and reproduction in any medium, provided attribution to the author(s) and the published article's title, journal citation, and DOI are maintained. Please note that some figures may have been included with permission from other third parties. It is your responsibility to obtain the proper permission from the rights holder directly for these figures.

Export citation

Export citation

Choose format for download:

Download Citation
  • Open Access

Membrane-associated self-assembly for cellular decision-making

Samuel L. Foley* and Margaret E. Johnson†

  • *Contact author: sfoley13@jhu.edu
  • †Contact author: margaret.johnson@jhu.edu

Phys. Rev. Research 8, 023280 – Published 11 June, 2026

DOI: https://doi.org/10.1103/cnfz-qffz

Abstract

Cellular decision-making based on information received from the external environment is frequently initiated by transmembrane receptors. These receptors are known to propagate such information by triggering a series of irreversible, energy-consuming reactions. While this active mechanism ensures switchlike responses, here we show how spontaneous self-assembly of native three-dimensional subunits on a two-dimensional substrate can similarly act as a tunable and robust switch for detecting receptors at physiological concentrations. This mechanism is much more sensitive than other passive mechanisms for receptor detection. We derive analytical expressions for the critical receptor density driving stable subunit assembly, in close agreement with stochastic reaction-diffusion simulations. The theory provides testable predictions for how lipids, subunits, and receptors each can control decision boundaries and magnitude of response.

View figure in article

Physics Subject Headings (PhySH)

Article Text

References (59)

  1. C. Barata-Antunes, R. Alves, G. Talaia, M. Casal, H. Gerós, R. Mans, and S. Paiva, Endocytosis of nutrient transporters in fungi: The art of connecting signaling and trafficking, Comput. Struct. Biotechnol. J. 19, 1713 (2021).
  2. A. Sorkin and C. M. Waters, Endocytosis of growth factor receptors, BioEssays 15, 375 (1993).
  3. C. M. Cadwell, W. Su, and A. P. Kowalczyk, Cadherin tales: Regulation of cadherin function by endocytic membrane trafficking, Traffic 17, 1262 (2016).
  4. D. A. Lauffenburger and J. J. Linderman, Receptors: Models for Binding, Trafficking, and Signaling (Oxford University Press, Oxford, UK, 1996).
  5. J. E. Ferrell and S. H. Ha, Ultrasensitivity. Part III: Cascades, bistable switches, and oscillators, Trends Biochem. Sci. 39, 612 (2014).
  6. G. Tkačik and W. Bialek, Information processing in living systems, Annu. Rev. Condens. Matter Phys. 7, 89 (2016).
  7. P. François and G. Altan-Bonnet, The case for absolute ligand discrimination: Modeling information processing and decision by immune T cells, J. Stat. Phys. 162, 1130 (2016).
  8. G. Tkačik and P. R. ten Wolde, Information processing in biochemical networks, Annu. Rev. Biophys. 54, 249 (2025).
  9. M. Mettlen, P.-H. Chen, S. Srinivasan, G. Danuser, and S. L. Schmid, Regulation of clathrin-mediated endocytosis, Annu. Rev. Biochem. 87, 871 (2018).
  10. S. Mondal, K. Narayan, S. Botterbusch, I. Powers, J. Zheng, H. P. James, R. Jin, and T. Baumgart, Multivalent interactions between molecular components involved in fast endophilin mediated endocytosis drive protein phase separation, Nat. Commun. 13, 5017 (2022).
  11. C. Malinverno, S. Corallino, F. Giavazzi, M. Bergert, Q. Li, M. Leoni, A. Disanza, E. Frittoli, A. Oldani, E. Martini, et al., Endocytic reawakening of motility in jammed epithelia, Nat. Mater. 16, 587 (2017).
  12. S. M. Troyanovsky, Adherens junction: The ensemble of specialized cadherin clusters, Trends Cell Biol. 33, 374 (2023).
  13. D. B. McAffee, M. K. O’Dair, J. J. Lin, S. T. Low-Nam, K. B. Wilhelm, S. Kim, S. Morita, and J. T. Groves, Discrete LAT condensates encode antigen information from single pMHC: TCR binding events, Nat. Commun. 13, 7446 (2022).
  14. A. Jhaveri, S. Loggia, Y. Qian, and M. E. Johnson, Discovering optimal kinetic pathways for self-assembly using automatic differentiation, Proc. Natl. Acad. Sci. USA 121, e2403384121 (2024).
  15. G. Ercolani, Assessment of cooperativity in self-assembly, J. Am. Chem. Soc. 125, 16097 (2003).
  16. A. Zlotnick, To build a virus capsid: An equilibrium model of the self assembly of polyhedral protein complexes, J. Mol. Biol. 241, 59 (1994).
  17. W. M. Jacobs, A. Reinhardt, and D. Frenkel, Rational design of self-assembly pathways for complex multicomponent structures, Proc. Natl. Acad. Sci. USA 112, 6313 (2015).
  18. W. M. Jacobs, Self-assembly of biomolecular condensates with shared components, Phys. Rev. Lett. 126, 258101 (2021).
  19. W. Zhong, D. J. Schwab, and A. Murugan, Associative pattern recognition through macro-molecular self-assembly, J. Stat. Phys. 167, 806 (2017).
  20. C. G. Evans, J. O’Brien, E. Winfree, and A. Murugan, Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly, Nature (London) 625, 500 (2024).
  21. G. Adam and M. Delbrück, Reduction of dimensionality in biological diffusion processes, in Structural Chemistry and Molecular Biology, edited by A. Rich and N. Davidson (Caltech, California, 1968), pp. 198–215.
  22. L. Würthner, F. Brauns, G. Pawlik, J. Halatek, J. Kerssemakers, C. Dekker, and E. Frey, Bridging scales in a multiscale pattern-forming system, Proc. Natl. Acad. Sci. USA 119, e2206888119 (2022).
  23. G.-K. Xu, J. Hu, R. Lipowsky, and T. R. Weikl, Binding constants of membrane-anchored receptors and ligands: A general theory corroborated by Monte Carlo simulations, J. Chem. Phys. 143, 243136 (2015).
  24. O. N. Yogurtcu and M. E. Johnson, Cytosolic proteins can exploit membrane localization to trigger functional assembly, PLoS Comput. Biol. 14, e1006031 (2018).
  25. S.-K. Guo, A. J. Sodt, and M. E. Johnson, Large self-assembled clathrin lattices spontaneously disassemble without sufficient adaptor proteins, PLoS Comput. Biol. 18, e1009969 (2022).
  26. Z. Toprakcioglu, A. Kamada, T. C. Michaels, M. Xie, J. Krausser, J. Wei, A. Saric, M. Vendruscolo, and T. P. Knowles, Adsorption free energy predicts amyloid protein nucleation rates, Proc. Natl. Acad. Sci. USA 119, e2109718119 (2022).
  27. F. Brauns, G. Pawlik, J. Halatek, J. Kerssemakers, E. Frey, and C. Dekker, Bulk-surface coupling identifies the mechanistic connection between Min-protein patterns in vivo and in vitro, Nat. Commun. 12, 3312 (2021).
  28. N. A. Araújo, L. M. Janssen, T. Barois, G. Boffetta, I. Cohen, A. Corbetta, O. Dauchot, M. Dijkstra, W. M. Durham, A. Dussutour, et al., Steering self-organisation through confinement, Soft Matter 19, 1695 (2023).
  29. M. Rouches, S. L. Veatch, and B. B. Machta, Surface densities prewet a near-critical membrane, Proc. Natl. Acad. Sci. USA 118, e2103401118 (2021).
  30. X. Zhao, G. Bartolucci, A. Honigmann, F. Jülicher, and C. A. Weber, Thermodynamics of wetting, prewetting and surface phase transitions with surface binding, New J. Phys. 23, 123003 (2021).
  31. W. D. Kaplan, D. Chatain, P. Wynblatt, and W. C. Carter, A review of wetting versus adsorption, complexions, and related phenomena: The Rosetta stone of wetting, J. Mater. Sci. 48, 5681 (2013).
  32. J. W. Cahn, Critical point wetting, J. Chem. Phys. 66, 3667 (1977).
  33. N. Goldenfeld, Lectures on Phase Transitions and the Renormalization Group (CRC Press, Boca Raton, Florida, USA, 2018).
  34. L. M. Traub, Sorting it out: AP-2 and alternate clathrin adaptors in endocytic cargo selection, J. Cell Biol. 163, 203 (2003).
  35. Y. Wu, J. Vendome, L. Shapiro, A. Ben-Shaul, and B. Honig, Transforming binding affinities from three dimensions to two with application to cadherin clustering, Nature (London) 475, 510 (2011).
  36. M. J. Varga, Y. Fu, S. Loggia, O. N. Yogurtcu, and M. E. Johnson, Nerdss: A nonequilibrium simulator for multibody self-assembly at the cellular scale, Biophys. J. 118, 3026 (2020).
  37. M. Smoluchowski, Mathematical theory of the kinetics of the coagulation of colloidal solutions, Z. Phys. Chem. 19, 129 (1917).
  38. M. E. Johnson and G. Hummer, Free-propagator reweighting integrator for single-particle dynamics in reaction-diffusion models of heterogeneous protein-protein interaction systems, Phys. Rev. X 4, 031037 (2014).
  39. S. L. Foley and M. E. Johnson, GitHub repository of simulation setup scripts, 2026, https://github.com/mjohn218/sensingbyassembly, accessed 21 May 2026.
  40. M. F. Hagan, Modeling viral capsid assembly, in Advances in Chemical Physics, edited by S. A. Rice and A. R. Dinner (John Wiley and Sons, Ltd., 2014), Vol. 155.
  41. S. Sigismund, L. Lanzetti, G. Scita, and P. P. Di Fiore, Endocytosis in the context-dependent regulation of individual and collective cell properties, Nat. Rev. Mol. Cell Biol. 22, 625 (2021).
  42. D. Duan, M. Hanson, D. O. Holland, and M. E. Johnson, Integrating protein copy numbers with interaction networks to quantify stoichiometry in clathrin-mediated endocytosis, Sci. Rep. 12, 5413 (2022).
  43. E. Boucrot, S. Saffarian, R. Massol, T. Kirchhausen, and M. Ehrlich, Role of lipids and actin in the formation of clathrin-coated pits, Exp. Cell Res. 312, 4036 (2006).
  44. B. Pearse and R. Crowther, Structure and assembly of coated vesicles, Annu. Rev. Biophys. Biophys. Chem. 16, 49 (1987).
  45. B. T. Kelly, S. C. Graham, N. Liska, P. N. Dannhauser, S. Höning, E. J. Ungewickell, and D. J. Owen, AP2 controls clathrin polymerization with a membrane-activated switch, Science 345, 459 (2014).
  46. W. F. Zeno, J. B. Hochfelder, A. S. Thatte, L. Wang, A. K. Gadok, C. C. Hayden, E. M. Lafer, and J. C. Stachowiak, Clathrin senses membrane curvature, Biophys. J. 120, 818 (2021).
  47. S. J. Bryant and B. B. Machta, Physical constraints in intracellular signaling: The cost of sending a bit, Phys. Rev. Lett. 131, 068401 (2023).
  48. W. S. Hlavacek, A. Redondo, H. Metzger, C. Wofsy, and B. Goldstein, Kinetic proofreading models for cell signaling predict ways to escape kinetic proofreading, Proc. Natl. Acad. Sci. USA 98, 7295 (2001).
  49. I. Levental and S. L. Veatch, The continuing mystery of lipid rafts, J. Mol. Biol. 428, 4749 (2016).
  50. T. Baumgart, A. T. Hammond, P. Sengupta, S. T. Hess, D. A. Holowka, B. A. Baird, and W. W. Webb, Large-scale fluid/fluid phase separation of proteins and lipids in giant plasma membrane vesicles, Proc. Natl. Acad. Sci. USA 104, 3165 (2007).
  51. F. Frey and U. S. Schwarz, Coat stiffening can explain invagination of clathrin-coated membranes, Phys. Rev. E 110, 064403 (2024).
  52. R. D. Cadena-Nava, M. Comas-Garcia, R. F. Garmann, A. Rao, C. M. Knobler, and W. M. Gelbart, Self-assembly of viral capsid protein and RNA molecules of different sizes: Requirement for a specific high protein/RNA mass ratio, J. Virol. 86, 3318 (2012).
  53. C. Floyd, A. R. Dinner, A. Murugan, and S. Vaikuntanathan, Limits on the computational expressivity of non-equilibrium biophysical processes, Nat. Commun. 16, 7184 (2025).
  54. M. Thomas and R. Schwartz, Quantitative computational models of molecular self-assembly in systems biology, Phys. Biol. 14, 035003 (2017).
  55. X.-S. Wu, B. D. McNeil, J. Xu, J. Fan, L. Xue, E. Melicoff, R. Adachi, L. Bai, and L.-G. Wu, Ca2+ and calmodulin initiate all forms of endocytosis during depolarization at a nerve terminal, Nat. Neurosci. 12, 1003 (2009).
  56. W. Bialek and S. Setayeshgar, Physical limits to biochemical signaling, Proc. Natl. Acad. Sci. USA 102, 10040 (2005).
  57. P. R. ten Wolde, N. B. Becker, T. E. Ouldridge, and A. Mugler, Fundamental limits to cellular sensing, J. Stat. Phys. 162, 1395 (2016).
  58. D. Loerke, M. Mettlen, D. Yarar, K. Jaqaman, H. Jaqaman, G. Danuser, and S. L. Schmid, Cargo and dynamin regulate clathrin-coated pit maturation, PLoS Biol. 7, e1000057 (2009).
  59. B. Mishra and M. E. Johnson, Speed limits of protein assembly with reversible membrane localization, J. Chem. Phys. 154, 194101 (2021).

Outline

Information

Sign In to Your Journals Account

Filter

Filter

Article Lookup

Enter a citation