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  • Open Access

Designing complex behaviors using transition-based allosteric self-assembly

Jakob Metson*

  • *Contact author: jakob.metson@ds.mpg.de

Phys. Rev. Research 7, 033044 – Published 10 July, 2025

DOI: https://doi.org/10.1103/hx18-tm3p

Abstract

Allosteric interactions occur when binding at one part of a complex affects the interactions at another part. Allostery offers a high degree of control in multispecies processes, and these interactions play a crucial role in many biological and synthetic contexts. Leveraging allosteric principles in synthetic systems holds great potential for designing materials and systems that can autonomously adapt, reconfigure, or replicate. In this work we establish a basic allosteric model and develop an intuitive design process, which we demonstrate by constructing systems to exhibit four different complex behaviors: controlled fiber growth, shape shifting, sorting, and self-replication. In order to verify that the systems evolve according to the pathways we have developed, we also calculate and measure key length and time scales. Our findings demonstrate that with minimal interaction rules, allosteric systems can be engineered to achieve sophisticated emergent behaviors, opening new avenues for the design of responsive and adaptive materials.

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References (81)

  1. J. Liu and R. Nussinov, Allostery: An overview of its history, concepts, methods, and applications, PLoS Comput. Biol. 12, e1004966 (2016).
  2. N. V. Bhagavan, CHAPTER 7 - Enzymes II: Regulation, in Medical Biochemistry (Fourth Edition), edited by N. V. Bhagavan (Academic Press, San Diego, 2002), pp. 109–119.
  3. Q. Cui and M. Karplus, Allostery and cooperativity revisited, Protein Sci. 17, 1295 (2008).
  4. S. J. Wodak, E. Paci, N. V. Dokholyan, I. N. Berezovsky, A. Horovitz, J. Li, V. J. Hilser, I. Bahar, J. Karanicolas, G. Stock, P. Hamm, R. H. Stote, J. Eberhardt, Y. Chebaro, A. Dejaegere, M. Cecchini, J.-P. Changeux, P. G. Bolhuis, J. Vreede, P. Faccioli et al., Allostery in its many disguises: From theory to applications, Structure 27, 566 (2019).
  5. A. Cooper and D. T. F. Dryden, Allostery without conformational change, Eur. Biophys. J. 11, 103 (1984).
  6. J. Monod, J. Wyman, and J.-P. Changeux, On the nature of allosteric transitions: A plausible model, J. Mol. Biol. 12, 88 (1965).
  7. K. Reiss, V. S. Batista, and J. P. Loria, Allosteric control of enzyme activity: From ancient origins to recent gene-editing technologies, Biochemistry 59, 1711 (2020).
  8. J. P. England, Y. Hao, L. Bai, V. Glick, H. C. Hodges, S. S. Taylor, and R. A. Maillard, Switching of the folding-energy landscape governs the allosteric activation of protein kinase A, Proc. Natl. Acad. Sci. USA 115, E7478 (2018).
  9. L. Kovbasyuk and R. Krämer, Allosteric supramolecular receptors and catalysts, Chem. Rev. 104, 3161 (2004).
  10. D. L. Caspar, Movement and self-control in protein assemblies. Quasi-equivalence revisited, Biophys. J. 32, 103 (1980).
  11. C. Packianathan, S. P. Katen, C. E. Dann, and A. Zlotnick, Conformational changes in the hepatitis b virus core protein are consistent with a role for allostery in virus assembly, J. Virol. 84, 1607 (2010).
  12. I. Dubanevics and T. C. B. McLeish, Computational analysis of dynamic allostery and control in the SARS-CoV-2 main protease, J. R. Soc. Interface. 18, 20200591 (2021).
  13. G. R. Lazaro and M. F. Hagan, Allosteric control of icosahedral capsid assembly, J. Phys. Chem. B 120, 6306 (2016).
  14. S. Hamilton, T. Modi, P. Šulc, and S. B. Ozkan, RNA-induced allosteric coupling drives viral capsid assembly, PRX Life 2, 013012 (2024).
  15. A. Perez-Riba, M. Synakewicz, and L. S. Itzhaki, Folding cooperativity and allosteric function in the tandem-repeat protein class, Philos. Trans. R. Soc. B: Biol. Sci. 373, 20170188 (2018).
  16. Y. Chebaro, I. Amal, N. Rochel, C. Rochette-Egly, R. H. Stote, and A. Dejaegere, Phosphorylation of the retinoic acid receptor alpha induces a mechanical allosteric regulation and changes in internal dynamics, PLoS Comput. Biol. 9, e1003012 (2013).
  17. R. Nussinov, C.-J. Tsai, and J. Liu, Principles of allosteric interactions in cell signaling, J. Am. Chem. Soc. 136, 17692 (2014).
  18. D. Thirumalai and C. Hyeon, Signalling networks and dynamics of allosteric transitions in bacterial chaperonin GroEL: Implications for iterative annealing of misfolded proteins, Philos. Trans. R. Soc. B: Biol. Sci. 373, 20170182 (2018).
  19. R. Nussinov and C.-J. Tsai, Allostery in disease and in drug discovery, Cell 153, 293 (2013).
  20. A. F. Abdel-Magid, Allosteric Modulators: An emerging concept in drug discovery, ACS Med. Chem. Lett. 6, 104 (2015).
  21. M. Cecchini and J.-P. Changeux, The nicotinic acetylcholine receptor and its prokaryotic homologues: Structure, conformational transitions & allosteric modulation, Neuropharmacology, 96, 137 (2015), The nicotinic acetylcholine receptor: From molecular biology to cognition.
  22. N. V. Dokholyan, Controlling allosteric networks in proteins, Chem. Rev. 116, 6463 (2016).
  23. L. Pauling, The oxygen equilibrium of hemoglobin and its structural interpretation, Proc. Natl. Acad. Sci. USA 21, 186 (1935).
  24. J. Monod and F. Jacob, General conclusions: Teleonomic mechanisms in cellular metabolism, growth, and differentiation, Cold Spring Harbor Symp. Quant. Biol. 26, 389 (1961).
  25. M. Takeuchi, M. Ikeda, A. Sugasaki, and S. Shinkai, Molecular design of artificial molecular and ion recognition systems with allosteric guest responses, Acc. Chem. Res. 34, 865 (2001).
  26. C. Kremer and A. Lützen, Artificial allosteric receptors, Chem. A Eur. J. 19, 6162 (2013).
  27. H.-J. Schneider, Efficiency parameters in artificial allosteric systems, Org. Biomol. Chem. 14, 7994 (2016).
  28. J. W. Rocks, N. Pashine, I. Bischofberger, C. P. Goodrich, A. J. Liu, and S. R. Nagel, Designing allostery-inspired response in mechanical networks, Proc. Natl. Acad. Sci. USA 114, 2520 (2017).
  29. H. Flechsig, Design of elastic networks with evolutionary optimized long-range communication as mechanical models of allosteric proteins, Biophys. J. 113, 558 (2017).
  30. J.-H. Ha and S. N. Loh, Construction of allosteric protein switches by alternate frame folding and intermolecular fragment exchange, in Synthetic Protein Switches: Methods and Protocols, edited by V. Stein (Springer, New York, NY, 2017), pp. 27–41.
  31. T. Huang, Z. Zhu, R. Xue, T. Wu, P. Liao, Z. Liu, Y. Xiao, J. Huang, and Y. Yan, Allosteric self-assembly of coordinating terthiophene amphiphile for triggered light harvesting, Langmuir 34, 5935 (2018).
  32. L. A. Campos, R. Sharma, S. Alvira, F. M. Ruiz, B. Ibarra-Molero, M. Sadqi, C. Alfonso, G. Rivas, J. M. Sanchez-Ruiz, A. Romero Garrido, J. M. Valpuesta, and V. Muñoz, Engineering protein assemblies with allosteric control via monomer fold-switching, Nat. Commun. 10, 5703 (2019).
  33. C. Zhang, X. Ma, X. Zheng, Y. Ke, K. Chen, D. Liu, Z. Lu, J. Yang, and H. Yan, Programmable allosteric DNA regulations for molecular networks and nanomachines, Sci. Adv. 8, eabl4589 (2022).
  34. T. Plaper, E. Merljak, T. Fink, T. Satler, A. Ljubetič, D. Lainšček, V. Jazbec, M. Benčina, S. Stevanoska, S. Džeroski, and R. Jerala, Designed allosteric protein logic, Cell Discovery 10, 8 (2024).
  35. Y. Zhang, A. McMullen, L.-L. Pontani, X. He, R. Sha, N. C. Seeman, J. Brujic, and P. M. Chaikin, Sequential self-assembly of DNA functionalized droplets, Nat. Commun. 8, 21 (2017).
  36. J. Evans and P. Šulc, Designing 3D multicomponent self-assembling systems with signal-passing building blocks, J. Chem. Phys. 160, 084902 (2024).
  37. T. D. Nguyen, E. Jankowski, and S. C. Glotzer, Self-assembly and reconfigurability of shape-shifting particles, ACS Nano 5, 8892 (2011).
  38. N. Denkov, S. Tcholakova, I. Lesov, D. Cholakova, and S. K. Smoukov, Self-shaping of oil droplets via the formation of intermediate rotator phases upon cooling, Nature (London) 528, 392 (2015).
  39. S. Osat and R. Golestanian, Non-reciprocal multifarious self-organization, Nat. Nanotechnol. 18, 79 (2023).
  40. J. Metson, S. Osat, and R. Golestanian, Continuous-time multifarious systems – Part II: Non-reciprocal multifarious self-organization, arXiv:2506.07649.
  41. H. Shen, E. M. Lynch, S. Akkineni, J. L. Watson, J. Decarreau, N. P. Bethel, I. Benna, W. Sheffler, D. Farrell, F. DiMaio, E. Derivery, J. J. De Yoreo, J. Kollman, and D. Baker, De novo design of pH-responsive self-assembling helical protein filaments, Nat. Nanotechnol. 19, 1016 (2024).
  42. A. Nagarkar, W.-K. Lee, D. J. Preston, M. P. Nemitz, N.-N. Deng, G. M. Whitesides, and L. Mahadevan, Elastic-instability–enabled locomotion, Proc. Natl. Acad. Sci. USA 118, e2013801118 (2021).
  43. N. Sarraf, K. R. Rodriguez, and L. Qian, Modular reconfiguration of DNA origami assemblies using tile displacement, Sci. Rob. 8, eadf1511 (2023).
  44. A. Z. Barabas, I. Sequeira, Y. Yang, A. H. Barajas-Aguilar, T. Taniguchi, K. Watanabe, and J. D. Sanchez-Yamagishi, Mechanically reconfigurable van der Waals devices via low-friction gold sliding, Sci. Adv. 9, eadf9558 (2023).
  45. C. G. Knott, Life and Scientific Work of Peter Guthrie Tait Supplementing the Two Volumes of Scientific Papers Published in 1898 and 1900 (Cambridge University Press, 1911), pp. 213–215.
  46. The sorting Demon of Maxwell, Nature (London) 20, 126 (1879).
  47. A. J. Thubagere, W. Li, R. F. Johnson, Z. Chen, S. Doroudi, Y. L. Lee, G. Izatt, S. Wittman, N. Srinivas, D. Woods, E. Winfree, and L. Qian, A cargo-sorting DNA robot, Science 357, eaan6558 (2017).
  48. E. S. Andersen, M. Dong, M. M. Nielsen, K. Jahn, R. Subramani, W. Mamdouh, M. M. Golas, B. Sander, H. Stark, C. L. P. Oliveira, J. S. Pedersen, V. Birkedal, F. Besenbacher, K. V. Gothelf, and J. Kjems, Self-assembly of a nanoscale DNA box with a controllable lid, Nature (London) 459, 73 (2009).
  49. X. Chang, Q. Yang, J. Y. Lee, D. Perumal, and F. Zhang, Reconfigurable DNA Nanocage for protein encapsulation and regulation, J. Am. Chem. Soc. 146, 26131 (2024).
  50. L. S. Penrose, Self-Reproducing Machines, Sci. Am. 200, 105 (1959).
  51. J. V. Neumann, Theory of Self-Reproducing Automata, edited by A. W. Burks (University of Illinois Press, USA, 1966).
  52. A. Keenan, R. Schweller, and X. Zhong, Exponential replication of patterns in the signal tile assembly model, in DNA Computing and Molecular Programming, edited by D. Soloveichik and B. Yurke (Springer International Publishing, Cham, 2013), pp. 118–132.
  53. A. Alseth, D. Hader, and M. J. Patitz, Universal shape replication via self-assembly with signal-passing tiles, Nat. Comput. 23, 627 (2024).
  54. R. Lano, Mechanical mechanism for self-replication, Q. Appl. Math. (2025).
  55. Z. Zeravcic and M. P. Brenner, Self-replicating colloidal clusters, Proc. Natl. Acad. Sci. USA 111, 1748 (2014).
  56. R. A. Freitas and R. C. Merkle, Kinematic Self-Replicating Machines (Landes Bioscience, Georgetown, Tex., 2004).
  57. X. He, R. Sha, R. Zhuo, Y. Mi, P. M. Chaikin, and N. C. Seeman, Exponential growth and selection in self-replicating materials from DNA origami rafts, Nat. Mater. 16, 993 (2017).
  58. J. E. Padilla, M. J. Patitz, R. Pena, R. T. Schweller, N. C. Seeman, R. Sheline, S. M. Summers, and X. Zhong, Asynchronous signal passing for tile self-assembly: Fuel efficient computation and efficient assembly of shapes, in Unconventional Computation and Natural Computation, edited by G. Mauri, A. Dennunzio, L. Manzoni, and A. E. Porreca (Springer, Berlin, Heidelberg, 2013), pp. 174–185.
  59. A. A. Cantu, A. Luchsinger, R. Schweller, and T. Wylie, Signal passing self-assembly simulates tile automata, in 31st International Symposium on Algorithms and Computation (ISAAC 2020), Leibniz International Proceedings in Informatics (LIPIcs) (Schloss Dagstuhl – Leibniz-Zentrum für Informatik, 2020), Vol. 181, pp. 531–5317.
  60. E. Winfree, Algorithmic self-assembly of DNA, Ph.D. thesis, California Institute of Technology, 1998.
  61. P. W. K. Rothemund, Theory and experiments in algorithmic self-assembly, Ph.D. thesis, University of Southern California, 2001.
  62. J. I. Lathrop, J. H. Lutz, and S. M. Summers, Strict Self-assembly of Discrete Sierpinski Triangles, in Computation and Logic in the Real World, edited by S. B. Cooper, B. Löwe, and A. Sorbi (Springer, Berlin, Heidelberg, 2007), pp. 455–464.
  63. K. Onan, J. Jr. Rebek, T. Costello, and L. Marshall, Allosteric effects: Structural and thermodynamic origins of binding in cooperativity in a subunit model, J. Am. Chem. Soc. 105, 6759 (1983).
  64. R. J. Hawkins and T. C. B. McLeish, Coupling of global and local vibrational modes in dynamic allostery of proteins, Biophys. J. 91, 2055 (2006).
  65. C.-J. Tsai and R. Nussinov, A unified view of “How allostery works”, PLoS Comput. Biol. 10, e1003394 (2014).
  66. M. V. LeVine and H. Weinstein, AIM for allostery: Using the ising model to understand information processing and transmission in allosteric biomolecular systems, Entropy 17, 2895 (2015).
  67. R. Nussinov and C.-J. Tsai, Allostery without a conformational change? Revisiting the paradigm, Curr. Opin. Struct. Biol. 30, 17 (2015), Folding and binding/nucleic acids and their protein complexes.
  68. T. McLeish, C. Schaefer, and A. C. von der Heydt, The ‘allosteron’ model for entropic allostery of self-assembly, Philos. Trans. R. Soc. B: Biol. Sci. 373, 20170186 (2018).
  69. S. Dutta, J.-P. Eckmann, A. Libchaber, and T. Tlusty, Green function of correlated genes in a minimal mechanical model of protein evolution, Proc. Natl. Acad. Sci. USA 115, 4559 (2018).
  70. M. Vossel, B. L. de Groot, and A. Godec, The allosteric lever: Towards a principle of specific allosteric response, arXiv:2311.12025.
  71. M. Segers, A. Voorspoels, T. Sakaue, and E. Carlon, Mechanisms of DNA-Mediated Allostery, Phys. Rev. Lett. 131, 238402 (2023).
  72. J. E. Padilla, R. Sha, M. Kristiansen, J. Chen, N. Jonoska, and N. C. Seeman, A signal-passing DNA-strand-exchange mechanism for active self-assembly of DNA nanostructures, Angew. Chem. 127, 6037 (2015).
  73. G. Chatterjee, N. Dalchau, R. A. Muscat, A. Phillips, and G. Seelig, A spatially localized architecture for fast and modular DNA computing, Nat. Nanotechnol. 12, 920 (2017).
  74. C. M. Grinstead and J. L. Snell, Grinstead and Snell's Introduction to Probability (American Mathematical Society, Providence, Rhode Island, US, 2006), pp. 416–420.
  75. C. L. Bassani, G. van Anders, U. Banin, D. Baranov, Q. Chen, M. Dijkstra, M. S. Dimitriyev, E. Efrati, J. Faraudo, O. Gang, N. Gaston, R. Golestanian, G. I. Guerrero-Garcia, M. Gruenwald, A. Haji-Akbari, M. Ibáñez, M. Karg, T. Kraus, B. Lee, R. C. Van Lehn et al., Nanocrystal assemblies: Current advances and open problems, ACS Nano 18, 14791 (2024).
  76. S. Osat, J. Metson, M. Kardar, and R. Golestanian, Escaping kinetic traps using nonreciprocal interactions, Phys. Rev. Lett. 133, 028301 (2024).
  77. S. F. Navas and S. H. L. Klapp, Impact of non-reciprocal interactions on colloidal self-assembly with tunable anisotropy, J. Chem. Phys. 161, 054908 (2024).
  78. Q.-Z. Zhu, C. X. Du, E. M. King, and M. P. Brenner, Proofreading mechanism for colloidal self-assembly, Phys. Rev. Res. 6, L042057 (2024).
  79. F. C. Simmel, B. Yurke, and H. R. Singh, Principles and applications of nucleic acid strand displacement reactions, Chem. Rev. 119, 6326 (2019).
  80. E. Poppleton, M. Matthies, D. Mandal, F. Romano, P. Šulc, and L. Rovigatti, oxDNA: Coarse-grained simulations of nucleic acids made simple, J. Open Source Software 8, 4693 (2023).
  81. J. Metson, Designing complex behaviors using transition-based allosteric self-assembly, Edmond, Version 1, 2025, https://doi.org/10.17617/3.TTLGU4.

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