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| Main Authors: | , |
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| Format: | Preprint |
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2025
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| Online Access: | https://arxiv.org/abs/2511.16362 |
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| _version_ | 1866915628582961152 |
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| author | Benoist, Félix Sartori, Pablo |
| author_facet | Benoist, Félix Sartori, Pablo |
| contents | The cytoplasm is a heterogeneous mixture containing many types of proteins that self-assemble into a wide variety of complexes. The accuracy and speed of cytoplasmic self-assembly is astonishing because it involves the correct identification of components shared among different structures, despite pervasive thermal fluctuations. Typical toy models of self-assembly are based on the specificity of binding energies among components and neglect kinetic effects. However, kinetics plays a key role in biological self-assembly, often catalyzed by a plethora of assembly factors. Building on this observation, we extend a previous heteropolymer growth model to describe the retrieval of two-dimensional structures. We find that the self-assembly of structures in this model is subject to strong speed and encoding bottlenecks. Moreover, we show that these bottlenecks can be suppressed by increasing the connectivity of a small fraction of components. This mechanism of kinetically controlling a small number of critical binding events provides a simple explanation for the timely assembly of large protein, and suggests a unifying principle for the role of assembly factors. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2511_16362 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Resolving Speed and Encoding Bottlenecks in Fast Heteromeric Self-Assembly Benoist, Félix Sartori, Pablo Statistical Mechanics The cytoplasm is a heterogeneous mixture containing many types of proteins that self-assemble into a wide variety of complexes. The accuracy and speed of cytoplasmic self-assembly is astonishing because it involves the correct identification of components shared among different structures, despite pervasive thermal fluctuations. Typical toy models of self-assembly are based on the specificity of binding energies among components and neglect kinetic effects. However, kinetics plays a key role in biological self-assembly, often catalyzed by a plethora of assembly factors. Building on this observation, we extend a previous heteropolymer growth model to describe the retrieval of two-dimensional structures. We find that the self-assembly of structures in this model is subject to strong speed and encoding bottlenecks. Moreover, we show that these bottlenecks can be suppressed by increasing the connectivity of a small fraction of components. This mechanism of kinetically controlling a small number of critical binding events provides a simple explanation for the timely assembly of large protein, and suggests a unifying principle for the role of assembly factors. |
| title | Resolving Speed and Encoding Bottlenecks in Fast Heteromeric Self-Assembly |
| topic | Statistical Mechanics |
| url | https://arxiv.org/abs/2511.16362 |