Iterative Annealing Mechanism for Protein and RNA Chaperones
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arXiv
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| Format: | Preprint |
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2025
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| _version_ | 1866911006602559488 |
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| author | Hyeon, Changbong Thirumalai, D. |
| author_facet | Hyeon, Changbong Thirumalai, D. |
| contents | Molecular chaperones are machines that consume copious amount of ATP to drive misfolded proteins or RNA to fold into functionally competent native states. Because the folding landscapes of biomolecules with complex native state topology are rugged consisting of multiple minima that are separated by large free energy barriers, folding occurs by the kinetic partitioning mechanism according to which only a small fraction of the molecules reach the folded state in biologically viable times. The rescue of such proteins and RNA require chaperones. Although the protein and RNA chaperones are profoundly different in their structure and action, the principles underlying their activity to produce the folded structures can be understood using a unified theoretical framework based on iterative annealing mechanism (IAM). Our theory shows that both these machines have evolved to the maximize the production of the steady state yield on biological times. Strikingly, theory predicts that only at a moderate level of RNA chaperone activity is the yield of the self-splicing pre-RNA is maximized in \textit{in vivo}. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2506_12645 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Iterative Annealing Mechanism for Protein and RNA Chaperones Hyeon, Changbong Thirumalai, D. Biological Physics Soft Condensed Matter Biomolecules Molecular chaperones are machines that consume copious amount of ATP to drive misfolded proteins or RNA to fold into functionally competent native states. Because the folding landscapes of biomolecules with complex native state topology are rugged consisting of multiple minima that are separated by large free energy barriers, folding occurs by the kinetic partitioning mechanism according to which only a small fraction of the molecules reach the folded state in biologically viable times. The rescue of such proteins and RNA require chaperones. Although the protein and RNA chaperones are profoundly different in their structure and action, the principles underlying their activity to produce the folded structures can be understood using a unified theoretical framework based on iterative annealing mechanism (IAM). Our theory shows that both these machines have evolved to the maximize the production of the steady state yield on biological times. Strikingly, theory predicts that only at a moderate level of RNA chaperone activity is the yield of the self-splicing pre-RNA is maximized in \textit{in vivo}. |
| title | Iterative Annealing Mechanism for Protein and RNA Chaperones |
| topic | Biological Physics Soft Condensed Matter Biomolecules |
| url | https://arxiv.org/abs/2506.12645 |