Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory.
The nuclear pore complex (NPC), a channel within the nuclear envelope filled with intrinsically disordered proteins, regulates the transport of macromolecules between the nucleus and the cytoplasm. Recent studies have highlighted the NPC's ability to adjust its diameter in response to the membr...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2025-04-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1012909 |
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| author | Atsushi Matsuda Mohammad R K Mofrad |
| author_facet | Atsushi Matsuda Mohammad R K Mofrad |
| author_sort | Atsushi Matsuda |
| collection | DOAJ |
| description | The nuclear pore complex (NPC), a channel within the nuclear envelope filled with intrinsically disordered proteins, regulates the transport of macromolecules between the nucleus and the cytoplasm. Recent studies have highlighted the NPC's ability to adjust its diameter in response to the membrane tension, underscoring the importance of exploring how variations in pore size influence molecular transport through the NPC. In this study, we investigated the relationship between pore size and transport rate and proposed a mathematical model describing this connection. We began by theoretically analyzing how the pore size scales with the characteristic dimensions of the mesh-like structure within the pore. By introducing key assumptions about how the meshwork structure influences molecular diffusion, we derived a mathematical expression for the transport rate based on the size of the pore and the transported molecules. To validate our model, we conducted Brownian dynamics simulations using a coarse-grained representation of the NPC. These simulations, performed across a range of pore sizes, demonstrated strong agreement with our model's predictions, confirming its accuracy and applicability. Our model is specifically tailored for small-to-medium-sized molecules, approximately 5 nanometers in size, making it relevant to a wide range of transcription factors and signaling molecules. It also extends to molecules with weak and transient interactions with FG-Nups, such as importin-β. By presenting this model formula, our study offers a quantitative framework for analyzing the effects of pore dilation on nucleocytoplasmic transport. |
| format | Article |
| id | doaj-art-48a6fd774dda45aa97a77e330038d85c |
| institution | DOAJ |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-48a6fd774dda45aa97a77e330038d85c2025-08-20T03:08:31ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582025-04-01214e101290910.1371/journal.pcbi.1012909Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory.Atsushi MatsudaMohammad R K MofradThe nuclear pore complex (NPC), a channel within the nuclear envelope filled with intrinsically disordered proteins, regulates the transport of macromolecules between the nucleus and the cytoplasm. Recent studies have highlighted the NPC's ability to adjust its diameter in response to the membrane tension, underscoring the importance of exploring how variations in pore size influence molecular transport through the NPC. In this study, we investigated the relationship between pore size and transport rate and proposed a mathematical model describing this connection. We began by theoretically analyzing how the pore size scales with the characteristic dimensions of the mesh-like structure within the pore. By introducing key assumptions about how the meshwork structure influences molecular diffusion, we derived a mathematical expression for the transport rate based on the size of the pore and the transported molecules. To validate our model, we conducted Brownian dynamics simulations using a coarse-grained representation of the NPC. These simulations, performed across a range of pore sizes, demonstrated strong agreement with our model's predictions, confirming its accuracy and applicability. Our model is specifically tailored for small-to-medium-sized molecules, approximately 5 nanometers in size, making it relevant to a wide range of transcription factors and signaling molecules. It also extends to molecules with weak and transient interactions with FG-Nups, such as importin-β. By presenting this model formula, our study offers a quantitative framework for analyzing the effects of pore dilation on nucleocytoplasmic transport.https://doi.org/10.1371/journal.pcbi.1012909 |
| spellingShingle | Atsushi Matsuda Mohammad R K Mofrad Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory. PLoS Computational Biology |
| title | Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory. |
| title_full | Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory. |
| title_fullStr | Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory. |
| title_full_unstemmed | Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory. |
| title_short | Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory. |
| title_sort | role of pore dilation in molecular transport through the nuclear pore complex insights from polymer scaling theory |
| url | https://doi.org/10.1371/journal.pcbi.1012909 |
| work_keys_str_mv | AT atsushimatsuda roleofporedilationinmoleculartransportthroughthenuclearporecomplexinsightsfrompolymerscalingtheory AT mohammadrkmofrad roleofporedilationinmoleculartransportthroughthenuclearporecomplexinsightsfrompolymerscalingtheory |