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Modeling the ribosome as a bipartite graph
Developing mathematical representations of biological systems that can allow predictions is a challenging and important research goal. It is demonstrated here how the ribosome, the nano-machine responsible for synthesizing all proteins necessary for cellular life, can be represented as a bipartite n...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Public Library of Science
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9803165/ https://www.ncbi.nlm.nih.gov/pubmed/36584020 http://dx.doi.org/10.1371/journal.pone.0279455 |
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author | Calvet, Laurie E. |
author_facet | Calvet, Laurie E. |
author_sort | Calvet, Laurie E. |
collection | PubMed |
description | Developing mathematical representations of biological systems that can allow predictions is a challenging and important research goal. It is demonstrated here how the ribosome, the nano-machine responsible for synthesizing all proteins necessary for cellular life, can be represented as a bipartite network. Ten ribosomal structures from Bacteria and six from Eukarya are explored. Ribosomal networks are found to exhibit unique properties despite variations in the nodes and edges of the different graphs. The ribosome is shown to exhibit very large topological redundancies, demonstrating mathematical resiliency. These results can potentially explain how it can function consistently despite changes in composition and connectivity. Furthermore, this representation can be used to analyze ribosome function within the large machinery of network theory, where the degrees of freedom are the possible interactions, and can be used to provide new insights for translation regulation and therapeutics. |
format | Online Article Text |
id | pubmed-9803165 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-98031652022-12-31 Modeling the ribosome as a bipartite graph Calvet, Laurie E. PLoS One Research Article Developing mathematical representations of biological systems that can allow predictions is a challenging and important research goal. It is demonstrated here how the ribosome, the nano-machine responsible for synthesizing all proteins necessary for cellular life, can be represented as a bipartite network. Ten ribosomal structures from Bacteria and six from Eukarya are explored. Ribosomal networks are found to exhibit unique properties despite variations in the nodes and edges of the different graphs. The ribosome is shown to exhibit very large topological redundancies, demonstrating mathematical resiliency. These results can potentially explain how it can function consistently despite changes in composition and connectivity. Furthermore, this representation can be used to analyze ribosome function within the large machinery of network theory, where the degrees of freedom are the possible interactions, and can be used to provide new insights for translation regulation and therapeutics. Public Library of Science 2022-12-30 /pmc/articles/PMC9803165/ /pubmed/36584020 http://dx.doi.org/10.1371/journal.pone.0279455 Text en © 2022 Laurie E. Calvet https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Calvet, Laurie E. Modeling the ribosome as a bipartite graph |
title | Modeling the ribosome as a bipartite graph |
title_full | Modeling the ribosome as a bipartite graph |
title_fullStr | Modeling the ribosome as a bipartite graph |
title_full_unstemmed | Modeling the ribosome as a bipartite graph |
title_short | Modeling the ribosome as a bipartite graph |
title_sort | modeling the ribosome as a bipartite graph |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9803165/ https://www.ncbi.nlm.nih.gov/pubmed/36584020 http://dx.doi.org/10.1371/journal.pone.0279455 |
work_keys_str_mv | AT calvetlauriee modelingtheribosomeasabipartitegraph |