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Self-organized emergence of folded protein-like network structures from geometric constraints
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino acids, the biochemical environment and the temporal sequence of d...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7046222/ https://www.ncbi.nlm.nih.gov/pubmed/32106258 http://dx.doi.org/10.1371/journal.pone.0229230 |
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author | Molkenthin, Nora Mühle, Steffen Mey, Antonia S. J. S. Timme, Marc |
author_facet | Molkenthin, Nora Mühle, Steffen Mey, Antonia S. J. S. Timme, Marc |
author_sort | Molkenthin, Nora |
collection | PubMed |
description | The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino acids, the biochemical environment and the temporal sequence of distinct interactions yield a complex folding process that cannot yet be easily tracked for all proteins. To gain qualitative insights into the fundamental mechanisms behind the folding dynamics and generic features of the folded structure, we propose a simple model of structure formation that takes into account only fundamental geometric constraints and otherwise assumes randomly paired connections. We find that despite its simplicity, the model results in a network ensemble consistent with key overall features of the ensemble of Protein Residue Networks we obtained from more than 1000 biological protein geometries as available through the Protein Data Base. Specifically, the distribution of the number of interaction neighbors a unit (amino acid) has, the scaling of the structure’s spatial extent with chain length, the eigenvalue spectrum and the scaling of the smallest relaxation time with chain length are all consistent between model and real proteins. These results indicate that geometric constraints alone may already account for a number of generic features of protein tertiary structures. |
format | Online Article Text |
id | pubmed-7046222 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-70462222020-03-09 Self-organized emergence of folded protein-like network structures from geometric constraints Molkenthin, Nora Mühle, Steffen Mey, Antonia S. J. S. Timme, Marc PLoS One Research Article The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino acids, the biochemical environment and the temporal sequence of distinct interactions yield a complex folding process that cannot yet be easily tracked for all proteins. To gain qualitative insights into the fundamental mechanisms behind the folding dynamics and generic features of the folded structure, we propose a simple model of structure formation that takes into account only fundamental geometric constraints and otherwise assumes randomly paired connections. We find that despite its simplicity, the model results in a network ensemble consistent with key overall features of the ensemble of Protein Residue Networks we obtained from more than 1000 biological protein geometries as available through the Protein Data Base. Specifically, the distribution of the number of interaction neighbors a unit (amino acid) has, the scaling of the structure’s spatial extent with chain length, the eigenvalue spectrum and the scaling of the smallest relaxation time with chain length are all consistent between model and real proteins. These results indicate that geometric constraints alone may already account for a number of generic features of protein tertiary structures. Public Library of Science 2020-02-27 /pmc/articles/PMC7046222/ /pubmed/32106258 http://dx.doi.org/10.1371/journal.pone.0229230 Text en © 2020 Molkenthin et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://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 Molkenthin, Nora Mühle, Steffen Mey, Antonia S. J. S. Timme, Marc Self-organized emergence of folded protein-like network structures from geometric constraints |
title | Self-organized emergence of folded protein-like network structures from geometric constraints |
title_full | Self-organized emergence of folded protein-like network structures from geometric constraints |
title_fullStr | Self-organized emergence of folded protein-like network structures from geometric constraints |
title_full_unstemmed | Self-organized emergence of folded protein-like network structures from geometric constraints |
title_short | Self-organized emergence of folded protein-like network structures from geometric constraints |
title_sort | self-organized emergence of folded protein-like network structures from geometric constraints |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7046222/ https://www.ncbi.nlm.nih.gov/pubmed/32106258 http://dx.doi.org/10.1371/journal.pone.0229230 |
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