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The complexity of protein interactions unravelled from structural disorder

The importance of unstructured biology has quickly grown during the last decades accompanying the explosion of the number of experimentally resolved protein structures. The idea that structural disorder might be a novel mechanism of protein interaction is widespread in the literature, although the n...

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Autores principales: Seoane, Beatriz, Carbone, Alessandra
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7846008/
https://www.ncbi.nlm.nih.gov/pubmed/33417598
http://dx.doi.org/10.1371/journal.pcbi.1008546
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author Seoane, Beatriz
Carbone, Alessandra
author_facet Seoane, Beatriz
Carbone, Alessandra
author_sort Seoane, Beatriz
collection PubMed
description The importance of unstructured biology has quickly grown during the last decades accompanying the explosion of the number of experimentally resolved protein structures. The idea that structural disorder might be a novel mechanism of protein interaction is widespread in the literature, although the number of statistically significant structural studies supporting this idea is surprisingly low. At variance with previous works, our conclusions rely exclusively on a large-scale analysis of all the 134337 X-ray crystallographic structures of the Protein Data Bank averaged over clusters of almost identical protein sequences. In this work, we explore the complexity of the organisation of all the interaction interfaces observed when a protein lies in alternative complexes, showing that interfaces progressively add up in a hierarchical way, which is reflected in a logarithmic law for the size of the union of the interface regions on the number of distinct interfaces. We further investigate the connection of this complexity with different measures of structural disorder: the standard missing residues and a new definition, called “soft disorder”, that covers all the flexible and structurally amorphous residues of a protein. We show evidences that both the interaction interfaces and the soft disordered regions tend to involve roughly the same amino-acids of the protein, and preliminary results suggesting that soft disorder spots those surface regions where new interfaces are progressively accommodated by complex formation. In fact, our results suggest that structurally disordered regions not only carry crucial information about the location of alternative interfaces within complexes, but also about the order of the assembly. We verify these hypotheses in several examples, such as the DNA binding domains of P53 and P73, the C3 exoenzyme, and two known biological orders of assembly. We finally compare our measures of structural disorder with several disorder bioinformatics predictors, showing that these latter are optimised to predict the residues that are missing in all the alternative structures of a protein and they are not able to catch the progressive evolution of the disordered regions upon complex formation. Yet, the predicted residues, when not missing, tend to be characterised as soft disordered regions.
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spelling pubmed-78460082021-02-04 The complexity of protein interactions unravelled from structural disorder Seoane, Beatriz Carbone, Alessandra PLoS Comput Biol Research Article The importance of unstructured biology has quickly grown during the last decades accompanying the explosion of the number of experimentally resolved protein structures. The idea that structural disorder might be a novel mechanism of protein interaction is widespread in the literature, although the number of statistically significant structural studies supporting this idea is surprisingly low. At variance with previous works, our conclusions rely exclusively on a large-scale analysis of all the 134337 X-ray crystallographic structures of the Protein Data Bank averaged over clusters of almost identical protein sequences. In this work, we explore the complexity of the organisation of all the interaction interfaces observed when a protein lies in alternative complexes, showing that interfaces progressively add up in a hierarchical way, which is reflected in a logarithmic law for the size of the union of the interface regions on the number of distinct interfaces. We further investigate the connection of this complexity with different measures of structural disorder: the standard missing residues and a new definition, called “soft disorder”, that covers all the flexible and structurally amorphous residues of a protein. We show evidences that both the interaction interfaces and the soft disordered regions tend to involve roughly the same amino-acids of the protein, and preliminary results suggesting that soft disorder spots those surface regions where new interfaces are progressively accommodated by complex formation. In fact, our results suggest that structurally disordered regions not only carry crucial information about the location of alternative interfaces within complexes, but also about the order of the assembly. We verify these hypotheses in several examples, such as the DNA binding domains of P53 and P73, the C3 exoenzyme, and two known biological orders of assembly. We finally compare our measures of structural disorder with several disorder bioinformatics predictors, showing that these latter are optimised to predict the residues that are missing in all the alternative structures of a protein and they are not able to catch the progressive evolution of the disordered regions upon complex formation. Yet, the predicted residues, when not missing, tend to be characterised as soft disordered regions. Public Library of Science 2021-01-08 /pmc/articles/PMC7846008/ /pubmed/33417598 http://dx.doi.org/10.1371/journal.pcbi.1008546 Text en © 2021 Seoane, Carbone 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
Seoane, Beatriz
Carbone, Alessandra
The complexity of protein interactions unravelled from structural disorder
title The complexity of protein interactions unravelled from structural disorder
title_full The complexity of protein interactions unravelled from structural disorder
title_fullStr The complexity of protein interactions unravelled from structural disorder
title_full_unstemmed The complexity of protein interactions unravelled from structural disorder
title_short The complexity of protein interactions unravelled from structural disorder
title_sort complexity of protein interactions unravelled from structural disorder
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7846008/
https://www.ncbi.nlm.nih.gov/pubmed/33417598
http://dx.doi.org/10.1371/journal.pcbi.1008546
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