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Physical Motif Clustering within Intrinsically Disordered Nucleoporin Sequences Reveals Universal Functional Features

Bioinformatics of disordered proteins is especially challenging given high mutation rates for homologous proteins and that functionality may not be strongly related to sequence. Here we have performed a novel bioinformatic analysis, based on the spatial clustering of physically relevant features suc...

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Detalles Bibliográficos
Autores principales: Ando, David, Colvin, Michael, Rexach, Michael, Gopinathan, Ajay
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3774778/
https://www.ncbi.nlm.nih.gov/pubmed/24066078
http://dx.doi.org/10.1371/journal.pone.0073831
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author Ando, David
Colvin, Michael
Rexach, Michael
Gopinathan, Ajay
author_facet Ando, David
Colvin, Michael
Rexach, Michael
Gopinathan, Ajay
author_sort Ando, David
collection PubMed
description Bioinformatics of disordered proteins is especially challenging given high mutation rates for homologous proteins and that functionality may not be strongly related to sequence. Here we have performed a novel bioinformatic analysis, based on the spatial clustering of physically relevant features such as binding motifs and charges within disordered proteins, on thousands of Nuclear Pore Complex (NPC) FG motif containing proteins (FG nups). The biophysical mechanism by which FG nups regulate nucleocytoplasmic transport has remained elusive. Our analysis revealed a set of highly conserved spatial features in the sequence structure of individual FG nups, such as the separation, localization, and ordering of FG motifs and charged residues along the protein chain. These functionally conserved features provide insight into the particular biophysical mechanisms responsible for regulation of nucleocytoplasmic traffic in the NPC, strongly constraining current models. Additionally this method allows us to identify potentially functionally analogous disordered proteins across distantly related species.
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spelling pubmed-37747782013-09-24 Physical Motif Clustering within Intrinsically Disordered Nucleoporin Sequences Reveals Universal Functional Features Ando, David Colvin, Michael Rexach, Michael Gopinathan, Ajay PLoS One Research Article Bioinformatics of disordered proteins is especially challenging given high mutation rates for homologous proteins and that functionality may not be strongly related to sequence. Here we have performed a novel bioinformatic analysis, based on the spatial clustering of physically relevant features such as binding motifs and charges within disordered proteins, on thousands of Nuclear Pore Complex (NPC) FG motif containing proteins (FG nups). The biophysical mechanism by which FG nups regulate nucleocytoplasmic transport has remained elusive. Our analysis revealed a set of highly conserved spatial features in the sequence structure of individual FG nups, such as the separation, localization, and ordering of FG motifs and charged residues along the protein chain. These functionally conserved features provide insight into the particular biophysical mechanisms responsible for regulation of nucleocytoplasmic traffic in the NPC, strongly constraining current models. Additionally this method allows us to identify potentially functionally analogous disordered proteins across distantly related species. Public Library of Science 2013-09-16 /pmc/articles/PMC3774778/ /pubmed/24066078 http://dx.doi.org/10.1371/journal.pone.0073831 Text en © 2013 Ando 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, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Ando, David
Colvin, Michael
Rexach, Michael
Gopinathan, Ajay
Physical Motif Clustering within Intrinsically Disordered Nucleoporin Sequences Reveals Universal Functional Features
title Physical Motif Clustering within Intrinsically Disordered Nucleoporin Sequences Reveals Universal Functional Features
title_full Physical Motif Clustering within Intrinsically Disordered Nucleoporin Sequences Reveals Universal Functional Features
title_fullStr Physical Motif Clustering within Intrinsically Disordered Nucleoporin Sequences Reveals Universal Functional Features
title_full_unstemmed Physical Motif Clustering within Intrinsically Disordered Nucleoporin Sequences Reveals Universal Functional Features
title_short Physical Motif Clustering within Intrinsically Disordered Nucleoporin Sequences Reveals Universal Functional Features
title_sort physical motif clustering within intrinsically disordered nucleoporin sequences reveals universal functional features
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3774778/
https://www.ncbi.nlm.nih.gov/pubmed/24066078
http://dx.doi.org/10.1371/journal.pone.0073831
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