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Residues crucial for maintaining short paths in network communication mediate signaling in proteins

Here, we represent protein structures as residue interacting networks, which are assumed to involve a permanent flow of information between amino acids. By removal of nodes from the protein network, we identify fold centrally conserved residues, which are crucial for sustaining the shortest pathways...

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Detalles Bibliográficos
Autores principales: del Sol, Antonio, Fujihashi, Hirotomo, Amoros, Dolors, Nussinov, Ruth
Formato: Texto
Lenguaje:English
Publicado: 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1681495/
https://www.ncbi.nlm.nih.gov/pubmed/16738564
http://dx.doi.org/10.1038/msb4100063
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author del Sol, Antonio
Fujihashi, Hirotomo
Amoros, Dolors
Nussinov, Ruth
author_facet del Sol, Antonio
Fujihashi, Hirotomo
Amoros, Dolors
Nussinov, Ruth
author_sort del Sol, Antonio
collection PubMed
description Here, we represent protein structures as residue interacting networks, which are assumed to involve a permanent flow of information between amino acids. By removal of nodes from the protein network, we identify fold centrally conserved residues, which are crucial for sustaining the shortest pathways and thus play key roles in long-range interactions. Analysis of seven protein families (myoglobins, G-protein-coupled receptors, the trypsin class of serine proteases, hemoglobins, oligosaccharide phosphorylases, nuclear receptor ligand-binding domains and retroviral proteases) confirms that experimentally many of these residues are important for allosteric communication. The agreement between the centrally conserved residues, which are key in preserving short path lengths, and residues experimentally suggested to mediate signaling further illustrates that topology plays an important role in network communication. Protein folds have evolved under constraints imposed by function. To maintain function, protein structures need to be robust to mutational events. On the other hand, robustness is accompanied by an extreme sensitivity at some crucial sites. Thus, here we propose that centrally conserved residues, whose removal increases the characteristic path length in protein networks, may relate to the system fragility.
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spelling pubmed-16814952007-01-25 Residues crucial for maintaining short paths in network communication mediate signaling in proteins del Sol, Antonio Fujihashi, Hirotomo Amoros, Dolors Nussinov, Ruth Mol Syst Biol Article Here, we represent protein structures as residue interacting networks, which are assumed to involve a permanent flow of information between amino acids. By removal of nodes from the protein network, we identify fold centrally conserved residues, which are crucial for sustaining the shortest pathways and thus play key roles in long-range interactions. Analysis of seven protein families (myoglobins, G-protein-coupled receptors, the trypsin class of serine proteases, hemoglobins, oligosaccharide phosphorylases, nuclear receptor ligand-binding domains and retroviral proteases) confirms that experimentally many of these residues are important for allosteric communication. The agreement between the centrally conserved residues, which are key in preserving short path lengths, and residues experimentally suggested to mediate signaling further illustrates that topology plays an important role in network communication. Protein folds have evolved under constraints imposed by function. To maintain function, protein structures need to be robust to mutational events. On the other hand, robustness is accompanied by an extreme sensitivity at some crucial sites. Thus, here we propose that centrally conserved residues, whose removal increases the characteristic path length in protein networks, may relate to the system fragility. 2006-05-02 /pmc/articles/PMC1681495/ /pubmed/16738564 http://dx.doi.org/10.1038/msb4100063 Text en Copyright © 2006, EMBO and Nature Publishing Group
spellingShingle Article
del Sol, Antonio
Fujihashi, Hirotomo
Amoros, Dolors
Nussinov, Ruth
Residues crucial for maintaining short paths in network communication mediate signaling in proteins
title Residues crucial for maintaining short paths in network communication mediate signaling in proteins
title_full Residues crucial for maintaining short paths in network communication mediate signaling in proteins
title_fullStr Residues crucial for maintaining short paths in network communication mediate signaling in proteins
title_full_unstemmed Residues crucial for maintaining short paths in network communication mediate signaling in proteins
title_short Residues crucial for maintaining short paths in network communication mediate signaling in proteins
title_sort residues crucial for maintaining short paths in network communication mediate signaling in proteins
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1681495/
https://www.ncbi.nlm.nih.gov/pubmed/16738564
http://dx.doi.org/10.1038/msb4100063
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