Reuse of structural domain–domain interactions in protein networks
<p>Abstract</p> <p>Background</p> <p>Protein interactions are thought to be largely mediated by interactions between structural domains. Databases such as <it>i</it>Pfam relate interactions in protein structures to known domain families. Here, we investigate...
Main Authors: | , |
---|---|
Format: | Article |
Language: | English |
Published: |
BMC
2007-07-01
|
Series: | BMC Bioinformatics |
Online Access: | http://www.biomedcentral.com/1471-2105/8/259 |
id |
doaj-8962a8cd9fa24983951b99f95ea8f5f8 |
---|---|
record_format |
Article |
spelling |
doaj-8962a8cd9fa24983951b99f95ea8f5f82020-11-25T00:15:21ZengBMCBMC Bioinformatics1471-21052007-07-018125910.1186/1471-2105-8-259Reuse of structural domain–domain interactions in protein networksBateman AlexSchuster-Böckler Benjamin<p>Abstract</p> <p>Background</p> <p>Protein interactions are thought to be largely mediated by interactions between structural domains. Databases such as <it>i</it>Pfam relate interactions in protein structures to known domain families. Here, we investigate how the domain interactions from the <it>i</it>Pfam database are distributed in protein interactions taken from the HPRD, MPact, BioGRID, DIP and IntAct databases.</p> <p>Results</p> <p>We find that known structural domain interactions can only explain a subset of 4–19% of the available protein interactions, nevertheless this fraction is still significantly bigger than expected by chance. There is a correlation between the frequency of a domain interaction and the connectivity of the proteins it occurs in. Furthermore, a large proportion of protein interactions can be attributed to a small number of domain interactions. We conclude that many, but not all, domain interactions constitute reusable modules of molecular recognition. A substantial proportion of domain interactions are conserved between <it>E. coli</it>, <it>S. cerevisiae </it>and <it>H. sapiens</it>. These domains are related to essential cellular functions, suggesting that many domain interactions were already present in the last universal common ancestor.</p> <p>Conclusion</p> <p>Our results support the concept of domain interactions as reusable, conserved building blocks of protein interactions, but also highlight the limitations currently imposed by the small number of available protein structures.</p> http://www.biomedcentral.com/1471-2105/8/259 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Bateman Alex Schuster-Böckler Benjamin |
spellingShingle |
Bateman Alex Schuster-Böckler Benjamin Reuse of structural domain–domain interactions in protein networks BMC Bioinformatics |
author_facet |
Bateman Alex Schuster-Böckler Benjamin |
author_sort |
Bateman Alex |
title |
Reuse of structural domain–domain interactions in protein networks |
title_short |
Reuse of structural domain–domain interactions in protein networks |
title_full |
Reuse of structural domain–domain interactions in protein networks |
title_fullStr |
Reuse of structural domain–domain interactions in protein networks |
title_full_unstemmed |
Reuse of structural domain–domain interactions in protein networks |
title_sort |
reuse of structural domain–domain interactions in protein networks |
publisher |
BMC |
series |
BMC Bioinformatics |
issn |
1471-2105 |
publishDate |
2007-07-01 |
description |
<p>Abstract</p> <p>Background</p> <p>Protein interactions are thought to be largely mediated by interactions between structural domains. Databases such as <it>i</it>Pfam relate interactions in protein structures to known domain families. Here, we investigate how the domain interactions from the <it>i</it>Pfam database are distributed in protein interactions taken from the HPRD, MPact, BioGRID, DIP and IntAct databases.</p> <p>Results</p> <p>We find that known structural domain interactions can only explain a subset of 4–19% of the available protein interactions, nevertheless this fraction is still significantly bigger than expected by chance. There is a correlation between the frequency of a domain interaction and the connectivity of the proteins it occurs in. Furthermore, a large proportion of protein interactions can be attributed to a small number of domain interactions. We conclude that many, but not all, domain interactions constitute reusable modules of molecular recognition. A substantial proportion of domain interactions are conserved between <it>E. coli</it>, <it>S. cerevisiae </it>and <it>H. sapiens</it>. These domains are related to essential cellular functions, suggesting that many domain interactions were already present in the last universal common ancestor.</p> <p>Conclusion</p> <p>Our results support the concept of domain interactions as reusable, conserved building blocks of protein interactions, but also highlight the limitations currently imposed by the small number of available protein structures.</p> |
url |
http://www.biomedcentral.com/1471-2105/8/259 |
work_keys_str_mv |
AT batemanalex reuseofstructuraldomaindomaininteractionsinproteinnetworks AT schusterbocklerbenjamin reuseofstructuraldomaindomaininteractionsinproteinnetworks |
_version_ |
1725387302000132096 |