Detection of alpha-rod protein repeats using a neural network and application to huntingtin.
A growing number of solved protein structures display an elongated structural domain, denoted here as alpha-rod, composed of stacked pairs of anti-parallel alpha-helices. Alpha-rods are flexible and expose a large surface, which makes them suitable for protein interaction. Although most likely origi...
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| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2009-03-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000304&type=printable |
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| _version_ | 1850182896508207104 |
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| author | Gareth A Palidwor Sergey Shcherbinin Matthew R Huska Tamas Rasko Ulrich Stelzl Anup Arumughan Raphaele Foulle Pablo Porras Luis Sanchez-Pulido Erich E Wanker Miguel A Andrade-Navarro |
| author_facet | Gareth A Palidwor Sergey Shcherbinin Matthew R Huska Tamas Rasko Ulrich Stelzl Anup Arumughan Raphaele Foulle Pablo Porras Luis Sanchez-Pulido Erich E Wanker Miguel A Andrade-Navarro |
| author_sort | Gareth A Palidwor |
| collection | DOAJ |
| description | A growing number of solved protein structures display an elongated structural domain, denoted here as alpha-rod, composed of stacked pairs of anti-parallel alpha-helices. Alpha-rods are flexible and expose a large surface, which makes them suitable for protein interaction. Although most likely originating by tandem duplication of a two-helix unit, their detection using sequence similarity between repeats is poor. Here, we show that alpha-rod repeats can be detected using a neural network. The network detects more repeats than are identified by domain databases using multiple profiles, with a low level of false positives (<10%). We identify alpha-rod repeats in approximately 0.4% of proteins in eukaryotic genomes. We then investigate the results for all human proteins, identifying alpha-rod repeats for the first time in six protein families, including proteins STAG1-3, SERAC1, and PSMD1-2 & 5. We also characterize a short version of these repeats in eight protein families of Archaeal, Bacterial, and Fungal species. Finally, we demonstrate the utility of these predictions in directing experimental work to demarcate three alpha-rods in huntingtin, a protein mutated in Huntington's disease. Using yeast two hybrid analysis and an immunoprecipitation technique, we show that the huntingtin fragments containing alpha-rods associate with each other. This is the first definition of domains in huntingtin and the first validation of predicted interactions between fragments of huntingtin, which sets up directions toward functional characterization of this protein. An implementation of the repeat detection algorithm is available as a Web server with a simple graphical output: http://www.ogic.ca/projects/ard. This can be further visualized using BiasViz, a graphic tool for representation of multiple sequence alignments. |
| format | Article |
| id | doaj-art-e5001745c12f4778a1e58afef071e9d0 |
| institution | OA Journals |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2009-03-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-e5001745c12f4778a1e58afef071e9d02025-08-20T02:17:29ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582009-03-0153e100030410.1371/journal.pcbi.1000304Detection of alpha-rod protein repeats using a neural network and application to huntingtin.Gareth A PalidworSergey ShcherbininMatthew R HuskaTamas RaskoUlrich StelzlAnup ArumughanRaphaele FoullePablo PorrasLuis Sanchez-PulidoErich E WankerMiguel A Andrade-NavarroA growing number of solved protein structures display an elongated structural domain, denoted here as alpha-rod, composed of stacked pairs of anti-parallel alpha-helices. Alpha-rods are flexible and expose a large surface, which makes them suitable for protein interaction. Although most likely originating by tandem duplication of a two-helix unit, their detection using sequence similarity between repeats is poor. Here, we show that alpha-rod repeats can be detected using a neural network. The network detects more repeats than are identified by domain databases using multiple profiles, with a low level of false positives (<10%). We identify alpha-rod repeats in approximately 0.4% of proteins in eukaryotic genomes. We then investigate the results for all human proteins, identifying alpha-rod repeats for the first time in six protein families, including proteins STAG1-3, SERAC1, and PSMD1-2 & 5. We also characterize a short version of these repeats in eight protein families of Archaeal, Bacterial, and Fungal species. Finally, we demonstrate the utility of these predictions in directing experimental work to demarcate three alpha-rods in huntingtin, a protein mutated in Huntington's disease. Using yeast two hybrid analysis and an immunoprecipitation technique, we show that the huntingtin fragments containing alpha-rods associate with each other. This is the first definition of domains in huntingtin and the first validation of predicted interactions between fragments of huntingtin, which sets up directions toward functional characterization of this protein. An implementation of the repeat detection algorithm is available as a Web server with a simple graphical output: http://www.ogic.ca/projects/ard. This can be further visualized using BiasViz, a graphic tool for representation of multiple sequence alignments.https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000304&type=printable |
| spellingShingle | Gareth A Palidwor Sergey Shcherbinin Matthew R Huska Tamas Rasko Ulrich Stelzl Anup Arumughan Raphaele Foulle Pablo Porras Luis Sanchez-Pulido Erich E Wanker Miguel A Andrade-Navarro Detection of alpha-rod protein repeats using a neural network and application to huntingtin. PLoS Computational Biology |
| title | Detection of alpha-rod protein repeats using a neural network and application to huntingtin. |
| title_full | Detection of alpha-rod protein repeats using a neural network and application to huntingtin. |
| title_fullStr | Detection of alpha-rod protein repeats using a neural network and application to huntingtin. |
| title_full_unstemmed | Detection of alpha-rod protein repeats using a neural network and application to huntingtin. |
| title_short | Detection of alpha-rod protein repeats using a neural network and application to huntingtin. |
| title_sort | detection of alpha rod protein repeats using a neural network and application to huntingtin |
| url | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000304&type=printable |
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