The identification of protein domains that mediate functional interactions between Rab-GTPases and RabGAPs using 3D protein modeling
Jeremiah J Davie, Silviu L Faitar Department of Biology and Mathematics, School of Arts, Sciences, and Education, D’Youville College, Buffalo, NY, USA Abstract: Currently, time-consuming serial in vitro experimentation involving immunocytochemistry or radiolabeled materials is required to...
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| Format: | Article |
| Language: | English |
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Dove Medical Press
2017-04-01
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| Series: | Advances and Applications in Bioinformatics and Chemistry |
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| Online Access: | https://www.dovepress.com/the-identification-of-protein-domains-that-mediate-functional-interact-peer-reviewed-article-AABC |
| _version_ | 1811256521575628800 |
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| author | Davie JJ Faitar SL |
| author_facet | Davie JJ Faitar SL |
| author_sort | Davie JJ |
| collection | DOAJ |
| description | Jeremiah J Davie, Silviu L Faitar Department of Biology and Mathematics, School of Arts, Sciences, and Education, D’Youville College, Buffalo, NY, USA Abstract: Currently, time-consuming serial in vitro experimentation involving immunocytochemistry or radiolabeled materials is required to identify which of the numerous Rab-GTPases (Rab) and Rab-GTPase activating proteins (RabGAP) are capable of functional interactions. These interactions are essential for numerous cellular functions, and in silico methods of reducing in vitro trial and error would accelerate the pace of research in cell biology. We have utilized a combination of three-dimensional protein modeling and protein bioinformatics to identify domains present in Rab proteins that are predictive of their functional interaction with a specific RabGAP. The RabF2 and RabSF1 domains appear to play functional roles in mediating the interaction between Rabs and RabGAPs. Moreover, the RabSF1 domain can be used to make in silico predictions of functional Rab/RabGAP pairs. This method is expected to be a broadly applicable tool for predicting protein–protein interactions where existing crystal structures for homologs of the proteins of interest are available. Keywords: GTP hydrolysis, Rab proteins, RabGAPs, protein–protein interactions, structural informatics, computational biology, Evi5, Evi5L |
| first_indexed | 2024-04-12T17:41:28Z |
| format | Article |
| id | doaj.art-648289d13d074cbb90d23c3c0a551ad3 |
| institution | Directory Open Access Journal |
| issn | 1178-6949 |
| language | English |
| last_indexed | 2024-04-12T17:41:28Z |
| publishDate | 2017-04-01 |
| publisher | Dove Medical Press |
| record_format | Article |
| series | Advances and Applications in Bioinformatics and Chemistry |
| spelling | doaj.art-648289d13d074cbb90d23c3c0a551ad32022-12-22T03:22:47ZengDove Medical PressAdvances and Applications in Bioinformatics and Chemistry1178-69492017-04-01Volume 10475632292The identification of protein domains that mediate functional interactions between Rab-GTPases and RabGAPs using 3D protein modelingDavie JJFaitar SLJeremiah J Davie, Silviu L Faitar Department of Biology and Mathematics, School of Arts, Sciences, and Education, D’Youville College, Buffalo, NY, USA Abstract: Currently, time-consuming serial in vitro experimentation involving immunocytochemistry or radiolabeled materials is required to identify which of the numerous Rab-GTPases (Rab) and Rab-GTPase activating proteins (RabGAP) are capable of functional interactions. These interactions are essential for numerous cellular functions, and in silico methods of reducing in vitro trial and error would accelerate the pace of research in cell biology. We have utilized a combination of three-dimensional protein modeling and protein bioinformatics to identify domains present in Rab proteins that are predictive of their functional interaction with a specific RabGAP. The RabF2 and RabSF1 domains appear to play functional roles in mediating the interaction between Rabs and RabGAPs. Moreover, the RabSF1 domain can be used to make in silico predictions of functional Rab/RabGAP pairs. This method is expected to be a broadly applicable tool for predicting protein–protein interactions where existing crystal structures for homologs of the proteins of interest are available. Keywords: GTP hydrolysis, Rab proteins, RabGAPs, protein–protein interactions, structural informatics, computational biology, Evi5, Evi5Lhttps://www.dovepress.com/the-identification-of-protein-domains-that-mediate-functional-interact-peer-reviewed-article-AABCGTP HydrolysisRab ProteinsRabGAPsProtein-Protein InteractionsStructural InformaticsComputational Biology |
| spellingShingle | Davie JJ Faitar SL The identification of protein domains that mediate functional interactions between Rab-GTPases and RabGAPs using 3D protein modeling Advances and Applications in Bioinformatics and Chemistry GTP Hydrolysis Rab Proteins RabGAPs Protein-Protein Interactions Structural Informatics Computational Biology |
| title | The identification of protein domains that mediate functional interactions between Rab-GTPases and RabGAPs using 3D protein modeling |
| title_full | The identification of protein domains that mediate functional interactions between Rab-GTPases and RabGAPs using 3D protein modeling |
| title_fullStr | The identification of protein domains that mediate functional interactions between Rab-GTPases and RabGAPs using 3D protein modeling |
| title_full_unstemmed | The identification of protein domains that mediate functional interactions between Rab-GTPases and RabGAPs using 3D protein modeling |
| title_short | The identification of protein domains that mediate functional interactions between Rab-GTPases and RabGAPs using 3D protein modeling |
| title_sort | identification of protein domains that mediate functional interactions between rab gtpases and rabgaps using 3d protein modeling |
| topic | GTP Hydrolysis Rab Proteins RabGAPs Protein-Protein Interactions Structural Informatics Computational Biology |
| url | https://www.dovepress.com/the-identification-of-protein-domains-that-mediate-functional-interact-peer-reviewed-article-AABC |
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