Structured Tandem Repeats in Protein Interactions
Tandem repeats (TRs) in protein sequences are consecutive, highly similar sequence motifs. Some types of TRs fold into structural units that pack together in ensembles, forming either an (open) elongated domain or a (closed) propeller, where the last unit of the ensemble packs against the first one....
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| Language: | English |
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MDPI AG
2024-03-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/25/5/2994 |
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| author | Juan Mac Donagh Abril Marchesini Agostina Spiga Maximiliano José Fallico Paula Nazarena Arrías Alexander Miguel Monzon Aimilia-Christina Vagiona Mariane Gonçalves-Kulik Pablo Mier Miguel A. Andrade-Navarro |
| author_facet | Juan Mac Donagh Abril Marchesini Agostina Spiga Maximiliano José Fallico Paula Nazarena Arrías Alexander Miguel Monzon Aimilia-Christina Vagiona Mariane Gonçalves-Kulik Pablo Mier Miguel A. Andrade-Navarro |
| author_sort | Juan Mac Donagh |
| collection | DOAJ |
| description | Tandem repeats (TRs) in protein sequences are consecutive, highly similar sequence motifs. Some types of TRs fold into structural units that pack together in ensembles, forming either an (open) elongated domain or a (closed) propeller, where the last unit of the ensemble packs against the first one. Here, we examine TR proteins (TRPs) to see how their sequence, structure, and evolutionary properties favor them for a function as mediators of protein interactions. Our observations suggest that TRPs bind other proteins using large, structured surfaces like globular domains; in particular, open-structured TR ensembles are favored by flexible termini and the possibility to tightly coil against their targets. While, intuitively, open ensembles of TRs seem prone to evolve due to their potential to accommodate insertions and deletions of units, these evolutionary events are unexpectedly rare, suggesting that they are advantageous for the emergence of the ancestral sequence but are early fixed. We hypothesize that their flexibility makes it easier for further proteins to adapt to interact with them, which would explain their large number of protein interactions. We provide insight into the properties of open TR ensembles, which make them scaffolds for alternative protein complexes to organize genes, RNA and proteins. |
| first_indexed | 2024-04-25T00:28:01Z |
| format | Article |
| id | doaj.art-a5901b4ef39441deb91eb3af2906b338 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-04-25T00:28:01Z |
| publishDate | 2024-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-a5901b4ef39441deb91eb3af2906b3382024-03-12T16:47:10ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672024-03-01255299410.3390/ijms25052994Structured Tandem Repeats in Protein InteractionsJuan Mac Donagh0Abril Marchesini1Agostina Spiga2Maximiliano José Fallico3Paula Nazarena Arrías4Alexander Miguel Monzon5Aimilia-Christina Vagiona6Mariane Gonçalves-Kulik7Pablo Mier8Miguel A. Andrade-Navarro9Science and Technology Department, National University of Quilmes, Bernal B1876, ArgentinaNational Scientific and Technical Research Council (CONICET), Buenos Aires C1033AAJ, ArgentinaScience and Technology Department, National University of Quilmes, Bernal B1876, ArgentinaLaboratory of Bioactive Compound Research and Development, Faculty of Exact Sciences, University of La Plata, La Plata 1900, ArgentinaDepartment of Biomedical Sciences, University of Padova, Via U. Bassi 58/b, 35121 Padova, ItalyDepartment of Information Engineering, University of Padova, Via Giovanni Gradenigo 6/B, 35131 Padova, ItalyInstitute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, GermanyInstitute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, GermanyInstitute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, GermanyInstitute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, GermanyTandem repeats (TRs) in protein sequences are consecutive, highly similar sequence motifs. Some types of TRs fold into structural units that pack together in ensembles, forming either an (open) elongated domain or a (closed) propeller, where the last unit of the ensemble packs against the first one. Here, we examine TR proteins (TRPs) to see how their sequence, structure, and evolutionary properties favor them for a function as mediators of protein interactions. Our observations suggest that TRPs bind other proteins using large, structured surfaces like globular domains; in particular, open-structured TR ensembles are favored by flexible termini and the possibility to tightly coil against their targets. While, intuitively, open ensembles of TRs seem prone to evolve due to their potential to accommodate insertions and deletions of units, these evolutionary events are unexpectedly rare, suggesting that they are advantageous for the emergence of the ancestral sequence but are early fixed. We hypothesize that their flexibility makes it easier for further proteins to adapt to interact with them, which would explain their large number of protein interactions. We provide insight into the properties of open TR ensembles, which make them scaffolds for alternative protein complexes to organize genes, RNA and proteins.https://www.mdpi.com/1422-0067/25/5/2994tandem repeatsprotein–protein interactionsprotein structureprotein evolutionprotein flexibility |
| spellingShingle | Juan Mac Donagh Abril Marchesini Agostina Spiga Maximiliano José Fallico Paula Nazarena Arrías Alexander Miguel Monzon Aimilia-Christina Vagiona Mariane Gonçalves-Kulik Pablo Mier Miguel A. Andrade-Navarro Structured Tandem Repeats in Protein Interactions International Journal of Molecular Sciences tandem repeats protein–protein interactions protein structure protein evolution protein flexibility |
| title | Structured Tandem Repeats in Protein Interactions |
| title_full | Structured Tandem Repeats in Protein Interactions |
| title_fullStr | Structured Tandem Repeats in Protein Interactions |
| title_full_unstemmed | Structured Tandem Repeats in Protein Interactions |
| title_short | Structured Tandem Repeats in Protein Interactions |
| title_sort | structured tandem repeats in protein interactions |
| topic | tandem repeats protein–protein interactions protein structure protein evolution protein flexibility |
| url | https://www.mdpi.com/1422-0067/25/5/2994 |
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