Constructing networks for comparison of collagen types
Collagens are structural proteins that are predominantly found in the extracellular matrix of multicellular animals, where they are mainly responsible for the stability and structural integrity of various tissues. All collagens contain polypeptide strands (α-chains). There are several types of colla...
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
De Gruyter
2024-07-01
|
| Series: | Journal of Integrative Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1515/jib-2024-0020 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1846143527231160320 |
|---|---|
| author | Wesp Valentin Scholz Lukas Ziermann-Canabarro Janine M. Schuster Stefan Stark Heiko |
| author_facet | Wesp Valentin Scholz Lukas Ziermann-Canabarro Janine M. Schuster Stefan Stark Heiko |
| author_sort | Wesp Valentin |
| collection | DOAJ |
| description | Collagens are structural proteins that are predominantly found in the extracellular matrix of multicellular animals, where they are mainly responsible for the stability and structural integrity of various tissues. All collagens contain polypeptide strands (α-chains). There are several types of collagens, some of which differ significantly in form, function, and tissue specificity. Because of their importance in clinical research, they are grouped into subdivisions, the so-called collagen families, and their sequences are often analysed. However, problems arise with highly homologous sequence segments. To increase the accuracy of collagen classification and prediction of their functions, the structure of these collagens and their expression in different tissues could result in a better focus on sequence segments of interest. Here, we analyse collagen families with different levels of conservation. As a result, clusters with high interconnectivity can be found, such as the fibrillar collagens, the COL4 network-forming collagens, and the COL9 FACITs. Furthermore, a large cluster between network-forming, FACIT, and COL28a1 α-chains is formed with COL6a3 as a major hub node. The formation of clusters also signifies, why it is important to always analyse the α-chains and why structural changes can have a wide range of effects on the body. |
| format | Article |
| id | doaj-art-b926ba0f65ef4acea3e37237a89fd7c0 |
| institution | Kabale University |
| issn | 1613-4516 |
| language | English |
| publishDate | 2024-07-01 |
| publisher | De Gruyter |
| record_format | Article |
| series | Journal of Integrative Bioinformatics |
| spelling | doaj-art-b926ba0f65ef4acea3e37237a89fd7c02024-12-02T12:04:10ZengDe GruyterJournal of Integrative Bioinformatics1613-45162024-07-0121321110.1515/jib-2024-0020Constructing networks for comparison of collagen typesWesp Valentin0Scholz Lukas1Ziermann-Canabarro Janine M.2Schuster Stefan3Stark Heiko4Department of Bioinformatics, 64341Friedrich-Schiller-University Jena, Jena, GermanyDepartment of Bioinformatics, 64341Friedrich-Schiller-University Jena, Jena, GermanyDepartment of Anatomy, Howard University College of Medicine, Washington, DC, USADepartment of Bioinformatics, 64341Friedrich-Schiller-University Jena, Jena, GermanyDepartment of Bioinformatics, 64341Friedrich-Schiller-University Jena, Jena, GermanyCollagens are structural proteins that are predominantly found in the extracellular matrix of multicellular animals, where they are mainly responsible for the stability and structural integrity of various tissues. All collagens contain polypeptide strands (α-chains). There are several types of collagens, some of which differ significantly in form, function, and tissue specificity. Because of their importance in clinical research, they are grouped into subdivisions, the so-called collagen families, and their sequences are often analysed. However, problems arise with highly homologous sequence segments. To increase the accuracy of collagen classification and prediction of their functions, the structure of these collagens and their expression in different tissues could result in a better focus on sequence segments of interest. Here, we analyse collagen families with different levels of conservation. As a result, clusters with high interconnectivity can be found, such as the fibrillar collagens, the COL4 network-forming collagens, and the COL9 FACITs. Furthermore, a large cluster between network-forming, FACIT, and COL28a1 α-chains is formed with COL6a3 as a major hub node. The formation of clusters also signifies, why it is important to always analyse the α-chains and why structural changes can have a wide range of effects on the body.https://doi.org/10.1515/jib-2024-0020α-chainsalphafoldcollagenhigh-confidence regionnetwork analysis |
| spellingShingle | Wesp Valentin Scholz Lukas Ziermann-Canabarro Janine M. Schuster Stefan Stark Heiko Constructing networks for comparison of collagen types Journal of Integrative Bioinformatics α-chains alphafold collagen high-confidence region network analysis |
| title | Constructing networks for comparison of collagen types |
| title_full | Constructing networks for comparison of collagen types |
| title_fullStr | Constructing networks for comparison of collagen types |
| title_full_unstemmed | Constructing networks for comparison of collagen types |
| title_short | Constructing networks for comparison of collagen types |
| title_sort | constructing networks for comparison of collagen types |
| topic | α-chains alphafold collagen high-confidence region network analysis |
| url | https://doi.org/10.1515/jib-2024-0020 |
| work_keys_str_mv | AT wespvalentin constructingnetworksforcomparisonofcollagentypes AT scholzlukas constructingnetworksforcomparisonofcollagentypes AT ziermanncanabarrojaninem constructingnetworksforcomparisonofcollagentypes AT schusterstefan constructingnetworksforcomparisonofcollagentypes AT starkheiko constructingnetworksforcomparisonofcollagentypes |