Constructing networks for comparison of collagen types.
AlphaFold
collagen
high-confidence region
network analysis
α-chains
Journal
Journal of integrative bioinformatics
ISSN: 1613-4516
Titre abrégé: J Integr Bioinform
Pays: Germany
ID NLM: 101503361
Informations de publication
Date de publication:
15 Jul 2024
15 Jul 2024
Historique:
received:
03
05
2024
accepted:
15
05
2024
medline:
13
7
2024
pubmed:
13
7
2024
entrez:
13
7
2024
Statut:
aheadofprint
Résumé
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.
Identifiants
pubmed: 38997817
pii: jib-2024-0020
doi: 10.1515/jib-2024-0020
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© 2024 the author(s), published by De Gruyter, Berlin/Boston.
Références
Huxley-Jones, J, Robertson, DL, Boot-Handford, RP. On the origins of the extracellular matrix in vertebrates. Matrix Biol 2007;26:2–11. https://doi.org/10.1016/j.matbio.2006.09.008 .
doi: 10.1016/j.matbio.2006.09.008
LeBleu, VS, MacDonald, B, Kalluri, R. Structure and function of basement membranes. Exp Biol Med 2007;232:1121–9. https://doi.org/10.3181/0703-mr-72 .
doi: 10.3181/0703-mr-72
Patino, MG, Neiders, ME, Andreana, S, Noble, B, Cohen, RE. Collagen: an overview. Implant Dent 2002;11:280–5. https://doi.org/10.1097/00008505-200207000-00014 .
doi: 10.1097/00008505-200207000-00014
Salamito, M, Nauroy, P, Ruggiero, F. The collagen superfamily: everything you always wanted to know. In: The collagen superfamily and collagenopathies . Berlin, Germany: Springer; 2021, 8:1–22 pp.
Ahmed, MS, Kamruzzaman, M, Rana, M, Akond, Z, Mollah, M. In silico analyses of human collagen protein function prediction. J Biol Sci 2016;24:55–65.
Bornstein, P, Sage, H. Structurally distinct collagen types. Annu Rev Biochem 1980;49:957–1003. https://doi.org/10.1146/annurev.bi.49.070180.004521 .
doi: 10.1146/annurev.bi.49.070180.004521
Kucharz, EJ. The collagens: biochemistry and pathophysiology . Berlin, Germany: Springer Science & Business Media; 2012.
Miller, EJ, Gay, S. Collagen: an overview. Methods Enzymol 1982;82:3–32. https://doi.org/10.1016/0076-6879(82)82058-2 .
doi: 10.1016/0076-6879(82)82058-2
Zhao, C, Xiao, Y, Ling, S, Pei, Y, Ren, J. Structure of collagen. Fibrous proteins: design, synthesis, and assembly . In: Ling, S. (eds) Fibrous proteins. methods in molecular biology . New York, NY: Humana; 2021, 2347:17–25 pp.
van Der Rest, M, Garrone, R. Collagen family of proteins. Faseb J 1991;5:2814–23. https://doi.org/10.1096/fasebj.5.13.1916105 .
doi: 10.1096/fasebj.5.13.1916105
Tajbakhsh, S, Spörle, R. Somite development: constructing the vertebrate body. Cell 1998;92:9–16. https://doi.org/10.1016/s0092-8674(00)80894-6 .
doi: 10.1016/s0092-8674(00)80894-6
Duband, JL, Thiery, JP. Distribution of laminin and collagens during avian neural crest development. Development 1987;101:461–78. https://doi.org/10.1242/dev.101.3.461 .
doi: 10.1242/dev.101.3.461
Leivo, I, Vaheri, A, Timpl, R, Wartiovaara, J. Appearance and distribution of collagens and laminin in the early mouse embryo. Dev Biol 1980;76:100–14. https://doi.org/10.1016/0012-1606(80)90365-6 .
doi: 10.1016/0012-1606(80)90365-6
Gonçalves, TJM, Boutillon, F, Lefebvre, S, Goffin, V, Iwatsubo, T, Wakabayashi, T, et al.. Collagen XXV promotes myoblast fusion during myogenic differentiation and muscle formation. Sci Rep 2019;9:5878. https://doi.org/10.1038/s41598-019-42296-6 .
doi: 10.1038/s41598-019-42296-6
Gordon, MK, Hahn, RA. Collagens. Cell Tissue Res 2010;339:247–57. https://doi.org/10.1007/s00441-009-0844-4 .
doi: 10.1007/s00441-009-0844-4
Mayne, R, Brewton, RG. New members of the collagen superfamily. Curr Opin Cell Biol 1993;5:883–90. https://doi.org/10.1016/0955-0674(93)90039-s .
doi: 10.1016/0955-0674(93)90039-s
Maynes, R. Structure and function of collagen types . Orlando, FL: Elsevier; 2012.
Vuorio, E, de Crombrugghe, B. The family of collagen genes. Annu Rev Biochem 1990;59:837–72. https://doi.org/10.1146/annurev.biochem.59.1.837 .
doi: 10.1146/annurev.biochem.59.1.837
Ricard-Blum, S. The collagen family. Cold Spring Harbor Perspect Biol 2011;3:a004978. https://doi.org/10.1101/cshperspect.a004978 .
doi: 10.1101/cshperspect.a004978
Exposito, JY, Valcourt, U, Cluzel, C, Lethias, C. The fibrillar collagen family. Int J Mol Sci 2010;11:407–26. https://doi.org/10.3390/ijms11020407 .
doi: 10.3390/ijms11020407
Franzke, CW, Tasanen, K, Schumann, H, Bruckner-Tuderman, L. Collagenous transmembrane proteins: collagen XVII as a prototype. Matrix Biol 2003;22:299–309. https://doi.org/10.1016/s0945-053x(03)00051-9 .
doi: 10.1016/s0945-053x(03)00051-9
Knupp, C, Squire, JM. Molecular packing in network-forming collagens. Adv Protein Chem 2005;70:375–403. https://doi.org/10.1016/s0065-3233(05)70011-5 .
doi: 10.1016/s0065-3233(05)70011-5
Ricard-Blum, S, Ruggiero, F. The collagen superfamily: from the extracellular matrix to the cell membrane. Pathol Biol 2005;53:430–42. https://doi.org/10.1016/j.patbio.2004.12.024 .
doi: 10.1016/j.patbio.2004.12.024
Brodsky, B, Persikov, AV. Molecular structure of the collagen triple helix. Adv Protein Chem 2005;70:301–39. https://doi.org/10.1016/s0065-3233(05)70009-7 .
doi: 10.1016/s0065-3233(05)70009-7
Connizzo, BK, Yannascoli, SM, Soslowsky, LJ. Structure–function relationships of postnatal tendon development: a parallel to healing. Matrix Biol 2013;32:106–16. https://doi.org/10.1016/j.matbio.2013.01.007 .
doi: 10.1016/j.matbio.2013.01.007
McAlinden, A, Smith, TA, Sandell, LJ, Ficheux, D, Parry, DA, Hulmes, DJ. α-Helical coiled-coil oligomerization domains are almost ubiquitous in the collagen superfamily. J Biol Chem 2003;278:42200–7. https://doi.org/10.1074/jbc.m302429200 .
doi: 10.1074/jbc.m302429200
Francomano, CA. Key role for a minor collagen. Nat Genet 1995;9:6–8. https://doi.org/10.1038/ng0195-6 .
doi: 10.1038/ng0195-6
Brinckmann, J. Collagens at a glance. In: Collagen: Primer in Structure, Processing and Assembly . Springer; 2005, 247:1–6 pp.
Gelse, K, Pöschl, E, Aigner, T. Collagens—structure, function, and biosynthesis. Adv Drug Deliv Rev 2003;55:1531–46. https://doi.org/10.1016/j.addr.2003.08.002 .
doi: 10.1016/j.addr.2003.08.002
Hulmes, D. Collagen diversity, synthesis and assembly. In: Collagen: structure and mechanics . Springer; 2008:15–47 pp.
Linsenmayer, T. Collagen. In: Cell Biology of Extracellular Matrix , 2nd ed Springer; 1991:7–44 pp.
Birk, DE, Bruckner, P. Collagen suprastructures. In: Collagen: primer in structure, processing and assembly ; 2005:185–205 pp.
Fratzl, P. Collagen: structure and mechanics, an introduction. In: Collagen: Structure and Mechanics . Springer; 2008:1–13 pp.
Goh, KL, Listrat, A, Béchet, D. Hierarchical mechanics of connective tissues: integrating insights from nano to macroscopic studies. J Biomed Nanotechnol 2014;10:2464–507. https://doi.org/10.1166/jbn.2014.1960 .
doi: 10.1166/jbn.2014.1960
Heino, J. The collagen family members as cell adhesion proteins. Bioessays 2007;29:1001–10. https://doi.org/10.1002/bies.20636 .
doi: 10.1002/bies.20636
Nimni, ME, Harkness, RD. Molecular structure and functions of collagen. In: Collagen , 1st ed. CRC Press; 2018:1–78 pp.
Kim, MS, Pinto, SM, Getnet, D, Nirujogi, RS, Manda, SS, Chaerkady, R, et al.. A draft map of the human proteome. Nature 2014;509:575–81. https://doi.org/10.1038/nature13302 .
doi: 10.1038/nature13302
Uhlén, M, Fagerberg, L, Hallström, BM, Lindskog, C, Oksvold, P, Mardinoglu, A, et al.. Tissue-based map of the human proteome. Science 2015;347:1260419. https://doi.org/10.1126/science.1260419 .
doi: 10.1126/science.1260419
Oh, SP, Griffith, CM, Hay, ED, Olsen, BR. Tissue-specific expression of type XII collagen during mouse embryonic development. Dev Dynam 1993;196:37–46. https://doi.org/10.1002/aja.1001960105 .
doi: 10.1002/aja.1001960105
Arseni, L, Lombardi, A, Orioli, D. From structure to phenotype: impact of collagen alterations on human health. Int J Mol Sci 2018;19:1407. https://doi.org/10.3390/ijms19051407 .
doi: 10.3390/ijms19051407
Jumper, J, Evans, R, Pritzel, A, Green, T, Figurnov, M, Ronneberger, O, et al.. Highly accurate protein structure prediction with AlphaFold. Nature 2021;596:583–9. https://doi.org/10.1038/s41586-021-03819-2 .
doi: 10.1038/s41586-021-03819-2
Varadi, M, Anyango, S, Deshpande, M, Nair, S, Natassia, C, Yordanova, G, et al.. AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res 2022;50:D439–44. https://doi.org/10.1093/nar/gkab1061 .
doi: 10.1093/nar/gkab1061
Brown, JC, Timpl, R. The collagen superfamily. Int Arch Allergy Immunol 1995;107:484–90. https://doi.org/10.1159/000237090 .
doi: 10.1159/000237090
Beck, K, Brodsky, B. Supercoiled protein motifs: the collagen triple-helix and the α-helical coiled coil. J Struct Biol 1998;122:17–29. https://doi.org/10.1006/jsbi.1998.3965 .
doi: 10.1006/jsbi.1998.3965
Marro, J, Pfefferli, C, de Preux Charles, AS, Bise, T, Jaźwińska, A. Collagen XII contributes to epicardial and connective tissues in the zebrafish heart during ontogenesis and regeneration. PLoS One 2016;11:e0165497. https://doi.org/10.1371/journal.pone.0165497 .
doi: 10.1371/journal.pone.0165497
Mereness, JA, Mariani, TJ. The critical role of collagen VI in lung development and chronic lung disease. Matrix Biol Plus 2021;10:100058. https://doi.org/10.1016/j.mbplus.2021.100058 .
doi: 10.1016/j.mbplus.2021.100058
Kuivaniemi, H, Tromp, G, Prockop, DJ. Mutations in collagen genes: causes of rare and some common diseases in humans. Faseb J 1991;5:2052–60. https://doi.org/10.1096/fasebj.5.7.2010058 .
doi: 10.1096/fasebj.5.7.2010058
Nassa, M, Anand, P, Jain, A, Chhabra, A, Jaiswal, A, Malhotra, U, et al.. Analysis of human collagen sequences. Bioinformation 2012;8:26. https://doi.org/10.6026/97320630008026 .
doi: 10.6026/97320630008026
Mak, KM, Png, CYM, Lee, DJ. Type V collagen in health, disease, and fibrosis. Anat Rec 2016;299:613–29. https://doi.org/10.1002/ar.23330 .
doi: 10.1002/ar.23330
Imamura, Y, Scott, IC, Greenspan, DS. The Pro-α3 (V) Collagen Chain: complete primary structure, expression domains in adult and developing tissues, and comparison to the structures and expression domains of the other types V and XI procollagen chains. J Biol Chem 2000;275:8749–59. https://doi.org/10.1074/jbc.275.12.8749 .
doi: 10.1074/jbc.275.12.8749
Steinmann, B, Royce, PM, Superti-Furga, A. The Ehlers-Danlos syndrome. In: Connective tissue and its heritable disorders: molecular, genetic, and medical aspects , 1st ed. Springer; 2002, 802:431–523 pp.
Malfait, F, Wenstrup, RJ, De Paepe, A. Clinical and genetic aspects of Ehlers-Danlos syndrome, classic type. Genet Med 2010;12:597–605. https://doi.org/10.1097/gim.0b013e3181eed412 .
doi: 10.1097/gim.0b013e3181eed412
Khoshnoodi, J, Pedchenko, V, Hudson, BG. Mammalian collagen IV. Microsc Res Tech 2008;71:357–70. https://doi.org/10.1002/jemt.20564 .
doi: 10.1002/jemt.20564
Roig-Rosello, E, Rousselle, P. The human epidermal basement membrane: a shaped and cell instructive platform that aging slowly alters. Biomolecules 2020;10:1607. https://doi.org/10.3390/biom10121607 .
doi: 10.3390/biom10121607
Brittingham, R, Uitto, J, Fertala, A. High-affinity binding of the NC1 domain of collagen VII to laminin 5 and collagen IV. Biochem Biophys Res Commun 2006;343:692–9. https://doi.org/10.1016/j.bbrc.2006.03.034 .
doi: 10.1016/j.bbrc.2006.03.034
De Gregorio, V, Caparali, EB, Shojaei, A, Ricardo, S, Barua, M. Alport syndrome: clinical Spectrum and therapeutic advances. Kidney Med 2023;5:100631. https://doi.org/10.1016/j.xkme.2023.100631 .
doi: 10.1016/j.xkme.2023.100631
Imafuku, A, Nozu, K, Sawa, N, Hasegawa, E, Hiramatsu, R, Kawada, M, et al.. Autosomal dominant form of type IV collagen nephropathy exists among patients with hereditary nephritis difficult to diagnose clinicopathologically. Nephrology 2018;23:940–7. https://doi.org/10.1111/nep.13115 .
doi: 10.1111/nep.13115
Shulman, C, Liang, E, Kamura, M, Udwan, K, Yao, T, Cattran, D, et al.. Type IV collagen variants in CKD: performance of computational predictions for identifying pathogenic variants. Kidney Med 2021;3:257–66. https://doi.org/10.1016/j.xkme.2020.12.007 .
doi: 10.1016/j.xkme.2020.12.007
Deltas, C. Pos-435 next generation sequencing identifies candidate genetic modifiers potentially exacerbating kidney disease in col4a3/a4 heterozygous patients. Kidney Int Rep 2022;7:S194. https://doi.org/10.1016/j.ekir.2022.01.462 .
doi: 10.1016/j.ekir.2022.01.462
Cascella, R, Strafella, C, Caputo, V, Errichiello, V, Zampatti, S, Milano, F, et al.. Towards the application of precision medicine in Age-Related Macular Degeneration. Prog Retinal Eye Res 2018;63:132–46. https://doi.org/10.1016/j.preteyeres.2017.11.004 .
doi: 10.1016/j.preteyeres.2017.11.004
Zhang, J, Patel, DV. The pathophysiology of Fuchs’ endothelial dystrophy–a review of molecular and cellular insights. Exp Eye Res 2015;130:97–105. https://doi.org/10.1016/j.exer.2014.10.023 .
doi: 10.1016/j.exer.2014.10.023
Cescon, M, Gattazzo, F, Chen, P, Bonaldo, P. Collagen VI at a glance. J Cell Sci 2015;128:3525–31. https://doi.org/10.1242/jcs.169748 .
doi: 10.1242/jcs.169748
Tonelotto, V, Trapani, V, Bretaud, S, Heumüller, SE, Wagener, R, Ruggiero, F, et al.. Spatio-temporal expression and distribution of collagen VI during zebrafish development. Sci Rep 2019;9:19851. https://doi.org/10.1038/s41598-019-56445-4 .
doi: 10.1038/s41598-019-56445-4
Bushby, KM, Collins, J, Hicks, D. Collagen type VI myopathies. In: Progress in Heritable Soft Connective Tissue Diseases , 1st ed. Springer; 2014, 802:185–99 pp.
Murphy, AP, Straub, V. The classification, natural history and treatment of the limb girdle muscular dystrophies. J Neuromuscul Dis 2015;2:S7–19. https://doi.org/10.3233/jnd-150105 .
doi: 10.3233/jnd-150105
Dowling, P, Gargan, S, Murphy, S, Zweyer, M, Sabir, H, Swandulla, D, et al.. The dystrophin node as integrator of cytoskeletal organization, lateral force transmission, fiber stability and cellular signaling in skeletal muscle. Proteomes 2021;9:9. https://doi.org/10.3390/proteomes9010009 .
doi: 10.3390/proteomes9010009
Robin, NH, Moran, RT, Ala-Kokko, L. Stickler syndrome . In: GeneReviews®, 1993 . Seattle, WA: GeneReviews, University of Washington; 2021.
Trainor, PA, Krumlauf, R. Hox genes, neural crest cells and branchial arch patterning. Curr Opin Cell Biol 2001;13:698–705. https://doi.org/10.1016/s0955-0674(00)00273-8 .
doi: 10.1016/s0955-0674(00)00273-8
Liu, Q, Gibson, MP, Sun, H, Qin, C. Dentin sialophosphoprotein (DSPP) plays an essential role in the postnatal development and maintenance of mouse mandibular condylar cartilage. J Histochem Cytochem 2013;61:749–58. https://doi.org/10.1369/0022155413502056 .
doi: 10.1369/0022155413502056
Marneros, AG, Olsen, BR. The role of collagen-derived proteolytic fragments in angiogenesis. Matrix Biol 2001;20:337–45. https://doi.org/10.1016/s0945-053x(01)00151-2 .
doi: 10.1016/s0945-053x(01)00151-2
Seppinen, L, Pihlajaniemi, T. The multiple functions of collagen XVIII in development and disease. Matrix Biol 2011;30:83–92. https://doi.org/10.1016/j.matbio.2010.11.001 .
doi: 10.1016/j.matbio.2010.11.001
Stover, DA, Verrelli, BC. Comparative vertebrate evolutionary analyses of type I collagen: potential of COL1a1 gene structure and intron variation for common bone-related diseases. Mol Biol Evol 2011;28:533–42. https://doi.org/10.1093/molbev/msq221 .
doi: 10.1093/molbev/msq221
Iozzo, RV, Gubbiotti, MA. Extracellular matrix: the driving force of mammalian diseases. Matrix Biol 2018;71:1–9. https://doi.org/10.1016/j.matbio.2018.03.023 .
doi: 10.1016/j.matbio.2018.03.023
Fichtner, M, Schuster, S, Stark, H. Determination of scoring functions for protein damage susceptibility. Biosystems 2020;187:104035. https://doi.org/10.1016/j.biosystems.2019.104035 .
doi: 10.1016/j.biosystems.2019.104035