Bioinformatic Analysis of Human Collagen Sequence Mutations on Osteogenesis Imperfecta

Öz

Collagen has been implicated in a number of pathological conditions. When an amino acid in triple helix is replaced with other amino acids, the collagen structure is destroyed. The deterioration in the collagen structure causes various hereditary diseases and dysfunctions. In this study, the mutations on the alpha-1 chain of type I collagen, which is the most common in the human body, were examined using Python programming language. Based on the previous studies, brittle bone disease (OI) type 2 caused by mutations in type-I collagen alpha-1 chains, has been focused on. UniprotKB database were used for the mutations reported. The mutations obtained were combined in an alpha-I chain and it was seen that the most mutated amino acid was glycine (Gly). Since glycine amino acid affects the stability of the helix structure of the collagen alpha-I chain, it can be considered to influence collagen-induced diseases. The most frequently recurring mutations (glycine (G)> arginine (R), glycine (G)> serine (S), glycine (G)>aspartate (D)) were detected. As a result of comparison, increase in molecular mass, change in isoelectric point, decrease in hydropathy index, change in charge state and acid-base properties were observed. The effect of these changed features on brittle bone disease (OI) has been interpreted.

Anahtar Kelimeler

• Alpha-1 chain
• Collagen
• Extracellular matrix
• Osteogenesis imperfecta
• Python

Kaynakça

1. Cen, L., et al., Collagen tissue engineering: development of novel biomaterials and applications. Pediatric research, 2008. 63(5): p. 492-496.
2. Ileana, R. and K. Francois, Biopolymers for application in photonics. NBI-technologies, 2014(4).
3. Gelse, K., E. Pöschl, and T. Aigner, Collagens—structure, function, and biosynthesis. Advanced drug delivery reviews, 2003. 55(12): p. 1531-1546.
4. Rauch, F. and F.H. Glorieux, Osteogenesis imperfecta. The Lancet, 2004. 363(9418): p. 1377-1385.
5. Bodian, D.L., et al., Predicting the clinical lethality of osteogenesis imperfecta from collagen glycine mutations. Biochemistry, 2008. 47(19): p. 5424-5432.
6. van Dijk, F.S., et al., Lethal/severe osteogenesis imperfecta in a large family: a novel homozygous LEPRE1 mutation and bone histological findings. Pediatric and Developmental Pathology, 2011. 14(3): p. 228-234.
7. Arjadi, R., et al., A systematic review of online interventions for mental health in low and middle income countries: a neglected field. Global Mental Health, 2015. 2.
8. Bahadıroğlu, S., et al., ORGANİZMAMIZ İÇİN NİASİN.

9. Wagner, I. and H. Musso, New naturally occurring amino acids. Angewandte Chemie International Edition in English, 1983. 22(11): p. 816-828.
10. Aryal, S., Amino Acids- Properties, Structure, Classification and Functions. August 9, 2018.
11. Fforde, A., From plan to market: The economic transition in Vietnam. 2019: Routledge.
12. Idrees, M., et al., Multimodal role of amino acids in microbial control and drug development. Antibiotics, 2020. 9(6): p. 330.
13. Biro, J., Amino acid size, charge, hydropathy indices and matrices for protein structure analysis. Theoretical Biology and Medical Modelling, 2006. 3(1): p. 15.
14. Mitaku, S., T. Hirokawa, and T. Tsuji, Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane–water interfaces. Bioinformatics, 2002. 18(4): p. 608-616.
15. Bodian, D.L., et al., Mutation and polymorphism spectrum in osteogenesis imperfecta type II: implications for genotype–phenotype relationships. Human molecular genetics, 2009. 18(3): p. 463-471.
16. Nassa, M., et al., Analysis of human collagen sequences. Bioinformation, 2012. 8(1): p. 26.
17. Green, E.D., The human genome project and its impact on the study of human disease. The genetic basis of human cancer, 1997: p. 33-64.
18. Lander, E.S., et al., Erratum: Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium (Nature (2001) 409 (860-921)). Nature, 2001. 412(6846): p. 565-566.
19. Prockop, D.J., Mutations in collagen genes as a cause of connective-tissue diseases. New England Journal of Medicine, 1992. 326(8): p. 540-546.