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Comparative Analysis And Characterization Of Various Syndromes Associated Human Collagen Proteins Using Computational Tools And Online Servers

K.Sivakumar, S.Balaji, Ganga Radhakrishnan

Collagen is the most abundant protein in the human body. Collagen forms a major part of connective tissue, which can be described as the supportive tissue of the organs of the body. Defect in collagen causes various syndromes. Here, we report the analysis and characterization studies on various syndromes [Alport syndrome (AS), Ehlers–Danlos syndrome (EDS), Goodpasture’s syndrome (GPS) and Stickler syndrome (SS)] associated 13 human collagen proteins retrieved from Swiss- Prot database to provide more detailed description about these proteins. The results of primary structure analysis suggest that the AS, EDS and SS associated collagen proteins are rich in glycine (23% to 28%) and proline (15% to 23%) residues. The GPS associated collagen protein is rich in Glu (9%) and Ser (9%) residues. The computed pI values of collagens P02452, P02461, P20908, P05997 (EDS associated proteins), the collagen Q9Y5P4 (GPS associated protein), the collagens P12107, P13942 (SS associated collagens) reveals that these are acidic (pI<7) in character. The computed pI of all alport syndrome associated human collagen proteins (P29400, P53420, Q01955 and Q14031), the protein P08123 (EDS associated collagen) and the protein P02458 (SS associated collagen) infers that these are basic (pI>7) in character. The number of basic and acidic amino acids in each collagen proteins correlates well with the corresponding pI computed. The low aliphatic index (37-59) of most of the syndromes associated proteins infers that the collagen proteins may become unstable at high temperature. The biocomputed half-life of AS, GPS and SS associated collagen is 30hrs and greater than 20hrs for EDS associated collagens. Expasy’s ProtParam classifies the GPS associated collagen as unstable on the basis of instability index (II>40) and all the other collagen proteins as stable (II<40). Secondary structure analysis shows that all the collagens are found to be predominant coil structure content. The SSCP server classifies the GPS associated collagen (Q9Y5P4) as mixed secondary structure class and all the other collagens as irregular secondary structure class proteins. The irregular structure of collagen proteins is due to the rich content of more flexible glycine and hydrophobic proline amino acids. The server SOSUI classifies all the four AS associated collagen proteins and the protein P02458 (SS associated collagen protein) as membrane protein and all the other proteins as soluble proteins. The identified transmembrane regions were visualized and analyzed using helical wheel plot generated by EMBOSS pepwheel tool and it is found that the helical wheel consists of more hydrophobic residues. This is the first report on characterization and comparative studies of AS, EDS, GPS and SS associated human collagen proteins.