Freshwater Fish Myeloid Differentiation Primary Response Protein MyD88: Characterisation and Homology Modelling by Using Computational Tools

MyD88 is a mediator to trigger the downstream signal in Toll/Toll-like receptor pathway which plays an important role in the innate immune system. In this study, computational tools were used to analyse the properties and structures of freshwater fish MyD88 proteins. The MyD88 proteins from fish species, including Cyprinus carpio Linnaeus 1758, Carassius carassius (Linnaeus 1758), Oreochromis niloticus (Linnaeus 1758), Danio rerio (Hamilton 1822), and Ictalurus punctatus (Rafinesque 1818) were used in this study. Physicochemical characterisations were performed by computing molecular weight, theoretical isoelectric point,amino acid composition, total number of positive and negative residues, extinction coefficient,instability index, aliphatic index, and grand average of hydropathicity. Cysteine residues were found in all MyD88s, excepting channel catfish MyD88; disulphide bond pattern of pairs were predicted in common carp, crucian carp, Nile tilapia and zebrafish. Random coils were dominating among secondary elements, followed by helices and strands. Three dimensional structures of proteins were analysed and validated by using PROCHECK’s Ramachandran plot,ProQ and ProSA. The results indicated that all predicted models may be used as structures for investigated fish MyD88s. This study provides basic knowledge of the properties, structures and functions of MyD88 proteins from freshwater fish species and is useful for further studies on specific functions of this protein.