CHARACTERISATION AND HOMOLOGY MODELLING OF FINFISH NF-KAPPA B INHIBITOR ALPHA USING IN SILICO ANALYSIS

Abstract

     NFκB plays an important role in the immune system in all organisms. In this study, physicochemical properties and modelling of finfish NFκBIα protein was analysed using in silico approach. Finfish species: guppy (Poecilia reticulate), Bicolor damselfish (Stegastes partitus), Channel catfish (Ictalurus punctatus), Coelacanth (Latimeria chalumnae), and Australian ghostshark (Callorhinchus milii) were used in this study. Physicochemical characteristics, molecular weight (Mol. Wt.: 33160.2 – 42977.9), theoretical isoelectric point (pI: 4.37 – 5.09), extinction coefficient (EC: 17920– 37650 / 17420 – 36900), aliphatic index (AI: 85.88 – 98.83), instability index (II: 39.83 – 49.09), total number of negatively charged residues (-R: 47 – 55) and positively charged residues (+R: 19 – 29), and grand

average of hydropathicity (GRAVY: -0.611 – -0.241) were obtained. The results showed that except NFκBIα from P. reticulate all were defined as soluble proteins. Possible pairing and pattern of cysteine residues were found in all protein sequences and the most probable pattern of pairs of cysteine. Secondary structure analysis revealed approximately equal parts of random coils and helices, followed by strands. Three dimensional homology modelling for NFκBIα from finfish was performed and evaluated as credible models based on PROCHECK’s Ramachandran plot, ProQ and ProSA analysis.