AN IN SILICO PRIMARY AND SECONDARY STRUCTURE PREDICTION OF HUMAN INTERFERON ALPHA RECEPTOR 2 PROTEIN
Background: Structural analysis of human interferon alpha receptor 2 (IFNAR-2) protein is important to determine its structure and function because that information is needed to understand the role and mechanism of IFNAR-2 protein in human immune system. Therefore, this study was conducted to find out composition of amino acids contributing in primary and secondary structure of IFNAR-2 protein. Methods: Protein sequences of human IFNAR-2 were retrieved from â€˜The Universal Protein Resource (UniProt)â€™ and â€˜National Center for Biotechnology Information (NCBI)â€™ databases. The Basic Local Alignment Search Tool (BLAST) was used to search for every IFNAR-2 protein sequence in NCBI database. Human IFNAR-2 protein sequences were further refined according to set criteria for experimental analysis. All retrieved IFNAR-2 protein sequences were aligned by using computational tool â€˜Clustal Omegaâ€™. Consensus protein sequence was obtained from aligned protein dataset. Furthermore, consensus protein sequence of IFNAR-2 was subjected for secondary structure prediction analysis. Protein topology was predicted by using Expert Protein Analysis System (ExPASy) server and Transmembrane Helices; Hidden Markov Model. Results: Alignment data set revealed that IFNAR-2 protein consisted of 515 amino acids long chain, having total 37 identical positions with 6.446% identity. Protein topology analysis predicted that human IFNAR-2 protein consists of verities of secondary structures such as alpha-helix, turn and beta sheets. Alpha-helixes mainly form three topological domains (i) inner (1â€“6 amino acids), (ii) outer (7â€“29 amino acids) and (iii) trans-membrane domain (30â€“515 amino acids). Conclusion: Human IFNAR-2 protein consists of 515 amino acids having hydrophobic, polar and aromatic characteristics. Alpha-helixes, turn, beta sheets and three topological domains constitute secondary structure and predicted topological domains contribute in the subcellular compartmentalization.
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