AN IN SILICO PRIMARY AND SECONDARY STRUCTURE PREDICTION OF HUMAN INTERFERON ALPHA RECEPTOR 2 PROTEIN

  • Gulshan Ara Trali Associate Professor, Department of Biochemistry, HITEC Institute of Medical Sciences Taxila Cantt., Pakistan
  • Ambreen Javed Department of Biochemistry, HITEC-Institute of Medical Sciences, Taxila Cantt., Pakistan
  • Alia Sadiq Department of Biochemistry, HITEC Institute of Medical Sciences Taxila Cantt., Pakistan
Keywords: Human IFNAR-2, In silico analysis, Protein secondary structure, Subcellular compartmentalization

Abstract

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 ‘The Universal Protein Resource (UniProt)’ and ‘National Center for Biotechnology Information (NCBI)’ 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 ‘Clustal Omega’. 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 (1–6 amino acids), (ii) outer (7–29 amino acids) and (iii) trans-membrane domain (30–515 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.

Pak J Physiol 2018;14(1):40–3

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How to Cite
1.
Trali GA, Javed A, Sadiq A. AN IN SILICO PRIMARY AND SECONDARY STRUCTURE PREDICTION OF HUMAN INTERFERON ALPHA RECEPTOR 2 PROTEIN. PJP [Internet]. 1 [cited 19Aug.2018];14(1):40-. Available from: http://pjp.pps.org.pk/index.php/PJP/article/view/278