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

Authors

  • 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

DOI:

https://doi.org/10.69656/pjp.v14i1.278

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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Pak J Physiol 2018;14(1)

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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. Pak J Phsyiol [Internet]. 2018 Mar. 31 [cited 2024 Nov. 21];14(1):40-3. Available from: https://pjp.pps.org.pk/index.php/PJP/article/view/278

Issue

Vol. 14 No. 1 (2018): Pakistan Journal of Physiology

Section

Original Article

License

Pakistan Journal of Physiology, Pak J Physiol, PJP is FREE for research and academic purposes. It can be freely downloaded and stored, printed, presented, projected, cited and quoted with full reference of, and acknowledgement to the author(s) and the PJP. The contents are published with an international CC-BY-ND-4.0 License.