An in Silico Primary and Secondary Structure Prediction of Human Interferon Alpha Receptor 2 Protein. | [Pakistan Journal of Physiology • 2018]

Author(s):

1. Gulshan Ara Trali: Department of Biochemistry, HITEC-Institute of Medical Sciences, Taxila Cantt, Pakistan

2. Ambreen Javed: Department of Biochemistry, HITEC-Institute of Medical Sciences, Taxila Cantt, Pakistan

3. Alia Sadiq: Department of Biochemistry, HITEC-Institute of Medical Sciences, Taxila Cantt, Pakistan

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.

Page(s): 40-43

DOI: DOI not available

Published: Journal: Pakistan Journal of Physiology, Volume: 14, Issue: 1, Year: 2018

Keywords:

Keywords are not available for this article.

References:

[1] SinghN,UpadhyayS,JaiswarA,MishraN., 2016.In silico Analysis of Protein,J Bioinform Genomics Proteomics 1 1007 -

[2] NovickD,CohenB,RubinsteinM., 1994.The human interferon alpha/beta receptor: characterization and molecular cloning,Cell 77 391 -400

[3] KumaranJ,ColamoniciOR,FishEN, 2000.Structure-function study of the extracellular domain of the human type I interferon receptor (IFNA)-1 subunit,J Interferon Cytokine Res 20 479 -85

[4] de WeerdNA,NguyenT., 2012.The interferons and their receptors, distribution and regulation,Immunol Cell Biol 90 483 -91

[5] NagaokiY,ImamuraM,AikataH,DaijoK1,TeraokaY1,HondaF, 2017.The risks of hepatocellular carcinoma development after HCV eradication are similar between patients treated with peg-interferon plus ribavirin and direct-acting antiviral therapy,PLoS One 12 e0182710d -

[6] SalemR,MillerFH,YaghmaiV,LewandowskiRJ, 2013.Efficacy of interferon-based antiviral therapy on the risk of hepatocellular carcinoma of patients with chronic hepatitis C: Further evidence in decompensation cirrhosis,J Hepatol 58 1258 -66

[7] SongX,JinP,QinS,ChenL, 2012.The Evolution and Origin of Animal Toll-Like Receptor Signaling Pathway Revealed by Network-Level Molecular Evolutionary Analyses,PLoS One 7 e51657 -

[8] Söding, 2005.Protein homology detection by HMM-HMM comparison',Bioinformatics 21 951 -60

[9] ErtugrulF,IbrahimK., 2014.In silico sequence analysis and homology modeling of predicted beta-amylase 7-like protein in Brachypodium distachyon L,J BioSci Biotech 3 61 -7

[10] ArtimoP,JonnalageddaM,ArnoldK,BaratinD,CsardiG,de CastroE, 2012.ExPASy: SIB bioinformatics resource portal,Nucleic Acids Res 40 W597 -603

[11] LailaCR,JacobP,Jean-YvesT,HaroldAS,GideonS., 2001.Structure of the interferon-receptor complex determined by distance constraints from double-mutant cycles and flexible docking,PNAS 98 13231 -6

[12] de WeerdNA,SamarajiwaSA,HertzogPJ,BiologicalFunctions, 2007.Type I Interferon Receptors: Biochemistry,J Biol Chem 282 20053 -7

[13] HuayuX,BrianLB,Hong-mingS,MichaelHH, 1995.Periodicity of polar and nonpolar amino acids is the major determinant of secondary structure in self-assembling oligomeric peptides,Proc Natl Acad Sci USA 92 6349 -53

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