Identification of HLA-A*0201-restricted CTL epitopes from the receptor-binding domain of MERS-CoV spike protein using a combinatorial in silico approach

Naghmeh POORINMOHAMMAD, (Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran)
Hassan MOHABATKAR (Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran)
Turkish Journal of Biology
1 0
Yıl: 2014 Cilt: 38 Sayı: 5 Sayfa Aralığı: 628 - 632 Metin Dili: İngilizce İndeks Tarihi: 29-07-2022

Identification of HLA-A*0201-restricted CTL epitopes from the receptor-binding domain of MERS-CoV spike protein using a combinatorial in silico approach

Öz:
A novel SARS-like illness called Middle East respiratory syndrome coronavirus (MERS-CoV), caused by an emerging coronavirus, has been a recent cause for concern due to its fatality and pandemic potential. Developing a peptide-based vaccine could be helpful in fighting against the virus. Since the experimental procedure is time-consuming and expensive, computational analysis can play an important role in accelerating the process. Therefore, the aim of this study was to computationally identify cytotoxic T-lymphocyte epitopes presented by the human leukocyte antigen (HLA)-A*0201, as this is the most frequent HLA class I allele among Middle Eastern populations. The receptor-binding domain of the spike glycoprotein of MERS-CoV, by which the virus binds to its entry receptor to further infect host cells, is a potential candidate used here for running our in silico epitope identification process. The results include predicted epitopes together with their interaction properties with major histocompatibility complex (MHC) molecules and also the binding behavior of MHC-epitope complexes to human T-cell receptor. Predicted epitopes with the most preferable binding properties are beneficial for vaccine development. Therefore, the huge experimental workload for epitope-based vaccine design will be minimized.
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Konular: Biyoloji
Belge Türü: Makale Makale Türü: Araştırma Makalesi Erişim Türü: Erişime Açık
  • Bhasin M, Raghava G (2007). A hybrid approach for predicting promiscuous MHC class I restricted T cell epitopes. J Biosciences 32: 31–42.
  • Comeau SR, Gatchell DW, Vajda S, Camacho CJ (2004a). ClusPro: a fully automated algorithm for protein–protein docking. Nucleic Acids Res 32: W96–W99.
  • Comeau SR, Gatchell DW, Vajda S, Camacho CJ (2004b). ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics 20: 45–50.
  • Doytchinova IA, Guan P, Flower DR (2006). EpiJen: a server for multistep T cell epitope prediction. BMC Bioinformatics 7: 131.
  • Du L, He Y, Zhou Y, Liu S, Zheng BJ, Jiang S (2009). The spike protein of SARS-CoV—a target for vaccine and therapeutic development. Nat Rev Microbiol 7: 226–236.
  • Ferrante A, Gorski J (2007). Cooperativity of hydrophobic anchor interactions: evidence for epitope selection by MHC class II as a folding process. J Immunol 178: 7181–7189.
  • Hatipoğlu İ, Söğüt İ, Ercan D, Aksu S, Sivas H, Başalp A (2013). Stimulation of dendritic cells with vaccine and vaccine- antibody complex and effect on immune response. Turk J Biol 37: 457–463.
  • He Y, Lu H, Siddiqui P, Zhou Y, Jiang S (2005). Receptor-binding domain of severe acute respiratory syndrome coronavirus spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies. J Immunol 174: 4908–4915.
  • Jiang S, Bottazzi ME, Du L, Lustigman S, Tseng CTK, Curti E, Jones K, Zhan B, Hotez PJ (2012). Roadmap to developing a recombinant coronavirus S protein receptor-binding domain vaccine for severe acute respiratory syndrome. Expert Rev Vaccines 11: 1405–1413.
  • Kaur H, Garg A, Raghava G (2007). PEPstr: a de novo method for tertiary structure prediction of small bioactive peptides. Protein Pept Lett 14: 626–631.
  • Kozakov D, Brenke R, Comeau SR, Vajda S (2006). PIPER: an FFT‐ based protein docking program with pairwise potentials. Proteins 65: 392–406.
  • Kozakov D, Hall DR, Beglov D, Brenke R, Comeau SR, Shen Y, Li K, Zheng J, Vakili P, Paschalidis IC (2010). Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13–19. Proteins 78: 3124–3130.
  • Larsen MV, Lundegaard C, Lamberth K, Buus S, Lund O, Nielsen M (2007). Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinformatics 8: 424.
  • Lisowska E (2002). The role of glycosylation in protein antigenic properties. Cell Mol Life Sci 59: 445–455.
  • Lu G, Hu Y, Wang Q, Qi J, Gao F, Li Y, Zhang Y, Zhang W, Yuan Y, Bao J (2013). Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor CD26. Nature 500: 227–231.
  • Lundegaard C, Nielsen M, Lund O (2006). The validity of predicted T-cell epitopes. Trends Biotechnol 24: 537–538.
  • Magrane M (2011). UniProt Knowledgebase: a hub of integrated protein data. Database 2011; 2011: bar009.
  • Mou H, Raj VS, van Kuppeveld FJ, Rottier PJ, Haagmans BL, Bosch BJ (2013). The receptor binding domain of the new MERS coronavirus maps to a 231-residue region in the spike protein that efficiently elicits neutralizing antibodies. J Virol 87: 9379–9383.
  • Öztürk MA (2013). Computational design of a pentapeptide inhibitor for fibroblast growth factor receptor 3b (FGFR3b). Turk J Biol 37: 675–682.
  • Peters B, Bulik S, Tampe R, Van Endert PM, Holzhütter HG (2003). Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors. J Immunol 171: 1741–1749.
  • Raj VS, Mou H, Smits SL, Dekkers DH, Müller MA, Dijkman R, Muth D, Demmers JA, Zaki A, Fouchier RA et al. (2013). Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC. Nature 495: 251–254.
  • Sheth KV, Edwards JA, Godwin JT (1985). Study of the HLA gene and antigen frequency from a Saudi Arabian hospital. Tissue Antigens 25: 156–162.
  • Szabó TG, Palotai R, Antal P, Tokatly I, Tóthfalusi L, Lund O, Nagy G, Falus A, Buzás EI (2009). Critical role of glycosylation in determining the length and structure of T cell epitopes. Immunome Res 5: 4.
  • Valluei V, Mustafa M, Santhosh A, Middleton D, Alvales M, El Haj E, Gumama O, Abdel‐Waieth L (2005). Frequencies of HLA‐A, HLA‐B, HLA‐DR, and HLA‐DQ phenotypes in the United Arab Emirates population. Tissue Antigens 66: 107–113.
  • Wang N, Shi X, Jiang L, Zhang S, Wang D, Tong P, Guo D, Fu L, Cui Y, Liu X et al. (2013). Structure of MERS-CoV spike receptor- binding domain complexed with human receptor DPP4. Cell Res 23: 986–993.
  • Wodarz D, Nowak MA (2000). Correlates of cytotoxic T–lymphocyte– mediated virus control: implications for immunosuppressive infections and their treatment. Philos T R Soc Lon B 355: 1059–1070.
  • Zaki AM, van Boheemen S, Bestebroer TM, Osterhaus AD, Fouchier RA (2012). Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. New Engl J Med 367: 1814–1820.
APA POORINMOHAMMAD N, MOHABATKAR H (2014). Identification of HLA-A*0201-restricted CTL epitopes from the receptor-binding domain of MERS-CoV spike protein using a combinatorial in silico approach. , 628 - 632.
Chicago POORINMOHAMMAD Naghmeh,MOHABATKAR Hassan Identification of HLA-A*0201-restricted CTL epitopes from the receptor-binding domain of MERS-CoV spike protein using a combinatorial in silico approach. (2014): 628 - 632.
MLA POORINMOHAMMAD Naghmeh,MOHABATKAR Hassan Identification of HLA-A*0201-restricted CTL epitopes from the receptor-binding domain of MERS-CoV spike protein using a combinatorial in silico approach. , 2014, ss.628 - 632.
AMA POORINMOHAMMAD N,MOHABATKAR H Identification of HLA-A*0201-restricted CTL epitopes from the receptor-binding domain of MERS-CoV spike protein using a combinatorial in silico approach. . 2014; 628 - 632.
Vancouver POORINMOHAMMAD N,MOHABATKAR H Identification of HLA-A*0201-restricted CTL epitopes from the receptor-binding domain of MERS-CoV spike protein using a combinatorial in silico approach. . 2014; 628 - 632.
IEEE POORINMOHAMMAD N,MOHABATKAR H "Identification of HLA-A*0201-restricted CTL epitopes from the receptor-binding domain of MERS-CoV spike protein using a combinatorial in silico approach." , ss.628 - 632, 2014.
ISNAD POORINMOHAMMAD, Naghmeh - MOHABATKAR, Hassan. "Identification of HLA-A*0201-restricted CTL epitopes from the receptor-binding domain of MERS-CoV spike protein using a combinatorial in silico approach". (2014), 628-632.
APA POORINMOHAMMAD N, MOHABATKAR H (2014). Identification of HLA-A*0201-restricted CTL epitopes from the receptor-binding domain of MERS-CoV spike protein using a combinatorial in silico approach. Turkish Journal of Biology, 38(5), 628 - 632.
Chicago POORINMOHAMMAD Naghmeh,MOHABATKAR Hassan Identification of HLA-A*0201-restricted CTL epitopes from the receptor-binding domain of MERS-CoV spike protein using a combinatorial in silico approach. Turkish Journal of Biology 38, no.5 (2014): 628 - 632.
MLA POORINMOHAMMAD Naghmeh,MOHABATKAR Hassan Identification of HLA-A*0201-restricted CTL epitopes from the receptor-binding domain of MERS-CoV spike protein using a combinatorial in silico approach. Turkish Journal of Biology, vol.38, no.5, 2014, ss.628 - 632.
AMA POORINMOHAMMAD N,MOHABATKAR H Identification of HLA-A*0201-restricted CTL epitopes from the receptor-binding domain of MERS-CoV spike protein using a combinatorial in silico approach. Turkish Journal of Biology. 2014; 38(5): 628 - 632.
Vancouver POORINMOHAMMAD N,MOHABATKAR H Identification of HLA-A*0201-restricted CTL epitopes from the receptor-binding domain of MERS-CoV spike protein using a combinatorial in silico approach. Turkish Journal of Biology. 2014; 38(5): 628 - 632.
IEEE POORINMOHAMMAD N,MOHABATKAR H "Identification of HLA-A*0201-restricted CTL epitopes from the receptor-binding domain of MERS-CoV spike protein using a combinatorial in silico approach." Turkish Journal of Biology, 38, ss.628 - 632, 2014.
ISNAD POORINMOHAMMAD, Naghmeh - MOHABATKAR, Hassan. "Identification of HLA-A*0201-restricted CTL epitopes from the receptor-binding domain of MERS-CoV spike protein using a combinatorial in silico approach". Turkish Journal of Biology 38/5 (2014), 628-632.
Sayfa Oluşturulma Tarihi
22-04-2024 20:23

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