Generation of in silico predicted coxsackievirus B3-derived MHC class I epitopes by proteasomes.
Proteasomes are known to be the main suppliers of MHC class I (MHC-I) ligands. In an attempt to identify coxsackievirus B3 (CVB3)-MHC-I epitopes, a combined approach of in silico MHC-I/transporters associated with antigen processing (TAP)-binding and proteasomal cleavage prediction was applied. Accordingly, 13 potential epitopes originating from the structural and non-structural protein region of CVB3 were selected for further in vitro processing analysis by proteasomes. Mass spectrometry demonstrated the generation of seven of the 13 predicted MHC-I ligands or respective ligand precursors by proteasomes. Detailed processing analysis of three adjacent MHC-I ligands with partially overlapping sequences, i.e. VP2(273-281), VP2(284-292) and VP2(285-293), revealed the preferential generation predominantly of the VP2(285-293) epitope by immunoproteasomes due to altered cleavage site preferences. The VP2(285-293) peptide was identified to be a high affinity binder, rendering VP2(285-293) a likely candidate for CD8 T cell immunity in CVB3 infection. In conclusion, the concerted usage of different in silico prediction methods and in vitro epitope processing/presentation studies was supportive in the identification of CVB3 MHC-I epitopes.
Voigt
Antje
A
Clinic for Cardiology and Angiology, Charité-Universitätsmedizin Berlin, Campus Mitte, 10117, Berlin, Germany.
Jäkel
Sandra
S
Textoris-Taube
Kathrin
K
Keller
Christin
C
Drung
Ilse
I
Szalay
Gudrun
G
Klingel
Karin
K
Henklein
Peter
P
Stangl
Karl
K
Kloetzel
Peter M
PM
Kuckelkorn
Ulrike
U
D000818:Animals; D019295:Computational Biology; D029822:Enterovirus B, Human / Q000737:chemistry* / Q000276:immunology*; D000939:Epitopes / Q000276:immunology* / Q000378:metabolism*; D015395:Histocompatibility Antigens Class I / Q000276:immunology*; D008024:Ligands; D051379:Mice; D008810:Mice, Inbred C57BL; D046988:Proteasome Endopeptidase Complex / Q000378:metabolism*
D000939:Epitopes; D015395:Histocompatibility Antigens Class I; D008024:Ligands; D046988:Proteasome Endopeptidase Complex