Table 2.
Conserved HIV-1-derived HLA-DRB1-restricted epitopes recognized by CD4+ T cells.
| Peptide No. | Protein (HXB2 Position) | Stimulatory Peptides | IFN-γ/TNF-α | Responder’s HLA-DRB1 | Predicted HLA-DRB1 | Reported Epitopes | Reported Epitopes’ Restriction | Epitope Core | Epitope Core HLA-DRB1 |
|---|---|---|---|---|---|---|---|---|---|
| HC003 | Gag (167–181) | EVIPMFTALSEGATP EVIPMFTALSEGAT EVIPMFTALSEGA EVIPMFTALSEG EVIPMFTALSE EVIPMFTALS |
IFN-γ ≈ TNF-α | *04:01 *07:01 | *04:01 *07:01 |
PMFTALSEGAT PEVIPMFSALSEGA EVIPMFSALS |
Human DR1 *01:01 DR4 |
EVIPMFTALS FTALSEGAT VIPMFT LSEGAT |
*04:01 *04:01 *07:01 *07:01 |
| HC017 | Gag (269–283) | GLNKIVRMYSPVSIL GLNKIVRMYSPVSI GLNKIVRMYSPVS |
IFN-γ > TNF-α | *04:01 *07:01 | *04:01 *07:01 |
GLNKIVRMYSPVSIL GLNKIVRMYSPTSIL LNKIVRMYSPVSILD LNKIVRMYSPTSILD KIVRMYSPTS KIVRMYSPT |
human *01:01 human human DR4 *01:01 |
LNKIVRMYS IVRMYS |
*04:01 *07:01 |
| LNKIVRMYSPVSIL NKIVRMYSPVSIL KIVRMYSPVSIL | |||||||||
| HC078 | Pol (270–284) | YFSVPLDEGFRKYTA FSVPLDEGFRKYTA SVPLDEGFRKYTA VPLDEGFRKYTA PLDEGFRKYTA |
IFN-γ > TNF-α IFN-γ TNF-α |
*01:01 *07:01 | |||||
| HC079 | Pol (274–288) | PLDEGFRKYTAFTIP FRKYTAFTIP |
TNF-α IFN-γ |
*01:01 *07:01 | |||||
| HC080 | Pol (278–292) | GFRKYTAFTIPSINN GFRKYTAFTIPSIN GFRKYTAFTIPSI GFRKYTAFTIPS |
IFN-γ ≈ TNF-α | *03:01 *09:01 | *07:01 | FRKYTAFTIPSINNE | DR supermotif | ||
| FRKYTAFTIPSINN RKYTAFTIPSINN KYTAFTIPSINN YTAFTIPSINN | |||||||||
| HC081 | Pol (282–296) | YTAFTIPSINNETPG TIPSINNETPG |
TNF-α IFN-γ < TNF-α |
*11:04 *15:01 | |||||
| HC088 | Pol (311–325) | GSPAIFQSSMTKILE. GSPAIFQSSMTKIL |
IFN-γ ≈ TNF-α | *03:01 *09:01 | *04:01 | GSPAIFQSSMTKILE SPAIFQSSMTKILEP |
human DR supermotif | ||
| SPAIFQSSMTKILE PAIFQSSMTKILE AIFQSSMTKILE IFQSSMTKILE FQSSMTKILE | |||||||||
| HC093 | Pol (330–344) |
KNPEIVIYQYMDDLYV KNPEIVIYQYMD NPEIVIYQYMDDLYV IVIYQYMDDLYV |
TNF-α TNF-α |
*11:04 *15:01 *01:01 *07:01 |
IVIYQYM | *15:01 | |||
| HC094 | Pol (334–348) | VIYQYMDDLYVGSDL VIYQYMDDLYVGS VIYQYMDDL |
IFN-γ < TNF-α | *11:01 *15:01 | *11:01 | ||||
| YQYMDDLYVGSDL YMDDLYVGSDL DDLYVGSDL | |||||||||
| HC102 | Vif (12–26) | ----RMRIRTWKSLVK | IFN-γ < TNF-α | *07:01 *16:01 | *07:01 | IRTWKS | *07:01 | ||
| HC103 | Vif (16–28) | MRIRTWKSLVKHH-LT MRIRTWKSLVKHH MRIRTWKSLVKH RIRTWKSLVKHH-LT |
IFN-γ < TNF-α | *07:01 *16:01 | *07:01 | ||||
| HC103 | Vif (16–28) | MRIRTWKSLVKHH-LT MRIRTWKSLVK |
IFN-γ < TNF-α | *03:01 *15:01 | *03:01 *15:01 |
IRTWKSLV | *03:01 *15:01 |
||
| HC115 | Pol (560–573) | KQ-YWQATWIPEWEFVN QATWIPEWEFVN |
IFN-γ < TNF-α | *01:02 *04:01 | |||||
| HC123 | gp160 (91–106) | KNFNMWKNDMVDQMHE FNMWKNDMVDQMHE NMWKNDMVDQMHE MWKNDMVDQMHE NDMVDQMHE |
IFN-γ < TNF-α TNF-α | *11:01 *15:01 | NVTENFNMWKNNMVEQMH | *11:01 *15:01 *15:02 |
|||
| HC145 | Pol (767–782) | GQVDCSPGIWQLDCTH GQVDCSPGIWQL GQVDCSPGIW CSPGIWQLDCTH SPGIWQLDCTH |
IFN-γ ≈ TNF-α | *13:01 *13:02 | |||||
| HC164 | Pol (891–906) | VQMAVFIHNFKRKGGI VQMAVFIHN VFIHNFKRKGGI |
IFN-γ < TNF-α | *13:01 *13:02 | *13:01 | KTAVQMAVFIHNFKR | DR supermotif | ||
| HC176 | Pol (974–988) | VVPRRKAKIIRDYGK VVPRRKAKIIR VVPRRKAKII |
IFN-γ < TNF-α | *03:01 *11:01 | *11:01 | SDIKVVPRRKAKIIR | human | ||
| VPRRKAKIIRDYGK RKAKIIRDYGK KAKIIRDYGK AKIIRDYGK | |||||||||
| HC177 | Pol (978–992) | RKAKIIRDYGKQMAG RKAKIIRDYGKQMA RKAKIIRDYGKQM RKAKIIRDYG |
IFN-γ ≈ TNF-α | *03:01 *15:01 | *03:01 | IIRDYGKQM | *03:01 | ||
| KAKIIRDYGKQMAG AKIIRDYGKQMAG KIIRDYGKQMAG IIRDYGKQMAG IRDYGKQMAG RDYGKQMAG | |||||||||
| HC178 | Pol (982–996) | IIRDYGKQMAGADCV IIRDYGKQMAG |
IFN-γ < TNF-α | *07:01 *16:01 | |||||
| HC190 | gp160 (745–760) | LLRAIEAQQHLLQLT LLRAIEAQQHLL LLRAIEAQQHL LLRAIEAQQHLLQLT IEAQQHLLQLT |
*01:02 *04:01 | *01:02 | LLRAIEAQQ | *04:01 |