Figure 6

Conserved regions around the Mamu-B*008 epitopes Vif RL9 and Nef RL10 that can be targeted by HLA and Patr class I molecules. P2 and PΩ (carboxyl-terminus) represent the anchor-binding positions of the MHC class I molecules; amino acids that are preferred on these position are indicated by the conventional one-letter code, whereas amino acids indicated between brackets are tolerated. The epitopes Vif RL9 and Nef RL10 in SIV_mac239 are indicated by a red line [118]. For HIV-1 (HBX2) and SIV_cpz the consensus sequences surrounding these Vif and Nef epitopes are given (http://www.hiv.lanl.gov). A lower-case letter in the SIV_cpz consensus indicates a variable position. A red arrow indicates that the respective MHC class I molecule is predicted to target the SIV_mac239 consensus sequence. A grey arrow indicates prediction of the MHC molecule to target the SIV_cpz/HBX2 consensus sequence. SB stands for solid binding (affinity < 100 nM); WB stands for weak binding (affinity between 100 to 700 nM). Binding affinity of the peptides was predicted using the NetMHCpan algorithm [119], except for Patr-B*03:01 (white dotted arrows), for which binding was assumed based on agreement in the anchor binding positions.