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Figure 6 | Retrovirology

Figure 6

From: The HIV-1 pandemic: does the selective sweep in chimpanzees mirror humankind’s future?

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 SIVmac239 are indicated by a red line [118]. For HIV-1 (HBX2) and SIVcpz the consensus sequences surrounding these Vif and Nef epitopes are given (http://www.hiv.lanl.gov). A lower-case letter in the SIVcpz consensus indicates a variable position. A red arrow indicates that the respective MHC class I molecule is predicted to target the SIVmac239 consensus sequence. A grey arrow indicates prediction of the MHC molecule to target the SIVcpz/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.

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