How that peptides containing Protease epitopes overlap with regions expected to
How that peptides containing Protease epitopes overlap with regions expected to be under pharmacologic selection pressure in those persons fortunate to have access to Protease inhibitor therapy.Page 9 of(page number not for citation purposes)Journal of Translational Medicine 2004,http://www.translational-medicine.com/content/2/1/Amino acid position 1 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1 0 Clade B sequences, smoothed (n=34) All sequences, smoothed (n=155) Number of subjects with responsesFigure 4 Correlation of amino acid sequence variability with MGCD516 site frequency of CD8 T cell responses targeting Protease. Correlation of amino acid sequence variability with frequency of CD8 T cell responses targeting Protease. For Protease, amino acid sequences were obtained from at the HIV-1 Molecular Immunology Database (27), and aligned relative to the HIV-1 clade B consensus sequence. Entropy scores for each amino acid residue were calculated based on this alignment, smoothed over nine amino acids, and plotted for all sequences (n=155, blue line, left axis) and clade B sequences only (n=34, red line, left axis). Entropy scores of 1 correspond to 100 conserved residues, while lower scores (plotted here on an inverse scale) correspond to increasing sequence variability. The number of responses in the 56 study subjects against peptides containing each amino acid was also plotted (purple line, right axis) to correlate regions with high sequence variability with regions targeted by CD8 T cells. Spearman’s rank-order correlation coefficient was calculated to correlate CD8 T cell responses against sequence variability for each protein.67ProteaseClade B, rs = -0.20, P = 0.02 All sequences, rs = -0.004, P = 0.Number of CD8+ T lymphocyte responsesNormalized entropyPage 10 of(page number not for citation purposes)Journal of Translational Medicine 2004,http://www.translational-medicine.com/content/2/1/Amino acid position 1 0.6 0.Normalized entropyIntegraseNumber of CD8+ T lymphocyte responsesClade B sequences, rs = -0.26, P <0.0001 All sequences, rs = -0.06, P = 0.0.7 0.75 0.8 0.85 0.9 0.95 1 Clade B sequences, smoothed (n=34) All sequences, smoothed (n=155) Number of subjects with responsesFigure 5 Correlation of amino acid sequence variability with frequency of CD8 T cell responses targeting Integrase Correlation of amino acid sequence variability with frequency of CD8 T cell responses targeting Integrase. For Integrase, amino PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/27797473 acid sequences were obtained from at the HIV-1 Molecular Immunology Database (27), and aligned relative to the HIV-1 clade B consensus sequence. Entropy scores for each amino acid residue were calculated based on this alignment, smoothed over nine amino acids, and plotted for all sequences (n = 155, blue line, left axis) and clade B sequences only (n = 34, red line, left axis). Entropy scores of 1 correspond to 100 conserved residues, while lower scores (plotted here on an inverse scale) correspond to increasing sequence variability. The number of responses in the 56 study subjects against peptides containing each amino acid was also plotted (purple line, right axis) to correlate regions with high sequence variability with regions targeted by CD8 T cells. Spearman’s rank-order correlation coefficient was calculated to correlate CD8 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26437915 T cell responses against sequence variability for each protein.Although studies of CD8 responses to the pol gene product have been conducted [10,11,39], few Protease and Integrase epitopes had been described, eve.