Compressed sensing (CS), mutual information (MI), and ensemble classifier predictions of HIV-1 Env positions constituting bnMAb epitopes for PGT 123, 123, 125, and 126.

<p>The experimentally identified positions are defined as those at which alanine point mutations were observed to increase the measured IC₅₀ of the mutant by more than 30-fold relative to that of the wild type JR-CSF. Alanine scans were performed as part of the present work for PGT 143 and 145; data for PGT 121–135 were taken from Ref. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone.0080562-Walker2" target="_blank">[51]</a>.</p><p><i>Footnote</i>: For each of the ten HIV-1 broadly neutralizing monoclonal antibodies (bnMAb) considered in this study, we report the residues identified by the compressed sensing (CS) classifier, positions identified by the mutual information (MI) classifier, and positions identified by the ensemble classifier (formed by combining the CS and MI predictions) predicted to lie within the bnMAb epitope. The number of residues identified by the CS classifier, <i>n_CS</i>, number of positions identified by the MI classifier, <i>n_MI</i>, number of positions predicted by the ensemble classifier, <i>n_ENS</i>, and number of positions identified by alanine scans, <i>n_EXPT</i>, may differ between bnMAbs.</p

Compressed sensing (CS), mutual information (MI), and ensemble classifier predictions of HIV-1 Env positions constituting bnMAb epitopes for PGT 127, 128, and 130.

<p>The experimentally identified positions are defined as those at which alanine point mutations were observed to increase the measured IC₅₀ of the mutant by more than 30-fold relative to that of the wild type JR-CSF. Alanine scans were performed as part of the present work for PGT 143 and 145; data for PGT 121–135 were taken from Ref. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone.0080562-Walker2" target="_blank">[51]</a>.</p><p><i>Footnote</i>: See footnote to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone-0080562-t001" target="_blank">Table 1</a>.</p

Compressed sensing (CS), mutual information (MI), and ensemble classifier predictions of HIV-1 Env positions constituting bnMAb epitopes for PGT 135, 143, and 145.

<p>The experimentally identified positions are defined as those at which alanine point mutations were observed to increase the measured IC₅₀ of the mutant by more than 30-fold relative to that of the wild type JR-CSF. Alanine scans were performed as part of the present work for PGT 143 and 145; data for PGT 121–135 were taken from Ref. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone.0080562-Walker2" target="_blank">[51]</a>.</p><p><i>Footnote</i>: See footnote to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone-0080562-t001" target="_blank">Table 1</a>.</p

Mutual information (MI) selection of PGT-123 epitope positions.

<p>The redundancy spectrum produced by application of the mutual information classification algorithm to the neutralization activity of bnMAb PGT-123 against a panel of 141 HIV-1 pseudoviruses (cf. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone.0080562.s001" target="_blank">Table S1</a>) using an IC₅₀ cutoff of 10 µg/ml. The ordinate records the computed redundancy of the residue identity in each position with the observed neutralization activity. The abscissa lists the positions of the protein in decreasing order of redundancy. The dashed line indicates the cutoff computed by the shuffling procedure described in Materials and Methods, <i>R_cutoff</i> = 0.15, above which redundancy values should be considered statistically significant. These results suggest that the three top ranked positions – respectively, 332, 334 and 330– be retained in the model (cf. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone-0080562-t001" target="_blank">Table 1</a>). For clarity of viewing, plots are terminated at the 100-component model.</p

Compressed sensing (CS) selection of PGT-123 epitope residues.

<p>Results of the application of the compressed sensing classification algorithm to the neutralization activity of bnMAb PGT-123 against a panel of 141 HIV-1 pseudoviruses (cf. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone.0080562.s001" target="_blank">Table S1</a>). In each panel, the abscissa indicates the number of non-zero elements in the signal vector computed by the LASSO algorithm, and therefore the number of residues incorporated into the regularized least squares fit of the neutralization data (Eqn. 3). For clarity of viewing, plots are terminated at the 100-component model. As indicated by the arrows, knees in the (a) mean squared error (MSE) over the complete data set and (b) leave-one-out cross-validation mean squared error (LOOCV-MSE) curves were identified using the L method at 11 and 9 residues, respectively <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone.0080562-Salvador1" target="_blank">[77]</a>. The mean of these values motivated the selection of the ten residues constituting this model: I323, H330, N332, N334, S334, S612, N671, Q740, V815, and V843 (c.f. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone-0080562-t001" target="_blank">Table 1</a>).</p

Logo plot of the variability of selected positions in HIV-1 Env within the 141-strain pseudovirus panel.

<p>We present data for all positions identified in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone-0080562-t001" target="_blank">Tables 1</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080562#pone-0080562-t003" target="_blank">3</a> as significant determinants of bnMAb neutralization activity by either the ensemble classifier or experimental alanine scan data.</p

Maximum neutralization activity of bnMAbs in PBMC assays.

<p>(A) Each point on the graph represents the percent at which the neutralization curve plateaued for a single PBMC-grown clade B virus assayed in PBMC cells. The dotted line designates 90%. (B) Each point on the graph represents the percent at which the neutralization curve plateaued for a single molecular clone virus against the bnMAbs listed above the data points. Virus clones were produced in both 293T cells and PBMCs as indicated on the x-axis. The data points are colored according to which site the bnMAb targets: high-mannose patch (magenta), CD4bs (red), V2 apex (blue), gp41-gp120 interface (green). The bars represent the medians and the whiskered bars represent the interquartile range.</p

Percentage of viruses neutralized with a maximum neutralization.

<p>^a total number of viruses with IC₅₀ < 1μg/ml.</p><p>Percentage of viruses neutralized with a maximum neutralization.</p

Maximum neutralization activity of bnMAbs in a U87 target cell assay.

<p>(A) The bnMAbs are ordered from left to right according to decreasing medians of percent maximum neutralization. Each point on the graph represents the percent at which the neutralization curve plateaued for a single virus. The percentages above the bars group bnMAb medians that have the same values. The dotted line designates 90%. The bars represent the medians and the whiskered bars represent the interquartile range. The data points are colored according to which site the bnMAb targets: high-mannose patch (magenta), CD4bs (red), V2 apex (blue), and MPER (green). (B) Percent viruses neutralized with a maximum neutralization of >95% (blue), >90% (green), and >65% (red). BnMAb groups are indicated above the figure in black and described in the text.</p

Maximum neutralization activity of bnMAbs in a TZM-bl target cell assay.

<p>(A) The bnMAbs are ordered from left to right according to decreasing medians of MPN. Each point on the graph represents the percent at which the neutralization curve plateaued for a single virus. The dotted line designates 90%. The bars represent the medians and the whiskered bars represent the interquartile range. The data points are colored according to which site the bnMAb targets: high-mannose patch (magenta), CD4bs (red), V2 apex (blue), and gp41 (green). (B) Percent viruses neutralized with a MPN of >65% (red), >90% (green), and >95% (blue). (C) Each point on the graph represents the percent at which the neutralization curve plateaued for a single virus against either PGT121 (magenta), PG9 (blue) or PGV04 (red). The assay system used to measure neutralization is indicated above the data points, which are filled circles for the monogram U87 assay and unfilled squares for the CAVD TZM-bl assay.</p