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), 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

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

The neutralization of nine HIV-1 pseudoviruses by mAb 2191 using U87 as target cells.

<p>The neutralization curves of anti-V3 mAb 2191 against nine selected HIV-1 pseudoviruses are shown with their corresponding AUC and IC₅₀ values. Fifty percent neutralization is denoted by the dashed line. Significant neutralization at the confidence level of p<0.001 (denoted with * after AUC values) was determined statistically based on comparison with the AUC values of the negative controls together with the slopes of the titration curves as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010254#s2" target="_blank">Materials and Methods</a>. For viruses coming from patients where the date of infection is known, viruses are denoted as coming from acutely- or chronically-infected patients, and the clade of the virus is denoted by the capital letter in its name (A, B, C or D).</p

The IC₅₀ values of anti-V3 mAbs against 57 HIV-1 pseudoviruses tested using the U87 target cell line.

<p>The IC₅₀ values were estimated from the titration curves of all mAb/psV combinations and are highlighted according to the color-coded scale. Pseudoviruses expressing Envs of JRCSF, NL3.4, and SF162 were tested as positive controls, whereas the irrelevant anti-parvovirus mAb 860 and aMLV Env-expressing psV were used as negative controls. When 50% neutralization was not achieved at the highest mAb concentration tested (50 µg/ml), the IC₅₀ values are shown as >50.</p

Neutralization curves of anti-V3 mAbs against representative HIV-1 psVs tested using the TZM.bl target cell line.

<p>Seven anti-V3 mAbs were tested against HIV-1 psVs in the TZM.bl experiment. The titration curves observed against nine selected viruses are shown. The background neutralization observed with the irrelevant control mAb 860 is also shown for comparison. Curve fitting was performed using the polynomial regression (quadratic) model described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010254#s2" target="_blank">Materials and Methods</a>. Fifty percent neutralization is denoted by the dashed line.</p

The AUC values of anti-V3 mAbs against 41 HIV-1 pseudoviruses tested using the TZM.bl target cell line.

<p>The AUC values were calculated from the titration curves as described in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010254#s2" target="_blank">Materials and Methods</a> section. All mAb/psV pairs with statistically significant neutralization at p<0.001 are color-coded according to the designated scale. The irrelevant anti-parvovirus mAb 1418 was used together with three other control mAbs (data not shown) as negative controls.</p