Fraction of Circulating HIV Strains Worldwide That Contain the Sequence Motifs for anti-V3 mAb Epitopes.

<p>The column headings for each of the subtypes displays the subtype name and, in parentheses, the percentage of the whole set of worldwide circulating viruses that belong to that subtype. Each cell shows the percentage of worldwide viruses, all of that subtype, that contain the sequence motif targeted by the indicated mAb of that row: thus “11%” for 3074 and subtype A indicates that 11% of the 12% of worldwide viruses that are subtype A contain the 3074 targeted epitope. Each cell in the Total column indicates the percentage of worldwide circulating viruses that contain the signature motif of the epitope targeted by the indicated mAb of that row.</p

Radar graphs illustrating the data on the global cross-HIV-1-strain conservation neutralization epitopes targeted by mAbs.

<p>The mAb is indicated in black bold letters above its graph. Each radar graph is a polygon, each point of which is representative of each subtype and each axis of which is proportional to the fraction of that subtype in the whole set of circulating worldwide strains. Thus the point labeled “C” is subtype C and its axis from the center of the polygon is as long as all the other axes combined, because subtype C represents half (50%) of the worldwide population of viruses. The percentage of each subtype that contains the neutralization epitope targeted by the mAb is plotted on each axis. Connecting each one of these plotted points traces out an inner polygon colored red that is visually representative of the population of circulating viruses that contain the sequence motif for the neutralization epitope targeted by that mAb. Thus, if most of the area enclosed by the polygon is colored red, most of the circulating HIV-1 viruses in the human population worldwide contain the epitope targeted by the indicated mAb in their sequences.</p

Results of the <i>in silico</i> modeling of amino acid substitutions in V3 loop epitopes.

<p>For each mAb epitope resolved crystallographically, <i>in silico</i> substitutions were made to the structure of the complex, the perturbation of the change was minimized conformationally and the change in energy of the complex was calculated as described in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015994#s2" target="_blank">Methods</a> (right column). Only amino acid substitutions occurring naturally in the viral population in more than 4% at each position were considered in the study. Red colored values indicate energetically silent or non-disruptive substitutions that retained a similar mAb contact and which were then added to the motif describing the epitope. *One change resulted in energetic improvement but a conformational change such that contact with the mAb was lost, thus not contributing to the motif.</p

Sequence Motifs for Epitopes Targeted by Individual anti-V3 mAbs Derived from 3D Structures of mAbs:V3 Complexes.

<p>Infecting Donor HIV Subtype indicates the subtype of the virus infecting the patient from which the mAb was isolated. V3 loop numbering is as described in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015994#s2" target="_blank">Methods</a>. “x” in the sequence motifs indicates that any amino acid may occupy that position.</p

Fraction of HIV-1 Pseudoviruses of five subtypes Neutralized by anti-V3 mABs.

<p>Summary of neutralization breadth of individual mAbs from previously published experiments. The column headings for each of the subtypes displays the subtype name and the number of HIV-1 pseudoviruses of that subtype tested for neutralization by the indicated anti-V3 mAbs. Each cell shows the percentage of tested HIV-1 pseudoviruses which are neutralized by the indicated mAb of that row. The <i>in vitro</i> neutralization data from Hioe et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015994#pone.0015994-Hioe1" target="_blank">[35]</a> was summarized in this table.</p

mAb 3074, 2557, and 268-D bound to V3 loop peptides.

<p>(A) Structure of mAb 3074 (grey molecular surface) bound to a peptide (red ribbon and blue stick depiction) with the same sequence as the crown of the V3 loop of subtype AG isolate VI191. (B) Structure of mAb 2557 (grey molecular surface) bound to a peptide (red ribbon and blue stick depiction) with the same sequence as the crown of the V3 loop of subtype B isolate NY5. (C) Structure of mAb 268-D (grey molecular surface) bound to a peptide (red ribbon and blue stick depiction) with the same sequence as the crown of the V3 loop of subtype B isolate MN. The side-chains of the V3 peptide that are buried in the molecular surface of the mAb are colored blue and labeled.</p

Library of signature motifs mapped to the V3 regions of AIDSVAX immunogens.

<p>Signature motifs recognized by each monoclonal antibody are shown in the second column: the numbers indicate the recognized positions in the V3 loop and the letters indicate the amino acid residues at each position required for recognition by that monoclonal antibody. Positions numbering is in the correspondence with the standard V3 loop numbering described elsewhere <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0027279#pone.0027279-Cardozo1" target="_blank">[19]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0027279#pone.0027279-Swetnam1" target="_blank">[20]</a>. Colored rectangles in the sequence column indicate the amino acid residues composing the signature motif in each of the gp120s. Sequences without colored rectangles do not contain a given motif.</p

Screening for the signature motifs in datasets of gp120 sequences of HIV-1 strains infecting volunteers during AIDSVAX Phase III clinical trials.

<p>Screening for the signature motifs in datasets of gp120 sequences of HIV-1 strains infecting volunteers during AIDSVAX Phase III clinical trials.</p

Epitope Mapping of Conformational V2-specific Anti-HIV Human Monoclonal Antibodies Reveals an Immunodominant Site in V2

<div><p>In the case-control study of the RV144 vaccine trial, the levels of antibodies to the V1V2 region of the gp120 envelope glycoprotein were found to correlate inversely with risk of HIV infection. This recent demonstration of the potential role of V1V2 as a vaccine target has catapulted this region into the focus of HIV-1 research. We previously described seven human monoclonal antibodies (mAbs) derived from HIV-infected individuals that are directed against conformational epitopes in the V1V2 domain. In this study, using lysates of SF162 pseudoviruses carrying V1V2 mutations, we mapped the epitopes of these seven mAbs. All tested mAbs demonstrated a similar binding pattern in which three mutations (F176A, Y177T, and D180L) abrogated binding of at least six of the seven mAbs to ≤15% of SF162 wildtype binding. Binding of six or all of the mAbs was reduced to ≤50% of wildtype by single substitutions at seven positions (168, 180, 181, 183, 184, 191, and 193), while one change, V181I, increased the binding of all mAbs. When mapped onto a model of V2, our results suggest that the epitope of the conformational V2 mAbs is located mostly in the disordered region of the available crystal structure of V1V2, overlapping and surrounding the α4β7 binding site on V2.</p></div

Summary of binding of conformational V2 mAbs to wildtype and mutant SF162 pseudovirus lysates.

*<p>The values are normalized to CD4-IgG2 (as described in Methods) and expressed as percentages of SF162 wildtype binding (100%). The means of 3–5 experiments are shown.</p