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

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

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

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

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

Computational Prediction of Neutralization Epitopes Targeted by Human Anti-V3 HIV Monoclonal Antibodies

<div><p>The extreme diversity of HIV-1 strains presents a formidable challenge for HIV-1 vaccine design. Although antibodies (Abs) can neutralize HIV-1 and potentially protect against infection, antibodies that target the immunogenic viral surface protein gp120 have widely variable and poorly predictable cross-strain reactivity. Here, we developed a novel computational approach, the Method of Dynamic Epitopes, for identification of neutralization epitopes targeted by anti-HIV-1 monoclonal antibodies (mAbs). Our data demonstrate that this approach, based purely on calculated energetics and 3D structural information, accurately predicts the presence of neutralization epitopes targeted by V3-specific mAbs 2219 and 447-52D in any HIV-1 strain. The method was used to calculate the range of conservation of these specific epitopes across all circulating HIV-1 viruses. Accurately identifying an Ab-targeted neutralization epitope in a virus by computational means enables easy prediction of the breadth of reactivity of specific mAbs across the diversity of thousands of different circulating HIV-1 variants and facilitates rational design and selection of immunogens mimicking specific mAb-targeted epitopes in a multivalent HIV-1 vaccine. The defined epitopes can also be used for the purpose of epitope-specific analyses of breakthrough sequences recorded in vaccine clinical trials. Thus, our study is a prototype for a valuable tool for rational HIV-1 vaccine design.</p></div

Percentage of HIV-1 strains of different clades that contains epitopes of mAbs 2219 and 447-52D.

<p>Percentage of HIV-1 strains of different clades that contains epitopes of mAbs 2219 and 447-52D.</p