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It should be noted that epitope competition assays only offer an approximate mapping of binding epitopes rather than any precise level of molecular detail.
The idea that weak binding epitopes, rather than high affinity peptides, underlie type 1 diabetes (Suri et al., Curr Op Immunol, 2008 [ 56]) appears to run counter to our hypothesis.
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Lastly, we noticed a focus on pol epitopes, rather than env and gag.
We reasoned that sequence divergence in L2 epitopes rather than the lack of proper display of those epitopes could explain the lack of cross-neutralization.
Indeed, the higher antibody titers seen against both the immunogen and HBc in all the volunteers could imply that the targeted epitopes in the immunogen are shared HBc epitopes, rather than malaria epitopes.
The residual reactivity with the convalescent sera following the addition of reductant is likely due to the small portion of polyclonal antibodies that recognize linear epitopes rather than conformational epitopes.
We used predicted epitopes rather than epitopes for which CTL reactivity was actually demonstrated [36] as to prevent a bias in our analyses towards better investigated HIV-1 genes (Gag) and HLA types (HLA A*02, B*57 and B*27).
This method can accurately predict the more useful antibody-specific epitopes rather than antigenic residues.
The method has advantages relative to both immunoPCR (because no signal is produced by background binding) and the proximity ligation assay (PLA) (because only one epitope, rather than two epitopes, on a protein surface must be bound).
We reasoned that if gp41 MPER tetramer binding to B cells represents an inherently unique feature of the gp41 MPER epitope (rather than specificity and/or avidity issues exhibited by all HIV-1 epitope-specific tetramer reagents), then gp41 ID and V3-specific tetramers should bind B cells at frequencies seen by conventional antigens.
These findings led us to hypothesize that the H120 antibody was recognizing a conformational epitope rather than a linear epitope, a relatively frequent event according to published studies[44].
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