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In large part this is due to the challenges that one faces in dealing with protein binding epitopes compared to, e.g., enzyme binding pockets.
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This may reflect the fact that the antibodies used to detect the total forms of each protein have different binding affinities and potentially different numbers of epitopes compared to the antibodies directed against the hyperphosphorylated forms.
We have demonstrated that TCRs bind more weakly to cancer epitopes compared to pathogenic epitopes [ 4, 5].
We hypothesized that the inability to neutralize HPV45 was either due to sequence divergence, or conformational differences in L2 epitopes compared to HPV16 that hindered antibody binding.
We observed that specific amino acids were unusually enriched or depleted in epitopes compared to non-epitopes.
However, in the oxalate extracts, both C. clariflavum strains exhibited increased depletion of xylan epitopes (as indicated by the reduced intensities of mAb binding) compared to that of the C. thermocellum strain.
Interestingly we found that memory "inflating" epitopes demonstrate reduced immunoproteasome dependence compared to non-inflating epitopes.
The epitope is localized closer to the C-terminus, compared to the ETS binding domain, which is essential for its binding to DNA [ 29].
Remarkably, two times more strong-binding epitopes for HLA DRB1 were found in panitumumab compared to zalutumumab (Table 1).
We used peptides that were modified in one amino acid compared to the original epitopes in order to enhance HLA binding affinity.
We subsequently found that the two CTL escape variants in the A11-AK11 epitope (G9S) and the B7-IL9 epitope (R3T) also mediated stronger binding interactions of the corresponding peptide/MHC class I complexes to monocytes compared to the respective wild type epitopes.
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