The Tat peptide, penetrain and pVEC are short peptides (∼20-mers) derived from the basic domain of the HIV-1 trans-activator of transcription (Tat) protein, the third helix of the Antennapedia homeodomain and cadherin, respectively.
This response is mediated by interleukin 15 (a typical cytokine of the innate immune system) and elicited by the toxic peptide, p31-49 (19-mer), derived from alpha-gliadin [31].
One peptide in particular, a 33-mer derived from in vitro gastrointestinal proteolysis of α2-gliadin, possesses all of these characteristics and activates proliferation in all celiac patient-derived T cell lines tested so far [2], [19].
Curdlan is a linear β-1, 3-glucan of ∼500-mers derived from the bacterium Alcaligenes faecal.
We first identified HIV-1 segments with sequence identity (4-, 5- and 6-mers) or high similarity (9-mers) to human proteins by comparing all possible 4, 5, 6 or 9-mers derived from HIV-1 B consensus 2001 to the human proteome.
The software program "Deconvolute This" was used to create sets of pooled peptides, such that each peptide from the overlapping 15-mers (derived from the three envs, gag, pol, and nef antigens contained in the vaccine) is present in five different pools.
Among analogues of an 18-mer derived from the Bim BH3 domain and an 8-mer derived from secreted phospholipase-2 (sPLA2), we find that recognition by antibodies raised against the prototype α-peptide is suppressed by periodic α → β replacements.
BayesHammer is unable to distinguish these correct k-mers from similar incorrect k-mers derived from the same antibody.
We also performed this analysis for a randomized set of 30-mers derived from the same repeat sequence.
The reference assembler uses a library of spaced 20-mers derived from the sites conserved across squamates.
