Furthermore, heparin completely blocked the interaction with LPS as well as antimicrobial activity, confirming that heparin interacting sequences of PrP mediate LPS binding, and thus, antimicrobial activity (not shown).
We hypothesize that there is a mismatch between coevolved sets of interacting sequences in the two parental inbred strains, for example transcription factors and proteins that activate them, that leads to this bias.
Strikingly, our inclusion-targeting strategy failed to reveal the presence of interacting sequences within domain 5, in spite that this domain has been previously shown to be an essential inclusion-forming player by orientating monomer-to-monomer interactions [11].
With a continuous three-letter protein model, we explore the free-energy landscape of pairs of interacting sequences and how it is impacted by 1), variations in the binding mechanism; and 2), the addition of disordered flanks to the binding region.
The identified ATAF2 interacting sequences were upstream and within 3000 bp of a translation start codon.
Comparisons of the proline-rich region of Scotin (residues 157 240) with AIP1/Alix and TSG101 revealed that the N-terminal part of this region (residues 157 177) has highest similarity with the ALG-2 interacting sequence of AIP1/ALIX (residues 794 812), which has been shown to be sufficient for the interaction with ALG-2 [13].
A variety of clathrin boxes has previously been identified [31], [33], and we propose that the CHC interacting sequence of SNX4 functions as a clathrin box.
SG2000 (SJG-136, NSC694501) is a rationally designed pyrrolobenzodiazepine dimer which interacts sequence selectively in the minor groove of DNA [ 4, 5].
If in one species multiple sequences were best hits with one of the two interacting sequences we combined each of those with the best hits in that species of its interaction partner.
The substrate binding domain of Hsp70 recognizes and interacts with sequences of hydrophobic amino acid residues of newly synthesized proteins that emerge from the ribosomes.
