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Interestingly, the U. maydis sid2 protein, which has only a single terminal T-C, contains two complete A-T-C modules predicted to charge AHO.
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The charged groups on the AF488 moiety are predicted to interact with charged amino acid residues on the ELs of the receptor to stabilize the high-affinity complex.
The disulfide cross-linked, N- and C-terminal domains of SP-B have been theoretically predicted to fold as charged, amphipathic helices, suggesting their participation in surfactant activities.
We made conservative mutations that would be predicted to neutralise these charged patches, but not affect the folding of the protein.
In addition, the observation that substitution of asparagines by aspartic acids in DsbA-IGFBP-3 fusion proteins improved solubility [ 12] is consistent with the solubility formula because the fusion protein is already predicted to be negatively charged (data not shown).
As shown in figure 2, 16 of the 43 serpin, sequences that have RCLs are predicted to possess basic charged amino acid residues, "R" or "K" at their P1 site (figure 4).
In contrast, only one fragment hit is predicted to bear negative charge, with the remaining 15 hits neutral at this pH.
The positive charge is predicted to interact with the negatively charged phosphate group of the phospholipids in the lipid bilayer, and this interaction perhaps prevents the transmembrane protein from sinking down to the ε-cleavage site.
Compound 1 was predicted to interact with positively charged arginines at the AMP allosteric site in the docking model.
The surface of the enzyme is predicted to be highly negatively charged, like other proteins of extreme halophiles.
The C-terminal region of DOR is predicted to form a positively charged alpha-helix structure and has no transcriptional activation capacity; in contrast, the presence of the C-terminal region reduces the transcriptional activity of the N-terminal half.
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