Second, substitutions within the EWKER motif (RanBP3 residues 49SWVER) are predicted to disrupt salt bridge interactions with the Ran effector loop (Figure 4B).
All of the mutations examined were in the serine and glutamic acid residues predicted to anchor the bridge to the enzyme.
WSC domains are approx. 100 amino acid long with eight conserved cysteines, which are predicted to form disulfide bridges.
(A ) Structural modeling of zebrafish TAAR13c bound to cadaverine (yellow) reveals two aspartates (D1123.32 and D2025.42) with carboxylates (red) predicted to form salt bridges to ligand amino groups (blue).
The additional cysteine residues in these MMPs are also predicted to form disulfide bridges with the cysteine residue from the switch motif, possibly representing constitutively active forms of the enzyme.
Instead, its C5 cysteine residue is predicted to form a disulphide bridge with a C (non-exist in other similar proteins analyzed) that is directly adjacent to C3 [9].
Insert position in the secretion incompetent construct E99 is juxtaposed to the highly conserved sequence DFS at positions 104 106 (Fig. 3C), where Asp104 is predicted to form a salt bridge with Arg170 stabilizing loop 165.
Arg161 is conserved in all SPATE passenger domains (see also Fig. 3C, sequence conservation of loop 165) and is predicted to build a salt bridge with Asp346, whereas Tyr121 interacts via hydrogen bonds with Lys312 and Tyr313 (Fig. 7B).
According to their respective positions within the leucine zipper heptads, this residue is predicted to form a salt bridge with arginine (Arg) in all the Eurotiomycetes and lysine (Lys) in the Dothideomycetes, Sordariomycetes and Leotiomycetes orthologs (Figure 2; Figure S1, light blue highlight).
According to the Scratch protein predictor server [ 20] this residue is predicted to form a disulfide bridge with Cys 118 in the cysteine switch motif.
