We predicted secondary structure and disorder to investigate the characteristics of the protein structure of the intracellular third loop containing the Glu repeats. For the analysis of disorder prediction, we used DISOPRED2 [50 (link)], and for the analysis of the secondary structure, we predicted protein structure using PSI-PRED [51 (link)].
As we hypothesized that the Glu repeats forms a helix structure, we prepared a helical structure of the 8–12 residues in each poly-Glu repeats sequence by artificial measures. The three-dimensional structures of the amino acid variants from the 8–12 poly-Glu repeats were constructed using the MOE program with default parameters (Chemical Computing Group, Montreal, Canada). The structural models of the 8–12 poly-Glu repeats were docked into the X-ray structure of the Gi α-subunit from the co-crystal structure of the GPCR and G proteins (PDB-ID: 3sn6) [52 (link)] using the docking simulation program ClusPro (Boston University, Boston, MA) [53 (link)] with the “Electrostatic Favored” interaction energy score.
As we hypothesized that the Glu repeats forms a helix structure, we prepared a helical structure of the 8–12 residues in each poly-Glu repeats sequence by artificial measures. The three-dimensional structures of the amino acid variants from the 8–12 poly-Glu repeats were constructed using the MOE program with default parameters (Chemical Computing Group, Montreal, Canada). The structural models of the 8–12 poly-Glu repeats were docked into the X-ray structure of the Gi α-subunit from the co-crystal structure of the GPCR and G proteins (PDB-ID: 3sn6) [52 (link)] using the docking simulation program ClusPro (Boston University, Boston, MA) [53 (link)] with the “Electrostatic Favored” interaction energy score.
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