A Post-Synaptic Scaffold at the Origin of the Animal Kingdom (original) (raw)
Figure 2
(A) Sponge PDZ3—CRIPT Homology Model.
The last five residues of the CRIPT protein (yellow) interact with PDZ3 residues (blue and orange) by making van der Waals contacts, hydrogen bonds, or electrostatic interactions of greater than 0.1 kcal/mol in magnitude in any of the PDZ3 homology models. (Figure S4). The subset of residues painted blue represent the core union set that interact directly with the ligand in the PDZ1 co-crystal (2I1N), the PDZ2 co-crystal (2G2L), or the PDZ3 co-crystal (1BE9) by either van der Waals contacts of 3.9 Å or shorter or by hydrogen-bond lengths of 3.5 Å or shorter. (B) Ligand-binding residues are very highly conserved within a specific type of PDZ domain. Conservation of the 13 binding residues compared to the remaining 61 more distant residues for 16 types of PDZ domains from Homo, Drosophila, Nematostella and Amphimedon. These frequencies are also calculated across all those domains at once (column 1). Comparison of the conservation of binding residues versus non-binding residues; *, p<0.05; **, p<0.01; ***, p<0.001 (Probability associated with a Student's two-sample unequal variance t-Test).