Structural Modeling of Protein Interactions by Analogy: Application to PSD-95
Figure 3
Two Binding Modes of the Core Fragment of Rat PSD-95
The PDZ3 domain is shown in blue, SH3 in red, and GK in yellow. The grey spheres correspond to the residues of the interdomain linker between PDZ3 and SH3. Locations of the hydrophobic cleft (Cleft) and PXXP motif (PXXP) in PDZ3, PRBS in SH3, and the GBS in GK are shown by arrows. (A) The domain architecture of the core fragment. (B) The first predicted configuration. (C) The second predicted configuration. The difference between the theoretically calculated SAXS spectra of the first (red) and second (blue) configurations is significantly larger than the anticipated experimental error.