Structural Modeling of Protein Interactions by Analogy: Application to PSD-95
Figure 5
The PDZ3–SH3–GK and SH3–GK Domains Are Stable Fragments
(A) Coomassie-stained gel (10% acrylamide) of aliquots from limited proteolysis of PSD-95 by Subtilisin proteinase: panels 1 and 3, Precision Plus Protein molecular weight marker (Bio-Rad, http://www.bio-rad.com); panel 2, starting sample prior to proteinase addition; panels 4, Lanes 4–9, Aliquots at 5, 30, 60, 90, 120 min, and 8 h after protease addition (as labeled). Arrows point to stable fragments that were excised from the gel and analyzed by mass spectrometry as described in Methods.
(B) Sequence of Rat PSD-95: underlined are the peptide sequences identified by mass spectrometry from the ∼34 kDa stable fragment corresponding to residues 429–721 (33,944 kDa). In bold are the sequences derived from the ∼48 kDa stable fragment comprising residues 300–721 (47,796 kDa).