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The allosteric response ratio profiles and ribbon diagrams of hPTP1E and PSD-95.

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posted on 06.10.2011, 02:01 by Z. Nevin Gerek, S. Banu Ozkan

The allosteric response ratio plots as a function of residue index for (A) hPTP1E PDZ2 (PDB entry: 3LNX) and (C) PSD-95 PDZ3 (PDB entry: 1BFE) along with the ribbon diagrams colored with respect to allosteric response ratio profiles (B and D). The key residues obtained from recent experimental studies are illustrated with red dots in these plots. The residues that give the highest mean square fluctuation response upon perturbation of binding pocket residues from PRS are displayed in the corresponding ribbon diagrams. The residues whose perturbation leads to a high response (χi>1.00 for hPTP1E and PSD-95) are red, whereas residues with a low response are shown in blue within a color spectrum of red-orange-yellow-green-cyan and blue. The residues that match with experimentally determined ones are shown in stick representation. In hPTP1E PDZ2, distal surface 1 (DS1) contains residues in the N terminal of β6 and the anti-parallel β strand formed by β4 and β5 (Val61, Val64 and Val85) and distal surface 2 (DS2) located next to helix α1 consists of residues Val40 and Ile41. The figures were drawn using PYMOL [67].