Inhibitor-induced conformational changes for PH domain structures.
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A. Heavy atom RMSDs for the residues with conformational changes. RMSD of each residue is calculated from the snapshots taken from three independent MD simulations and compared with the unbound control structure. W107GAB1 and W106IRS1 (in black) are used as the controls for no conformational change. Red: Region I residues; Blue: Region II residues; Magenta: Region III residues. “..” for p<0.1; “*” for p<0.05; “**” for p<0.01. B–E. The critical residues in the three regions are shown in sticks. Pink: the protein in unbound state; Green: the protein in inhibitor-bound state. The inhibitors are depicted with gray sticks and surfaces. The arrows illustrate large conformational changes. B. GAB1 PH domain in complex with GAB-001; C. GAB1 PH domain in complex with GAB-017; D. IRS1 PH domain in complex with GAB-007; E. IRS1 PH domain in complex with GAB-010.