Ligand binding extended conformations

We have previously calculated conformational free energy differences for a well-suited model system, the catalytic subunit of cAMP-dependent protein kinase (cAPK), which is the best characterized member of the protein kinase family. It has been crystallized in three different conformations and our main focus was on how ligand binding shifts the equilibrium among these ([Helms and McCammon 1997]). As an example using state-of-the-art computational techniques, we summarize the main conclusions of this study and discuss a variety of methods that may be used to extend this study into the dynamic regime of protein domain motion. 

The most notable difference between the acid and basic forms of the PBP is the conformation of the C-terminus. In the basic form the C-terminus is extended, on the surface of the protein (Sandler et al., 2000), while in the acid form the C-terminus forms a seventh a-helix, which occupies the pheromonebinding cavity. The loop with two vicinal histidine residues (69 and 70) has also moved significantly between the two forms, suggesting that titration of one of these residues has a profound effect on the conformation of the PBP (Horst et al., 2001). Consistent with this, mutation of histidines 69 and 70 to alanine, abolished a conformational change detectable upon ligand binding (Mohl et al., 2002). 

The peptidase inhibitors, (82) and (83), are actually amino acid and transition-state mimics pieced together to emulate the typical ligand-bound extended p-strand inhibitor conformation. The structurally distinct heterocyclic aspartic protease inhibitors (85-86) and (87-88) are non-peptide peptidomimetics because of their remote structural relationship to native peptide substrates. Yet these two distinct peptidomimeticclasses bind to the same active site topography. These structurally distinct peptidomimetics selectively stabilize closely related enzyme conformations. 

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