Computational modeling of cAMP-dependent protein kinase allostery

Allosteric regulation by ATP of peptide binding with a cAMP-dependent protein kinase catalytic subunit was computationally modeled by combining conventional docking analysis and molecular dynamics calculations. It was found that the peptide docking energy was dependent on peptide structure, and, moreover, this energy was also different for the free enzyme and the enzyme-ATP complex. This difference was used to model the allosteric effect of ATP on peptide binding. The same computational analysis revealed that ligand binding reduced the root-mean-square fluctuation (RMSF) values of the enzyme backbone alpha C atoms, pointing to a ligand-induced reduction in intrinsic conformational dynamics of the protein. As this stiffening of the conformation was induced by the binding of ATP as well as peptides, and its magnitude was in correlation with the ligand binding energy, it was suggested that the modulation of protein conformational dynamics may be responsible for the allosteric regulation of binding effectiveness through the alteration of ligand off-rate from the binding site. This means that the atomic network of interactions, which determines the molecular recognition of the peptide substrate in its binding site, is not changed by allostery, but the intensity of these interactions is affected. This change modulates the overall ligand binding effectiveness and is recognized as an allosteric effect.