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The second messenger cyclic Adenosine MonoPosphate (cAMP) mediates many biological process by interacting with structurally conserved nucleotide binding domains (cNBD's). Here, we use molecular dynamics simulations on RIIbeta-PKA, one of the best characterized members of the cNBD family, in presence and absence of cAMP. The results of our calculations are fully consistent with the available experimental data and suggest that the key factor of the cAMP allosteric mechanism in cNBDS's is the increased flexibility of the protein upon ligand release along with a mechanical coupling between helical segments. In addition, our calculations provide a rationale for the experimentally observed cAMP selective binding to PKA.

Original publication




Journal article



Publication Date





2679 - 2685


Allosteric Regulation, Binding Sites, Computer Simulation, Crystallography, X-Ray, Cyclic AMP, Cyclic AMP-Dependent Protein Kinases, Gene Deletion, Hydrogen Bonding, Kinetics, Ligands, Models, Molecular, Protein Binding, Protein Conformation, Protein Isoforms, Protein Structure, Secondary, Protein Structure, Tertiary, Sodium, Water, X-Ray Diffraction