Water-mediated conformational preselection mechanism in substrate binding cooperativity to protein kinase A

Cooperativity in substrate binding to a protein often involves some kind of interaction between distant binding sites mediated by the protein structure. Experimental studies indicate that the cooperative effect in protein kinase A relies on a shift in conformational equilibrium of the catalytic subunit, but its exact molecular basis remains unclear. Our molecular dynamics simulations provide atomistic insight into conformational states visited by the enzyme and its complexes and suggest a plausible mechanistic model contributing to cooperative substrate binding. Intriguingly, an important role seems to be played by water molecules that occupy two conserved hydration sites within the catalytic subunit.Substrate binding cooperativity in protein kinase A (PKA) seems to involve allosteric coupling between the two binding sites. It received significant attention, but its molecular basis still remains not entirely clear. Based on long molecular dynamics of PKA and its complexes, we characterized an allosteric pathway that links ATP binding to the redistribution of states adopted by a protein substrate positioning segment in favor of those that warrant correct binding. We demonstrate that the cooperativity mechanism critically depends on the presence of water in two distinct, buried hydration sites. One holds just a single water molecule, which acts as a switchable hydrogen bond bridge along the allosteric pathway. The second, filled with partially disordered solvent, is essential for providing a smooth free energy landscape underlying conformational transitions of the peptide binding region. Our findings remain in agreement with experimental data, also concerning the cooperativity abolishing effect of the Y204A mutation, and indicate a plausible molecular mechanism contributing to experimentally observed binding cooperativity of the two substrates.