Dynamic Fluctuations Provide the Basis of a Conformational Switch Mechanism in Apo Cyclic AMP Receptor Protein

Escherichia coli cyclic AMP Receptor Protein (CRP) undergoes conformational changes with cAMP binding and allosterically promotes CRP to bind specifically to the DNA. In that, the structural and dynamic properties of apo CRP prior to cAMP binding are of interest for the comprehension of the activation mechanism. Here, the dynamics of apo CRP monomer/dimer and holo CRP dimer were studied by Molecular Dynamics (MD) simulations and Gaussian Network Model (GNM). The interplay of the inter-domain hinge with the cAMP and DNA binding domains are pre-disposed in the apo state as a conformational switch in the CRP's allosteric communication mechanism. The hinge at L134-D138 displaying intra- and inter-subunit coupled fluctuations with the cAMP and DNA binding domains leads to the emergence of stronger coupled fluctuations between the two domains and describes an on state. The flexible regions at K52-E58, P154/D155 and I175 maintain the dynamic coupling of the two domains. With a shift in the inter-domain hinge position towards the N terminus, nevertheless, the latter correlations between the domains loosen and become disordered; L134-D138 dynamically interacts only with the cAMP and DNA binding domains of its own subunit, and an off state is assumed. We present a mechanistic view on how the structural dynamic units are hierarchically built for the allosteric functional mechanism; from apo CRP monomer to apo-to-holo CRP dimers.Author Summary: Protein dynamics are central in allosteric communication. The cooperative character of atomic motions is key in the propagation of the allosteric signal and in the protein functioning. Here, we explored the dynamics of cAMP Receptor Protein (CRP) as an apo unbound monomer/dimer and a holo dimer by molecular dynamics simulations combined with the Gaussian network model analysis. The cAMP binding allosterically promotes CRP to bind specifically to the DNA. To this, our results show how the residue fluctuations provide the basis of an allosteric communication mechanism and describe a conformational switch with its off and on states and how this behavior is evolved from apo CRP monomer to apo-to-holo CRP dimers. The dynamic infrastructure needed for the coordination between the effector and DNA binding domains is largely observed in apo CRP monomer. This is an example of the pre-existence of functional dynamic states in the smaller subunits of the structure and the functional importance of the inter-domain hinges. The dynamics of the holo state pre-exist in the apo state, but disorganized in the way the cAMP and DNA binding sites interact. The cAMPs organize the couplings and elicit proper communication.