Molecular Dynamics Simulations of Phosphorylation-induced Conformational Transitions in the Mycobacterium tuberculosis Response Regulator PrrA

Abstract

Phosphorylation-mediated activation of response regulators (RRs) is predominantly used by microorganisms as a central strategy in the regulatory activities of their two-component systems, the underlying molecular mechanisms are however far from fully understood. In this work we have conducted molecular dynamics simulations of the phosphorylation-induced conformational transitions in the Mycobacterium tuberculosis RR, PrrA, to obtain the dynamical details that are relevant to the RR activation. From the full-length structure of unphosphorylated PrrA we generated a computational model for the phosphorylated PrrA state by changing the phospho-accepting aspartic acid Asp-58 in the regulatory domain to the phosphoaspartate phos-Asp-58. The resultant structural relaxations were simulated through a rapid sampling of protein motions using a conformation-biased all heavy-atom potential energy function without explicit solvent. Marked structural rearrangements have been observed across the interdomain interface of the phosphorylated PrrA, manifesting the global effect of the local phosphorylation upon a single residue of aspartate. Such changes have also been found to involve the domain-crossing motions that disrupt the hydrophilic and hydrophobic interactions within the interdomain space and thus transform PrrA from a compact structure to a more extended conformation featuring a wider domain-domain separation and a more exposed transactivation loop. These simulated motions reflect the essential early-stage activation dynamics for the relief of the inhibitory role of the regulatory domain in PrrA. In effect, each more extended PrrA becomes more suited to interact with DNA and RNA polymerase; the activation of many proteins also shifts the population-equilibrium of PrrA towards more active states, therefore leading to a phosphorylation-enhanced allosteric regulation for the control of transcription.