Electrostatic Switch Function in the Mechanism of Protein Kinase A I? Activation: Results of the Molecular Dynamics Simulation.

ABSTRACT: We used molecular dynamics to find the average path of the A-domain H ? B conformational transition in protein kinase A I?. We obtained thirteen productive trajectories and processed them sequentially using factor and cross-correlation analyses. The conformational transition is presented as partly deterministic sequence of six events. Event B represents H ? B transition of the phosphate binding cassette. Main participants of this event form electrostatic switch cAMP(O6)-A202(N-H)-G199(C=O). Through this switch, cAMP transmits information about its binding to hydrophobic switch L203-Y229 and thus triggers conformational transition of A-domain. Events C and D consist in N3A-motif displacement towards phosphate binding cassette and B/C-helix rotation. Event E involves an increase in interaction energy between Y229 and ?-subdomain. Taken together, events B, E, and D correspond to the hinge movement towards ?-barrel. Transition of B/C-helix turn (a.a. 229-234) from ?-form to ?-form accounts for event F. Event G implies that ?-helical turn is replaced by kink. Emerging in the resulting conformation, electrostatic interaction R241-E200 facilitates kink formation. The obtained data on the mechanism of cAMP-dependent activation of PKA I? may contribute to new approaches to designing pharmaceuticals based on cAMP analogs.

SUBMITTER: Rogacheva ON 

PROVIDER: S-EPMC5359514 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature