Langevin Dynamics Simulation of AKAP-PKA Complex: Re-Envisioning the Local Concentration Mechanism for Directing PKA Phosphorylation

Abstract

The second messenger cAMP and its effector cAMP-dependent protein kinase A (PKA) constitute a ubiquitous cell signaling system. Many receptor types existing within the same cell may use this signaling system and compartmentation of signaling is thought to occur due to A-Kinase Anchoring Proteins (AKAPs), which act to co-localize PKA with specific substrates. The molecular mechanism allowing AKAPs to direct PKA phosphorylation to a particular substrate remains unknown. A large body of evidence suggests that the catalytic subunit, which is highly diffusible, is released in response to cAMP. Recent studies have shown however that inside living cells, the catalytic subunit may not be released from the AKAP complex, and alterations in the structure of the PKA regulatory subunit tether affect substrate phosphorylation. We used a novel computational software based on Langevin dynamics to simulate the AKAP-PKA complex to investigate the possible molecular mechanisms for tether length and flexibility influence on phosphorylation and whether or not AKAPs can direct PKA phosphorylation to a particular substrate if the catalytic subunit is released from the complex. We find that short and flexible tethers contribute to a decrease in the average characteristic time of binding, which yields faster characteristic times of phosphorylation. We further demonstrate that release of the catalytic subunit from the AKAP complex abrogates the effect of tethering, with characteristic times of phosphorylation similar to non-AKAP bound PKA. The data suggests that AKAPs likely do not release the catalytic subunit and target PKA activity by increasing the efficiency of phosphorylation of AKAP-bound substrates.