Theoretical Physics

Research Area: Theory and simulation of phosphotransfer in protein kinases 

Current Project: Simulating the ADP release of the PKA-C cycle under the presence of different number of Magnesium ions

Background and previous work

The modification of biomolecules by addition of phosphates (phosphorylation/dephosphorylation) is essential for the regulation of vital cell processes as growth, division or morphogenesis. The protein kinase A (PKA) is responsible for important phosphorylation processes. The rate limiting process in the catalytic cycle of PKA is the release of ADP and the so-called Mg2 magnesium ion. The details and actual molecular dynamics of the ADP release are not well resolved. To observe the sub-millisecond behavior of the ADP release, we performed molecular dynamics (MD) simulations utilizing GROMACS v2016.3 and GROMACS v2018, with the AMBER99SB-ILDN force-fields, based on the crystallized structure of PKA-C with ADP and Mg2+ using a generalized Amber force-field (GAFF) to parameterize ADP. Since the normally present second Mg2+ is believed to only have an “linchpin” role stabilizing the process, it can be considered as irrelevant for the phosphorylation process, only slowing down the ADP release. Thus, we used the crystal structure PKA-C with ADP and only one Mg2+. This structure is already in an intermediate state between the open and the closed conformation, depending on the positions of the Gly-rich loop and C-terminal tail.

Specific aims

While simulating the dynamics of the ADP release we investigate the influence of the Mg2+ quantity by running the simulations (i) without any Mg2+ ions, (ii) with one Mg2+ ion.

Specifically, we will address the question of the detailed pathway on which ADP leaves PKA-C during complex dissociation.

Work programme

•    Preparation of PKA-C and ADP input structures and topologies.

•    Simulation of the ADP release dynamics with different Magnesium quantities and settings of special ADP parameters.

•    Analysis of the kinetics of the ADP release.

Graphical Abstract