Berlin 2018 – scientific programme

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BP: Fachverband Biologische Physik

BP 9: Postersession I

BP 9.8: Poster

Monday, March 12, 2018, 17:30–19:30, Poster A

Simulating the ADP release of the PKAC cycle with different Magnesium quantities approximated by static charge and dummy-atom models — •Robert C. König, Alexander Lipskij, Bernhard Reuter, and Martin E. Garcia — Theoretische Physik II, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany

The modification of biomolecules by addition of phosphates (phospho- rylation/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, with the AMBER03 and AMBER99SB-ILDN force-fields, based on the crystallized structure of PKAC with ADP and 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. While simulating the ADP release we investigated the influence of the Mg quantity by running the simulations (i) without any Mg ions, (ii) with one Mg ion and (iii) with two Mg ions, with the second magnesium ion added at the position of the linchpin magnesium ion, termed Mg1. To approximate the effect of the Mg charge we used both a standard static charge and a dummy-atom model, imitating the coordination number of Mg.