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BP: Fachverband Biologische Physik

BP 19: Poster VII

BP 19.12: Poster

Dienstag, 17. März 2020, 14:00–16:00, P2/3OG

Markov Modeling of an Allosteric Transition — •Georg Diez, Daniel Nagel, Benjamin Lickert, and Gerhard Stock — Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany

Allostery plays a fundamental role in regulatory biological processes, in which a functional change of a protein is triggered at one site by the binding of a ligand to another, distant site. It yet remains unclear what forces drive the underlying mechanisms, especially if they are of structural or dynamical nature. In order to investigate allostery, here we study molecular dynamics data of a PDZ domain, in which the binding of a ligand causing an allosteric transition is mimicked by an azobenzene photoswitch.

Markov State Models are a powerful tool for accessing the full dynamics of a system since they only require locally converged trajectories instead of one single long trajectory. This allows us to analyze an ensemble of equilibrium and non-equilibrium trajectories which in total cover more than 400   µs [1].

The chances to make predictions about the dynamical and conformational change of the system will be illustrated. At the same time, the virtues and shortcomings of constructing a Markov State Model will be addressed.

[1] S. Buchenberg, F. Sittel, and G. Stock, "Time-resolved observation of protein allosteric communication," Proc. Natl. Acad. Sci. U.S.A. 114,E6804 (2017)