Dynlon | P8

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Mechanisms of ion channel regulation investigated by extensive simulation and Markov state modeling

Institution:

Freie Universität Berlin

Fachbereich Mathematik und Informatik

Director:

Financial support:

German Research Foundation (DFG)

Term:

Jun 01, 2017 — May 31, 2020

The DFG Research Unit initiative "DynIon - Functional dynamics of ion channels and transporters" combines experimental and computational strategies to study ion channels and transporters. In this project, we will provide our expertise in long-timescale simulation and Markov state modeling from both experimental and simulation data to the research unit. By combining extensive GPU-driven MD simulations (100 microsecond to milliseconds) with recently developed adaptive sampling techniques and multi-ensemble estimators, we will explore the conformational dynamics of binding domains in AMPA-type glutamate receptors and their modulation by binding auxiliary proteins. Methodologically, we will develop new Bayesian inference methods to learn MSMs from single-channel data and optimally combine them with simulation data.