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Our group studies the structure of drug-like molecules and characterizes their interactions with proteins. We apply a variety of experimental and computational methods including NMR spectroscopy and molecular dynamics simulations.
By leveraging a combination of computational and experimental approaches, we aim to deepen our understanding of membrane transport mechanisms to pharmacologically target relevant disease processes for intervention.
Our research focuses on understanding membrane transport mechanisms at the atomistic scale and rationally designing tool compounds for pharmacological intervention. Biological membranes serve as central barriers that separate the extracellular and intracellular environments, as well as the major compartments within cells. Understanding how ions, substrates, drugs, and delivery systems move across these membranes is not only crucial for elucidating physiological processes and disease mechanisms but also essential for developing drug-like molecules and improving drug delivery strategies. On the theoretical side, our group develops and applies advanced molecular modeling techniques, state-of-the-art molecular dynamics (MD), quantum mechanics/molecular mechanics (QM/MM) simulations, and machine learning. Experimentally, we develop novel solution NMR-based methods to probe the conformational dynamics and molecular interactions of both organic molecules and biomolecules.
During conduction in C1C2 channelrhodopsin, the density of K+ ions within the pore was very low, with typically only one K+ ion passing through the pore at a time.
DOI: doi.org/10.1021/jacs.4c15402
© Songhwan Hwang
Ion permeation in the TREK-2 K2P channel visualized by computational electrophysiology
DOI: doi.org/10.1038/s41467-024-48823-y
DOI: doi.org/10.1126/science.1261512
DOI: doi.org/10.1016/j.bpj.2011.06.010
© Berke Türkaydin
CNG channel (Cyclic nucleotide–gated ion channel) DOI: doi.org/10.1101/2024.12.19.629380
© Haoran Liu
HCN channel (hyperpolarization-activated cyclic nucleotide-gated cation channel). doi: doi.org/10.1073/pnas.2422533122
© Haoran Liu
K+ permeation through K2P channel. DOI: doi.org/10.1101/2025.01.08.631886
© Yessenbek Aldakul
K+ permeation in NaK channel. DOI: doi.org/10.1038/s41467-018-03179-y
K+ permeation GluA2 AMPA receptor. DOI: doi.org/10.1073/pnas.2012843118
© Johann Biedermann
Group Retreat 2023
© Bernd Rupp
Group 2023
© Bernd Rupp
Group 2022
© Bernd Rupp
Group Retreat 2022
© Bernd Rupp
Group Retreat 2022
© Bernd Rupp
Group Retreat 2021
© Bernd Rupp
People
MD simulations of ion channels
MD simulations of ion channels
Free energy calculations
NMR for natural products.
MD simulations of ion channels
NMR analysis of cyclic peptides.
MD simulations of membrane transport mechanism.
NMR investigation of natural products
Computational investigation of ion channel modulation.
Cell Painting analysis.
Free energy calculations
The Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) is part of the Forschungsverbund Berlin e.V. (FVB), which legally represents seven non-university research institutes - members of the Leibniz Association - in Berlin.
Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP)
Campus Berlin-Buch
Robert-Roessle-Str. 10,
13125 Berlin, Germany
