Highlight: Lipids Nosing Around the Drug Binding Sites in Membrane Proteins (Previous Highlights) Tweet
The serotonin transporter (SERT) is a protein in the cellular membrane of neurons that is responsible for the uptake of the neurotransmitter serotonin from the synapse back into the cell. Lipid-protein interactions have been demonstrated to regulate the transport properties of SERT. To understand the underlying mechanism, we collaborated with Eric Gouaux's lab at OHSU and investigated the binding of lipids to SERT using cryo-EM and molecular dynamics simulations. Our enhanced sampling simulations (performed in NAMD and analyzed in VMD) successfully captured a specific lipid that binds to a binding site in SERT. This site can also accommodate the substrate serotonin to trigger its transport. Therefore, binding of lipids to it is a putative mechanism for lipid-modulated function of SERT. For more details, see our recent publication in PNAS.
The Future of Biomolecular Modeling
A 2015 TCBG Symposium brought together scientists from across the Midwest to brainstorm about what's on the horizon for computational modeling. See a summary of what these experts foresee.
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Computer Modeling in Bionanotechnology-The History
Since 2001 Illinois scientists have innovatively used molecular dynamics to simulate biological molecules combined with nanodevices. It turns out that the computational microscope is the quintessential imaging tool for these bionano systems. By Lisa Pollack.
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Recent Publications All Publications
- Application Experiences on a GPU-Accelerated Arm-based HPC Testbed. Association for Computing Machinery, HPC Asia '23 Workshops. 2023.
- VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations. J. Chem. Inf. Model., 63:4664-4678. 2023.
- Quinoline Thiourea-Based Zinc Ionophores with Antibacterial Activity. J. Med. Chem., 66:11078-11093. 2023.
- Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants. Proc. Natl. Acad. Sci. USA, 2023.
- End-to-end AI framework for interpretable prediction of molecular and crystal properties. Machine Learning: Science and Technology, 2023.
- Insights into substrate transport and water permeation in the mycobacterial transporter MmpL3. Biophys. J., 2023.
- Tuning phenylalanine fluorination to assess aromatic contributions to protein function and stability in cells. Nat. Commun., 14:59. 2023.
- Differential dynamics and direct interaction of bound ligands with lipids in multidrug transporter ABCG2. Proc. Natl. Acad. Sci. USA, 120:e2213437120. 2022.
- Cryo-EM structures of human ABCA7 provide insights into its phospholipid translocation mechanisms. EMBO Journal, 42:e111065. 2022.
- Backbone amides are key determinants of Cl- selectivity in CLC ion channels. Nat. Commun., 13:7508. 2022.
