ArticlePLoS computational biology2015
Molecular dynamics simulations of the bacterial UraA H+-uracil symporter in lipid bilayers reveal a closed state and a selective interaction with cardiolipin.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 43 citations in OpenAlex.
- Design, Synthesis of Novel Quinazolinone Derivatives and Evaluation of EGFR Kinase Inhibition Activity via In Vitro and In Silico Studies.Chemical biology & drug design · 2026Article
- Insight into the mechanism of HProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Molecular Biophysics of Class A G Protein Coupled Receptors-Lipids Interactome at a Glance-Highlights from the ABiomolecules · 2023Review
- mPPases create a conserved anionic membrane fingerprint as identified via multi-scale simulations.PLoS computational biology · 2022Article
- Organization and Dynamics of the Red Blood Cell Band 3 Anion Exchanger SLC4A1: Insights From Molecular Dynamics Simulations.Frontiers in physiology · 2022Review
- The Transporter-Mediated Cellular Uptake and Efflux of Pharmaceutical Drugs and Biotechnology Products: How and Why Phospholipid Bilayer Transport Is Negligible in Real Biomembranes.Molecules (Basel, Switzerland) · 2021Review
- Structure and function of an Arabidopsis thaliana sulfate transporter.Nature communications · 2021Article
- Monolysocardiolipin (MLCL) interactions with mitochondrial membrane proteins.Biochemical Society transactions · 2020Review
- Emerging Diversity in Lipid-Protein Interactions.Chemical reviews · 2019Review
- Computational Modeling of Realistic Cell Membranes.Chemical reviews · 2019Review
- Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation.Chemical reviews · 2019Review
- Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance.Chemical reviews · 2019Article
- Interaction of the human erythrocyte Band 3 anion exchanger 1 (AE1, SLC4A1) with lipids and glycophorin A: Molecular organization of the Wright (Wr) blood group antigen.PLoS computational biology · 2018Article
- Cardiolipin dynamics and binding to conserved residues in the mitochondrial ADP/ATP carrier.Biochimica et biophysica acta. Biomembranes · 2018Article
- Structure of the SLC4 transporter Bor1p in an inward-facing conformation.Protein science : a publication of the Protein Society · 2017Article
- Atomistic insight into lipid translocation by a TMEM16 scramblase.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Structural and Functional Basis for Lipid Synergy on the Activity of the Antibacterial Peptide ABC Transporter McjD.The Journal of biological chemistry · 2016Article
- Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale.Current opinion in structural biology · 2016Review
- Lipid interaction sites on channels, transporters and receptors: Recent insights from molecular dynamics simulations.Biochimica et biophysica acta · 2016Review
- Model parameters for simulation of physiological lipids.Journal of computational chemistry · 2016Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
The Escherichia coli UraA H+-uracil symporter is a member of the nucleobase/ascorbate transporter (NAT) family of proteins, and is responsible for the proton-driven uptake of uracil. Multiscale molecular dynamics simulations of the UraA symporter in phospholipid bilayers consisting of: 1) 1-palmitoyl 2-oleoyl-phosphatidylcholine (POPC); 2) 1-palmitoyl 2-oleoyl-phosphatidylethanolamine (POPE); and 3) a mixture of 75% POPE, 20% 1-palmitoyl 2-oleoyl-phosphatidylglycerol (POPG); and 5% 1-palmitoyl 2-oleoyl-diphosphatidylglycerol/cardiolipin (CL) to mimic the lipid composition of the bacterial inner membrane, were performed using the MARTINI coarse-grained force field to self-assemble lipids around the crystal structure of this membrane transport protein, followed by atomistic simulations. The overall fold of the protein in lipid bilayers remained similar to the crystal structure in detergent on the timescale of our simulations. Simulations were performed in the absence of uracil, and resulted in a closed state of the transporter, due to relative movement of the gate and core domains. Anionic lipids, including POPG and especially CL, were found to associate with UraA, involving interactions between specific basic residues in loop regions and phosphate oxygens of the CL head group. In particular, three CL binding sites were identified on UraA: two in the inner leaflet and a single site in the outer leaflet. Mutation of basic residues in the binding sites resulted in the loss of CL binding in the simulations. CL may play a role as a "proton trap" that channels protons to and from this transporter within CL-enriched areas of the inner bacterial membrane.
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