ArticleBiophysical journal2004
Lipid-protein interactions of integral membrane proteins: a comparative simulation study.
Article in Biophysical journal, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Differential effects of lipid composition on the thermal and functional properties of membrane associated CYP2J2.Protein science : a publication of the Protein Society · 2026Article
- Extracellular and Membrane Protein: Structure, Biological Functions, Diseases, and an Emerging Modality for Drug Discovery.MedComm · 2026Review
- Cerebellar lipid dysregulation in SCA3: A comparative study in patients and mice.Neurobiology of disease · 2025Article
- Probing the Hydrophobic Region of a Lipid Bilayer at Specific Depths Using Vibrational Spectroscopy.Journal of the American Chemical Society · 2023Article
- Lipid-mediated prestin organization in outer hair cell membranes and its implications in sound amplification.Nature communications · 2022Article
- Volleying plasma membrane proteins from birth to death: Role of J-domain proteins.Frontiers in molecular biosciences · 2022Review
- A Single Mutation in the Outer Lipid-Facing Helix of a Pentameric Ligand-Gated Ion Channel Affects Channel Function Through a Radially-Propagating Mechanism.Frontiers in molecular biosciences · 2021Article
- Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation.Chemical reviews · 2019Review
- Influence of membrane lipid composition on the structure and activity of γ-secretase.Physical chemistry chemical physics : PCCP · 2018Article
- The Role of Lipid Interactions in Simulations of the α-Hemolysin Ion-Channel-Forming Toxin.Biophysical journal · 2018Article
- Structural Insights into the Yersinia pestis Outer Membrane Protein Ail in Lipid Bilayers.The journal of physical chemistry. B · 2017Article
- Structural features and lipid binding domain of tubulin on biomimetic mitochondrial membranes.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Direct Interaction between the Voltage Sensors Produces Cooperative Sustained Deactivation in Voltage-gated H+ Channel Dimers.The Journal of biological chemistry · 2016Article
- Membrane-induced structural rearrangement and identification of a novel membrane anchor in talin F2F3.Biophysical journal · 2014Article
- Assembly and stability of Salmonella enterica ser. Typhi TolC protein in POPE and DMPE.Journal of biological physics · 2014Article
- Molecular dynamics simulation of human serum paraoxonase 1 in DPPC bilayer reveals a critical role of transmembrane helix H1 for HDL association.European biophysics journal : EBJ · 2014Article
- Identification of novel cholesterol-binding regions in Kir2 channels.The Journal of biological chemistry · 2013Article
- Molecular dynamics simulations reveal the HIV-1 Vpu transmembrane protein to form stable pentamers.PloS one · 2013Article
- Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data.BMC biophysics · 2011Article
- Membrane protein dynamics in different environments: simulation study of the outer membrane protein X in a lipid bilayer and in a micelle.European biophysics journal : EBJ · 2011Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The interactions between membrane proteins and their lipid bilayer environment play important roles in the stability and function of such proteins. Extended (15-20 ns) molecular dynamics simulations have been used to explore the interactions of two membrane proteins with phosphatidylcholine bilayers. One protein (KcsA) is an alpha-helix bundle and embedded in a palmitoyl oleoyl phosphatidylcholine bilayer; the other (OmpA) is a beta-barrel outer-membrane protein and is in a dimyristoyl phosphatidylcholine bilayer. The simulations enable analysis in detail of a number of aspects of lipid-protein interactions. In particular, the interactions of aromatic amphipathic side chains (i.e., Trp, Tyr) with lipid headgroups, and "snorkeling" interactions of basic side chains (i.e., Lys, Arg) with phosphate groups are explored. Analysis of the number of contacts and of H-bonds reveal fluctuations on an approximately 1- to 5-ns timescale. There are two clear bands of interacting residues on the surface of KcsA, whereas there are three such bands on OmpA. A large number of Arg-phosphate interactions are seen for KcsA; for OmpA, the number of basic-phosphate interactions is smaller and shows more marked fluctuations with respect to time. Both classes of interaction occur in clearly defined interfacial regions of width approximately 1 nm. Analysis of lateral diffusion of lipid molecules reveals that "boundary" lipid molecules diffuse at about half the rate of bulk lipid. Overall, these simulations present a dynamic picture of lipid-protein interactions: there are a number of more specific interactions but even these fluctuate on an approximately 1- to 5-ns timescale.
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