ArticlePloS one2013
Aggregation of lipid-anchored full-length H-Ras in lipid bilayers: simulations with the MARTINI force field.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
26 citing papers in PubMed, 47 citations in OpenAlex.
- KRAS4a and KRAS4b show distinct lipid-dependent regulation of RAS-RAF membrane dynamics.The Journal of biological chemistry · 2026Article
- Advanced computational approaches to understand protein aggregation.Biophysics reviews · 2024Review
- RAS G-domains allosterically contribute to the recognition of lipid headgroups and acyl chains.The Journal of cell biology · 2024Article
- RAS GTPases and Interleaflet Coupling in the Plasma Membrane.Cold Spring Harbor perspectives in biology · 2023Review
- Measuring pico-Newton Forces with Lipid Anchors as Force Sensors in Molecular Dynamics Simulations.The journal of physical chemistry. B · 2023Article
- Remodeling of the Plasma Membrane by Surface-Bound Protein Monomers and Oligomers: The Critical Role of Intrinsically Disordered Regions.The Journal of membrane biology · 2022Review
- Molecular Mechanisms Underlying Caveolin-1 Mediated Membrane Curvature.The Journal of membrane biology · 2022Review
- Approaches to inhibiting oncogenic K-Ras.Small GTPases · 2021Review
- Guardians of the Cell: State-of-the-Art of Membrane Proteins from a Computational Point-of-View.Methods in molecular biology (Clifton, N.J.) · 2021Article
- RAS Nanoclusters Selectively Sort Distinct Lipid Headgroups and Acyl Chains.Frontiers in molecular biosciences · 2021Review
- Probing the Conformational and Energy Landscapes of KRAS Membrane Orientation.The journal of physical chemistry. B · 2019Article
- Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation.Chemical reviews · 2019Review
- Computational Modeling of Realistic Cell Membranes.Chemical reviews · 2019Review
- Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance.Chemical reviews · 2019Article
- Interplay between Membrane Curvature and Cholesterol: Role of Palmitoylated Caveolin-1.Biophysical journal · 2019Article
- Interactions of the EphA2 Kinase Domain with PIPs in Membranes: Implications for Receptor Function.Structure (London, England : 1993) · 2018Article
- Spatiotemporal Analysis of K-Ras Plasma Membrane Interactions Reveals Multiple High Order Homo-oligomeric Complexes.Journal of the American Chemical Society · 2017Article
- Geodesic curvature driven surface microdomain formation.Journal of computational physics · 2017Article
- Domain Stability in Biomimetic Membranes Driven by Lipid Polyunsaturation.The journal of physical chemistry. B · 2016Article
- Ras Dimer Formation as a New Signaling Mechanism and Potential Cancer Therapeutic Target.Mini reviews in medicinal chemistry · 2016Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Lipid-anchored Ras oncoproteins assemble into transient, nano-sized substructures on the plasma membrane. These substructures, called nanoclusters, were proposed to be crucial for high-fidelity signal transmission in cells. However, the molecular basis of Ras nanoclustering is poorly understood. In this work, we used coarse-grained (CG) molecular dynamics simulations to investigate the molecular mechanism by which full-length H-ras proteins form nanoclusters in a model membrane. We chose two different conformations of H-ras that were proposed to represent the active and inactive state of the protein, and a domain-forming model bilayer made up of di16:0-PC (DPPC), di18:2-PC (DLiPC) and cholesterol. We found that, irrespective of the initial conformation, Ras molecules assembled into a single large aggregate. However, the two binding modes, which are characterized by the different orientation of the G-domain with respect to the membrane, differ in dynamics and organization during and after aggregation. Some of these differences involve regions of Ras that are important for effector/modulator binding, which may partly explain observed differences in the ability of active and inactive H-ras nanoclusters to recruit effectors. The simulations also revealed some limitations in the CG force field to study protein assembly in solution, which we discuss in the context of proposed potential avenues of improvement.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.