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Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers
2014
PLoS Computational Biology
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A larger scale simulation of a model plasma membrane containing 6000 lipid molecules revealed correlations between curvature of the bilayer surface and clustering of lipid molecules. ...
In summary, these simulations explore the nanoscale dynamics of model bilayers which mimic the in vivo lipid composition of mammalian plasma membranes, revealing emergent nanoscale membrane organization ...
Correlation between bilayer surface curvature and the clustering of lipid molecules Visualization of the PM6000 simulation suggested a correlation between the curvature in the PM6000 bilayer surface and ...
doi:10.1371/journal.pcbi.1003911
pmid:25340788
pmcid:PMC4207469
fatcat:2kwcswptrvhsndukckw7eddmpu
Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale
2016
Current Opinion in Structural Biology
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Building on the success of protein-lipid interaction simulations, larger scale simulations reveal crowding and clustering of proteins, resulting in slow and anomalous diffusional dynamics, within realistic ...
All atom and coarse-grained simulations may be used to explore in detail the interactions of membrane proteins and specific lipids, yielding predictions of lipid binding sites in good agreement with available ...
Acknowledgements This study was supported by grants from the Wellcome Trust, the BBSRC, and the EPSRC. ...
doi:10.1016/j.sbi.2016.06.007
pmid:27341016
pmcid:PMC5404110
fatcat:4pfcurn6xfaqvjfktzauqjtvra
Molecular mechanisms of spontaneous curvature and softening in complex lipid bilayer mixtures
[article]
2022
bioRxiv
pre-print
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We identify two mechanisms of bilayer softening: Diffusional softening, which is driven by the dynamic coupling between lipid distributions and membrane undulations, and conformational softening, which ...
The curvature preference of populations of lipid conformations were inferred from their redistribution on a dynamically fluctuating bilayer. ...
The correlation of state (i.e., molecular structure) and curvature is recorded and compared with Helfrich/Canham theory. ...
doi:10.1101/2022.02.17.480963
fatcat:2mylkbas3jat3klt2h6gvqyaj4
Assembly of Lipid Bilayers in Large Scaffold Arrays
2010
Biophysical Journal
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Using a combination of all-atom and coarse-grained molecular dynamics simulations to interpret a range of x-ray scattering experiments, we aim to understand the role of membrane deformation in the action ...
Our simulation results have led to the hypothesis that aS flattens curved membranes by screening the repulsive interactions between negatively charged, acidic headgroups, thereby reducing the effective ...
This tendency of flip-flop motions is strongly correlated with the relative positions of the lipids to the bilayer membranes: CHOL stays almost at the center of the membrane, whereas the head group of ...
doi:10.1016/j.bpj.2009.12.2661
fatcat:n7wzv5vbanf6padipnjlyavbhq
Calcium ions promote membrane fusion by forming negative-curvature inducing clusters on specific anionic lipids
[article]
2020
bioRxiv
pre-print
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This allows us to trace the origin of lipid-calcium selectivity in membrane fusion to the formation of lipid clusters with long-range correlations that induce negative curvature on the membrane surface ...
We show how the combined effects of calcium binding to membranes lower the barriers along the fusion pathway that lead to the formation of the fusion stalk as well as the fusion pore. ...
FIG. 3 . 3 Top panel: Clustering of lipids by Ca 2+ from simulations. ...
doi:10.1101/2020.04.29.068221
fatcat:xgrzfcojnbhvhkll4b4h74tqwu
Molecular simulations of glycolipids: Towards mammalian cell membrane models
2016
Biochimie
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This glycolipid is included in simulations of a mixed lipid bilayer model reflecting the compositional complexity of a mammalian cell membrane. ...
Recent advances in molecular dynamics methods, especially the development of coarse-grained models, have enabled simulations of increasingly complex models of cell membranes. ...
G.H. is supported by a fellowship from the MRC and the Department of Biochemistry, University of Oxford. ...
doi:10.1016/j.biochi.2015.09.033
pmid:26427555
pmcid:PMC4710579
fatcat:yagbmxkf5vg45ne3oaucmuadti
Computational Modeling of Realistic Cell Membranes
2018
Biophysical Journal
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Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. ...
Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. ...
al. 483 revealed the molecular organization of syntaxin clusters and showed that syntaxin clustering is mediated by electrostatic interactions with the strongly anionic lipid phosphatidylinositol-4,5 ...
doi:10.1016/j.bpj.2017.11.2032
fatcat:opnbavtgknhqvhjfvosyawur2u
Computational Modeling of Realistic Cell Membranes
2019
Chemical Reviews
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Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. ...
Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. ...
al. 483 revealed the molecular organization of syntaxin clusters and showed that syntaxin clustering is mediated by electrostatic interactions with the strongly anionic lipid phosphatidylinositol-4,5 ...
doi:10.1021/acs.chemrev.8b00460
pmid:30623647
pmcid:PMC6509646
fatcat:ioyxru5wtnehbbhcjfkghs4kbi
Entropic forces drive clustering and spatial localization of influenza A M2 during viral budding
2018
Proceedings of the National Academy of Sciences of the United States of America
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The authors declare no conflict of interest. ...
M2 clustering, as accentuated in bilayers with stiff lipids, is driven by an entropic force that can be suppressed by raising the temperature of the system (compare the simulations of M2 in stiff 10e at ...
M2 clustering, as accentuated in bilayers with stiff lipids, is driven by an entropic force that can be suppressed by raising the temperature of the system (compare the simulations of M2 in stiff 10e at ...
doi:10.1073/pnas.1805443115
pmid:30150411
fatcat:vpj5bensnvg7ffqotpkbeoneue
Aggregation of Model Membrane Proteins, Modulated by Hydrophobic Mismatch, Membrane Curvature, and Protein Class
2011
Biophysical Journal
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The nature and extent of aggregation are shown to be influenced by membrane curvature and the shape or orientation of the protein. ...
Using coarse-grained molecular dynamics simulations, we have studied model membranes comprising~7000 lipids and 16 identical copies of model cylindrical proteins of either a-helical or b-barrel types. ...
, such as protein class (a-helical or b-barrel), lipid bilayer hydrophobic thickness, and membrane curvature (by comparing planar bilayer systems to vesicle systems). ...
doi:10.1016/j.bpj.2011.06.048
pmid:21806937
pmcid:PMC3145270
fatcat:vmtac6jbbzbgdhlzeyt266c3vu
Multiscale Modeling of Four Component Lipid Mixtures: Coarse Grained and United Atom Simulations Reveal Trends in Phase Separation
2014
Biophysical Journal
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The simulations indicate stabilization of curved areas by lipid nano-domains and a tight correlation between lipid species and curvature. ...
Advances in lipidomics are detailing the compositional and dynamic complexity of cell membranes such as leaflet asymmetry, lipid nanodomains, local curvature, lipid diffusion and lipid composition and ...
The simulations indicate stabilization of curved areas by lipid nano-domains and a tight correlation between lipid species and curvature. ...
doi:10.1016/j.bpj.2013.11.1700
fatcat:y3mxhzcdnbaoha2fg2ue3jrxkm
'In vivo in Silico': Effects of Membrane Complexity on Protein-Lipid Interactions, Lipid Nano-Domains and Curvature
2015
Biophysical Journal
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Our simulations indicate stabilization of curved areas by lipid nano-domains and a correlation between composition and curvature. ...
reveal the compositional complexity of cell membranes. ...
Our simulations indicate stabilization of curved areas by lipid nano-domains and a correlation between composition and curvature. ...
doi:10.1016/j.bpj.2014.11.469
fatcat:74gbemd4hrd5xhf4m5ozbzhnc4
Membrane Cytoskeletal Changes during In-Situ to Invasive Progression of Breast Cancer Cells Observed by Multi-Scale Diffusion Analysis of Transmembrane Proteins
2015
Biophysical Journal
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Due to their bulky sugar headgroup, GM1 molecules introduce substantial disorder to the lipid bilayer, which results in formation of lipid domains with unique molecular organization. ...
as Revealed by Advanced Time-Resolved Fluorescence Techniques Russian Federation. ...
Our simulations indicate stabilization of curved areas by lipid nano-domains and a correlation between composition and curvature. ...
doi:10.1016/j.bpj.2014.11.468
fatcat:lge2mbgnwbhcllkjld5bqutyni
Curvature and Lipid Clustering within Asymmetric Biologically Relevant Membrane Models
2014
Biophysical Journal
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The simulations indicate stabilization of curved areas by lipid nano-domains and a tight correlation between lipid species and curvature. ...
Advances in lipidomics are detailing the compositional and dynamic complexity of cell membranes such as leaflet asymmetry, lipid nanodomains, local curvature, lipid diffusion and lipid composition and ...
The simulations indicate stabilization of curved areas by lipid nano-domains and a tight correlation between lipid species and curvature. ...
doi:10.1016/j.bpj.2013.11.1699
fatcat:pmplohpwwfgxnfm233wiip3k4e
Organization, dynamics, and segregation of Ras nanoclusters in membrane domains
2012
Proceedings of the National Academy of Sciences of the United States of America
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As model systems, we chose the triply lipidated membrane targeting motif of H-ras (tH) and a large bilayer made up of di16∶0-PC (DPPC), di18∶2-PC (DLiPC), and cholesterol. ...
| lipidated Ras proteins | nanoclusters/nanodomains | plasma membrane | molecular dynamics simulation ...
Reyna for help with Fig. 6 . J.F.H. is supported by National Institutes of Health Grant R01GM066717. ...
doi:10.1073/pnas.1200773109
pmid:22562795
pmcid:PMC3361399
fatcat:aqcg5b2givcspa6eylngtkdaui
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