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Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers

Heidi Koldsø, David Shorthouse, Jean Hélie, Mark S. P. Sansom, Cécile Fradin
2014 PLoS Computational Biology  
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

Matthieu Chavent, Anna L Duncan, Mark SP Sansom
2016 Current Opinion in Structural Biology  
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]

Henry J Lessen, Kayla C Sapp, Andrew H Beaven, Rana Ashkar, Alexander J Sodt
2022 bioRxiv   pre-print
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

Jesper S. Hansen, Mark Perry, Jörg Vogel, Jesper Groth, Thomas Vissing, Jenny Emnéus, Claus H. Nielsen
2010 Biophysical Journal  
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]

Christoph Allolio, Daniel Harries
2020 bioRxiv   pre-print
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

David Shorthouse, George Hedger, Heidi Koldsø, Mark S.P. Sansom
2016 Biochimie  
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

Siewert J. Marrink
2018 Biophysical Journal  
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

Siewert J. Marrink, Valentina Corradi, Paulo C.T. Souza, Helgi I. Ingólfsson, D. Peter Tieleman, Mark S.P. Sansom
2019 Chemical Reviews  
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

Jesper J. Madsen, John M. A. Grime, Jeremy S. Rossman, Gregory A. Voth
2018 Proceedings of the National Academy of Sciences of the United States of America  
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

Daniel L. Parton, Jochen W. Klingelhoefer, Mark S.P. Sansom
2011 Biophysical Journal  
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

David G. Ackerman, Gerald W. Feigenson
2014 Biophysical Journal  
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

Heidi Koldsø, Mark S.P. Sansom
2015 Biophysical Journal  
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

Muhammed F. Simsek, Arnd Pralle
2015 Biophysical Journal  
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

Heidi Koldsø, Mark S.P. Sansom
2014 Biophysical Journal  
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

L. Janosi, Z. Li, J. F. Hancock, A. A. Gorfe
2012 Proceedings of the National Academy of Sciences of the United States of America  
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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