Literature DB >> 30075850

From Dynamics to Membrane Organization: Experimental Breakthroughs Occasion a "Modeling Manifesto".

Edward Lyman1, Chia-Lung Hsieh2, Christian Eggeling3.   

Abstract

New experimental techniques, especially in the context of observing molecular dynamics, reveal the plasma membrane to be heterogeneous and "scale rich," from nanometers to microns and from microseconds to seconds. This is critical information, which shows that scale-dependent transport governs the molecular encounters that underlie cellular signaling. The data are rich and reaffirm the importance of the cortical cytoskeleton, protein aggregates, and lipidomic complexity on the statistics of molecular encounters. Moreover, the data demand simulation approaches with a particular set of features, hence the "manifesto." Together with the experimental data, simulations that satisfy these requirements hold the promise of a deeper understanding of membrane spatiotemporal organization. Several experimental breakthroughs in measuring molecular membrane dynamics are reviewed, the constraints that they place on simulations are discussed, and the status of simulation approaches that aim to meet them are detailed.
Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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Year:  2018        PMID: 30075850      PMCID: PMC6103736          DOI: 10.1016/j.bpj.2018.07.012

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  81 in total

1.  Detection and spectroscopy of gold nanoparticles using supercontinuum white light confocal microscopy.

Authors:  K Lindfors; T Kalkbrenner; P Stoller; V Sandoghdar
Journal:  Phys Rev Lett       Date:  2004-07-15       Impact factor: 9.161

Review 2.  Revitalizing membrane rafts: new tools and insights.

Authors:  Kai Simons; Mathias J Gerl
Journal:  Nat Rev Mol Cell Biol       Date:  2010-10       Impact factor: 94.444

3.  Correlated diffusion of membrane proteins and their effect on membrane viscosity.

Authors:  Naomi Oppenheimer; Haim Diamant
Journal:  Biophys J       Date:  2009-04-22       Impact factor: 4.033

4.  Single molecule diffusion of membrane-bound proteins: window into lipid contacts and bilayer dynamics.

Authors:  Jefferson D Knight; Michael G Lerner; Joan G Marcano-Velázquez; Richard W Pastor; Joseph J Falke
Journal:  Biophys J       Date:  2010-11-03       Impact factor: 4.033

5.  Nanoscale fluorescence correlation spectroscopy on intact living cell membranes with NSOM probes.

Authors:  Carlo Manzo; Thomas S van Zanten; Maria F Garcia-Parajo
Journal:  Biophys J       Date:  2011-01-19       Impact factor: 4.033

Review 6.  Functional rafts in cell membranes.

Authors:  K Simons; E Ikonen
Journal:  Nature       Date:  1997-06-05       Impact factor: 49.962

7.  Phospholipids undergo hop diffusion in compartmentalized cell membrane.

Authors:  Takahiro Fujiwara; Ken Ritchie; Hideji Murakoshi; Ken Jacobson; Akihiro Kusumi
Journal:  J Cell Biol       Date:  2002-06-10       Impact factor: 10.539

8.  Divergent Diffusion Coefficients in Simulations of Fluids and Lipid Membranes.

Authors:  Martin Vögele; Gerhard Hummer
Journal:  J Phys Chem B       Date:  2016-07-22       Impact factor: 2.991

9.  Scanning STED-FCS reveals spatiotemporal heterogeneity of lipid interaction in the plasma membrane of living cells.

Authors:  Alf Honigmann; Veronika Mueller; Haisen Ta; Andreas Schoenle; Erdinc Sezgin; Stefan W Hell; Christian Eggeling
Journal:  Nat Commun       Date:  2014-11-20       Impact factor: 14.919

10.  Remodeling of the postsynaptic plasma membrane during neural development.

Authors:  Karolina Tulodziecka; Barbara B Diaz-Rohrer; Madeline M Farley; Robin B Chan; Gilbert Di Paolo; Kandice R Levental; M Neal Waxham; Ilya Levental
Journal:  Mol Biol Cell       Date:  2016-08-17       Impact factor: 4.138

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  11 in total

1.  Computer simulations of protein-membrane systems.

Authors:  Jennifer Loschwitz; Olujide O Olubiyi; Jochen S Hub; Birgit Strodel; Chetan S Poojari
Journal:  Prog Mol Biol Transl Sci       Date:  2020-02-26       Impact factor: 3.622

2.  Interdigitation of Lipids Induced by Membrane-Active Proteins.

Authors:  T Devanand; Sankaran Krishnaswamy; Satyavani Vemparala
Journal:  J Membr Biol       Date:  2019-06-11       Impact factor: 1.843

3.  Emerging Diversity in Lipid-Protein Interactions.

Authors:  Valentina Corradi; Besian I Sejdiu; Haydee Mesa-Galloso; Haleh Abdizadeh; Sergei Yu Noskov; Siewert J Marrink; D Peter Tieleman
Journal:  Chem Rev       Date:  2019-02-13       Impact factor: 60.622

4.  Persistent collective motion of a dispersing membrane domain.

Authors:  Benjamin Sorkin; Haim Diamant
Journal:  Biophys J       Date:  2021-03-17       Impact factor: 4.033

Review 5.  Computational Modeling of Realistic Cell Membranes.

Authors:  Siewert J Marrink; Valentina Corradi; Paulo C T Souza; Helgi I Ingólfsson; D Peter Tieleman; Mark S P Sansom
Journal:  Chem Rev       Date:  2019-01-09       Impact factor: 72.087

Review 6.  Tools for Understanding Nanoscale Lipid Regulation of Ion Channels.

Authors:  Carol V Robinson; Tibor Rohacs; Scott B Hansen
Journal:  Trends Biochem Sci       Date:  2019-05-03       Impact factor: 14.264

7.  Fluorescence strategies for mapping cell membrane dynamics and structures.

Authors:  Jagadish Sankaran; Thorsten Wohland
Journal:  APL Bioeng       Date:  2020-05-12

8.  Imaging FCS delineates subtle heterogeneity in plasma membranes of resting mast cells.

Authors:  Nirmalya Bag; David A Holowka; Barbara A Baird
Journal:  Mol Biol Cell       Date:  2020-01-02       Impact factor: 4.138

9.  Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics.

Authors:  Astrid F Brandner; Stepan Timr; Simone Melchionna; Philippe Derreumaux; Marc Baaden; Fabio Sterpone
Journal:  Sci Rep       Date:  2019-11-11       Impact factor: 4.379

Review 10.  Regulation of Membrane Calcium Transport Proteins by the Surrounding Lipid Environment.

Authors:  Louise Conrard; Donatienne Tyteca
Journal:  Biomolecules       Date:  2019-09-20
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