Literature DB >> 26743083

Computational 'microscopy' of cellular membranes.

Helgi I Ingólfsson1, Clément Arnarez1, Xavier Periole1, Siewert J Marrink2.   

Abstract

Computational 'microscopy' refers to the use of computational resources to simulate the dynamics of a molecular system. Tuned to cell membranes, this computational 'microscopy' technique is able to capture the interplay between lipids and proteins at a spatio-temporal resolution that is unmatched by other methods. Recent advances allow us to zoom out from individual atoms and molecules to supramolecular complexes and subcellular compartments that contain tens of millions of particles, and to capture the complexity of the crowded environment of real cell membranes. This Commentary gives an overview of the main concepts of computational 'microscopy' and describes the state-of-the-art methods used to model cell membrane processes. We illustrate the power of computational modelling approaches by providing a few in-depth examples of large-scale simulations that move up from molecular descriptions into the subcellular arena. We end with an outlook towards modelling a complete cell in silico.
© 2016. Published by The Company of Biologists Ltd.

Entities:  

Keywords:  Coarse-graining; Lipid bilayers; Membrane proteins; Molecular dynamics; Multiscaling; Simulations

Mesh:

Substances:

Year:  2016        PMID: 26743083     DOI: 10.1242/jcs.176040

Source DB:  PubMed          Journal:  J Cell Sci        ISSN: 0021-9533            Impact factor:   5.285


  38 in total

1.  CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides.

Authors:  Pin-Chia Hsu; Bart M H Bruininks; Damien Jefferies; Paulo Cesar Telles de Souza; Jumin Lee; Dhilon S Patel; Siewert J Marrink; Yifei Qi; Syma Khalid; Wonpil Im
Journal:  J Comput Chem       Date:  2017-08-03       Impact factor: 3.376

Review 2.  From Atoms to Cells: Using Mesoscale Landscapes to Construct Visual Narratives.

Authors:  David S Goodsell; Margaret A Franzen; Tim Herman
Journal:  J Mol Biol       Date:  2018-06-07       Impact factor: 5.469

3.  Piezo1 Forms Specific, Functionally Important Interactions with Phosphoinositides and Cholesterol.

Authors:  Amanda Buyan; Charles D Cox; Jonathan Barnoud; Jinyuan Li; Hannah S M Chan; Boris Martinac; Siewert J Marrink; Ben Corry
Journal:  Biophys J       Date:  2020-09-02       Impact factor: 4.033

4.  Multiple interactions between an Arf/GEF complex and charged lipids determine activation kinetics on the membrane.

Authors:  Deepti Karandur; Agata Nawrotek; John Kuriyan; Jacqueline Cherfils
Journal:  Proc Natl Acad Sci U S A       Date:  2017-09-18       Impact factor: 11.205

5.  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

6.  Cholesterol binding to a conserved site modulates the conformation, pharmacology, and transport kinetics of the human serotonin transporter.

Authors:  Louise Laursen; Kasper Severinsen; Kristina Birch Kristensen; Xavier Periole; Malene Overby; Heidi Kaastrup Müller; Birgit Schiøtt; Steffen Sinning
Journal:  J Biol Chem       Date:  2018-01-19       Impact factor: 5.157

Review 7.  Potassium channels in the heart: structure, function and regulation.

Authors:  Eleonora Grandi; Michael C Sanguinetti; Daniel C Bartos; Donald M Bers; Ye Chen-Izu; Nipavan Chiamvimonvat; Henry M Colecraft; Brian P Delisle; Jordi Heijman; Manuel F Navedo; Sergei Noskov; Catherine Proenza; Jamie I Vandenberg; Vladimir Yarov-Yarovoy
Journal:  J Physiol       Date:  2016-11-13       Impact factor: 5.182

Review 8.  Dynamic pattern generation in cell membranes: Current insights into membrane organization.

Authors:  Krishnan Raghunathan; Anne K Kenworthy
Journal:  Biochim Biophys Acta Biomembr       Date:  2018-05-09       Impact factor: 3.747

Review 9.  The Lateral Organization and Mobility of Plasma Membrane Components.

Authors:  Ken Jacobson; Ping Liu; B Christoffer Lagerholm
Journal:  Cell       Date:  2019-05-02       Impact factor: 41.582

Review 10.  Lipid interaction sites on channels, transporters and receptors: Recent insights from molecular dynamics simulations.

Authors:  George Hedger; Mark S P Sansom
Journal:  Biochim Biophys Acta       Date:  2016-03-03
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.