The Fats of Life: Using Computational Chemistry to Characterise the Eukaryotic Cell Membrane

2020 ◽  
Vol 73 (3) ◽  
pp. 85 ◽  
Author(s):  
Katie A. Wilson ◽  
Lily Wang ◽  
Hugo MacDermott-Opeskin ◽  
Megan L. O'Mara
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Current Knowledge ◽  
Computational Modelling ◽  
Eukaryotic Cell ◽  
Computational Techniques ◽  
Lipid Species ◽  
Dynamics Simulations ◽  
And Function

Our current knowledge of the structural dynamics and complexity of lipid bilayers is still developing. Computational techniques, especially molecular dynamics simulations, have increased our understanding significantly as they allow us to model functions that cannot currently be experimentally resolved. Here we review available computational tools and techniques, the role of the major lipid species, insights gained into lipid bilayer structure and function from molecular dynamics simulations, and recent progress towards the computational modelling of the physiological complexity of eukaryotic lipid bilayers.

The membranes of Gram-negative bacteria: progress in molecular modelling and simulation

2015 ◽  
Vol 43 (2) ◽  
pp. 162-167 ◽  
Author(s):  
Syma Khalid ◽  
Nils A. Berglund ◽  
Daniel A. Holdbrook ◽  
Yuk M. Leung ◽  
Jamie Parkin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Molecular Modelling ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Bacterial Membranes ◽  
Lipid Species ◽  
Membrane Models ◽  
Dynamics Simulations

Molecular modelling and simulations have been employed to study the membranes of Gram-negative bacteria for over 20 years. Proteins native to these membranes, as well as antimicrobial peptides and drug molecules have been studied using molecular dynamics simulations in simple models of membranes, usually only comprising one lipid species. Thus, traditionally, the simulations have reflected the majority of in vitro membrane experimental setups, enabling observations from the latter to be rationalized at the molecular level. In the last few years, the sophistication and complexity of membrane models have improved considerably, such that the heterogeneity of the lipid and protein composition of the membranes can now be considered both at the atomistic and coarse-grain levels of granularity. Importantly this means relevant biology is now being retained in the models, thereby linking the in silico and in vivo scenarios. We discuss recent progress in simulations of proteins in simple lipid bilayers, more complex membrane models and finally describe some efforts to overcome timescale limitations of atomistic molecular dynamics simulations of bacterial membranes.

Molecular dynamics simulations of rupture in lipid bilayers

2010 ◽  
Vol 235 (2) ◽  
pp. 181-188 ◽  
Author(s):  
Michael D Tomasini ◽  
Carlos Rinaldi ◽  
M Silvina Tomassone
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Dynamics Simulations

scholarly journals Molecular dynamics simulations of carbon nanotube porins in lipid bilayers

2018 ◽  
Vol 209 ◽  
pp. 341-358 ◽  
Author(s):  
Martin Vögele ◽  
Jürgen Köfinger ◽  
Gerhard Hummer
Keyword(s):  
Molecular Dynamics ◽  
Carbon Nanotube ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Lipid Membranes ◽  
Dynamics Simulations

Carbon nanotube porins embedded in lipid membranes are studied by molecular dynamics simulations.

scholarly journals Accurate Estimation of Membrane Capacitance from Atomistic Molecular Dynamics Simulations of Zwitterionic Lipid Bilayers

2020 ◽  
Vol 124 (38) ◽  
pp. 8278-8286 ◽  
Author(s):  
Vikram Reddy Ardham ◽  
Valeria Zoni ◽  
Sylvain Adamowicz ◽  
Pablo Campomanes ◽  
Stefano Vanni
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Membrane Capacitance ◽  
Accurate Estimation ◽  
Dynamics Simulations
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