Computational modeling of realistic cell membranes

SJ Marrink, V Corradi, PCT Souza, HI Ingolfsson… - Chemical …, 2019 - ACS Publications
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. The …

Perspective on the Martini model

SJ Marrink, DP Tieleman - Chemical Society Reviews, 2013 - pubs.rsc.org
The Martini model, a coarse-grained force field for biomolecular simulations, has found a
broad range of applications since its release a decade ago. Based on a building block …

The antibiotic darobactin mimics a β-strand to inhibit outer membrane insertase

H Kaur, RP Jakob, JK Marzinek, R Green, Y Imai… - Nature, 2021 - nature.com
Antibiotics that target Gram-negative bacteria in new ways are needed to resolve the
antimicrobial resistance crisis,–. Gram-negative bacteria are protected by an additional outer …

Computational lipidomics of the neuronal plasma membrane

HI Ingólfsson, TS Carpenter, H Bhatia, PT Bremer… - Biophysical journal, 2017 - cell.com
Membrane lipid composition varies greatly within submembrane compartments, different
organelle membranes, and also between cells of different cell stage, cell and tissue types …

Excessive aggregation of membrane proteins in the Martini model

M Javanainen, H Martinez-Seara, I Vattulainen - PloS one, 2017 - journals.plos.org
The coarse-grained Martini model is employed extensively to study membrane protein
oligomerization. While this approach is exceptionally promising given its computational …

Piezo1 forms specific, functionally important interactions with phosphoinositides and cholesterol

A Buyan, CD Cox, J Barnoud, J Li, HSM Chan… - Biophysical journal, 2020 - cell.com
Touch, hearing, and blood pressure regulation require mechanically gated ion channels that
convert mechanical stimuli into electrical currents. One such channel is Piezo1, which plays …

Computational analysis of local membrane properties

V Gapsys, BL de Groot, R Briones - Journal of computer-aided molecular …, 2013 - Springer
In the field of biomolecular simulations, dynamics of phospholipid membranes is of special
interest. A number of proteins, including channels, transporters, receptors and short peptides …

Triacylglycerols sequester monotopic membrane proteins to lipid droplets

L Caillon, V Nieto, P Gehan, M Omrane… - Nature …, 2020 - nature.com
Triacylglycerols (TG) are synthesized at the endoplasmic reticulum (ER) bilayer and
packaged into organelles called lipid droplets (LDs). LDs are covered by a single …

[HTML][HTML] Coarse-grain modelling of protein–protein interactions

M Baaden, SJ Marrink - Current opinion in structural biology, 2013 - Elsevier
Highlights•Coarse graining allows to model multi-protein aggregates of very large
scale.•Knowledge-based approaches promise to improve protein–protein interface …

Ganglioside-lipid and ganglioside-protein interactions revealed by coarse-grained and atomistic molecular dynamics simulations

RX Gu, HI Ingólfsson, AH De Vries… - The Journal of …, 2017 - ACS Publications
Gangliosides are glycolipids in which an oligosaccharide headgroup containing one or
more sialic acids is connected to a ceramide. Gangliosides reside in the outer leaflet of the …