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 …

Pore formation in regulated cell death

H Flores‐Romero, U Ros, AJ Garcia‐Saez - The EMBO journal, 2020 - embopress.org
The discovery of alternative signaling pathways that regulate cell death has revealed
multiple strategies for promoting cell death with diverse consequences at the tissue and …

Characterization of lipid–protein interactions and lipid-mediated modulation of membrane protein function through molecular simulation

MP Muller, T Jiang, C Sun, M Lihan, S Pant… - Chemical …, 2019 - ACS Publications
The cellular membrane constitutes one of the most fundamental compartments of a living
cell, where key processes such as selective transport of material and exchange of …

[HTML][HTML] Enhanced sampling in molecular dynamics using metadynamics, replica-exchange, and temperature-acceleration

C Abrams, G Bussi - Entropy, 2013 - mdpi.com
We review a selection of methods for performing enhanced sampling in molecular dynamics
simulations. We consider methods based on collective variable biasing and on tempering …

The MARTINI force field: coarse grained model for biomolecular simulations

SJ Marrink, HJ Risselada, S Yefimov… - The journal of …, 2007 - ACS Publications
We present an improved and extended version of our coarse grained lipid model. The new
version, coined the MARTINI force field, is parametrized in a systematic way, based on the …

[HTML][HTML] Permeability across lipid membranes

W Shinoda - Biochimica et Biophysica Acta (BBA)-Biomembranes, 2016 - Elsevier
Molecular permeation through lipid membranes is a fundamental biological process that is
important for small neutral molecules and drug molecules. Precise characterization of free …

The different interactions of lysine and arginine side chains with lipid membranes

L Li, I Vorobyov, TW Allen - The journal of physical chemistry B, 2013 - ACS Publications
The basic amino acids lysine (Lys) and arginine (Arg) play important roles in membrane
protein activity, the sensing of membrane voltages, and the actions of antimicrobial, toxin …

[HTML][HTML] Toroidal pores formed by antimicrobial peptides show significant disorder

D Sengupta, H Leontiadou, AE Mark… - Biochimica et Biophysica …, 2008 - Elsevier
A large variety of antimicrobial peptides have been shown to act, at least in vitro, by poration
of the lipid membrane. The nanometre size of these pores, however, complicates their …

[HTML][HTML] Lipid nanotechnology

S Mashaghi, T Jadidi, G Koenderink… - International journal of …, 2013 - mdpi.com
Nanotechnology is a multidisciplinary field that covers a vast and diverse array of devices
and machines derived from engineering, physics, materials science, chemistry and biology …

Molecular dynamics simulations suggest a mechanism for translocation of the HIV-1 TAT peptide across lipid membranes

HD Herce, AE Garcia - … of the National Academy of Sciences, 2007 - National Acad Sciences
The recombinant HIV-1 Tat protein contains a small region corresponding to residues
47YGRKKRRQRR57R, which is capable of translocating cargoes of different molecular …