Computational modeling of realistic cell membranes
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 …
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …
Pore formation in regulated cell death
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 …
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
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 …
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
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 …
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 …
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 …
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 …
protein activity, the sensing of membrane voltages, and the actions of antimicrobial, toxin …
[HTML][HTML] Toroidal pores formed by antimicrobial peptides show significant disorder
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 …
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 …
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
The recombinant HIV-1 Tat protein contains a small region corresponding to residues
47YGRKKRRQRR57R, which is capable of translocating cargoes of different molecular …
47YGRKKRRQRR57R, which is capable of translocating cargoes of different molecular …