Multiscale simulations of biological membranes: the challenge to understand biological phenomena in a living substance

G Enkavi, M Javanainen, W Kulig, T Róg… - Chemical …, 2019 - ACS Publications
Biological membranes are tricky to investigate. They are complex in terms of molecular
composition and structure, functional over a wide range of time scales, and characterized by …

Membrane lipid nanodomains

M Cebecauer, M Amaro, P Jurkiewicz… - Chemical …, 2018 - ACS Publications
Lipid membranes can spontaneously organize their components into domains of different
sizes and properties. The organization of membrane lipids into nanodomains might …

CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications

S Feng, S Park, YK Choi, W Im - Journal of chemical theory and …, 2023 - ACS Publications
Molecular dynamics simulations of membranes and membrane proteins serve as
computational microscopes, revealing coordinated events at the membrane interface. As G …

Unsaturated lipids facilitate partitioning of transmembrane peptides into the liquid ordered phase

S Park, I Levental, RW Pastor, W Im - Journal of Chemical Theory …, 2023 - ACS Publications
The affinity of single-pass transmembrane (TM) proteins for ordered membrane phases has
been reported to depend on their lipidation, TM length, and lipid accessible surface area. In …

Direct observation of cholesterol dimers and tetramers in lipid bilayers

MR Elkins, A Bandara, GA Pantelopulos… - The Journal of …, 2021 - ACS Publications
Cholesterol is a ubiquitous component of mammalian cell membranes and affects
membrane protein function. Although cholesterol-mediated formation of ordered membrane …

Cholesterol and Lipid Rafts in the Biogenesis of Amyloid-β Protein and Alzheimer's Disease

GA Pantelopulos, CB Abraham… - Annual Review of …, 2024 - annualreviews.org
Cholesterol has been conjectured to be a modulator of the amyloid cascade, the mechanism
that produces the amyloid-β (Aβ) peptides implicated in the onset of Alzheimer's disease …

Addressing the excessive aggregation of membrane proteins in the MARTINI model

A Majumder, JE Straub - Journal of chemical theory and …, 2021 - ACS Publications
The MARTINI model is a widely used coarse-grained force field popular for its capacity to
represent a diverse array of complex biomolecules. However, efforts to simulate increasingly …

Lateral heterogeneity and domain formation in cellular membranes

JJ Kinnun, D Bolmatov, MO Lavrentovich… - Chemistry and physics of …, 2020 - Elsevier
As early as the development of the fluid mosaic model for cellular membranes, researchers
began observing the telltale signs of lateral heterogeneity. Over the decades this has led to …

Raft-like lipid mixtures in the highly coarse-grained Cooke membrane model

M Varma, F Khuri-Makdisi, M Deserno - The Journal of Chemical …, 2024 - pubs.aip.org
Lipid rafts are nanoscopic assemblies of sphingolipids, cholesterol, and specific membrane
proteins. They are believed to underlie the experimentally observed lateral heterogeneity of …

On computing equilibrium binding constants for protein–protein association in membranes

A Majumder, S Kwon, JE Straub - Journal of Chemical Theory and …, 2022 - ACS Publications
Protein association in lipid membranes is fundamental to membrane protein function and of
great biomedical relevance. All-atom and coarse-grained models have been extensively …