Martini 3 Coarse-Grained Force Field for Carbohydrates.

The Martini 3 force field is a full reparametrization of the Martini coarse-grained model for biomolecular simulations. Due to the improved interaction balance, it allows for a more accurate description of condensed phase systems. In the present work, we develop a consistent strategy to parametrize carbohydrate molecules accurately within the framework of Martini 3.

Computational Virology: Molecular Simulations of Virus Dynamics and Interactions.

Molecular modelling and simulations play a key role in computational virology, allowing us to study viruses and their components. This allows experimental structures and related information to be integrated into a single coherent model, enabling predictions about the behaviour of a viral system to go beyond what could be obtained experimentally. In this way, computational approaches provide a powerful complement to more traditional experimental and structural methods.

Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries.

A necessary step prior to starting any membrane protein computer simulation is the creation of a well-packed configuration of protein(s) and lipids. Here, we demonstrate a method, , that can simultaneously and rapidly embed multiple proteins into arrangements of lipids described using either atomistic or coarse-grained force fields. During a short simulation, the interactions between the protein(s) and lipids are gradually switched on using a soft-core van der Waals potential.

Nothing to sneeze at: a dynamic and integrative computational model of an influenza A virion.

The influenza virus is surrounded by an envelope composed of a lipid bilayer and integral membrane proteins. Understanding the structural dynamics of the membrane envelope provides biophysical insights into aspects of viral function, such as the wide-ranging survival times of the virion in different environments. We have combined experimental data from X-ray crystallography, nuclear magnetic resonance spectroscopy, cryo-electron microscopy, and lipidomics to build a model of the intact influenza A virion.

NRas slows the rate at which a model lipid bilayer phase separates.

The Ras family of small membrane-associated GTP-ases are important components in many different cell signalling cascades. They are thought to cluster on the cell membrane through association with cholesterol-rich nanodomains. This process remains poorly understood.

Multiscale simulations reveal conserved patterns of lipid interactions with aquaporins.

Interactions of membrane proteins with lipid molecules are central to their stability and function. We have used multiscale molecular dynamics simulations to determine the extent to which interactions with lipids are conserved across the aquaporin (Aqp) family of membrane proteins. Simulation-based assessment of the lipid interactions made by Aqps when embedded within a simple phospholipid bilayer agrees well with the protein-lipid contacts determined by electron diffraction from 2D crystals.