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 …

Enhancing important fluctuations: Rare events and metadynamics from a conceptual viewpoint

O Valsson, P Tiwary, M Parrinello - Annual review of physical …, 2016 - annualreviews.org
Atomistic simulations play a central role in many fields of science. However, their usefulness
is often limited by the fact that many systems are characterized by several metastable states …

Molecular basis of SARS-CoV-2 infection and rational design of potential antiviral agents: modeling and simulation approaches

A Frances-Monerris, C Hognon, T Miclot… - Journal of Proteome …, 2020 - ACS Publications
The emergence in late 2019 of the coronavirus SARS-CoV-2 has resulted in the
breakthrough of the COVID-19 pandemic that is presently affecting a growing number of …

Atomistic simulations of membrane ion channel conduction, gating, and modulation

E Flood, C Boiteux, B Lev, I Vorobyov… - Chemical …, 2019 - ACS Publications
Membrane ion channels are the fundamental electrical components in the nervous system.
Recent developments in X-ray crystallography and cryo-EM microscopy have revealed what …

Molecular insights from conformational ensembles via machine learning

O Fleetwood, MA Kasimova, AM Westerlund… - Biophysical …, 2020 - cell.com
Biomolecular simulations are intrinsically high dimensional and generate noisy data sets of
ever-increasing size. Extracting important features from the data is crucial for understanding …

[HTML][HTML] Conformational landscapes of membrane proteins delineated by enhanced sampling molecular dynamics simulations

TJ Harpole, L Delemotte - Biochimica Et Biophysica Acta (BBA) …, 2018 - Elsevier
The expansion of computational power, better parameterization of force fields, and the
development of novel algorithms to enhance the sampling of the free energy landscapes of …

Enhanced sampling without borders: on global biasing functions and how to reweight them

AS Kamenik, SM Linker, S Riniker - Physical Chemistry Chemical …, 2022 - pubs.rsc.org
Molecular dynamics (MD) simulations are a powerful tool to follow the time evolution of
biomolecular motions in atomistic resolution. However, the high computational demand of …

Dynamics of activation in the voltage-sensing domain of Ciona intestinalis phosphatase Ci-VSP

SC Guo, R Shen, B Roux, AR Dinner - Nature Communications, 2024 - nature.com
The Ciona intestinalis voltage-sensing phosphatase (Ci-VSP) is a membrane protein
containing a voltage-sensing domain (VSD) that is homologous to VSDs from voltage-gated …

Computational methods for unlocking the secrets of potassium channels: Structure, mechanism, and drug design

L Wang, Q Zhang, HHY Tong, X Yao… - Wiley Interdisciplinary …, 2024 - Wiley Online Library
Potassium (K+) channels play vital roles in various physiological functions, including
regulating K+ flow in cell membranes, impacting nervous system signal transduction …

The interplay of excitation and electroporation in nanosecond pulse stimulation

AG Pakhomov, ON Pakhomova - Bioelectrochemistry, 2020 - Elsevier
Conventional electric stimuli of micro-and millisecond duration excite or activate cells at
voltages 10–100 times below the electroporation threshold. This ratio is remarkably different …