Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms
This paper reviews various enhanced conformational sampling methods and explicit/implicit
solvent/membrane models, as well as their recent applications to the exploration of the …
solvent/membrane models, as well as their recent applications to the exploration of the …
Molecular dynamics simulation of small molecules interacting with biological membranes
C Martinotti, L Ruiz‐Perez, E Deplazes… - …, 2020 - Wiley Online Library
Cell membranes protect and compartmentalise cells and their organelles. The semi‐
permeable nature of these membranes controls the exchange of solutes across their …
permeable nature of these membranes controls the exchange of solutes across their …
GENESIS 1.1: A hybrid‐parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms
GENeralized‐Ensemble SImulation System (GENESIS) is a software package for molecular
dynamics (MD) simulation of biological systems. It is designed to extend limitations in system …
dynamics (MD) simulation of biological systems. It is designed to extend limitations in system …
Accelerating membrane simulations with hydrogen mass repartitioning
C Balusek, H Hwang, CH Lau… - Journal of chemical …, 2019 - ACS Publications
The time step of atomistic molecular dynamics (MD) simulations is determined by the fastest
motions in the system and is typically limited to 2 fs. An increasingly popular approach is to …
motions in the system and is typically limited to 2 fs. An increasingly popular approach is to …
Cholesterol modulates the dimer interface of the β2-adrenergic receptor via cholesterol occupancy sites
X Prasanna, A Chattopadhyay, D Sengupta - Biophysical journal, 2014 - cell.com
The β 2-adrenergic receptor is an important member of the G-protein-coupled receptor
(GPCR) superfamily, whose stability and function are modulated by membrane cholesterol …
(GPCR) superfamily, whose stability and function are modulated by membrane cholesterol …
The energetics of protein–lipid interactions as viewed by molecular simulations
RA Corey, PJ Stansfeld… - Biochemical Society …, 2020 - portlandpress.com
Membranes are formed from a bilayer containing diverse lipid species with which membrane
proteins interact. Integral, membrane proteins are embedded in this bilayer, where they …
proteins interact. Integral, membrane proteins are embedded in this bilayer, where they …
Enzyme-substrate hybrid β-sheet controls geometry and water access to the γ-secretase active site
Abstract γ-Secretase is an aspartyl intramembrane protease that cleaves the amyloid
precursor protein (APP) involved in Alzheimer's disease pathology and other …
precursor protein (APP) involved in Alzheimer's disease pathology and other …
Interplay of G protein-coupled receptors with the membrane: insights from supra-atomic coarse grain molecular dynamics simulations
X Periole - Chemical reviews, 2017 - ACS Publications
G protein-coupled receptors (GPCRs) are central to many fundamental cellular signaling
pathways. They transduce signals from the outside to the inside of cells in physiological …
pathways. They transduce signals from the outside to the inside of cells in physiological …
Balancing force field protein–lipid interactions to capture transmembrane helix–helix association
Atomistic simulations have recently been shown to be sufficiently accurate to reversibly fold
globular proteins and have provided insights into folding mechanisms. Gaining similar …
globular proteins and have provided insights into folding mechanisms. Gaining similar …
Conformational heterogeneity of the HIV envelope glycan shield
To better understand the conformational properties of the glycan shield covering the surface
of the HIV gp120/gp41 envelope (Env) trimer, and how the glycan shield impacts the …
of the HIV gp120/gp41 envelope (Env) trimer, and how the glycan shield impacts the …