Plant protein-lipid interfaces studied by molecular dynamics simulations
M Neubergerová, R Pleskot - Journal of Experimental Botany, 2024 - academic.oup.com
The delineation of protein-lipid interfaces is essential for understanding the mechanisms of
various membrane-associated processes crucial to plant development and growth, including …
various membrane-associated processes crucial to plant development and growth, including …
OLIVES: A Go-like model for stabilizing protein structure via hydrogen bonding native contacts in the Martini 3 coarse-grained force field
KB Pedersen, L Borges-Araújo… - Journal of Chemical …, 2024 - ACS Publications
Coarse-grained molecular dynamics simulations enable the modeling of increasingly
complex systems at millisecond timescales. The transferable coarse-grained force field …
complex systems at millisecond timescales. The transferable coarse-grained force field …
Capturing chemical reactions inside biomolecular condensates with reactive Martini simulations
Biomolecular condensates are phase separated systems that play an important role in the
spatio-temporal organisation of cells. Their distinct physico-chemical nature offers a unique …
spatio-temporal organisation of cells. Their distinct physico-chemical nature offers a unique …
Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery
Lipid-mediated delivery of active pharmaceutical ingredients (API) opened new possibilities
in advanced therapies. By encapsulating an API into a lipid nanocarrier (LNC), one can …
in advanced therapies. By encapsulating an API into a lipid nanocarrier (LNC), one can …
Martini 3 OliGo̅mers: a scalable approach for multimers and fibrils in GROMACS
K Korshunova, J Kiuru, J Liekkinen… - Journal of Chemical …, 2024 - ACS Publications
Martini 3 is a widely used coarse-grained simulation method for large-scale biomolecular
simulations. It can be combined with a Go̅ model to realistically describe higher-order …
simulations. It can be combined with a Go̅ model to realistically describe higher-order …
Exploring the Ligand Binding and Conformational Dynamics of the Substrate-Binding Domain 1 of the ABC Transporter GlnPQ
M Nemchinova, GK Schuurman-Wolters… - The Journal of …, 2024 - ACS Publications
The adenosine triphosphate (ATP)-binding cassette (ABC) importer GlnPQ from
Lactococcus lactis has two sequential covalently linked substrate-binding domains (SBDs) …
Lactococcus lactis has two sequential covalently linked substrate-binding domains (SBDs) …
[HTML][HTML] Martini 3 Coarse-Grained Model for the Cofactors Involved in Photosynthesis
As a critical step in advancing the simulation of photosynthetic complexes, we present the
Martini 3 coarse-grained (CG) models of key cofactors associated with light harvesting …
Martini 3 coarse-grained (CG) models of key cofactors associated with light harvesting …
G-Protein-Coupled Receptor Surface Creates a Favorable Pathway for Membrane Permeation of Drug Molecules
C Gil Herrero, S Thallmair - The Journal of Physical Chemistry …, 2024 - ACS Publications
G-protein-coupled receptors (GPCRs) play a crucial role in modulating physiological
responses and serve as the main drug target. Specifically, salmeterol and salbutamol, which …
responses and serve as the main drug target. Specifically, salmeterol and salbutamol, which …
Charged peptides enriched in aromatic residues decelerate condensate ageing driven by cross-beta-sheet formation
Biomolecular condensates, formed through liquid-liquid phase separation, play wide-
ranging roles in cellular compartmentalization and biological processes. However, their …
ranging roles in cellular compartmentalization and biological processes. However, their …
[HTML][HTML] Simulation-based survey of TMEM16 family reveals that robust lipid scrambling requires an open groove
CA Stephens, N van Hilten, L Zheng, M Grabe - bioRxiv, 2024 - pmc.ncbi.nlm.nih.gov
Biological membranes are complex and dynamic structures with different populations of
lipids in their inner and outer leaflets. The Ca2+-activated TMEM16 family of membrane …
lipids in their inner and outer leaflets. The Ca2+-activated TMEM16 family of membrane …