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 …

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 …

Capturing chemical reactions inside biomolecular condensates with reactive Martini simulations

C Brasnett, A Kiani, S Sami, S Otto… - Communications …, 2024 - nature.com
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 …

Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery

M Paloncýová, M Valério, RN Dos Santos… - Molecular …, 2025 - ACS Publications
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 …

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 …

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) …

[HTML][HTML] Martini 3 Coarse-Grained Model for the Cofactors Involved in Photosynthesis

MG Chiariello, R Zarmiento-Garcia… - International Journal of …, 2024 - mdpi.com
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 …

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 …

Charged peptides enriched in aromatic residues decelerate condensate ageing driven by cross-beta-sheet formation

I Sanchez-Burgos, AR Tejedor, A Feito… - bioRxiv, 2024 - biorxiv.org
Biomolecular condensates, formed through liquid-liquid phase separation, play wide-
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 …