Two decades of Martini: Better beads, broader scope

SJ Marrink, L Monticelli, MN Melo… - Wiley …, 2023 - Wiley Online Library
The Martini model, a coarse‐grained force field for molecular dynamics simulations, has
been around for nearly two decades. Originally developed for lipid‐based systems by the …

Computational modeling of realistic cell membranes

SJ Marrink, V Corradi, PCT Souza, HI Ingolfsson… - Chemical …, 2019 - ACS Publications
Cell membranes contain a large variety of lipid types and are crowded with proteins,
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …

Structural basis of NINJ1-mediated plasma membrane rupture in cell death

M Degen, JC Santos, K Pluhackova, G Cebrero… - Nature, 2023 - nature.com
Eukaryotic cells can undergo different forms of programmed cell death, many of which
culminate in plasma membrane rupture as the defining terminal event,,,,,–. Plasma …

AI-based structure prediction empowers integrative structural analysis of human nuclear pores

S Mosalaganti, A Obarska-Kosinska, M Siggel… - Science, 2022 - science.org
INTRODUCTION The eukaryotic nucleus protects the genome and is enclosed by the two
membranes of the nuclear envelope. Nuclear pore complexes (NPCs) perforate the nuclear …

STING agonist delivery by tumour-penetrating PEG-lipid nanodiscs primes robust anticancer immunity

EL Dane, A Belessiotis-Richards, C Backlund… - Nature Materials, 2022 - nature.com
Activation of the innate immune STimulator of INterferon Genes (STING) pathway potentiates
antitumour immunity, but systemic delivery of STING agonists to tumours is challenging. We …

Martini 3: a general purpose force field for coarse-grained molecular dynamics

PCT Souza, R Alessandri, J Barnoud, S Thallmair… - Nature …, 2021 - nature.com
The coarse-grained Martini force field is widely used in biomolecular simulations. Here we
present the refined model, Martini 3 (http://cgmartini. nl), with an improved interaction …

Sequence-dependent material properties of biomolecular condensates and their relation to dilute phase conformations

D Sundaravadivelu Devarajan, J Wang… - Nature …, 2024 - nature.com
Material properties of phase-separated biomolecular condensates, enriched with disordered
proteins, dictate many cellular functions. Contrary to the progress made in understanding the …

Ubiquitination regulates ER-phagy and remodelling of endoplasmic reticulum

A González, A Covarrubias-Pinto, RM Bhaskara… - Nature, 2023 - nature.com
The endoplasmic reticulum (ER) undergoes continuous remodelling via a selective
autophagy pathway, known as ER-phagy. ER-phagy receptors have a central role in this …

Molecular dynamics simulation of an entire cell

JA Stevens, F Grünewald, PAM van Tilburg… - Frontiers in …, 2023 - frontiersin.org
The ultimate microscope, directed at a cell, would reveal the dynamics of all the cell's
components with atomic resolution. In contrast to their real-world counterparts …

Membrane thickness, lipid phase and sterol type are determining factors in the permeability of membranes to small solutes

J Frallicciardi, J Melcr, P Siginou, SJ Marrink… - Nature …, 2022 - nature.com
Cell membranes provide a selective semi-permeable barrier to the passive transport of
molecules. This property differs greatly between organisms. While the cytoplasmic …