Bottom-up coarse-graining: Principles and perspectives

J Jin, AJ Pak, AEP Durumeric, TD Loose… - Journal of chemical …, 2022 - ACS Publications
Large-scale computational molecular models provide scientists a means to investigate the
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …

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 …

[HTML][HTML] 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 …

Shared structural mechanisms of general anaesthetics and benzodiazepines

JJ Kim, A Gharpure, J Teng, Y Zhuang, RJ Howard… - Nature, 2020 - nature.com
Most general anaesthetics and classical benzodiazepine drugs act through positive
modulation of γ-aminobutyric acid type A (GABAA) receptors to dampen neuronal activity in …

Perspective: Advances, challenges, and insight for predictive coarse-grained models

WG Noid - The Journal of Physical Chemistry B, 2023 - ACS Publications
By averaging over atomic details, coarse-grained (CG) models provide profound
computational and conceptual advantages for studying soft materials. In particular, bottom …

[HTML][HTML] Structures of the TMC-1 complex illuminate mechanosensory transduction

H Jeong, S Clark, A Goehring… - Nature, 2022 - nature.com
The initial step in the sensory transduction pathway underpinning hearing and balance in
mammals involves the conversion of force into the gating of a mechanosensory transduction …

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 …

Charge-transfer electronic states in organic solar cells

V Coropceanu, XK Chen, T Wang, Z Zheng… - Nature Reviews …, 2019 - nature.com
In organic solar cells, the charge-transfer (CT) electronic states that form at the interface
between the electron-donor (D) and electron-acceptor (A) materials have a crucial role in …

Emerging diversity in lipid–protein interactions

V Corradi, BI Sejdiu, H Mesa-Galloso… - Chemical …, 2019 - ACS Publications
Membrane lipids interact with proteins in a variety of ways, ranging from providing a stable
membrane environment for proteins to being embedded in to detailed roles in complicated …

[HTML][HTML] Protein–ligand binding with the coarse-grained Martini model

PCT Souza, S Thallmair, P Conflitti… - Nature …, 2020 - nature.com
The detailed understanding of the binding of small molecules to proteins is the key for the
development of novel drugs or to increase the acceptance of substrates by enzymes …