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 …

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 …

Cross-linking mass spectrometry for investigating protein conformations and protein–protein interactions─ a method for all seasons

L Piersimoni, PL Kastritis, C Arlt, A Sinz - Chemical Reviews, 2021 - ACS Publications
Mass spectrometry (MS) has become one of the key technologies of structural biology. In this
review, the contributions of chemical cross-linking combined with mass spectrometry (XL …

Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy

JA Joseph, A Reinhardt, A Aguirre, PY Chew… - Nature Computational …, 2021 - nature.com
Various physics-and data-driven sequence-dependent protein coarse-grained models have
been developed to study biomolecular phase separation and elucidate the dominant …

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 …

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 …

Antimicrobial hybrid amphiphile via dynamic covalent bonds enables bacterial biofilm dispersal and bacteria eradication

Y Zhan, X Hu, Y Li, Y Wang, H Chen… - Advanced Functional …, 2023 - Wiley Online Library
To tackle the problems caused by bacterial biofilms, herein, this study reports an
antimicrobial hybrid amphiphile (aHA) via dynamic covalent bonds for eradicating …

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 …

[HTML][HTML] Structural basis of mitochondrial membrane bending by the I–II–III2–IV2 supercomplex

A Mühleip, RK Flygaard, R Baradaran, O Haapanen… - Nature, 2023 - nature.com
Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial
membrane. Here we show that a supercomplex containing all four respiratory chain …