Bottom-up coarse-graining: Principles and perspectives

J **, 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 …

Stable peptide-assembled nanozyme mimicking dual antifungal actions

Y Yuan, L Chen, K Song, M Cheng, L Fang… - Nature …, 2024 - nature.com
Natural antimicrobial peptides (AMPs) and enzymes (AMEs) are promising non-antibiotic
candidates against antimicrobial resistance but suffer from low efficiency and poor stability …

Rescaling protein-protein interactions improves Martini 3 for flexible proteins in solution

FE Thomasen, T Skaalum, A Kumar… - Nature …, 2024 - nature.com
Multidomain proteins with flexible linkers and disordered regions play important roles in
many cellular processes, but characterizing their conformational ensembles is difficult. We …

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 …