Bottom-up coarse-graining: Principles and perspectives
Large-scale computational molecular models provide scientists a means to investigate the
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …
Two decades of Martini: Better beads, broader scope
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 …
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 …
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
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 …
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
Various physics-and data-driven sequence-dependent protein coarse-grained models have
been developed to study biomolecular phase separation and elucidate the dominant …
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 …
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
Cell membranes provide a selective semi-permeable barrier to the passive transport of
molecules. This property differs greatly between organisms. While the cytoplasmic …
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 …
candidates against antimicrobial resistance but suffer from low efficiency and poor stability …
Rescaling protein-protein interactions improves Martini 3 for flexible proteins in solution
Multidomain proteins with flexible linkers and disordered regions play important roles in
many cellular processes, but characterizing their conformational ensembles is difficult. We …
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
To tackle the problems caused by bacterial biofilms, herein, this study reports an
antimicrobial hybrid amphiphile (aHA) via dynamic covalent bonds for eradicating …
antimicrobial hybrid amphiphile (aHA) via dynamic covalent bonds for eradicating …