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This work presents GōMartini 3, an improved coarse-grained protein model combining physics- and structure-based approaches. It boosts computational efficiency and accuracy for structured soluble and membrane as well as disordered peptides/proteins.

To facilitate the rational design of (nano)-materials and biomacromolecules by MD simulations, the authors present the polyply suite, featuring a graph matching algorithm and a random walk protocol for generating multi-scale polymeric topologies and initial coordinates.

Computer simulations of large-scale changes in membrane shape are challenging since they occur across a wide range of spatiotemporal scales. Here, authors present a multiscale algorithm that backmaps a continuum membrane model represented as a dynamically triangulated surface to its corresponding molecular model based on the coarse-grained Martini force field.

Computer-aided design of protein-ligand binding is important for the development of novel drugs. Here authors present an approach to use the recently re-parametrized coarse-grained Martini model to perform unbiased millisecond sampling of protein-ligand binding interactions of small drug-like molecules.

In neurons and glia, glutamate transporters catalyse the reuptake of this neurotransmitter by coupling it with cation transport. Here the authors combine X-ray crystallography and molecular dynamics simulations of the archeal glutamate transporter Glt_Tkto get insight into the coupled transport mechanism.

Martini 3.0 is an updated and reparametrized force field for coarse-grained molecular dynamics simulations with new bead types and an expanded ability to model molecular packing and interactions.

Here, the authors introduce Martini3-IDP, a refined model for disordered proteins that addresses prior over-compact structures. Validated across diverse systems, it captures IDP interactions and biomolecular condensates.

Membrane permeability of small molecules depends on the composition of the lipid bilayer. Here, authors compare permeability measured on membranes in different physical states and conclude that the yeast membrane exists in a highly ordered phase.

Plastoquinone (PLQ) shuttles electrons between photosystem II (PSII) and cytochrome b₆f. Here the authors perform molecular dynamics simulations and propose that PLQ enters the exchange cavity of PSII by a promiscuous diffusion mechanism whereby three different channels each act as entry and exit points.

Energy coupling factor (ECF) transporters are responsible for the uptake of micronutrients and consist of an integral membrane unit, the S-component, which confers substrate specificity. Here, authors present multi-scale molecular dynamics simulations and in vitro experiments to study the molecular toppling mechanism of the S-component of a folate-specific ECF transporter.

The mechanism of action of the antibacterial tripeptide AMC-109 is unclear. Here, Melcrová et al. show that AMC-109 self-assembles into stable aggregates with a cationic surface, and then individual peptides insert into the bacterial membrane and disrupt membrane nanodomains, thus affecting membrane function without forming pores.

The inherent toxicity of the aromatic compounds to the chassis strain hampers further improvement of bioproduction. Here, the authors show that membrane rigidifying effect of resveratrol can be attenuated by exogenous supplementation of palmitelaidic acid or linoleic acid in fermentation of Corynebacterium glutamicum.

ASCT2 is a Na⁺-dependent obligatory amino acid exchanger. Here, the authors untangle the structural basis of the exchange mechanism in ASCT2, revealing that structural rigidity and a high-affinity Na⁺ binding site effectively confine ASCT2 to an exchange mode.

Ceramides are lipids that act directly on mitochondria to trigger apoptosis, but the underlying mechanism remains largely unclear. Here authors use a photoactivatable ceramide probe combined with a computation approach and functional studies to identify the voltage-dependent anion channel VDAC2 as a direct effector of ceramide-mediated cell death.

The final step in an ECF transporters transport cycle involves the expulsion of the membrane embedded substrate binding protein (the S-component) from the motor (the ECF module). Here the authors show how the motor uses ATP binding to load a molecular spring, and adjusts the shape of the membrane, to achieve this step.

An integrated multiprotein nanopore has been fabricated using components from all three domains of life. This molecular machine opens the door to two approaches in single-molecule protein analysis, in which selected substrate proteins are unfolded, fed to into the proteasomal chamber and then processed either as fragmented peptides or intact polypeptides.

Achieved high thermoelectric figure of merit (ZT) in organic thermoelectric materials remains a challenge due to their low packing order and poor host/dopant miscibility. Here, the authors report side chain-engineered n-doped fullerene derivatives with record ZT >0.3 for organic thermoelectrics.

Although DNA nanopores are widely explored as synthetic membrane proteins, it is still unclear how the anionic DNA assemblies stably reside within the hydrophobic core of a lipid bilayer. Here, the authors use molecular dynamics simulations to reveal the key dynamic interactions and energetics stabilizing the nanopore-membrane interaction.

In the Big Data era, a change of paradigm in the use of molecular dynamics is required. Trajectories should be stored under FAIR (findable, accessible, interoperable and reusable) requirements to favor its reuse by the community under an open science paradigm.

Integrative molecular modelling of a mitochondrial crista demonstrates a pipeline for constructing biologically representative systems and addressing interactions in complex environments.

Biomolecular condensates show distinct physicochemical properties that may affect the rate of enzymatic activity and control cellular redox reactions, however, their influence on the other types of chemical reaction remains underexplored. Here, the authors use reactive Martini simulations to probe the non-enzymatic macrocyclization reaction of benzene-1,3-dithiol in the presence of peptide condensates.

MD simulations and experiments in cells reveal core structural and topological determinants that govern binding of hexokinase-I to mitochondrial VDAC channels, with the protonation status of a bilayerfacing glutamate on VDACs playing a crucial role.

Virtual screening, biochemical assays, and coarse-grained simulations identify an inhibitor of energy-coupling factor transporters and its potential mechanism of action.