The integration of coarse-grained (CG) approaches into docking workflows offers a powerful strategy for modeling large biomolecular assemblies with reduced computational costs. We present here the im...

Mitochondrial cristae are essential for respiration, yet the molecular basis of how the high curvature of these membrane folds is maintained remains unclear. Using structure prediction tools and multi...

We present an improved Martini-type coarse-grained (CG) model for polyethylene (PE) nanoplastics and benchmark its performance against three existing Martini PE models from the Martini 2 and Martini 3...

RNA–RNA interactions drive the formation of biomolecular condensates via liquid–liquid phase separation (LLPS), but their underlying molecular mechanisms remain poorly understood. Here, we employ Mart...

Metabolites are ubiquitous in all living cells and are essential mediators of biochemical processes, serving either as substrates or as cofactors to enable reactions. Capturing this diversity in compu...

Torsional parametrization remains one of the most persistent challenges and weaknesses of modern force fields, particularly for dihedrals whose asymmetry and multimodality evade traditional Fourier or...

Coarse-graining (CG) reduces molecular details to extend the time and length scales of molecular dynamics simulations to microseconds and micrometers. However, the CG approaches have long been limited...

An international team led by Dr. Adolfo Poma (IPPT PAN, Poland) shows that antibody effectiveness depends not only on binding strength but also on their stability under mechanical forces. The findings...

Biomolecular condensates organize cellular biochemistry not only by passive concentration modulation of molecules but also by potentially remodeling client protein conformations. However, the systematic principles governing such conformational editing are unknown. Here, we use coarse-grained simulations to demonstrate that diverse condensate environments remodel disordered client proteins in a scaffold-specific manner. Additionally, we explore the factors of this remodeling, establishing that the linear patterning of scaffold interaction motifs along sequence (sticker clustering) plays an important role, whereas an increased scaffold chain length primarily slows client dynamics while leaving their sequence-specific intrachain contact patterns largely preserved. This conformational remodeling is mediated by varied and nonuniform client–condensate interaction maps that are not solely encoded by primary sequence grammar but are cooperatively shaped by the emergent condensate architecture. Our work reveals that condensates function as sophisticated regulators of recruited disordered client conformation, with broad implications for cellular regulation and therapeutic intervention.

Unlike simplified IDR-only models, natural condensates with folded domains exhibit pronounced structural heterogeneity and attenuated dynamics, revealing folded domains as architectural keystones in n...

Perfluoroalkyl substances (PFAS) are a family of over seven million chemicals found in a vast number of industrial and consumer applications. Often referred to as the “forever chemicals,” they have ga...

Lipopolysaccharides (LPS), as critical components of the outer membrane (OM) of Gram-negative bacteria, play essential roles in maintaining bacterial integrity and mediating environmental interactions...

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PerFluoroAlkyl Substances (PFAS) are a family of over seven million chemicals found in a vast number of industrial and consumer applications. Often referred to as the "forever chemicals", they gained increasing attention due to their environmental and ...

Despite considerable advances in computational chemistry, bridging the gap between the accuracy of all-atom molecular dynamics (AA-MD) and the high-throughput capabilities of docking remains an unsolv...

Polypeptide coacervates exhibit remarkable cell membrane permeability for drug delivery, but the precise internalization mechanism is unclear. Here, taking histidine-rich beak derivative protein (HBpe...

Transport tunnels in enzymes with buried active sites are critical gatekeepers of enzymatic function, controlling substrate access, product release, and catalytic efficiency. Despite their importance,...

Membrane proteins play a vital role in numerous cellular processes, including ion transport, intercellular communication, and antibiotic resistance. Ensuring their accurate orientation within lipid bi...

Lipid nanoparticles (LNPs) represent a promising platform for advanced drug and gene delivery, yet optimizing these particles for specific cargos and cell targets poses a complex multifaceted challeng...

Multi-scale molecular dynamics simulations reveal that polymyxins form polymyxin-protein aggregates upon associating with the E. coli outer membrane thereby reducing lateral mobility of outer membrane...

Protein–lipid interactions play a crucial role in the stability and function of membrane proteins. While experimental approaches to characterize these interactions in a native-like membrane environment can be challenging, computational techniques offer a powerful alternative for identifying and analyzing potential binding sites. Recent advances in cofolding methods now enable the prediction of holo protein structures, capturing conformational changes that may occur upon lipid binding and thereby improving the accuracy of binding site characterization. However, the outputs from these methods often require postprocessing to ensure compatibility with widely used molecular dynamics force fields. In this work, we introduce CCD2MD, a modular toolkit designed to convert cofolding outputs into simulation-ready systems for GROMACS. CCD2MD supports both atomistic and coarse-grained representations with or without membrane embedding. While CCD2MD is exemplified here with protein–lipid systems, its modular design allows for straightforward adaptation to other cofolded biomolecular assemblies, incorporating complexes with nucleic acids, small molecules, carbohydrates, or metal ions, thereby enabling a variety of simulation setups across multiple scales.

Cu,Zn superoxide dismutase (SOD1) is one of the proteins with mutations linked to hereditary forms of the amyotrophic lateral sclerosis neurodegenerat…

Static protein structures can capture the association of lipids, but it is unclear whether the association is due to lipids acting as long-lived ligands or the solvation of preferred lipids around the protein. A computational-experimental framework has now shown that for the protein CLC-ec1, it is the change in lipid solvation energies that drives dimerization, with preferred lipids around the protein modulating this driving force.

P116 is an adaptive, all-in-one lipid acquisition machinery fit for any host environment.

This study explores the effect of charge on the bioactivity of peptide-based supramolecular materials. The design of a peptide library with varying charges that self-assemble into supramolecular fibe....

The Martini model is a coarse-grained force field allowing simulations of biomolecular systems as well as a range of materials including different types of nanomaterials of technological interest. Recently, a new version of the force field (version 3) has been released that includes new parameters for lipids, proteins, carbohydrates, and a number of small molecules, but not yet carbon nanomaterials. Here, we present new Martini models for three major types of carbon nanomaterials: fullerene, carbon nanotubes, and graphene. The new models were parametrized within the Martini 3 framework, and reproduce semiquantitatively a range of properties for each material. In particular, the model of fullerene yields excellent solid-state properties and good properties in solution, including correct trends in partitioning between different solvents and realistic translocation across lipid membranes. The models of carbon nanotubes reproduce the atomistic behavior of nanotube porins spanning lipid bilayers. The model of graphene reproduces structural and elastic properties, as well as trends in experimental adsorption enthalpies of organic molecules. All new models can be used in large-scale simulations to study the interaction with the wide variety of molecules already available in the Martini 3 force field, including biomolecular and synthetic systems.

Deep eutectic solvents (DESs) are often promoted as a more environmentally friendly alternative for ionic liquids and other ionic solvents. Like ionic liquids, DESs can be designed for specific tasks ...