Protein Structure and Dynamics

Integrating the MARTINI2 Coarse-Grained Force Field into HADDOCK3 for Faster Modelling of Large Biomolecular Complexes

The paper integrates the MARTINI2 force field into HADDOCK3 to enable faster modelling of large biomolecular complexes with reduced computational costs while maintaining accuracy.

Unraveling protein conformational plasticity with PROTEUS

The paper introduces PROTEUS, a method to assess protein conformational plasticity using a generative model, showing it correlates with molecular dynamics data and identifies functionally plastic proteins.

Structure of a sparsely populated chimeric intermediate that facilitates fold-switching of a metamorphic protein

The paper visualizes an invisible chimeric intermediate in the fold-switching pathway of a metamorphic protein using NMR techniques and shows its role as an on-pathway intermediate.

AlphaUnfold: Probing Potential Unfolding and Structural Fragility in AlphaFold3 Models via Short-Time High-Pressure MD

AlphaUnfold assesses structural fragility in AlphaFold3 models using high-pressure MD, finding lower pLDDT correlates with higher structural drift and RMSF.

Structure and Dynamics of a Long-Acting Insulin Analog in Hexameric and Dihexameric States

This study presents X-ray structures of detemir in hexameric and dodecameric forms, revealing structural dynamics and identifying key residues involved in conformational changes and stability.

Systematic Evaluation of AlphaFold2 and OpenFold3 on Protein-Peptide Complexes

This study benchmarks AlphaFold2 and OpenFold3 on protein-peptide complexes, finding AlphaFold2 outperforms OpenFold3 in success rate and high-quality model proportion.

An optimized contact map for GoMartini 3 enabling conformational changes in protein assemblies

The paper optimizes the contact map in GoMartini 3 by integrating dynamic contact information from AA-MD simulations, improving conformational sampling and representation in biomolecular assemblies.

Cooling fast and slow: Characterising the effects of vitrification in cryo-EM and the subsequent recovery of equilibrium populations

This study uses molecular dynamics simulations to investigate how vitrification affects the conformational ensemble of Trp-cage miniprotein and develops a thermodynamic inference framework to recover equilibrium populations from vitrified samples.

Improving AlphaFold3 by Engineering MSA and Template Inputs

This paper improves AlphaFold3 by using customized MSAs and templates, achieving higher accuracy in structure prediction for monomers, multimers, and protein-ligand complexes.

Generation of Pathway Signatures by Combining Normal Modes with Weighted Ensemble Simulations

This study combines normal modes with weighted ensemble simulations to generate unbiased protein pathways efficiently.

From foldamers to functional pores: a force field for oligourea-based desalination channels

This paper develops a CHARMM-based force field for oligourea foldamers to simulate their structural integrity and performance in desalination applications.

A molecular grammar for environmental sensitivity in intrinsically disordered protein regions

The paper identifies a molecular grammar that predicts environmental sensitivity in intrinsically disordered protein regions using sequence features and experimental validation.

SMC complex unidirectionally translocates DNA by coupling segment capture with an asymmetric kleisin path

This study uses molecular dynamics simulations to show that SMC complexes translocate DNA unidirectionally by capturing DNA segments and pumping them through an asymmetric kleisin path.

Using experimental results of protein design to guide biomolecular energy-function development

The paper uses experimental results from de novo protein designs to identify and resolve failure modes in the Rosetta energy function, improving its accuracy in predicting stable protein structures.

GeomMotif: A Benchmark for Arbitrary Geometric Preservation in Protein Generation

GeomMotif evaluates protein generation models' ability to preserve arbitrary structural fragments, revealing differences in performance based on structural and physicochemical context.

Protein inverse folding through joint modeling of surface and backbone geometry

This paper introduces Surleton, a framework for inverse protein folding that jointly models backbone and surface geometry, improving sequence recovery and predictive confidence on benchmark datasets.

Scaling k-Means for Multi-Million Frames: A Stratified NANI Approach for Large-Scale MD Simulations

The paper improves k-means clustering for MD simulations with new seeding strategies, reducing runtime without sacrificing clustering quality.

The Impact of Glycosylation on the Conformational Ensembles of β-, δ-, and γ-Sarcoglycans

This study investigates how glycosylation affects the conformational behavior of sarcoglycans and their heterotrimer, revealing structural changes that impact complex stability and muscular dystrophy.

Small Molecule Activators of Protein Phosphatase 2A Exert Global Stabilising Effects on the Scaffold PR65

The paper investigates how two small molecule activators of PP2A, ATUX-8385 and DBK-776, affect the structural stability of the PR65 scaffold using biophysical and computational methods.

Full-Atom MPNN Based Redesign of Plant Dehydrogenase Enables Thermostability Enhancement Without Loss of Stereoselectivity

The paper uses FAMPNN to redesign SrBDH1 for increased thermostability while maintaining stereoselectivity.

Natively entangled proteins are linked to human disease and pathogenic mutations likely due to a greater misfolding propensity

The paper investigates whether proteins with native entanglements are more prone to misfolding and associated with disease, finding significant statistical associations.

Mutation-induced biophysical destabilization as a key contributor to cancer-driving potential in the human structural protein interactome

The paper assesses how mutation-induced biophysical destabilization in the human structural protein interactome correlates with cancer-driving potential using fold difference metrics.

Detecting misfolded non-covalent lasso entanglements in protein structures, simulation trajectories, and mass spectrometry data

The paper introduces EntDetect, a tool to detect non-covalent lasso entanglements in protein structures, simulations, and mass spectrometry data, and demonstrates its application in identifying misfolded states.

Ionic strength modulates structural disorder and protein oligomerization in the marginally disordered Phd transcription factor

This paper shows how ionic strength affects the structural disorder and oligomerization of the Phd transcription factor, revealing its ability to function as a conformational rheostat.

Dynamic-Structure Redesign of Calmodulin Reveals Mechanistic Constraints on Ryr2 Regulation

The paper redesigns calmodulin to improve its function while preserving conformational dynamics, showing that structural flexibility is essential for physiological regulation.

Native entanglement misfolding contributes to age-associated structural changes across the Saccharomyces cerevisiae proteome

The paper examines age-related structural changes in yeast proteins using mass spectrometry and simulations, finding that entanglement misfolding contributes to proteome aging.

Sampling antibody conformational ensembles withABodyBuilder4-STEROIDS

ABB4-STEROIDS generates antibody conformational ensembles with state-of-the-art accuracy, outperforming existing methods in experimental benchmarks.

Generative design of intrinsically disordered proteins based on conditioned protein language models: Data is the limit

This paper presents a generative framework for designing intrinsically disordered proteins using protein language models, showing that large datasets are essential for accurate conformational control.

Thermoadaptation of EndoG proteins in the Xenopus frog genus

This study identifies structural differences in EndoG proteins between two Xenopus species adapted to different temperatures, suggesting temperature-driven adaptive evolution.

Proteome-wide identification and modeling of interactions between transactivation domains and arginine-glycine-rich regions

The paper identifies and models interactions between transactivation domains and arginine-glycine-rich regions using proteome-scale data and simulations, revealing electrostatic mechanisms driving TF-RBP coupling.