Protein Structure and Dynamics

A closely related pair of superoxide dismutase isozymes from Staphylococcus aureus show distinct stabilities and proton-exchange dynamics

This study compares the structural stability and proton-exchange dynamics of two closely related superoxide dismutase isozymes in Staphylococcus aureus, showing that the neofunctionalised camSOD is more stable than the ancestral MnSOD.

Distinct energetic blueprints diversify function of conserved protein folds

The paper decodes energetic blueprints of conserved protein folds to explain functional diversity and enables engineered transcription factors with ligand-driven responses.

Heuristic Multi-site Optimization for Protein Sequence Design using Masked Protein Language Models

This paper introduces ProtHMSO, a heuristic multi-site optimization framework using masked protein language models to design functional protein sequences more efficiently than existing methods.

A Bayesian approach to interpret time-resolved experiments using molecular simulations

This paper introduces a Bayesian method to interpret time-resolved experiments using molecular simulations, demonstrating its application to protein unfolding studies.

Modelling antibody structures at the speed of language

This paper introduces FlashABB, a model that predicts antibody structures faster than sequence embedding models, enabling efficient access to 3D information for antibody stability and developability prediction.

Deciphering the role of intrinsically disordered regions of FUS in recognizing U1 snRNA

This study uses molecular dynamics simulations to investigate how the intrinsically disordered regions of FUS recognize U1 snRNA, revealing distinct interaction mechanisms and structural changes upon RNA binding.

Rewiring V-type and K-type enzyme allostery through subunit interface mutations

This paper identifies specific interfacial residues in IGPS that modulate allosteric regulation through structural and dynamic changes induced by targeted mutations.

Language Modeling Materializes a World Model of Protein Biology

The paper uses language modeling to create a comprehensive representation of protein biology, enabling structure prediction and discovery of high-affinity protein interactions.

Decoding conformational heterogeneity across disordered proteomes

AI-IDP predicts conformational ensembles of disordered proteins by combining deep learning with physical restraints, revealing common structural features across proteomes.

Comparative Unfolding of the Trp-cage Miniprotein in Anionic and Cationic Surfactants

This study investigates how anionic and cationic surfactants affect the conformational stability of a cationic protein using molecular dynamics simulations.

Mapping the structural coverage of Arabidopsis thaliana plant developmental proteins: Insights from Experimental and AlphaFold Approaches

The paper maps structural coverage of Arabidopsis thaliana developmental proteins using experimental data and AlphaFold predictions, finding higher structural coverage in plants than in humans.

Intramolecular interactions between folded and disordered regions shape ubiquilin structure and function

The paper investigates how intramolecular interactions between folded and disordered regions of ubiquilin proteins influence their structure and function across different species.

Physics-guided design of intrinsically disordered proteins

This paper designs intrinsically disordered proteins using a physics-guided machine learning framework to encode complex signal processing and condensate properties.

A computational analysis of the glycoprotein LRP1 structure and the role of glycans as quaternary glue

This study models the structure of LRP1 using homology and neural network-based methods, revealing glycan-mediated dimerization and its role in stabilizing the protein's quaternary structure.

A functional amyloid scaffold shapes insect egg coats

The paper determines the atomic structure of insect chorion amyloid filaments and reveals their assembly principles, showing functional amyloids can operate in a regulated biological context.

DeepRank-Ab: a dedicated scoring function for antibody-antigen complexes based on geometric deep learning

DeepRank-Ab improves scoring of antibody-antigen complexes using geometric deep learning, outperforming existing methods in accuracy and ranking.

Multimodal dynamics control activity of a glial glutamate transporter

This study uses a combined experimental platform to analyze the conformational dynamics of EAAT1, revealing that multimodal dynamics regulate its function and identifying a mutation that inhibits transport by stabilizing a paused conformation.

Hierarchical latent representations reveal protein organization for functional discovery and design

This paper develops a hierarchical sequence-based framework to infer distributed protein organization, identifies novel ciliary proteins, and enables synthetic protein design.

Pressure-cooling remodeling of TMV coat protein reveals mechanically partitioned capsid dynamics and selective epitope masking

This paper uses pressure and temperature to study how TMV coat protein assembly changes, revealing localized structural dynamics and epitope masking under high pressure.

Structural characterisation of a spontaneous site 1 opening event in the insulin receptor

The paper reports a spontaneous structural transition in the insulin receptor during molecular dynamics simulation, revealing a conformation compatible with hybrid insulin binding sites.

Structures of protein folding intermediates on the ribosome

This study structures two co-translational folding intermediates of an immunoglobulin-like domain using NMR and MD simulations, revealing parallel folding pathways conserved within the domain family.

Antibody maturation increases rigidity in protein-contacting regions and flexibility at glycan interfaces

This study uses molecular dynamics simulations to show that antibody maturation increases rigidity in protein-contacting regions and flexibility at glycan interfaces.

Comparison of AI protein structure ensemble prediction tools

This study compares AI tools for predicting protein structural ensembles, finding they generate diverse but distinct conformational distributions, with limited coverage of experimental structures and minimal response to known mutations.

Structure can emerge from disorder under neutral evolution

The paper shows that neutral evolution can lead to increased structure in unstructured proteins and loss of structure in structured proteins, suggesting a diffuse sequence-structure landscape.

Accurate Identification of Functional Residues Across the Human Proteome with TAMALE

TAMALE identifies functional residues across the human proteome using structure models and variant effect predictions, validated through case studies and experimental validation.

AlphaInterp: Mechanistic Interpretability of AlphaFold 3 Reveals How Evolutionary Information Shapes Protein Structure Prediction

AlphaInterp analyzes AlphaFold 3's internal mechanisms to show how evolutionary data influences protein structure prediction, revealing dependencies on comparative context and phylogenetic diversity.

Objective curriculum-guided design of multi-property proteins

This paper introduces OCDesign, a curriculum-guided framework for multi-property protein design, showing that staged objective introduction improves success rates compared to one-shot optimization.

Preorganized RdRp-Thumb Dynamics Drives SARS-CoV-2 Polymerase Function

This study uses MD simulations to show that preorganized thumb-subdomain motions in SARS-CoV-2 polymerase drive functional transitions through structurally coupled regulatory regions.

ProtXAI: Explainable AI Reveals Structural Determinants of Protein Dynamics

ProtXAI combines molecular dynamics and explainable AI to identify residue-level determinants of protein conformational changes across diverse systems.

Conformational drugging pockets at the surface of c-MYC proto-oncongenes

This study identifies drugable pockets on c-MYC using simulations, showing 10074-G5 binds stably, offering a new approach to target this undruggable protein.