Protein Structure and Dynamics

Modulation of the internal dynamics of the Homer1 EVH1 domain by putative autism-associated mutations

The paper investigates how two autism-associated mutations in the Homer1 EVH1 domain affect its internal dynamics and binding properties using experimental and computational methods.

Sequence-independent protein domain detection and classification with PRISM

PRISM enables sequence-independent, one-shot fine-tuning for simultaneous protein domain segmentation and classification, improving accuracy for complex and novel architectures.

Protein entanglement misfolding determines divergent fates: proteasomal degradation or persistence in near-native misfolded states

The paper investigates how protein entanglement misfolding affects proteasomal degradation in human cells, finding that entangled proteins are more likely to be ubiquitinated and degraded.

De novo design of binder proteins targeting Helicobacter pylori adhesin BabA

This study designs compact protein binders targeting BabA, an H. pylori adhesin, using a structure-guided computational pipeline integrating structural, sequence, and evolutionary analyses.

SynFit: Synergistic Contrastive Learning for Multi-Objective Protein Fitness Prediction and Optimization

SynFit improves protein fitness prediction by learning shared and property-specific sequence representations, outperforming existing methods in multi-objective optimization.

Estimation of Protein Melting Temperatures Using Small-Ladder Replica Exchange Simulations

This study develops a method to estimate protein melting temperatures using small-ladder replica exchange simulations, showing improved efficiency with iterative temperature ladders.

Arginine versus Lysine: Molecular Determinants of Cation-π Interactions in Biomolecular Condensates

The paper quantifies differences in cation-π interaction strengths between Arg and Lys in biomolecular condensates, showing Arg is more effective than Lys due to higher dehydration penalty of Lys.

Structural studies of the C-terminal cysteine-rich domain of Aedes albopictus vitellogenin reveal an evolutionarily divergent, monomeric C-terminal cysteine knot (CTCK) architecture

This study determines the crystal structure of the C-terminal cysteine knot domain of Aedes albopictus vitellogenin, revealing a monomeric, evolutionarily divergent architecture that challenges prior assumptions about its oligomerization role.

The Martini 3 Metabolome

This paper parameterizes 186 common metabolites for the Martini 3 force field to enable realistic simulations of metabolite interactions in biological systems.

Computational prediction resolves thousands of homooligomeric phage protein structures

The paper predicts homooligomeric phage protein structures using a computational framework, confirming predictions for dimers and trimers and showing high accuracy in classifying homooligomeric states.

Cooperativity, dynamics, and the free-energy surfaces of charge-patterned IDPs

This study examines how charge patterning affects the conformational behavior and dynamics of intrinsically disordered proteins using experimental techniques and simulations.

Does the sequence of a disordered protein encode small molecule binding paths?

This study shows that disordered protein sequences encode characteristic small molecule binding pathways, identified through molecular dynamics simulations and machine learning.

A stickiness scale for disordered proteins

The paper develops a stickiness scale for disordered proteins based on biophysical experiments and compares it to existing hydropathy scales.

Pathway-resolved flux decomposition reveals hidden kinetic hierarchy in protein folding

The paper introduces a framework to decompose protein folding flux into pathway-specific kinetic contributions, revealing hidden kinetic hierarchies in folding mechanisms.

Adaptive disorder as the hallmark of nanobodies antigen-binding loops

This study identifies nanobody CDRs using deep learning and structural analysis, finding that their disorder and conformational diversity are adaptive features.

Scaffold-Lab: Critical Evaluation and Ranking of Protein Backbone Generation Methods in A Unified Framework

The paper evaluates and ranks protein backbone generation methods using a unified benchmark, identifying top-performing models in both unconditional and conditional generation.

Spatiotemporal graph neural networks reveal conformational binding signature in protein dynamics

This paper introduces a deep learning method to identify conformational binding signatures in protein dynamics from molecular simulations.

SuBMIT: A Software Toolkit for Facilitating Simulations of Coarse-Grained Structure-Based Models of Biomolecules.

SuBMIT generates input files for molecular dynamics simulations of coarse-grained structure-based models using GROMACS and OpenMM/OpenSMOG.

Discriminative Site-Directed Protein Engineering via Lightweight CASPE Platform

CASPE is a lightweight platform for site-directed protein engineering that improves the identification of beneficial mutations for thermostability and pH tolerance.

A Comprehensive Structural and Functional Analysis of Saccharomyces Killer Toxins.

The paper uses AlphaFold and molecular dynamics to model Saccharomyces killer toxins, revealing structural homology and functional insights into their mechanisms.

Accurate protein stability prediction for small domains using mega-scale experiments

The paper measures protein stability for 1.8 million domains using a new experimental method and develops models that accurately predict stability with high precision.

A Functional Map of the Human Intrinsically Disordered Proteome

The paper maps the functional landscape of the human intrinsically disordered proteome using evolutionary signatures to classify and predict IDR functions.

Deep Learning Structural Ensembles as Proxies for Protein Flexibility

This study evaluates deep learning models' ability to predict protein flexibility by comparing their structural ensembles with experimental data, finding AlphaFold3 performs best.

ConforFlux: Particle-Guided Trunk Repulsion for Diverse Protein Conformations

ConforFlux enhances protein structure prediction by sampling diverse conformations through trunk repulsion, improving success rates and coverage across multiple models and targets.

INTEGRATOR: Structural Elucidation of the INO80 Chromatin Remodeler via Experimentally Guided Molecular Simulations

The paper presents a computational model of the S. cerevisiae INO80 chromatin remodeling complex using integrative methods, revealing the structure and dynamics of key modules and introducing the INTEGRATOR workflow tool.

De novo design of peptides localizing at the interface of biomolecular condensates

This study designs peptides that localize at biomolecular condensate interfaces using a computational pipeline combining simulations, machine learning, and optimization, revealing charge-dependent localization mechanisms.

Functional Calmodulin States are Selected from an Electrostatically Tuned Free Energy Landscape

The paper uses simulations to identify CaM conformations under different calcium and salt conditions, showing how these factors influence its conformational dynamics.

Evolution of allostery without shape shifting: Internal dynamics drives functional diversification of a transcriptional repressor superfamily

The paper investigates how allostery evolves in the ArsR superfamily by showing that functional diversification arises from internal dynamics rather than large conformational changes.

De novo design of transmembrane accessory subunits for fold stabilization and expansion

This paper designs synthetic transmembrane subunits to stabilize and expand membrane proteins, demonstrating their utility in structural biology and disease treatment.

Ensemblify: a user-friendly tool for generating ensembles of intrinsically disordered regions of AlphaFold and user-defined models

Ensemblify generates and analyzes conformational ensembles of intrinsically disordered proteins using Monte Carlo sampling and AlphaFold confidence metrics.