Protein Structure and Dynamics

Correlated Motion-Based Residue Network Analysis Reveals the Distal Thermal Activation in Soybean Lipoxygenase

This study uses molecular dynamics and correlated motion analysis to reveal distal thermal activation pathways in soybean lipoxygenase, showing preferential communication through Leu546 over Leu754.

Structure of the Disulfide-rich Modules of a Striking Tandem Repeat Protein, Avian Cysteine-Rich Eggshell Membrane Protein

This paper determines the 3D structure of four disulfide-rich modules of CREMP, a structural protein in avian eggshell membrane, using NMR and compares it to other tandem repeat proteins.

Assessing the relation between protein phosphorylation, AlphaFold3 models and conformational variability

The paper evaluates AlphaFold models' ability to predict phosphorylation-induced structural changes in proteins using experimentally derived conformational ensembles.

Structural network comparison of domains across remote homologues arising from different domain architectures

The paper compares structural networks of remote homologous protein domains from different architectures to assess how domain combinations influence structural and evolutionary changes.

Divergent Side-Chain Networks of the Mineralocorticoid Receptor Control Mutation-Altered Drug Response

This study uses molecular dynamics simulations to show how the S810L mutation in the MR alters ligand-specific agonist/antagonist behavior by changing side-chain network interactions.

Defining the molecular determinants of titin kinase by analysing distantly evolved fish orthologues

The paper analyzes distantly evolved fish orthologues of titin kinase to identify conserved sequence motifs and classify titin gene duplicates into isoforms.

Glycopolymers stabilize protein folding and protein-protein interactions via enthalpic interactions

This study shows glycopolymers stabilize protein folding and interactions through enthalpic interactions, challenging simple volume exclusion models of crowding.

DynamicGT: a dynamic-aware geometric transformer model to predict protein binding interfaces in flexible and disordered regions

DynamicGT improves protein binding interface prediction by incorporating dynamic features and conformational changes, outperforming static models on flexible and disordered regions.

Biomolecular condensation using de novo designed globular proteins

This paper designs globular proteins that drive biomolecular condensation and demonstrates their use in forming dynamic condensates in cells.

ProFam: Open-Source Protein Family Language Modelling for Fitness Prediction and Design

ProFam is an open-source protein family language model that improves fitness prediction and design by leveraging evolutionary context through homologous sequences.

Generalizable and scalable protein stability prediction with rewired protein generative models

The paper introduces SPURS, a deep learning framework for protein stability prediction that integrates generative models and achieves accurate, scalable, and generalizable results.

Molecular basis for thermoresponsive protein condensation in plants

This study identifies a sequence-encoded mechanism in plant proteins that enables thermoresponsive phase separation through low-complexity domains.

The structural disorder of Dsup and its interaction with the human nucleosome: A computational study

This paper uses computational methods to study the structural disorder of Dsup and its interaction with the human nucleosome, revealing dynamic electrostatic shielding effects.

Alanine-scanning of the yeast killer toxin K2 reveals key residues for activity, gain-of-function variants, and supports prediction of precursor processing and 3D structure.

This study uses alanine scanning and computational methods to map sequence-function relationships in the yeast killer toxin K2, revealing key residues for activity and enabling engineering of enhanced toxicity and specificity.

Insight into Malt1 activation mechanism through synergetic approach of AlphaFold, MD Simulation and NMR dynamic analyses

The paper investigates MALT1 activation dynamics using a combination of AlphaFold, MD simulations, and NMR analyses, revealing how ionic strength influences its conformational states.

The transitional kinetics between open and closed Rep structures can be tuned by salt via two intermediate states

This study investigates the conformational transitions of Rep helicase using single-molecule techniques, revealing two intermediate states influenced by salt concentration.

De novo designed protein enables precise epitope-level control of Gremlin-1 antagonism

This study designs a protein that precisely controls Gremlin-1 antagonism by releasing BMPs, revealing the role of interface rigidity in antagonist function.

LoMuS: Low-Rank Adaptation with Multimodal Representations Improves Protein Stability Prediction

LoMuS improves protein stability prediction using a multimodal deep learning model that combines physicochemical descriptors with low-rank adapted embeddings from a protein language model.

Destabilization of Helix III Initiates Early Serum Amyloid A Misfolding by Exposing Its Amyloidogenic Core

This study identifies helix III destabilization as the initial trigger for SAA1-76 misfolding by exposing its amyloidogenic core through computational simulations.

Are frameworks independent from CDRs in antibodies? Exploring CDR-framework correlation networks of antibodies

This study uses molecular dynamics simulations to show that CDRs significantly influence antibody framework dynamics through CDR-FW correlation networks, highlighting their impact on structure and function.

An AI-Driven Platform for Deconstructing and Engineering Biomolecular Recognition

This paper introduces PS and IIOS, AI tools for analyzing and engineering molecular interactions by decomposing binding interfaces with stage-resolved force-wise insights.

On the variation of structural divergence among residues in enzyme evolution

The paper shows that structural divergence in enzymes correlates with residue flexibility and distance from the active site, arising from non-functional and functional evolutionary constraints.

An allosteric network governs Tom70 conformational dynamics to coordinate mitochondrial import

This study reveals the conformational dynamics of Tom70 through structural and computational analyses, showing how its allosteric network coordinates mitochondrial protein import and is modulated by viral interactions.

Depletion of the protein hydration shell with increasing temperature observed by small-angle X-ray scattering and molecular simulations

This study uses SAXS and simulations to show that protein hydration shells shrink with increasing temperature, revealing temperature-sensitive structural changes in the hydration shell.

Conformational Dynamics and Catalytic Backups in a Hyper-Thermostable Engineered Archaeal Protein Tyrosine Phosphatase

This paper describes an engineered archaeal PTP with enhanced thermostability and unique biochemical properties, revealing insights into enzyme evolution and biotechnological potential.

Capturing α-synuclein polymorphism with AlphaFold 3 and rivals

This paper evaluates AlphaFold 3 and other methods in predicting α-synuclein polymorphs using a reference set of known structures and finds they can generate fibril-like models, though performance varies with template use.

Topology-Encoded Polarity in Oppositely Charged Binary IDPP Condensates: Multiphase Organization from Non-Coacervating Partners as a Minimal Model of Complex Coacervation

This paper shows how oppositely charged IDPPs can form synthetic condensates with tunable properties through sequence-encoded phase behavior and micropolarity.

Engineering a Covalent Linkage into a Dimeric De Novo Enzyme Reveals a Novel Life-Sustaining Mechanism

The paper engineers a covalent linkage into a de novo enzyme, revealing that the modified protein rescues cells through upregulating siderophore biosynthesis rather than catalyzing iron release.

Full-Length Context Disrupts Folding of IgG-Binding Domains of Protein A

The paper shows that full-length Staphylococcal protein A fails to fold stably despite its individual domains being stable, challenging assumptions about modular protein folding and AI prediction accuracy.

The Heterogeneous Solution Ensemble of the DEAD-box Protein Dhh1 Reveals a Modular Architecture

The paper uses solution scattering and simulations to show that Dhh1's modular architecture allows structural heterogeneity while maintaining functional specificity.