protein structure

Binding of a Macrocyclic Nonapeptide Inhibitor to Histone Deacetylase 6

The paper reports the crystal structure of HDAC6 CD2 complexed with a macrocyclic nonapeptide inhibitor, revealing key interactions that contribute to its inhibitory potency.

Decoding CBM2 binding modes: how similar folds achieve distinct substrate preferences

This study investigates how CBM2 proteins achieve distinct substrate preferences through a balance of topological complementarity, hydrophobic dehydration, and hydrogen-bonding interactions.

Capturing domain-level detail of molecular interactions in the IMEx Consortium binding domain data set

The paper presents a manually curated dataset of protein binding domains, linking them to molecular interactions and genomic variations for benchmarking and disease mechanism studies.

Retroviral CA subdomains encode their immature assembly properties independently of strict subdomain co-pairing

This study shows that retroviral CA subdomains encode immature assembly properties independently, without requiring strict co-pairing or co-evolution between subdomains.

Nucleotide State Regulates Asymmetric Substrate-Binding Protein Docking in a Type II ABC Importer

This study determines the structural changes in a Type II ABC importer's substrate-binding protein in different nucleotide states, revealing how ATP binding and hydrolysis regulate its conformation and interaction with the transporter.

Complex enzyme active site scaffolding by iteratively detuned catalytic guidance

CaGE alternates guided structure prediction with sequence redesign, fading guidance each cycle, so sequences recover complex catalytic sites unaided; designed nonheme-iron and PLP-dependent enzymes were active.

The choice of structural template can create apparent links between predicted protein stability and longevity in tetrapods

The paper investigates how structural templates affect apparent links between protein stability predictions and longevity in tetrapods, finding that template choice can create spurious associations.

De novo design of metalloenzymes using Metal Mer

This paper introduces a computational pipeline for de novo metalloenzyme design using Metal Mer, achieving high selectivity and activity in catalytic reactions without directed evolution.

Nanoscopic Origin of Enhanced Tyrosine-Mediated Water Ordering over Canonical Threonine Motifs in a Bacterial Ice-Nucleating Protein

The paper identifies the glycine-tyrosine-glycine motif as a key site for ice-like water ordering in bacterial ice-nucleating proteins through molecular dynamics simulations.

The Signaling Pathway of a Bacterial Two-Component System Determined by cryo-EM

This study uses cryo-EM to determine the structure of a light-regulated bacterial two-component system, revealing how light affects signaling through changes in histidine kinase and response regulator interactions.

Temperature-responsive contacts in TRPV1 concentrate in the cytoplasmic coupling domains

This study identifies the cytoplasmic coupling domains of TRPV1 as the temperature-responsive region using simulations and analysis of contact networks.

Transfer seeding reveals divergent activation ensembles across tyrosine kinases

This study uses molecular dynamics simulations and Markov state models to compare activation mechanisms of tyrosine kinases, revealing kinase-specific conformational ensembles.

PDBe-SIFTS: an open-source tool for Structure Integration with Function, Taxonomy, and Sequences, featuring improved alignment, scoring scheme, and accelerated search

PDBe-SIFTS improves residue-level sequence-structure mapping with faster search, better scoring, and accurate alignment, comparable to expert curation.

A potent macrocyclic peptide binder enables effector-free crystallization of the GTPase RAB27A

The paper identifies a macrocyclic peptide binder, IMP2660, that disrupts RAB27A-effector interactions and enables crystallization of RAB27A without an effector, revealing its structural features.

E3 Ligase Ligandalyzer: A Structure-First, Ligand-Centric Platform for E3 Ligase Recruiter Selection

E3 Ligase Ligandalyzer provides a platform for exploring E3 ligase-recruiter complexes, enabling analysis of chemical and structural data to support degrader design.

NCI-Profiler: automated protein-ligand interaction detection and visualization

NCI-Profiler detects and visualizes nine types of protein-ligand non-covalent interactions with high accuracy and speed, outperforming existing tools in several categories.

High-plex protein imaging across thick tissue by synchronized amplification

This paper introduces ACE, a method for high-plex protein imaging in thick tissues, reducing imaging time and enabling uniform signal amplification across tissue depths.

De novo design of cysteine proteases

This study designs de novo cysteine proteases with high activity and structural novelty, achieving 19% success rate and up to 3 x 10^7 rate enhancement over background reactions.

Learning Dynamic Protein Representations at Scale with Distograms

Adding Boltz2 distogram edges and features to protein and RNA graph networks beats MD-correlation graphs on binding tasks and improves stability, interaction and RNA predictions without simulation.

Evidence-resolved benchmarks separate biological context recognition from direct-partner specificity in protein interaction models

The paper benchmarks protein interaction models to distinguish direct partners from non-binding or noncontacting proteins, showing that context recognition and direct specificity are separable capabilities.

OmniScore: Universal Scoring of Diverse Biomolecular Complexes via Equivariant Geometry-Aware Discrete Representation Learning

OmniScore learns shared geometric representations of diverse biomolecular complexes and improves quality assessment and interaction prediction across molecular classes.

BCell-Epitope-Prediction: A local, reproducible pipeline for multi-epitope vaccine design: integration and structural validation against a panel of PDB antigen-antibody complexes

This paper presents a pipeline for multi-epitope vaccine design that integrates multiple tools to predict B-cell epitopes and validates them against structural data.

Why 627 BindCraft2 trajectories produced zero binders

The paper reports that two BindCraft2 campaigns produced no binders despite high interface confidence, identifying issues with confidence metrics and a disabled feature.

Molecular Insights into the Collagen-binding Specificity of Discoidin Domain Receptors

This study identifies electrostatic interactions as the basis for collagen-binding specificity of DDR1 and DDR2, with implications for signaling and therapeutic design.

Unfolding of the disease-linked bank vole prion protein E200K in the context of PrPSc propagation

This study investigates the early unfolding events of the E200K mutant prion protein in bank voles, comparing it to the wild-type protein to understand its enhanced capacity to generate PrPSc.

A Structure-Based hERG Pose Selection Workflow Integrating Induced-Fit Docking, Shape Similarity, Interaction Fingerprints, and Molecular Dynamics

The paper evaluates a pose-selection framework using hERG structures to prioritize ligand poses, finding shape similarity and interaction fingerprints are effective for different ligand groups.

Structural Basis for Angiotensin II Type I Receptor G Protein-biased Signaling

The paper reports structures of the AT1R coupled to G protein and ligands, revealing a microswitch network that determines G protein-biased signaling.

Computational redesign of Chlamydomonas reinhardtii photosynthetic fructose-1,6-bisphosphatase from the Calvin-Benson-Bassham cycle improves both stability and catalytic capacities in vitro

The paper computationally redesigns Chlamydomonas reinhardtii FBPase to enhance stability and catalytic activity, revealing insights into redox regulation and tetrameric assembly.

Translational isoforms of mammalian heterochromatin protein 1 (HP1) tune its interactions with chromatin effectors

The paper shows that mammalian cells produce extended HP1β isoforms that alter effector binding preferences, affecting heterochromatin organization.

Computational design of metalloproteases

This paper designs de novo metalloproteases using RoseTTAFold Diffusion 2, achieving high activity and specificity for cleaving various substrates.