Enzyme Structure and Function

Two Glu/Asp Residues Cooperatively Mediate an Early Step of ATP Hydrolysis in GHKL ATPases MutL and GyrB

This study identifies two acidic residues that cooperatively mediate an early step of ATP hydrolysis in GHKL ATPases, refining the catalytic mechanism and linking it to disease-associated variants.

In-Cell Protein Crystallization via a Locally Flexible 24-mer Assembly Precursor

This study defines the assembly pathway of CipB, showing that a 24-mer precursor forms and packs into a cubic lattice, with N-terminal flexibility enabling crystallization.

Structural basis for covalent inhibition of sulfatases by sulfamate warheads

This paper investigates why aryl sulfatases are inhibited by sulfamate warheads while carbohydrate sulfatases are not, using structural and computational analyses.

Symmetry-Based Center and Rotation Refinement for Fiber Diffraction Patterns

This paper improves fiber diffraction pattern alignment by refining symmetry center and rotation using hybrid methods, achieving accuracy comparable to exhaustive search with faster runtime.

The evolution and mechanistic versatility of the bacterial NADH dehydrogenases type II

This study investigates the evolutionary and mechanistic diversity of bacterial NDH-2s, revealing lineage-specific catalytic mechanisms and their implications for drug development.

Graphene Device for High-Temperature Crystallography Visualizes How Enzymatic Reactivity is Rooted in Ensemble Probability

The paper develops a graphene device for high-temperature crystallography to study enzymatic reactivity across temperature ranges, revealing how transition state ensembles relate to catalytic rates.

Metabolites form a globally connected chemical network across protein families

The paper analyzes protein-ligand interactions to show that ancient metabolites form a globally connected network across protein families, while non-ancient metabolites expand this network without disrupting its connectivity.

Visualizing Reaction Pathways via Reciprocal Space Kinetic Decomposition

The paper introduces a method to decompose time-resolved crystallography data in reciprocal space to extract weak transient structural states from noisy datasets.

Resolution-standardized evaluation of ligand atomic coordinates in crystallographic structures using machine learning

The paper introduces aBCC, a machine learning-based metric for evaluating ligand coordinate-density consistency in crystallographic structures across different resolutions.

Conformational flexibility of soybean lipoxygenase is coupled to crystal solvent content in serial crystallography

This study determines two distinct structures of soybean lipoxygenase-1 from a single experiment, showing that conformational flexibility is influenced by crystal solvent content.

Conformational gating at histidine junctions coordinates proton translocation in respiratory complex I

The paper presents cryo-EM structures of bovine respiratory complex I under varying protonation conditions, revealing conformational changes at histidine junctions that coordinate proton translocation.

Ancestral proteins trace the emergence of substrate specificity and oligomerization within bacterial DEDDy dinucleases

This study reconstructs ancestral bacterial DEDDy dinucleases to trace the evolution of substrate specificity and oligomerization from a dimeric ancestor with intermediate preferences.

Use of photocaged molecular oxygen for time-resolved serial X-ray crystallography

This paper uses photocaged molecular oxygen to trigger oxygen binding in myoglobin crystals and captures structural changes using time-resolved serial X-ray crystallography.

XSSDense: Time-resolved X-ray Solution Scattering Density Reconstruction Using a Variational Autoencoder

XSSDense reconstructs electron density maps from X-ray scattering data using a variational autoencoder and genetic algorithm, capturing conformational heterogeneity in proteins.

Extraction of directional electron-density features from diffraction data using spherical-harmonic decomposition

The paper introduces a method to extract directional electron-density features from diffraction data using spherical-harmonic decomposition, revealing chemically interpretable dipolar features in crystallographic maps.

Quaternary structures of Streptococcus pneumoniae Nucleoside Diphosphate Kinase: from hexamers to supramolecular assemblies

This study reports the crystal and cryo-EM structures of Streptococcus pneumoniae NDK, revealing its hexameric form and higher-order supramolecular assemblies, and suggests these structures may modulate its function.

Structural analyses of Trichomonas vaginalis pyrophosphate-dependent phosphofructokinase (TvPPi-PFK)

This paper reports the purification, crystallization, and structure of Trichomonas vaginalis pyrophosphate-dependent phosphofructokinase (TvPPi-PFK), revealing its active site and additional ligand-binding sites.

Automating 3DED data processing at eBIC

The paper introduces an automated data processing workflow for 3DED datasets using AutoED, converting data to NeXus format and reducing workload for electron diffraction scientists.

Muscle Diffraction at the Life Science X-ray Scattering Beamline

The paper describes methodological advances at the LiX beamline for high-throughput muscle diffraction experiments on human and animal muscle tissues.

Filamentation and proline inhibition of glutamate kinase

This study investigates the filamentation and proline inhibition mechanisms of Escherichia coli glutamate kinase using cryogenic electron microscopy.

Open or closed? Exploring the conformational heterogeneity of human plasminogen across multiple resolution scales

This study characterizes the conformational states of human plasminogen using structural biology techniques, revealing closed and open conformations in recombinant and plasma-derived variants.

Anaerobic time-resolved serial crystallography captures CO dissociation and rebinding in oxygen-sensitive -hydrogenase

This study uses anaerobic time-resolved serial crystallography to capture CO dissociation and rebinding in [FeFe]-hydrogenase, revealing a rigid catalytic architecture.

Structure of human aldehyde oxidase under tris(2-carboxyethyl)phosphine-reducing conditions

This study shows that using TCEP instead of DTT for crystallizing hAOX1 prevents enzyme inactivation, enabling better crystallographic studies.

Evidence for lanthanide and PQQ dependent dehydrogenases in Eukarya

The paper identifies lanthanide-coordinating 8-bladed beta-propeller enzymes in eukaryotes using bioinformatics and modeling, suggesting lanthanide biology extends beyond bacteria.

Structural Determinants of Catalytic Bias in an AMP-Forming Acetyl-CoA Synthetase from Syntrophus aciditrophicus

This study identifies structural determinants of catalytic bias in SaAcs1, showing that residues G196 and T197 in the CoA-binding loop influence the preference for AMP formation.

Critical amino acid residues in the N-terminal domain of NADPH-dependent assimilatory sulfite reductase flavoprotein mediate octameric assembly

The paper identifies critical amino acid residues in the N-terminal domain of SiRFP that mediate octameric assembly, revealing their role in stabilizing the enzyme's structure.

Characterisation of the conformational changes of GlnH that stimulate PknG activity in Mycobacteria and Corynebacterium glutamicum

The paper determines the structures of GlnH from different organisms to understand how conformational changes in response to aspartate trigger signaling via GlnX.

Structural basis of the nucleotide incorporation cycle of bacterial DNA polymerase III

This study determines cryo-EM structures of bacterial DNA polymerase III complexes to elucidate the mechanism of nucleotide incorporation and proofreading.

CAGE-TRX expands the scope of time-resolved crystallography through genetically encoded active-site photocaging

The paper introduces CAGE-TRX, a method for time-resolved crystallography that uses photocaged amino acids to control enzyme activity and capture reaction intermediates.

Structural basis of half-site reactivity in the catalytic α-subunit of Class Ib ribonucleotide reductases

The paper determines cryo-EM structures of Class Ib RNR catalytic α-subunit in apo and holo states, revealing asymmetric nucleotide binding and conformational dynamics that drive half-site reactivity.