Enzyme Structure and Function

This paper introduces enhanced qFit software for building multiconformer models from structural biology data, improving accuracy and usability.

The paper identifies recurring 3D catalytic modules in enzymes using the M-CSA database, showing their conservation and role in catalysis and evolution.

This study characterizes the structure and biochemical properties of N-Carbamoyl-beta-Alanine Amidohydrolase from Rhizobium radiobacter MDC 8606, revealing its substrate specificity and potential for industrial applications.

The paper reports the crystal structure of puromycin-sensitive aminopeptidase and describes its interaction with polyglutamine.

This study develops an in-line anoxic small-angle X-ray scattering system to characterize oxygen-induced structural changes in the FNR transcription factor under anoxic conditions.

This paper demonstrates a method to identify multiple binding orientations of small molecule fragments using anomalous signals from sulphur and chlorine atoms, applied to SARS-CoV-2 nsp1 fragments.

BeEM converts mmCIF structure files to PDB format accurately and efficiently, handling complex chain IDs and outperforming existing tools.

The paper reports cryo-EM structures of hexameric CphA2 from Stanieria sp., with and without ATP and cyanophycin, and shows how hexamerization enhances cyanophycin synthesis.

The paper validates sequence assignment in protein crystal structure models using an automated method called checkMySequence, identifying register shift errors in PDB-deposited models.

The paper resolves the structure of the fungal E3-binding protein (E3BP) in complex with the PDC core and shows its orthology to mammalian E3BP, bridging evolutionary distance and suggesting E3-specificity discriminants.

The paper captures the release of a photopharmacological drug from tubulin using time-resolved serial crystallography and shows how ligand release triggers conformational changes.

The paper determines the structural assembly of yeast Oxalyl-CoA synthetase, revealing asymmetric hexameric arrangements and identifying key self-association interfaces.

This study refines multiconformer ensemble models from multi-temperature X-ray diffraction data of Proteinase K, revealing temperature-driven conformational changes and their functional implications.

This paper reviews advances in reciprocal space mapping for diffuse scattering analysis and provides a tutorial on using Python tools for data processing.

The paper introduces a method to analyze local heterogeneity in crystallographic and cryo-EM maps by estimating resolution and atomic displacement parameters.

This study discovers that native MCC from Leishmania tarentolae forms filaments, determines its structure, and proposes a new model for its catalytic mechanism.

AHoJ retrieves apo and holo protein structures for user-defined ligands by aligning and classifying structures based on binding site similarity.

The paper introduces ProtCAD, a database that clusters protein assembly structures from independent experiments to improve accuracy in biological assembly annotations.

The paper performs a comprehensive phylogenetic analysis of ribonucleotide reductase (RNR) family to identify an ancestral clade and trace evolutionary diversification through insertions and extensions.

The paper describes a new system for serial crystallography data collection using a 3D printed mesh-holder and high-performance computing pipeline, applied to two beta-lactamases.

The paper determines the structures of Cry11Aa and Cry11Ba toxins using serial femtosecond crystallography, revealing new insights into their in vivo crystallization patterns and toxicity.

xia2.multiplex merges multi-crystal data sets in macromolecular crystallography to improve data quality and facilitate analysis.

MrParse streamlines Molecular Replacement by consolidating homologue searches and rankings from PDB and EBI AlphaFold, using eLLG and structural predictions.

The paper introduces a multi-factor clustering method to classify diffraction data from dynamic proteins into polymorphs, using unit cell constants and intensities to cluster mixed-state data from chymotrypsinogen crystals.

This paper identifies two drug-like fragments that bind to a cryptic pocket in B. pseudomallei DsbA, showing weak binding but potential for optimization.

This study demonstrates a high-throughput drug screening protocol using serial femtosecond X-ray crystallography for SARS-CoV-2 main protease, achieving 120 images/second with a new detector.

The paper presents an automated pipeline to identify protein sequences from cryo-EM and crystallographic data, demonstrating its application on an unknown snake venom protein.

The paper investigates the tunable hetero-assembly of a plant pseudoenzyme-enzyme complex, revealing variable stoichiometry and structural insights into their interactions.

This paper evaluates CASP14 models for molecular replacement using a new metric, reLLG, which is independent of diffraction data and shows AlphaFold2 models outperform others.

The paper develops a new protein crystallisation screen (Shotgun II) using PDB data, showing it outperforms the previous Shotgun I screen in coverage and data input.