It started off as a Cys, how did it end up like this? Identifying the extent of unmodelled oxidatively modified cysteines within the Protein Data Bank

This work examines data contained within 118 215 structures in the Protein Data Bank for unmodelled difference density concomitant with unmodelled oxidatively damaged cysteines. This analysis demonstrates that site-specific oxidation of residues is a phenomenon of which the experimenter should be aware, and highlights the need for a suitable detection tool within refinement software.

Assessing protein-specific radiation damage in time-resolved X-ray solution-scattering experiments at high-brilliance synchrotrons using fast detector readout

Adenylate kinase was used to quantify how experimental parameters influence radiation damage during time-resolved X-ray solution scattering (TR-XSS) at a multipurpose SAXS beamline. The study provides general guidelines for minimizing radiation artifacts in TR-XSS.

AlignPCA-2D: PCA-reduced Euclidean vector alignment for 2D classification in cryo-EM

We introduce AlignPCA-2D, a PCA-space Euclidean alignment method for rapid and interpretable 2D classification of cryo-EM particle images. The approach preserves essential structural variability while greatly reducing computational cost, offering a lightweight alternative to existing large-scale cryo-EM classification pipelines.

Molecular architecture of the human citrate synthase–malate de­hydrogenase 2 metabolon

Human malate dehydrogenase forms a transient complex with citrate synthase.

Simulating neutron protein crystallography experiments: applications to the development of the NMX instrument at ESS

Monte Carlo simulations of neutron protein diffraction experiments provide useful data that models neutrons interacting with instrument components, as well as the crystal diffraction itself. These data can be applied to instrument development, such as the commissioning of the NMX Macromolecular Diffractometer at ESS.

Updating direct methods VI. The extended use of the information contained in the Patterson map

The Patterson map is used as prior information for estimating triplet invariants. The method makes use not only of the information contained in the individual Patterson peaks, but also of that contained in suitably selected triples of Patterson peaks: they provide a valuable additional contribution to the triplet invariant estimate.

Unusual backfolded binding poses of BAZ2A bromodomain binders

We identified BAZ2A-binding compounds assuming a peculiar, almost enclosed, conformation. These molecules pose a basis for the development of potent BAZ2A macrocyclic inhibitors, as performed for other bromodomains.

Biochemical and structural characterization of a tail-spike protein with depolymerase activity identified in a marine podovirus

The marine tail-spike protein Dpo31 degrades the exopolysaccharide of its host and has structural features similar to those of other members of this protein class, despite similarity not being detected at the sequence level.

Structure of the Arabidopsis receptor kinase SRF6 ectodomain determined from crystals obtained using the LRR crystallization screen

A crystallization screen that has enabled the structural analysis of various extracellular domains of plant membrane receptor kinases is described together with the structure of the LRR domain of the receptor SRF6.

Scotty: lattice coincidences for macromolecular crystallographic phasing

Scotty is a tool that leverages Niggli-cell matches to identify similar crystallographic lattices and perform phasing with difference Fourier methods.

Scotty: lattice coincidences in the Protein Data Bank

Scotty supports crystallographic comparisons of lattice coincidences, the interpretation of oligomeric assemblies and paracrystallinity.

Structural basis of regioselective double halogenation of the β-carboline tryptoline by the single-component halogenase AetF

A structure of the flavin-dependent single-component tryptophan halogenase AetF bound to the non-native tricyclic substrate tryptoline reveals a binding pose analogous to L-tryptophan that directs C6-first halogenation. Product analysis identifies 6,8-dibromotryptoline as the final product.

Miroslav Z. Papiz (1955–2026)

Miroslav Papiz is remembered.