Protein structure prediction by AlphaFold2: are attention and symmetries all you need?

This review discusses the AlphaFold2 system for protein structure prediction, including its conceptual and methodological advances, its amenability to interpretation and its achievements in the last Critical Assessment of protein Structure Prediction (CASP14) experiment.

CCD²: design constructs for protein expression, the easy way

CCD² is a software tool that aggregates sequence information for protein sequences (conservation, structure prediction, domain and disorder detection), enabling informed choices for expression-construct design, the single-click generation of PCR primers for cloning and easy data tracking.

The three-dimensional structure of Drosophila melanogaster (6–4) photolyase at room temperature

A crystal structure of a photolyase at room temperature confirms the structural information obtained from cryogenic crystallography and paves the way for time-resolved studies of the photolyase at an X-ray free-electron laser.

Structural and spectrophotometric investigation of two unnatural amino-acid altered chromophores in the superfolder green fluorescent protein

This work explores the structural and spectrophotometric implications of replacing a tyrosine residue in the chromophore of a fluorescent protein with two different unnatural amino acids.

Structure of a C1/C4-oxidizing AA9 lytic polysaccharide monooxygenase from the thermophilic fungus Malbranchea cinnamomea

The crystal structure of the lytic polysaccharide monooxygenase McAA9F, which is broadly active on both crystalline and soluble glycans and includes an unusual succinimide motif, is reported.

Structures of full-length VanR from Streptomyces coelicolor in both the inactive and activated states

Crystal structures are presented of the full-length VanR protein in both the inactive and activated states. Activation involves a disorder-to-order transition in a critical helix, which creates an interface for dimerization.

The β-link motif in protein architecture

The β-link, which is a motif consisting of a G1β β-bulge and a type II β-turn, is shown to play the specific role in protein architecture of connecting a β-sheet to another area of a protein in certain β-sandwiches, small β-barrels and β-sheet/α-helix proteins.

Structure of the unique tetrameric STENOFOLIA homeodomain bound with target promoter DNA

The STENOFOLIA homeodomain binds promoter DNA as a tetramer and the α3 helix binds DNA in both the major and minor grooves.

A GH13 α-glucosidase from Weissella cibaria uncommonly acts on short-chain maltooligosaccharides

Structures of α-glucosidase from Weissella cibaria BBK-1 (WcAG) in complex with various ligands, including a maltosyl N-linked enzyme intermediate, are reported. This work reveals a restricted active site of WcAG for short-chain maltooligosaccharides.

Mycobacterium tuberculosis ferritin: a suitable workhorse protein for cryo-EM development

A simple expression and purification protocol is presented which produces a high yield and good micrographs of the apoferritin bacterioferritin B (BfrB) from Mycobacterium tuberculosis. Its 2.12 Å resolution cryo-EM structure is presented, revealing a unique C-terminal extension (164–181), and it is discussed how BfrB could serve the growing cryo-EM community in characterizing and pushing the limits of their electron microscopes and workflows.

Structural studies of complexes of kallikrein 4 with wild-type and mutated forms of the Kunitz-type inhibitor BbKI

The crystal structures of complexes of human kallikrein 4 with BbKI, an inhibitor from Bauhinia bauhinioides, and of four of its reactive-site variants were determined in several crystal forms and were compared with the structures of complexes of Kunitz-type inhibitors with other serine proteases.

Exploring ligand dynamics in protein crystal structures with ensemble refinement

Ensemble refinement of six protein–ligand crystal structures indicates a much larger flexibility of some amino-acid side chains and ligand groups than is suggested by standard crystallographic refinement. Molecular-dynamics simulations and automatic generation of alternative conformations confirm the high flexibility of these groups, indicating that ensemble refinement can be used to identify such flexible groups.