Intracellular drug binding affinities by NMR

A commentary on the article by Luchinat et al. [(2021), Acta Cryst. D77, 1247–1258] where they describe an approach to identify the details of a compound binding to a molecular target using in-cell NMR to provide intracellular binding affinities.

Using photocaging for fast time-resolved structural biology studies

This review summarizes the best characterized and most relevant photocaging groups for time-resolved structural biology described in the literature to date. It provides a walkthrough of the essential factors to consider in designing a suitable photocaged molecule to address specific biological questions using time-resolved X-ray diffraction or solution-scattering methods.

On-grid and in-flow mixing for time-resolved cryo-EM

Time-resolved cryo-EM allows the study of proteins under non-equilibrium conditions on the millisecond timescale. Here, in-flow and on-grid mixing techniques are directly compared and it is found that on-grid reactions can be influenced by air–water interactions, whilst in-flow reactions give a broader distribution of reaction times due to laminar flow.

eSPC: an online data-analysis platform for molecular biophysics

eSPC is an online tool to analyze biophysical data from fluorescence, microscale thermophoresis and differential scanning fluorimetry experiments. The modules from the data-analysis platform contain classical thermodynamic models and clear user guidelines for the determination of dissociation constants (K_d) and thermal unfolding parameters such as melting temperatures (T_m).

Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography

Neutron protein crystallography provides insight into the structure and reaction mechanism of transition-state metal oxidoreductases without resulting in radiation-damage-induced artefacts.

Determination of intracellular protein–ligand binding affinity by competition binding in-cell NMR

Intracellular protein–ligand dissociation constants are measured by in-cell NMR spectroscopy by means of competition binding experiments with respect to a reference ligand. The method is applied to a set of carbonic anhydrase inhibitors, revealing intracellular binding with nanomolar affinity.

Cryo-EM single-particle structure refinement and map calculation using Servalcat

A new program, Servalcat, to facilitate atomic model refinement in cryo-EM single-particle analysis is presented. It implements a refinement pipeline using REFMAC5 and F_o − F_c map calculation.

A rush to explore protein–ligand electrostatic interaction energy with Charger

Embedded within the MoProViewer program, a new code library, Charger, contains an implementation of the analytical computation of the electrostatic interaction energy based on the multipolar atom. It was used to investigate the electrostatic interaction energies of benchmark dimers and glutathione transferase–benzophenone complexes.

Structure and mechanism of the γ-glutamyl-γ-aminobutyrate hydrolase SpuA from Pseudomonas aeruginosa

This article reports the structure and mechanism of SpuA, a class I glutamine amidotransferase from P. aeruginosa that forms part of a polyamine-utilization pathway.

Structural and catalytic characterization of Blastochloris viridis and Pseudomonas aeruginosa homospermidine synthases supports the essential role of cation–π interaction

The homospermidine synthases from P. aeruginosa and B. viridis, as well as their single-residue variants, are compared based on crystal structures and activity assays. A high structural similarity is demonstrated, suggesting the equivalent involvement of relevant residues in the reaction mechanism and catalytic dependence on cation–π interaction.

Crystal structures of a dodecameric multicopper oxidase from Marinithermus hydrothermalis

A two-domain multicopper oxidase (MCO) from Marinithermus hydrothermalis functions as a laccase and was crystallized in two distinct lattices as a dodecameric ball-like structure. Crystal structures are reported in cubic and orthorhombic lattices at 1.92 and 2.36 Å resolution, respectively. This MCO forms trimers similar to those found in other two-domain MCOs, but is unique in forming a higher order dodecameric structure.