forthcoming articles

The following articles are a selection of those recently accepted for publication in Acta Crystallographica Section D: Structural Biology.

See also Forthcoming articles in all IUCr journals.

Accepted 16 September 2021

Structure and metal-binding properties of PA4063, a novel player in periplasmic zinc trafficking by Pseudomonas aeruginosa

This paper presents the structural and zinc-binding properties of PA4063, one of the periplasmic proteins expressed by P. aeruginosa under zinc-deficient condition. PA4063 has a non-canonical ferredoxin-like fold. Two zinc binding sites with micromolar affinity are exposed and located on the same face of the structure. Two His-rich loops, disordered in the apo-protein, contribute to zinc coordination in one of the sites. These findings strongly suggest a role for PA4063 in zinc trafficking, possibly acting as a metal chaperon or as a regulator of some transport system.

Accepted 14 September 2021

Ambiguities and completeness of SAS data analysis of membrane proteins: the case of sensory rhodopsin II–transducer complex

Ambiguities and completeness of SAS data analysis of membrane proteins (MPs) are considered here in case of the sensory rhodopsin II – transducer complex solubilized in a detergent. A contribution of a detergent belt surrounding MPs is one of the main problems of SAS data analysis of MPs; the second problem addressed here is the influence of oligomerization polydispersity (which is a sufficiently common phenomenon for MPs) on the quality of SAS structural analysis.

Accepted 11 September 2021

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

We present a new program Servalcat to facilitate the atomic model refinement in cryo-EM single particle analysis. It implements a refinement pipeline using REFMAC5 and FoFc map calculation.

Accepted 10 September 2021

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 for cubic and orthorhombic lattices at 1.92 and 2.36 Å, respectively. This MCO forms trimers similar to those found in other two-domain MCOs but is unique in forming a higher order dodecameric structure.

Accepted 3 September 2021

Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM

The modification of a crystallographic molecular-replacement pipeline for use in fitting search models to cryo-EM is described.

Accepted 31 August 2021

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.

Accepted 31 August 2021

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.

Accepted 30 August 2021

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.

Accepted 30 August 2021

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 (Kd) and thermal unfolding parameters such as melting temperatures (Tm).

Accepted 27 August 2021

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.

Accepted 23 August 2021

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.

Accepted 23 August 2021

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.

Accepted 13 August 2021

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.

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