August 2023 issue
letters to the editor
A descriptor with a standard format and parameters is introduced for the large-area fixed targets used in serial crystallography. It is proposed that any fixed target used and developed by different facilities or groups could have its own version of this descriptor, facilitating their wider use and exchange.
Raynals is an online, user-friendly, free (for academia) and advanced tool for the analysis of single-angle dynamic light-scattering data. Estimation of the size distribution is performed through the Tikhonov–Phillips regularization.
A new protein structure validation method using hydrogen-bonding parameters is described.
The expression, characterization and structures of CeuE homologues from two thermophilic bacteria, Geobacillus stearothermophilus and Parageobacillus thermoglucosidasius, are described together with their ligand binding. The proteins show enhanced thermostability and resistance to organic chemicals; consequently, these thermophilic homologues offer advantages in the development of artificial metalloenzymes using the CeuE family.
The identification, characterization and X-ray structure of a novel fungal GH24 muramidase from Trichophaea saccata is described in which an SH3-like cell-wall-binding domain was identified by structure comparisons in addition to its catalytic domain. A domain-walking approach was then used to identify a group of fungal muramidases that belong to a new GH family containing homologous SH3-like cell-wall-binding modules, and X-ray structures of the independent catalytic and SH3-like domains of three of them are reported.
The first high-resolution 3D structure of Plasmodium vivax SUB1 complexed with a substrate-derived pseudo-peptide inhibitor is described. Subtle conformational changes in the enzyme–inhibitor complex define new pharmacophores for iterative cycles of structure-driven synthesis to accelerate the discovery of optimized SUB1 inhibitors that could represent a new generation of antimalarial candidates.
The first structures of Candida auris dihydrofolate reductase at near-atomic resolution are described, including apo and holo forms and complexes with two antifolate drugs: pyrimethamine and cycloguanil. C. auris is a highly significant globally emerging and resistant fungal pathogen and there is a great demand for research and progress towards novel therapeutics.
An E77 antibody with high binding affinity for the receptor-binding domain (RBD) of the prototype and Delta variant SARS-CoV-2 spike proteins was identified. The RBD–E77 Fab complex structure shows that the E77 antibody mimics the binding of angiotensin-converting enzyme 2 to RBD and that the N501Y mutation in variants of concern abolishes the binding potency of E77 to RBD.
High-resolution crystal structures of members of the purine class of FDA-approved drugs and phytochemical alkaloids complexed with hBRD2 bromodomains BD1 and BD2 revealed a new binding site by stacking the compounds against the WPF shelf of BD1 and BD2 in addition to the known acetyl-lysine binding site.
The two L-asparaginases ReAIV and ReAV encoded by the symbiotic bacterium R. etli were previously provisionally assigned to the same structural class 3. Here, it is shown that despite their low sequence identity, the constitutive enzyme ReAIV has the same architecture and active site as the inducible ReAV protein, although its kinetic characteristics are not identical to those of ReAV.