Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0

New computational biophysics pipelines for analysing the global dynamics of structural ensembles and large, dynamic complexes resolved by cryoEM are reviewed.

On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy

Single-particle analysis (SPA) by cryo-electron microscopy comprises the estimation of many parameters along its image-processing pipeline. Overfitting observed in SPA is normally due to misestimated parameters, and the only way to identify these is by comparing the estimates of multiple algorithms or, at least, multiple executions of the same algorithm.

Structural and functional analysis of the D-alanyl carrier protein ligase DltA from Staphylococcus aureus Mu50

The crystal structure and functional characterization of DltA from Staphylococcus aureus, a D-alanyl carrier protein ligase that is the first protein in the D-alanylation pathway, are reported.

Monomodular Pseudomonas aeruginosa phage JG004 lysozyme (Pae87) contains a bacterial surface-active antimicrobial peptide-like region and a possible substrate-binding subdomain

The structure of the monomodular Pseudomonas aeruginosa bacteriophage JG004 lysin Pae87 is presented and investigated in relation to repurposing its function as an antimicrobial agent. The structure with its peptidoglycan ligand revealed a possible cell-wall-binding region. A C-terminal antimicrobial peptide-like region is shown to be important for disrupting the bacterial cell wall.

Updated restraint dictionaries for carbohydrates in the pyranose form

New restraint dictionaries for carbohydrates in the pyranose form have been produced using the latest methods as released in CCP4. The new restraints allow users to keep pyranoside models in their lowest energy conformation during refinement.

CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures

CSSR, an algorithm for assigning secondary structures to RNA 3D structures with missing atoms, has been developed. The base-pair assignment accuracy is close to 90% for 3D structures in which only one atom per nucleotide can be empirically identified.

Molecular insight into 2-phosphoglycolate activation of the phosphatase activity of bis­phosphoglycerate mutase

Crystal structures of bisphosphoglycerate mutase (BPGM) with 2-phosphoglycolate in the presence and absence of 2,3-bisphosphoglycerate are reported. The structures identified a novel binding site for 2-phosphoglycolate at the dimer interface of BPGM, as well as showing a snapshot of the catalytic activity of BPGM.

Global fitting of multiple data frames from SEC–SAXS to investigate the structure of next-generation nanodiscs

A framework is presented for refining models from several data frames from the same size-exclusion chromatography small-angle scattering experiment. The method can be employed to drastically reduce the number of parameters refined from the data series.

Crystal structure of the putative cell-wall lipoglycan biosynthesis protein LmcA from Mycobacterium smegmatis

The first crystal structure of the putative cell-wall biosynthesis protein LmcA from Mycobacterium smegmatis is reported at 1.8 Å resolution. The structure revealed an elongated β-barrel fold enclosing two distinct cavities, indicating a possible lipid-binding function in lipomannan/lipoarabinomannan biosynthesis.

A scalable strategy to solve structures of PDZ domains and their complexes

This article describes a new strategy for the rapid crystallization of PDZ domains using annexin A2 as a crystallization chaperone.

The X-ray crystallography phase problem solved thanks to AlphaFold and RoseTTAFold models: a case-study report

The new artificial intelligence-based protein structure modeling programs such as AlphaFold and RoseTTAFold have raised great enthusiasm in the scientific community. Here, it is shown that the excellent overall quality of these models can solve the phase problem faced by structural biology using X-ray diffraction. This study also validates these in silico models.

Structural and functional identification of the uncharacterized metallo-β-lactamase superfamily protein TW9814 as a phosphodiesterase with unique metal coordination

The uncharacterized protein TW9814 was identified to be a phosphodiesterase (PDE) that is active towards bis(p-nitrophenyl)phosphate in the presence of manganese(II) or nickel(II). TW9814 has a unique metal coordination and shows remarkable catalytic efficiency compared with other PDEs.