Articles in 2023

Peptide epimerization is a common but enigmatic post-translational modification found in antibiotics formed from ribosomally synthesized and post-translationally modified peptides. Now, crystallographic snapshots, spectroscopy and biochemical investigations have provided insight into the mechanism of peptide epimerization catalyzed by radical S-adenosyl-l-methionine epimerases.

Cyclic peptides show promise for modulating difficult disease targets; however, they often cannot be administered orally. The authors developed a method to synthesize and screen large libraries of small cyclic peptides while enabling the simultaneous interrogation of activity and permeability. This approach was applied to the disease target thrombin to discover peptides with high affinity, stability and oral bioavailability of up to 18% in rats.

Macrocyclic peptides are promising scaffolds for chemical tools and potential therapeutics, but their synthesis is currently difficult. Here, the authors report the characterization of Ulm16, a peptide cyclase of the penicillin-binding protein (PBP)-type class of thioesterases, that catalyzes head-to-tail macrolactamization of nonribosmal peptides of 4–6 amino acids in length.

Qi et al. used phage-assisted evolution to optimize SlugCas9, a compact Cas9 nuclease, for NNG PAM recognition and developed a SlugCas9-NNG based adenine base editor for single AAV delivery.

A workflow integrating tools from bioinformatics, structural biology and synthetic biology has been developed that enables the rapid design of pili-enabled living materials. This approach allows mining of pili-producing nonpathogenic chassis, understanding of the pili structure and assembly, and engineering of pili-enabled living materials in a systematic and sequential manner.

Efforts to rationally engineer nonribosomal peptide synthetase (NRPS) enzymes have focused on making individual modifications. Here the authors describe a targeted random engineering approach that uses thousands of NRPS domains amplified from the soil metagenome for mass substitution experiments.

Oxygen sensitivity hampers applications of metal-dependent CO₂ reductases. Here, Oliveira et al. describe how an allosteric disulfide bond controls the activity of a CO₂ reductase, preventing its physiological reduction during transient O₂ exposure and allowing aerobic handling of the enzyme.

Cui et al. developed LAUNCHER, a single-component switch using potyviral protease, which offers a high signal-to-noise ratio for precise payload release, enabling versatile cellular applications and enhanced synthetic circuit performance.

Here, the authors describe the mechanistic flexibility and substrate promiscuity of the apramycin resistance enzyme ApmA. They identify additional clinical drugs susceptible to modification through a molecular mechanism that diverges from other enzymes within the left-handed β-helix superfamily.

Dumelie et al. asked whether biomolecular phase-separated condensates can establish microenvironments with distinct metabolomes and found that amphipathic lipids are highly enriched in these microenvironments and influence the properties of the condensates.

Ye et al. reveal the critical role of micropolarity in controlling the structure and miscibility of subcompartments in multiphasic biomolecular condensates, thereby providing new insights into multiphasic condensation regulation.

Development of chemically responsive bandpass filters mimics the signal-processing abilities of electronic circuits in mammalian cells by responding to chemical concentrations within a specific range and rejecting ones outside that range.

Methyl jasmonate in the root volatile organic compounds (rVOCs) signals to the soil microbiome to form biofilms with altered composition that benefits plant growth. This cross-kingdom VOCs-mediated signaling expands the zone of rhizosphere influence.

A chemical screen identified a small molecule inhibitor of CHEK2 that boosts insulin secretion in human β cells, including those from both healthy and type 2 diabetic human islets, as well as in diabetic mouse models and cynomolgus macaques.

Cofactorless oxygenases are rare in nature and natural product biosynthesis. Here the authors describe the biochemical and structural characterization of two such oxygenases catalyzing deformylation, ring cleavage and epoxidation in the biosynthesis of the enediyne natural product tiancimycin A.

Hydrogen–deuterium exchange–mass spectrometry and cryo-EM analysis revealed an allosteric mechanism involving the conformation of a single α-helix that controls the global conformation and activity of eIF2B, the core molecular machine of the integrated stress response.

The cryo-electron microscopy structure of the GPR101–Gs complex reveals the mechanism for its constitutive activity and facilitates the screening and identification of GPR101 ligands with rejuvenating potential.

Structural analysis of a type III effector protein CteC reveals that it represents a unique ‘D-E’ family of PARP-like ADP-ribosyltransferases, which harbors chimeric features from the enzymes of the R-S-E and H-Y-E classes.

Structural analysis of Crenotalea thermophila SPARTA reveals that guide-mediated target binding releases the auto-inhibition of SPARTA imposed by an acidic tail and triggers substantial conformational changes, resulting in the oligomerization of short Ago and TIR for SPARTA activation.

Zhang et al. determine multiple cryo-electron microscopy structures of inactive monomeric and active tetrameric short prokaryotic Ago/TIR–APAZ (SPARTA) complexes, providing structural basis of SPARTA assembly and activation that will facilitate the development of SPARTA-based biotechnological tools.