CIISB Research Highlights Archive

Catalytic metal clusters play critical roles in important enzymatic pathways such as carbon fixation and energy conservation. However, how ligand binding to the active-site metal regulates conformational changes critical for enzyme function is often not well understood. One carbon fixation pathway that relies heavily on metalloenzymes is the reductive acetyl-coenzyme A (acetyl-CoA) pathway. In this study, we investigated the catalysis of the last step of the reductive acetyl-CoA pathway by the CO-dehydrogenase (CODH)-acetyl-CoA synthase (ACS) complex from Carboxydothermushydrogenoformans, focusing on how ligand binding to the nickel atom in the active site affects the conformational equilibrium of the enzyme. We captured six intermediate states of the enzyme by cryo-electron microscopy, with resolutions of 2.5-1.9A, and visualized reaction products bound to cluster A (an Ni,Ni-[4Fe4S] cluster) and identified several previously uncharacterized conformational states of CODH-ACS. The structures demonstrate how substrate binding controls conformational changes in the ACS subunit to prepare for the next catalytic step. 

The rational design and selective self-assembly of flexible and unsymmetric ligands into large coordination complexes is an eminent challenge in supramolecular coordination chemistry. Here, we present the coordination-driven self-assembly of natural ursodeoxycholic-bile-acid-derived unsymmetric tris-pyridyl ligand (L) resulting in the selective and switchable formation of chiral stellated Pd6L8 and Pd12L16 cages. The selectivity of the cage originates in the adaptivity and flexibility of the arms of the ligand bearing pyridyl moieties. The interspecific transformations can be controlled by changes in the reaction conditions. The orientational self-sorting of L into a single constitutional isomer of each cage, i.e., homochiral quadruple and octuple right-handed helical species, was confirmed by a combination of molecular modelling and circular dichroism. The cages, derived from natural amphiphilic transport molecules, mediate the higher cellular uptake and increase the anticancer activity of bioactive palladium cations as determinedin studies using in vitro 3D spheroids of the human hepatic cells HepG2. 

Microtubules (MTs) undergo diverse posttranslational modifications that regulate their structural and functional properties. Among these, polyglutamylation-a dominant and conserved modification targeting unstructured tubulin C-terminal tails-plays a pivotal role in defining the tubulin code. Here, we describe a mechanism by which tubulin tyrosine ligase-like 11 (TTLL11) expands and diversifies the code. Cryo-electron microscopy revealed a unique bipartite MT recognition strategy wherein TTLL11 binding and catalytic domains engage adjacent MT protofilaments. Biochemical and cellular assays identifiedpreviously uncharacterized polyglutamylation patterns, showing that TTLL11 directly extends the primary polypeptide chains of alpha- and beta-tubulin in vitro, challenging the prevailing paradigms emphasizing lateral branching. Moreover, cell-based and in vivo data suggest a cross-talk between polyglutamylation and the detyrosination/tyrosination cycle likely linked to the TTLL11-mediated elongation of the primary alpha-tubulin chain. These findings unveil an unrecognized layer of complexity within the tubulin code and offer mechanistic insights into the molecular basis of functional specialization of MT cytoskeleton.

Untargeted high-resolution mass spectrometry is a key tool in clinical metabolomics, natural product discovery and exposomics, with compound identification remaining the major bottleneck. Currently, the standard workflow applies spectral library matching against tandem mass spectrometry (MS2) fragmentation data. Multi-stage fragmentation (MSn) yields more profound insights into substructures, enabling validation of fragmentation pathways; however, the community lacks open MSn reference data of diverse natural products and other chemicals. Here we describe MS(n)Lib, a machine learning-ready open resource of >2 million spectra in MSn trees of 30,008 unique small molecules, built with a high-throughput data acquisition and processing pipeline in the open-source software mzmine. 

Poly (ADP-ribose) polymerases (PARPs) are enzymes catalyzing the post-translational addition of chains of ADP-ribose moieties to proteins. In most eukaryotic cells, their primary protein targets are involved in DNA recombination, repair, and chromosome maintenance. Even though this group of enzymes is quite common in both eukaryotes and prokaryotes, no PARP homologs have been described so far in ascomycetous yeasts, leaving their potential roles in this group of organisms unexplored. Here, we characterize Pyl1 protein of Yarrowia lipolytica as the first candidate of PARP in yeasts. We show that the expression of PYL1 gene is increased in mutants lacking either subunit of telomerase and identified several of its candidate protein targets in vivo. We demonstrate that Pyl1p is a functional PARP that undergoes auto-PARylation and PARylates YlKu70/80 complex. We also show that overexpression of PYL1 in Y. lipolyticacells results in dissociation of YlKu80 from telomeres in vivo, supporting the role of Pyl1p in telomere protection and maintenance. Based on our observations, we propose Pyl1p and its homologs identified in other yeast species represent a distinct class of PARPs, thus substantiating a more detailed investigation of their roles in these organisms. 

Nedd4-2 is a key enzyme involved in regulating sodium levels by controlling the removal of sodium channels from cell membranes. This function is essential for the regulation of blood pressure and osmotic balance, and its disruption has been linked to diseases such as hypertension, kidney disease and some cancers. A new study by a team from the Institute of Physiology of the CAS and the Faculty of Science of Charles University has for the first time described in detail the structure of the entire Nedd4-2 enzyme and explained the mechanism of its regulation. Using advanced imaging and biochemical methods, the researchers found that the function of Nedd4-2 is blocked by interactions between its domains. The enzyme remains inactive until it binds to the cell membrane in the presence of calcium ions. This leads to the release of inter-domain interactions and the activation of Nedd4-2. The study also showed that the 14-3-3 proteins, which respond to hormonal signals and by their binding block both the enzymatic activity of Nedd4-2 and its ability to bind to the membrane, are also involved in the regulation of Nedd4-2.