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At least 199 records · Page 11

Sparsomycin inhibits translation through a conserved mechanism across all domains of life

Abstract Sparsomycin (SPA) is a broad-spectrum inhibitor of protein synthesis with activity across all three domains of life. Although SPA has long been known to target the ribosomal peptidyl transferase center (PTC), previous structural studies suggested that SPA binds differently to bacterial ribosomes compared to their archaeal and eukaryotic counterparts—an unexpected conclusion given the high evolutionary conservation of the ribosomal catalytic center. Here, we show that SPA inhibits a majority of elongation-competent bacterial ribosomal complexes and present X-ray crystal structures of Thermus thermophilus 70S ribosomes stalled by SPA at the initiation and early elongation stages of translation. These structures reveal that SPA binds to the bacterial ribosome in a manner essentially identical to that observed in archaeal and eukaryotic ribosomes, establishing a unified structural mechanism of SPA action across all domains of life. In this conserved binding mode, SPA occupies the A-site cleft of the PTC and forms an extensive network of interactions with universally conserved ribosomal RNA nucleotides and the CCA-end of the P-site transfer RNA (tRNA), thereby stabilizing the peptidyl-tRNA substrate while sterically blocking accommodation of an incoming aminoacyl-tRNA. By clarifying the mode of action of SPA on the bacterial ribosome, our work provides a structural framework for the rational design of SPA derivatives with improved potency and bacterial specificity.

Paranjpe, Madhura N [Department of Biological Scie↗

Lanthanum-Promoted Electrocatalyst for the Oxygen Evolution Reaction: Unique Catalyst or Oxide Deconstruction?

A conventional performance metric for electrocatalysts that promote the oxygen evolution reaction (OER) is the current density at a given overpotential. However, the assumption that increased current density at lower overpotentials indicates superior catalyst design is precarious for OER catalysts in the working environment, as the crystalline lattice is prone to deconstruction and amorphization, thus greatly increasing the concentration of catalytic active sites. We show this to be the case for La 3+ incorporation into Co 3 O 4 . Powder X-ray diffraction (PXRD), Raman spectroscopy and extended X-ray absorption fine structure (EXAFS) reveal smaller domain sizes with decreased long-range order and increased amorphization for La-modified Co 3 O 4 . This lattice deconstruction is exacerbated under the conditions of OER as indicated by operando spectroscopies. The overpotential for OER decreases with increasing La 3+ concentration, with maximum activity achieved at 17% La incorporation. HRTEM images and electron diffraction patterns clearly show the formation of an amorphous overlayer during OER catalysis that is accelerated with La 3+ addition. O 1s XPS spectra after OER show the loss of lattice-oxide and an increase in peak intensities associated with hydroxylated or defective O-atom environments, consistent with Co(O) x (OH) y species in an amorphous overlayer. Furthermore, our results suggest that improved catalytic activity of oxides incorporated with La 3+ ions (and likely other metal ions) is due to an increase in the number of terminal octahedral Co(O) x (OH) y edge sites upon Co 3 O 4 lattice deconstruction, rather than enhanced intrinsic catalysis.

Catalysts↗

Cryo-EM structures of engineered active bc 1- cbb 3 type CIII 2 CIV super-complexes and electronic communication between the complexes

Respiratory electron transport complexes are organized as individual entities or combined as large supercomplexes (SC). Gram-negative bacteria deploy a mitochondrial-like cytochrome (cyt) bc 1 (Complex III, CIII 2 ), and may have specific cbb 3 -type cyt c oxidases (Complex IV, CIV) instead of the canonical aa 3 -type CIV. Electron transfer between these complexes is mediated by soluble ( c 2 ) and membrane-anchored ( c y ) cyts. Here, we report the structure of an engineered bc 1 - cbb 3 type SC (CIII 2 CIV, 5.2Å resolution) and three conformers of native CIII 2 (3.3 Å resolution). The SC is active in vivo and in vitro, contains all catalytic subunits and cofactors, and two extra transmembrane helices attributed to cyt c y and the assembly factor CcoH. The cyt c y is integral to SC, its cyt domain is mobile and it conveys electrons to CIV differently than cyt c 2 . The successful production of a native-like functional SC and determination of its structure illustrate the characteristics of membrane-confined and membrane-external respiratory electron transport pathways in Gram-negative bacteria.

42 ENGINEERING↗

Structure and functional determinants of Rad6–Bre1 subunits in the histone H2B ubiquitin-conjugating complex

The conserved complex of the Rad6 E2 ubiquitin-conjugating enzyme and the Bre1 E3 ubiquitin ligase catalyzes histone H2B monoubiquitination (H2Bub1), which regulates chromatin dynamics during transcription and other nuclear processes. Here, we report a crystal structure of Rad6 and the non-RING domain N-terminal region of Bre1, which shows an asymmetric homodimer of Bre1 contacting a conserved loop on the Rad6 ‘backside’. This contact is distant from the Rad6 catalytic site and is the location of mutations that impair telomeric silencing in yeast. Mutational analyses validated the importance of this contact for the Rad6–Bre1 interaction, chromatin-binding dynamics, H2Bub1 formation and gene expression. Moreover, the non-RING N-terminal region of Bre1 is sufficient to confer nucleosome binding ability to Rad6 in vitro. Interestingly, Rad6 P43L protein, an interaction interface mutant and equivalent to a cancer mutation in the human homolog, bound Bre1 5-fold more tightly than native Rad6 in vitro, but showed reduced chromatin association of Bre1 and reduced levels of H2Bub1 in vivo. These surprising observations imply conformational transitions of the Rad6–Bre1 complex during its chromatin-associated functional cycle, and reveal the differential effects of specific disease-relevant mutations on the chromatin-bound and unbound states. Overall, our study provides structural insights into Rad6–Bre1 interaction through a novel interface that is important for their biochemical and biological responses.

59 BASIC BIOLOGICAL SCIENCES↗

Semiconducting to Metallic Electronic Landscapes in Defects-Controlled 2D π-d Conjugated Coordination Polymer Thin Films

Two-dimensional coordination polymers (2DCPs) have been predicted to exhibit exotic properties such as superconductivity, topological insulating behavior, catalytic activity, and superior ion transport for energy applications; experimentally, these materials have fallen short of their expectation due to the lack of synthesis protocols that yield continuous, large crystallite domains, and highly ordered thin films with controllable physical and chemical properties. Herein, the fabrication of large-area, highly ordered 2DCP thin films with large crystallite domains using chemical vapor deposition (CVD) approaches is described. It is demonstrated that defects and the packing motifs of 2DCP thin films may be controlled by adjusting the vapor–vapor and vapor–solid interactions of the metal and organic linker precursors during the CVD fabrication process. Such control allows for the fabrication of defects-controlled 2DCP thin films that show either semiconducting or metallic behavior. The findings provide the first demonstration of tuning the electrical properties of sub 100 nm-thick continuous 2DCP thin films by controlling their electronic landscape through defect engineering. As such, it is determined that large-area, highly ordered 2DCP thin films may undergo a semiconducting to metallic transition that is correlated to changes in morphology, crystalline domain sizes, crystallite orientation, defect interactions, and electronic structure.

2D coordination polymers↗

Structural basis of the promiscuity of the unusual Fe(II) and 2-oxoglutarate dependent human aspartate/asparagine-β-hydroxylase

Protein-hydroxylation catalysed by Fe(II) and 2-oxoglutarate (2OG) dependent oxygenases is an important regulatory mechanism in human biology. Such oxygenases typically coordinate their Fe(II) cofactor via a conserved triad of an aspartate- or glutamate- and two histidine-residues. By contrast, aspartate/asparagine β-hydroxylase (AspH), which catalyses asparagine/aspartate-residue oxidation in epidermal growth factor-like domains (EGFDs), has only two histidine-residues (H679, H725), with a water occupying the site normally occupied by an aspartate- or glutamate-residue. We describe mechanistic studies with catalytically active AspH crystals. Turnover studies with single crystals under cryogenic conditions give (3 R)-hydroxylated EGFDs with the product alcohol coordinating Fe(II) trans to H725. Time-resolved serial crystallography of microcrystals using an acoustic droplet ejection system, coupled to X-ray emission analyses, demonstrate turnover within 1.5 s, giving a product complex in which Fe(II) is regenerated. Solution and crystallographic studies with the O 2 surrogate nitric oxide imply O 2 binds to Fe(II) trans to H725. The additional Fe-chelating water is maintained throughout AspH catalysis and is not directly involved in substrate hydroxylation, because O 2 is the sole oxygen source in alcohol products, as shown by 18 O labelling studies. The results reveal how AspH accommodates both aspartate- and asparagine-substrates and will assist in efforts targeting AspH for cancer treatment.

de Munnik, Mariska↗

Nanorod length-dependent photodriven H2 production in 1D CdS–Pt heterostructures

Colloidal quantum confined semiconductor-metal heterostructures are promising candidates for solar energy conversion because their light absorbing semiconductor and catalytic components can be independently tuned and optimized. Although the light-to-hydrogen efficiencies of such systems have shown interesting dependences on the morphologies of the semiconductor and metal domains, the mechanisms of such dependences are poorly understood. Here, we use Pt tipped 0D CdS quantum dots (with ∼4.6 nm diameter) and 1D CdS nanorods (of ∼13.8, 27.8, 66.6, and 88.9 nm average rod lengths) as a model system to study the distance-dependence of charge separation and charge recombination times and their impacts on photo-driven H2 production. The H2 generation quantum efficiency increases from 0.2% ± 0.0% in quantum dots to 28.9% ± 0.4% at a rod length of 28 nm and shows negligible changes at longer rod lengths. The half-life time of electron transfer from CdS to Pt increases monotonically with rod length, from 0.7 ± 0.1 in quantum dots to 170.2 ± 29.5 ps in the longest rods, corresponding to a slight decrease in electron transfer quantum efficiency from 92% to 81%. The amplitude-weighted average lifetime of charge recombination of the electron in Pt with the hole in CdS increases from 4.7 ± 0.4 µs in quantum dots to 149 ± 34 µs in 28 nm nanorods, and the lifetime does not increase further in longer rods, resembling the trend in the observed H2 generation quantum efficiency. Our result suggests that the competition of the charge recombination process with the hole removal by the sacrificial electron donor plays a dominant role in the observed nanorod length dependent overall light driven H2 generation quantum efficiency.

Chemistry↗

Reagent to label proteins via lysine isopeptide bonds

Covalently cross-linked pilus polymers displayed on the cell surface of Gram-positive bacteria are assembled by class C sortase enzymes. These pilus-specific transpeptidases located on the bacterial membrane catalyze a two-step protein ligation reaction—first, cleaving the LPXTG motif of one pilin protomer to form an acyl-enzyme intermediate, and second, joining the terminal threonine to the nucleophilic lysine residue residing within the pilin motif of another pilin protomer. Informed by the high-resolution crystal structures of corynebacterial pilus-specific sortase (SrtA) and by developing structural variants of the sortase enzyme whose catalytic pocket has been unmasked by activating mutations, we have developed new reagents capable of forming isopeptide bonds in vitro. The reagents disclosed herein can catalyze ligation of isolated SpaA domains in vitro provide a facile and versatile new platform for protein engineering and bio-conjugation that has major implications for biotechnology.

Clubb, Robert T.↗

Calcium-stimulated autophosphorylation site of plant chimeric calcium/calmodulin-dependent protein kinase

The existence of two molecular switches regulating plant chimeric Ca(2+)/calmodulin-dependent protein kinase (CCaMK), namely the C-terminal visinin-like domain acting as Ca(2+)-sensitive molecular switch and calmodulin binding domain acting as Ca(2+)-stimulated autophosphorylation-sensitive molecular switch, has been described (Sathyanarayanan, P. V., Cremo, C. R., and Poovaiah, B. W. (2000) J. Biol. Chem. 275, 30417-30422). Here we report the identification of Ca(2+)-stimulated autophosphorylation site of CCaMK by matrix-assisted laser desorption ionization time of flight-mass spectrometry. Thr(267) was confirmed as the Ca(2+)-stimulated autophosphorylation site by post-source decay experiments and by site-directed mutagenesis. The purified T267A mutant form of CCaMK did not show Ca(2+)-stimulated autophosphorylation, autophosphorylation-dependent variable calmodulin affinity, or Ca(2+)/calmodulin stimulation of kinase activity. Sequence comparison of CCaMK from monocotyledonous plant (lily) and dicotyledonous plant (tobacco) suggests that the autophosphorylation site is conserved. This is the first identification of a phosphorylation site specifically responding to activation by second messenger system (Ca(2+) messenger system) in plants. Homology modeling of the kinase and calmodulin binding domain of CCaMK with the crystal structure of calcium/calmodulin-dependent protein kinase 1 suggests that the Ca(2+)-stimulated autophosphorylation site is located on the surface of the kinase and far from the catalytic site. Analysis of Ca(2+)-stimulated autophosphorylation with increasing concentration of CCaMK indicates the possibility that the Ca(2+)-stimulated phosphorylation occurs by an intermolecular mechanism.

Non-NASA Center↗

Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease

Abstract Long interspersed nuclear element-1 (L1) is an autonomous non-LTR retrotransposon comprising ∼20% of the human genome. L1 self-propagation causes genomic instability and is strongly associated with aging, cancer and other diseases. The endonuclease domain of L1’s ORFp2 protein (L1-EN) initiates de novo L1 integration by nicking the consensus sequence 5′-TTTTT/AA-3′. In contrast, related nucleases including structurally conserved apurinic/apyrimidinic endonuclease 1 (APE1) are non-sequence specific. To investigate mechanisms underlying sequence recognition and catalysis by L1-EN, we solved crystal structures of L1-EN complexed with DNA substrates. This showed that conformational properties of the preferred sequence drive L1-EN’s sequence-specificity and catalysis. Unlike APE1, L1-EN does not bend the DNA helix, but rather causes ‘compression’ near the cleavage site. This provides multiple advantages for L1-EN’s role in retrotransposition including facilitating use of the nicked poly-T DNA strand as a primer for reverse transcription. We also observed two alternative conformations of the scissile bond phosphate, which allowed us to model distinct conformations for a nucleophilic attack and a transition state that are likely applicable to the entire family of nucleases. This work adds to our mechanistic understanding of L1-EN and related nucleases and should facilitate development of L1-EN inhibitors as potential anticancer and antiaging therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗

Kinetic and substrate complex characterization of RamA, a corrinoid protein reductive activase from Methanosarcina barkeri

ABSTRACT In microbial corrinoid-dependent methyltransferase systems, adventitious Co(I)-corrinoid oxidation halts catalysis and necessitates repair by ATP-dependent reductive activases. RamA, an activase with a C-terminal ferredoxin domain with two [4Fe-4S] clusters from methanogenic archaea, has been far less studied than the bacterial activases bearing an N-terminal ferredoxin domain with one [2Fe-2S] cluster. These differences suggest RamA might prove to have other distinctive characteristics. Here, we examine RamA kinetics and the stoichiometry of the corrinoid protein:RamA complex. Like bacterial activases, K+ stimulates RamA. Potassium stimulation had been questioned due to differences in the primary structure of bacterial and methanogen activases. Unlike one bacterial activase, ATP is not inhibitory allowing the first determination of apparent kinetic parameters for any corrinoid activase. Unlike bacterial activases, a single RamA monomer complexes a single corrinoid protein monomer. Alanine replacement of a RamA serine residue corresponding to the serine of one bacterial activase which ligates the corrinoid cobalt during complex formation led to only moderate changes in the kinetics of RamA. These results reveal new differences in the two types of corrinoid activases, and provide direct evidence for the proposal that corrinoid activases act as catalytic monomers, unlike other enzymes that couple ATP hydrolysis to difficult reductions.

Microbiology↗

Application of machine learning interatomic potentials in heterogeneous catalysis

Heterogeneous catalysts are crucial in modern societies as they promote sustainability by enabling lower-energy pathways for various chemical reactions. While Density Functional Theory (DFT) computations can provide critical insights into how heterogeneous catalysts operate at the atomic level, they are limited by computational costs and unfavorable scaling with system size. Recently, machine learning interatomic potentials (MLIPs) have emerged as a promising alternative to DFT, offering near-DFT accuracy at significantly reduced cost. Here, in this perspective, we discuss the application of MLIPs in heterogeneous catalyst modeling as a surrogate for DFT. We detail how MLIPs have been applied in thermal catalysis to probe active sites, enable studying complex metallic and nanoporous catalysts, and investigate the reconstruction of catalytic surfaces. We review the use of MLIPs in electrocatalysis and photocatalysis, emphasizing their capabilities in studying transition metal oxide surfaces and solid–liquid interfaces. We also discuss the current limitations of MLIPs, particularly their challenges with transferability and description of non-local interactions. Finally, we conclude by identifying promising and underexplored domains in which MLIPs can further advance our understanding of heterogeneous catalysts.

Catalytic surfaces↗

Deep learning of electrochemical CO 2 conversion literature reveals research trends and directions

Large-scale and openly available material science databases are mainly composed of computer simulation results rather than experimental data. Some examples include the Materials Project, Open Quantum Materials Database, and Open Catalyst 2022. Unfortunately, building large-scale experimental databases remains challenging due to the difficulties in consolidating locally distributed datasets. In this work, focusing on the catalysis literature of CO 2 reduction reactions (CO 2 RRs), we present a machine learning (ML)-based protocol for selecting highly relevant papers and extracting important experimental data. First, we report a document embedding method (Doc2Vec) for collecting papers of greatest relevance to the specific target domain, which yielded 3154 CO 2 RR-related papers from six publishers. Next, we developed named entity recognition (NER) models to extract twelve entities related to material names (catalyst, electrolyte, etc.) and catalytic performance (Faradaic efficiency, current density, etc.). Further, among several tested models, the MatBERT-based approach achieved the highest accuracy, with an average F1-score of 90.4% and an F1-score of 95.2% in a boundary relaxation evaluation scheme. The accurate and accelerated NER-based data extraction from a large volume of catalysis literature enables temporal trend analyses of the CO 2 RR catalysts, products, and performances, revealing the potentially effective material space in CO 2 RRs. While this work demonstrates the effectiveness of our ML-based text mining methods for specifically CO 2 RR literature, the methods and approach are applicable to and may be used to accelerate the development of other catalytic chemical reactions.

36 MATERIALS SCIENCE↗

Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases

Replication-initiating HUH endonucleases (Reps) are sequence-specific nucleases that cleave and rejoin single-stranded DNA (ssDNA) during rolling-circle replication. These functions are mediated by covalent linkage of the Rep to its substrate post cleavage. Here, we describe the structures of the endonuclease domain from the Muscovy duck circovirus Rep in complex with its cognate ssDNA 10-mer with and without manganese in the active site. Structural and functional analyses demonstrate that divalent cations play both catalytic and structural roles in Reps by polarizing and positioning their substrate. Further structural comparisons highlight the importance of an intramolecular substrate Watson-Crick (WC) base pairing between the -4 and +1 positions. Subsequent kinetic and functional analyses demonstrate a functional dependency on WC base pairing between these positions regardless of the pair’s identity (i.e., A·T, T·A, G·C, or C·G), highlighting a structural specificity for substrate interaction. Finally, considering how well WC swaps were tolerated in vitro, we sought to determine to what extent the canonical -4T·+1A pairing is conserved in circular Rep-encoding single-stranded DNA viruses and found evidence of noncanonical pairings in a minority of these genomes. Altogether, our data suggest that substrate intramolecular WC base pairing is a universal requirement for separation and reunion of ssDNA in Reps.

59 BASIC BIOLOGICAL SCIENCES↗

Synergistic Enzyme Mixtures to Realize Near-Complete Depolymerization in Biodegradable Polymer/Additive Blends

Embedding catalysts inside of plastics affords accelerated chemical modification with programmable latency and pathways. Nanoscopically embedded enzymes can lead to near-complete degradation of polyesters via chain-end mediated processive depolymerization. The overall degradation rate and pathways have a strong dependence on the morphology of semicrystalline polyesters. Yet, most studies to date focus on pristine polymers instead of mixtures that contain additives and other components despite their nearly universal use in plastic production. Here, for this study, additives are introduced to purposely change the morphology of polycaprolactone (PCL) by increasing the bending and twisting of crystalline lamellae. These morphological changes immobilize chain ends preferentially at the crystalline/amorphous interfaces and limit chain-end accessibility by the embedded processive enzyme. This chain-end redistribution reduces the polymer-to-monomer conversion from >95% to less than 50%, causing formation of highly crystalline plastic pieces, including microplastics. By synergizing both random chain scission and processive depolymerization, it is feasible to navigate morphological changes in polymer/additive blends and to achieve near-complete depolymerization. The random scission enzymes in the amorphous domains create new chain ends that are subsequently bound and depolymerized by processive enzymes. Present studies further highlight the importance to consider how the host polymer's morphologies affect the reactions catalyzed by embedded catalytic species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nanometre-resolved observation of electrochemical microenvironment formation at the nanoparticle–ligand interface

The dynamic response of surface ligands on nanoparticles (NPs) to external stimuli critically determines the functionality of NP–ligand systems. For example, in electrocatalysis the collective dissociation of ligands on NP surfaces can lead to the creation of an NP/ordered-ligand interlayer, a microenvironment that is highly active and selective for CO 2 -to-CO conversion. However, the lack of in situ characterization techniques with high spatial resolution hampers a comprehensive molecular-level understanding of the mechanism of interlayer formation. Here, in this work, we utilize in situ infrared nanospectroscopy and surface-enhanced Raman spectroscopy, unveiling an electrochemical bias-induced consecutive bond cleavage mechanism of surface ligands leading to formation of the NP/ordered-ligand interlayer. This real-time molecular insight could influence the design of confined localized fields in multiple catalytic systems. Moreover, the demonstrated capability of capturing nanometre-resolved, dynamic molecular-scale events holds promise for the advancement of using controlled local molecular behaviour to achieve desired functionalities across multiple research domains in nanoscience.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Coupling sensor to enzyme in the voltage sensing phosphatase

Voltage-sensing phosphatases (VSPs) dephosphorylate phosphoinositide (PIP) signaling lipids in response to membrane depolarization. VSPs possess an S4-containing voltage sensor domain (VSD), resembling that of voltage-gated cation channels, and a lipid phosphatase domain (PD). The mechanism by which voltage turns on enzyme activity is unclear. Structural analysis and modeling suggest several sites of VSD-PD interaction that could couple voltage sensing to catalysis. Voltage clamp fluorometry reveals voltage-driven rearrangements in three sites implicated earlier in enzyme activation—the VSD-PD linker, gating loop and R loop—as well as the N-terminal domain, which has not yet been explored. N-terminus mutations perturb both rearrangements in the other segments and enzyme activity. Our results provide a model for a dynamic assembly by which S4 controls the catalytic site.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Differences in the dynamics of the tandem-SH2 modules of the Syk and ZAP-70 tyrosine kinases

The catalytic activity of Syk-family tyrosine kinases is regulated by a tandem Src homology 2 module (tSH2 module). In the autoinhibited state, this module adopts a conformation that stabilizes an inactive conformation of the kinase domain. The binding of the tSH2 module to phosphorylated immunoreceptor tyrosine-based activation motifs necessitates a conformational change, thereby relieving kinase inhibition and promoting activation. We determined the crystal structure of the isolated tSH2 module of Syk and find, in contrast to ZAP-70, that its conformation more closely resembles that of the peptide-bound state, rather than the autoinhibited state. Hydrogen–deuterium exchange by mass spectrometry, as well as molecular dynamics simulations, reveal that the dynamics of the tSH2 modules of Syk and ZAP-70 differ, with most of these differences occurring in the C-terminal SH2 domain. Our data suggest that the conformational landscapes of the tSH2 modules in Syk and ZAP-70 have been tuned differently, such that the autoinhibited conformation of the Syk tSH2 module is less stable. This feature of Syk likely contributes to its ability to more readily escape autoinhibition when compared to ZAP-70, consistent with tighter control of downstream signaling pathways in T cells.

59 BASIC BIOLOGICAL SCIENCES↗