Crystallography

Ricin is a potent plant toxin that targets the eukaryotic ribosome by depurinating an adenine from the sarcin-ricin loop (SRL), a highly conserved stem-loop of the rRNA. As a category-B agent for bioterrorism it is a prime target for therapeutic intervention with antibodies and enzyme blocking inhibitors since no effective therapy exists for ricin. Ricin toxin A subunit (RTA) depurinates the SRL by binding to the P-stalk proteins at a remote site. Stimulation of the N-glycosidase activity of RTA by the P-stalk proteins has been studied extensively by biochemical methods and by X-ray crystallography...

The pigmentation of the skin, modulated by different actors in melanogenesis, is mainly due to the melanins (protective pigments). In humans, these pigments' precursors are synthetized by an enzyme known as tyrosinase (TyH). The regulation of the enzyme activity by specific modulators (inhibitors or activators) can offer a means to fight hypo- and hyper-pigmentations responsible for medical, psychological and societal handicaps. Herein, we report the investigation of phenylalanine derivatives as TyH modulators...

All protein-directed syntheses of metal nanoclusters (NCs) and nanoparticles (NPs) have attracted considerable attention because protein scaffolds provide a unique metal coordination environment and can adjust the shape and morphology of NCs and NPs. However, the detailed formation mechanisms of NCs or NPs directed by protein templates remain unclear. In this study, by taking advantage of the ferritin nanocage as a biotemplate to monitor the growth of Fe-O NCs as a function of time, we synthesized a series of iron NCs with different sizes and shapes and subsequently solved their corresponding three-dimensional atomic-scale structures by X-ray protein crystallography and cryo-electron microscopy...

Metal-based complexes with their unique chemical properties, including multiple oxidation states, radio-nuclear capabilities and various coordination geometries yield value as potential pharmaceuticals. Understanding the interactions between metals and biological systems will prove key for site-specific coordination of new metal-based lead compounds. This study merges the concepts of target coordination with fragment-based drug methodologies, supported by varying the anomalous scattering of rhenium along with infrared spectroscopy, and has identified rhenium metal sites bound covalently with two amino acid types within the model protein...

Using knowledge from statistical thermodynamics and crystallography, we develop an image-image translation model, called SorbIIT, that uses three-dimensional grids of adsorbate-adsorbent interaction energies as input to predict the spatially resolved loading surface of nanoporous materials over a broad range of temperatures and pressures. SorbIIT consists of a closed-form differential model for loading-surface prediction and a U-Net to generate spatial differential distributions from the energy grids. SorbIIT is trained using the energy grids and adsorbate distributions (obtained from high-throughput simulations) of 50 synthesized and 70 hypothetical zeolites and applied for predicting the adsorption of carbon dioxide, hydrogen sulfide, n -butane, 2-methylpropane, krypton, and xenon in other zeolites from 256 to 400 K...

ReAV, the inducible Class-3 L-asparaginase from the nitrogen-fixing symbiotic bacterium Rhizobium etli , is an interesting candidate for optimizing its enzymatic potential for antileukemic applications. Since it has no structural similarity to known enzymes with this activity, it may offer completely new ways of approach. Also, as an unrelated protein, it would evade the immunological response elicited by other asparaginases. The crystal structure of ReAV revealed a uniquely assembled protein homodimer with a highly specific C135/K138/C189 zinc binding site in each subunit...

X-ray Free Electron Lasers (XFELs) allow the collection of high-quality serial femtosecond crystallography data. The next generation of megahertz superconducting FELs promises to drastically reduce data collection times, enabling the capture of more structures with higher signal-to-noise ratios and facilitating more complex experiments. Currently, gas dynamic virtual nozzles (GDVNs) stand as the sole delivery method capable of best utilizing the repetition rate of megahertz sources for crystallography. However, their substantial sample consumption renders their use impractical for many protein targets in serial crystallography experiments...

Prokaryotic Argonaute (pAgo) proteins, a class of DNA/RNA-guided programmable endonucleases, have been extensively utilized in nucleic acid-based biosensors. The specific binding and cleavage of nucleic acids by pAgo proteins, which are crucial processes for their applications, are dependent on the presence of Mn2+ bound in the pockets, as verified through X-ray crystallography. However, a comprehensive understanding of how dissociated Mn2+ in the solvent affects the catalytic cycle, and its underlying regulatory role in this structure-function relationship, remains underdetermined...

Two (BE)8 -[16]annulenes were prepared and fully characterized by experimental and quantum-chemical means ( 1 , E = N; 2 , E = O). The 1,8-naphthalenediyl-bridged diborane(6) 3 served as their common starting material, which was treated with [Al(NH3 )6 ]Cl3 to form 1 (91% yield) or with 1,8-naphthalenediboronic acid anhydride to form 2 (93% yield). As a result, the heteroannulenes 1 and 2 are supported by four aromatic "clamps" and may also be viewed as NH- or O-bridged cyclic tetramers of BNB- or BOB-doped phenalenyls...

A series of isomeric bis-2,6-(monoalkoxyphenyl)pyridine and bis-2,6-(dialkoxyphenyl)pyridine ligands were synthesized and characterized. In order to prepare their chlorogold(III) complexes, intermediate chloromercury(II) complexes were first prepared, but unlike observations from previous studies where they were obtained impure and at best in moderate yield, here pure complexes were synthesized, many in rather high yields. Depending on the substitution pattern of the alkoxy chains on the ligands, mono- and/or dimercurated complexes were obtained, characterized by 1 H, 13 C{1 H}, and 199 Hg NMR spectroscopy as well as, in several cases, by X-ray crystallography...

Cofactor mimicry represents an attractive strategy for the development of enzyme inhibitors but can lead to off-target effects due to the evolutionary conservation of binding sites across the proteome. Here, we uncover the ADP-ribose (ADPr) hydrolase NUDT5 as an unexpected, noncovalent, off-target of clinical BTK inhibitors. Using a combination of biochemical, biophysical, and intact cell NanoBRET assays as well as X-ray crystallography, we confirm catalytic inhibition and cellular target engagement of NUDT5 and reveal an unusual binding mode that is independent of the reactive acrylamide warhead...

In the search for mild agents for the oxidative cyclization of tetrapyrromethane to the corresponding corrole, we discovered a route that leads to a monoazaporphyrin with three meso -CF3 groups. Optimization studies that allowed access to appreciable amounts of this new macrocycle paved the way for the preparation of its cobalt, copper, nickel, zinc, and iron complexes. All complexes were fully characterized by various spectroscopic methods and X-ray crystallography. Their photophysical and electrochemical properties were determined and compared to those of analogous porphyrins in order to deduce the effect of the peripheral N atom...

Recently, we have developed novel Pim-1 kinase inhibitors starting from a dihydrobenzofuran core structure using a computational approach. Here, we report the design and synthesis of stilbene-based Pim-1 kinase inhibitors obtained by formal elimination of the dihydrofuran ring. These inhibitors of the first design cycle, which were obtained as inseparable cis/trans mixtures, showed affinities in the low single-digit micromolar range. To be able to further optimize these compounds in a structure-based fashion, we determined the X-ray structures of the protein-ligand-complexes...

Human ornithine aminotransferase ( h OAT), a pyridoxal 5'-phosphate (PLP)-dependent enzyme, has been shown to play an essential role in the metabolic reprogramming and progression of hepatocellular carcinoma (HCC). HCC accounts for approximately 75% of primary liver cancers and is within the top three causes of cancer death worldwide. As a result of treatment limitations, the overall 5-year survival rate for all patients with HCC is under 20%. The prevalence of HCC necessitates continued development of novel and effective treatment methods...

BACKGROUND: Organotin(IV) complexes of dithiocarbamate are vital in medicinal chemistry, exhibiting potential in targeting cancer cells due to their unique properties that enhance targeted delivery. This study aimed to synthesize and characterize organotin(IV) N-ethyl-N-benzyldithiocarbamate complexes (ONBDCs) and evaluate their cytotoxicity against A549 cells, which are commonly used as a model for human lung cancer research. METHOD: The two ONBDC derivatives - ONBDC 1 (dimethyltin(IV) N-ethyl-N-benzyldithiocarbamate) and ONBDC 2 (triphenyltin(IV) N-ethyl-N-benzyldithiocarbamate) - were synthesized via the reaction of tin(IV) chloride with N-ethylbenzylamine in the presence of carbon disulfide...

Categorization underlies understanding. Conceptualizing solid-state structures of organic molecules with `archetype crystal structures' bridges established categories of disorder, polymorphism and solid solutions and is herein extended to special position and high-Z' structures. The concept was developed in the context of disorder modelling [Dittrich, B. (2021). IUCrJ, 8, 305-318] and relies on adding quantum chemical energy differences between disorder components to other criteria as an explanation as to why disorder - and disappearing disorder - occurs in an average structure...

Trafficking receptors control protein localization through the recognition of specific signal sequences that specify unique cellular locations. Differences in luminal pH are important for the vectorial trafficking of cargo receptors. The KDEL receptor is responsible for maintaining the integrity of the ER by retrieving luminally localized folding chaperones in a pH-dependent mechanism. Structural studies have revealed the end states of KDEL receptor activation and the mechanism of selective cargo binding. However, precisely how the KDEL receptor responds to changes in luminal pH remains unclear...

Tethered nonplanar aromatics (TNAs) make up an important class of nonplanar aromatic compounds showing unique features. However, the knowledge on the synthesis, structures, and properties of TNAs remains insufficient. In this work, a new type of TNAs, the tethered aromatic lactams, is synthesized via Pd-catalyzed consecutive intramolecular direct arylations. These molecules possess a helical ladder-type conjugated system of up to 13 fused rings. The overall yields ranged from 3.4 to 4.3%. The largest of the tethered aromatic lactams, 6L-Bu-C 14 , demonstrates a guest-adaptive hosting capability of TNAs for the first time...

ConspectusThe growing list of physiologically important protein-protein interactions (PPIs) has amplified the need for compounds to target topologically complex biomolecular surfaces. In contrast to small molecules, peptide and protein mimics can exhibit three-dimensional shape complementarity across a large area and thus have the potential to significantly expand the "druggable" proteome. Strategies to stabilize canonical protein secondary structures without sacrificing side-chain content are particularly useful in the design of peptide-based chemical probes and therapeutics...

The coordination of hydrotris[3-(2'-furyl)pyrazol-1-yl]borate (Tp2-Fu , C21 H16 BN6 O3 ) to lanthanide(III) ions is achieved for the first time with the complex [Ln(Tp2-Fu )2 ](BPh4 )·xCH2 Cl2 (1-Ln has Ln = Ce and x = 2; 1-Dy has Ln = Dy and x = 1). This was accomplished via both hydrous (Ln = Ce) and anhydrous methods (Ln = Dy). When isolating the dysprosium analogue, the filtrate produced a second crop of crystals which were revealed to be the 1,2-borotropic-shifted product [Dy(κ4 -Tp2-Fu )(κ5 -Tp2-Fu *)](BPh4 ) (2) {Tp2-Fu * = hydrobis[3-(2'-furyl)pyrazol-1-yl][5-(2'-furyl)pyrazol-1-yl]borate}...