Human CaaX protease ZMPSTE24 expressed in yeast: Structure and inhibition by HIV protease inhibitors

The function and localization of proteins and peptides containing C‐terminal “CaaX” (Cys‐aliphatic‐aliphatic‐anything) sequence motifs are modulated by post‐translational attachment of isoprenyl groups to the cysteine sulfhydryl, followed by proteolytic cleavage of the aaX amino acids. The zinc metalloprotease ZMPSTE24 is one of two enzymes known to catalyze this cleavage. The only identified target of mammalian ZMPSTE24 is prelamin A, the precursor to the nuclear scaffold protein lamin A. ZMPSTE24 also cleaves prelamin A at a second site 15 residues upstream from the CaaX site. Mutations in ZMPSTE24 result in premature‐aging diseases and inhibition of ZMPSTE24 activity has been reported to be an off‐target effect of HIV protease inhibitors. We report here the expression (in yeast), purification, and crystallization of human ZMPSTE24 allowing determination of the structure to 2.0 Å resolution. Compared to previous lower resolution structures, the enhanced resolution provides: (1) a detailed view of the active site of ZMPSTE24, including water coordinating the catalytic zinc; (2) enhanced visualization of fenestrations providing access from the exterior to the interior cavity of the protein; (3) a view of the C‐terminus extending away from the main body of the protein; (4) localization of ordered lipid and detergent molecules at internal and external surfaces and also projecting through fenestrations; (5) identification of water molecules associated with the surface of the internal cavity. We also used a fluorogenic assay of the activity of purified ZMPSTE24 to demonstrate that HIV protease inhibitors directly inhibit the human enzyme in a manner indicative of a competitive mechanism.     

Deciphering metal ion preference and primary coordination sphere robustness of a designed zinc finger with high‐resolution mass spectrometry

Small zinc finger (ZnF) motifs are promising molecular scaffolds for protein design owing to their structural robustness and versatility. Moreover, their characterization provides important insights into protein folding in general. ZnF motifs usually possess an exceptional specificity and high affinity towards Zn(II) ion to drive folding. While the Zn(II) ion is canonically coordinated by two cysteine and two histidine residues, many other coordination spheres also exist in small ZnFs, all having four amino acid ligands. Here we used high‐resolution mass spectrometry to study metal ion binding specificity and primary coordination sphere robustness of a designed zinc finger, named MM1. Based on the results, MM1 possesses high specificity for zinc with sub‐micromolar binding affinity. Surprisingly, MM1 retains metal ion binding affinity even in the presence of selective alanine mutations of the primary zinc coordinating amino acid residues.     

The unique N‐terminal zinc finger of synaptotagmin‐like protein 4 reveals FYVE structure

Synaptotagmin‐like protein 4 (Slp4), expressed in human platelets, is associated with dense granule release. Slp4 is comprised of the N‐terminal zinc finger, Slp homology domain, and C2 domains. We synthesized a compact construct (the Slp4N peptide) corresponding to the Slp4 N‐terminal zinc finger. Herein, we have determined the solution structure of the Slp4N peptide by nuclear magnetic resonance (NMR). Furthermore, experimental, chemical modification of Cys residues revealed that the Slp4N peptide binds two zinc atoms to mediate proper folding. NMR data showed that eight Cys residues coordinate zinc atoms in a cross‐brace fashion. The Simple Modular Architecture Research Tool database predicted the structure of Slp4N as a RING finger. However, the actual structure of the Slp4N peptide adopts a unique C₄C₄‐type FYVE fold and is distinct from a RING fold. To create an artificial RING finger (ARF) with specific ubiquitin‐conjugating enzyme (E2)‐binding capability, cross‐brace structures with eight zinc‐ligating residues are needed as the scaffold. The cross‐brace structure of the Slp4N peptide could be utilized as the scaffold for the design of ARFs.     

Crystal structure of the UBR‐box from UBR6/FBXO11 reveals domain swapping mediated by zinc binding

The UBR‐box is a 70‐residue zinc finger domain present in the UBR family of E3 ubiquitin ligases that directly binds N‐terminal degradation signals in substrate proteins. UBR6, also called FBXO11, is an UBR‐box containing E3 ubiquitin ligase that does not bind N‐terminal signals. Here, we present the crystal structure of the UBR‐box domain from human UBR6. The dimeric crystal structure reveals a unique form of domain swapping mediated by zinc coordination, where three independent protein chains come together to regenerate the topology of the monomeric UBR‐box fold. Analysis of the structure suggests that the absence of N‐terminal residue binding arises from the lack of an amino acid binding pocket.     

Induction of reactive oxygen species by diphenyl diselenide is preceded by changes in cell morphology and permeability in Saccharomyces cerevisiae

Organoselenium compounds, such as diphenyl diselenide (PhSe)₂ and phenylselenium zinc chloride (PhSeZnCl), show protective activities related to their thiol peroxidase activity. However, depending on experimental conditions, organoselenium compounds can cause toxicity by oxidising thiol groups of proteins and induce the production of reactive oxygen species (ROS). Here, we analysed the toxicity of (PhSe)₂ and PhSeZnCl in yeast Saccharomyces cerevisiae. Cell growth of S. cerevisiae after 1, 2, 3, 4, 6, and 16?h of treatment with 2, 4, 6, and 10?μM of (PhSe)₂ was evaluated. For comparative purpose, PhSeZnCl was analysed only at 16?h of incubation at equivalent concentrations of selenium (i.e. 4, 8, 12, and 20?μM). ROS production (DCFH-DA), size, granularity, and cell membrane permeability (propidium iodide) were determined by flow cytometry. (PhSe)₂ inhibited cell growth at 2?h (10?μM) of incubation, followed by increase in cell size. The increase of cell membrane permeability and granularity (10?μM) was observed after 3?h of incubation, however, ROS production occurs only at 16?h of incubation (10?μM) with (PhSe)₂, indicating that ROS overproduction is a more likely consequence of (PhSe)₂ toxicity and not its determinant. All tested parameters showed that only concentration of 20?μM induced toxicity in samples incubated with PhSeZnCl. In summary, the results suggest that (PhSe)₂ toxicity in S. cerevisiae is time and concentration dependent, presenting more toxicity when compared with PhSeZnCl.     

Zinc supplementation imparts tolerance to arsenite stress in Hydrilla verticillata (L.f.) Royle

The present study was aimed to analyze the effects of external Zn supply on arsenic (As) toxicity in Hydrilla verticillata (L.f.) Royle. The plants were exposed to arsenite (AsIII; 10 μM) with or without 50 and 100 μM Zn. The level of As accumulation (μg g^?1 dw) after 2 and 4 days was not significantly affected by Zn supply. The plants showed a significant stimulation of the thiol metabolism (nonprotein thiols, cysteine, glutathione-S-transferase activity) upon As(III) exposure in the presence of Zn as compared to As(III) alone treatment. Besides, they did not experience significant toxicity, measured in terms of hydrogen peroxide and malondialdehyde accumulation, which are the indicators of oxidative stress. The minus Zn plants suffered from oxidative stress probably due to insufficient increase in thiols to counteract the stress. Stress amelioration by Zn supply was also evident from antioxidant enzyme activities, which came close to control levels with increasing Zn supply as compared to the increase observed in As(III) alone treatment. Variable Zn supply also modulated the level of photosynthetic pigments and restored them to control levels. In conclusion, an improved supply of Zn to plants was found to augment their ability to withstand As toxicity through enhanced thiol metabolism.     

Concentration‐dependent studies of Nd3+‐doped zinc phosphate glasses for NIR photoluminescence at 1.05 μm

Nd³⁺‐doped lead‐free zinc phosphate glasses with the chemical compositions (60‐x) NH₄H₂PO₄ + 20ZnO + 10BaF₂ + 10NaF + xNd₂O₃ (where x = 0.5, 1.0, 1.5, 2.0 and 2.5 mol%) were prepared using a melt quenching technique. Vibrational bands were assigned and clearly elucidated by Raman spectral profiles for all the glass samples. Judd–Ofelt (J–O) intensity parameters (Ω_λ: λ = 2, 4, 6) were obtained from the spectral intensities of different absorption bands of Nd³⁺ ions. Radiative properties such as radiative transition probabilities (A_R), radiative lifetimes (τ_R) and branching ratios (β_R) for different excited states were calculated using J–O parameters. The near infrared (NIR) photoluminescence spectra exhibited three emission bands (⁴F_3/2 level to ⁴I_13/2, ⁴I_11/2 and ⁴I_9/2 states) for all the concentrations of Nd³⁺ ions. Various luminescence properties were studied by varying the Nd³⁺ concentration for the three spectral profiles. Fluorescence decay curves of the ⁴F_3/2 level were recorded. The energy transfer mechanism that leads to quenching of the ⁴F_3/2 state lifetimes was discussed at higher concentration of Nd³⁺ ions. These glasses are suggested as suitable hosts to produce efficient lasing action in NIR region at 1.05 μm.     

A porphyrin‐based fluorescence method for zinc determination in commercial propolis extracts without sample pretreatment

The quantification of zinc in over‐the–counter drugs as commercial propolis extracts by molecular fluorescence technique using meso ‐tetrakis(4‐carboxyphenyl)porphyrin (H₂TCPP⁴) was developed for the first time. The calibration curve is linear from 6.60 to 100 nmol L^?1 of Zn²⁺. The detection and quantification limits were 6.22 nmol L^?1 and 19.0 nmol L^?1, respectively. The reproducibility and repeatability calculated as the percentage variation of slopes of seven calibration curves were 6.75% and 4.61%, respectively. Commercial propolis extract samples from four Brazilian states were analyzed and the results (0.329–0.797 mg/100 mL) obtained with this method are in good agreement with that obtained with the Atomic Absorption Spectroscopy (AAS) technique. The method is simple, fast, of low cost and allows the analysis of the samples without pretreatment. Moreover the major advantage is that Zn‐porphyrin complex presents fluorescent characteristic promoting the selectivity and sensitivity of the method.