The catalytic Mn2+ sites in the enolase-inhibitor complex: crystallography, single-crystal EPR, and DFT calculations

Crystals of Zn2+/Mn2+ yeast enolase with the inhibitor PhAH (phosphonoacetohydroxamate) were grown under conditions with a slight preference for binding of Zn2+ at the higher affinity site, site I. The structure of the Zn2+/Mn2+-PhAH complex was solved at a resolution of 1.54 A, and the two catalytic metal binding sites, I and II, show only subtle displacement compared to that of the corresponding complex with the native Mg2+ ions. Low-temperature echo-detected high-field (W-band, 95 GHz) EPR (electron paramagnetic resonance) and 1H ENDOR (electron-nuclear double resonance) were carried out on a single crystal, and rotation patterns were acquired in two perpendicular planes. Analysis of the rotation patterns resolved a total of six Mn2+ sites, four symmetry-related sites of one type and two out of the four of the other type. The observation of two chemically inequivalent Mn2+ sites shows that Mn2+ ions populate both sites I and II and the zero-field splitting (ZFS) tensors of the Mn2+ in the two sites were determined. The Mn2+ site with the larger D value was assigned to site I based on the 1H ENDOR spectra, which identified the relevant water ligands. This assignment is consistent with the seemingly larger deviation of site I from octahedral symmetry, compared to that of site II. The ENDOR results gave the coordinates of the protons of two water ligands, and adding them to the crystal structure revealed their involvement in a network of H bonds stabilizing the binding of the metal ions and PhAH. Although specific hyperfine interactions with the inhibitor were not determined, the spectroscopic properties of the Mn2+ in the two sites were consistent with the crystal structure. Density functional theory (DFT) calculations carried out on a cluster representing the catalytic site, with Mn2+ in site I and Zn2+ in site II, and vice versa, gave overestimated D values on the order of the experimental ones, although the larger D value was found for Mn2+ in site II rather than in site I. This discrepancy was attributed to the high sensitivity of the ZFS parameters to the Mn-O bond lengths and orientations, such that small, but significant, differences between the optimized and crystal structures alter the ZFS considerably, well above the difference between the two sites.     

GdIII-19F Distance Measurements for Proteins in Cells by Electron-Nuclear Double Resonance

Studies of protein structure and dynamics are usually carried out in dilute buffer solutions, conditions that differ significantly from the crowded environment in the cell. The double electron-electron resonance (DEER) technique can track proteins’ conformations in the cell by providing distance distributions between two attached spin labels. This technique, however, cannot access distances below 1.8 nm. Here, we show that Gd^III-¹⁹F Mims electron-nuclear double resonance (ENDOR) measurements can cover part of this short range. Low temperature solution and in-cell ENDOR measurements, complemented with room temperature solution and in-cell Gd^III-¹⁹F PRE (paramagnetic relaxation enhancement) NMR measurements, were performed on fluorinated GB1 and ubiquitin (Ub), spin-labeled with rigid Gd^III tags. The proteins were delivered into human cells via electroporation. The solution and in-cell derived Gd^III-¹⁹F distances were essentially identical and lie in the 1–1.5 nm range revealing that both, GB1 and Ub, retained their overall structure in the Gd^III and ¹⁹F regions in the cell.     

Optically Controlled Construction of Three-Dimensional Protein Arrays

Protein crystallization is an important tool for structural biology and nanostructure preparation. Here, we report on kinetic pathway-dependent protein crystals that are controlled by light. Photo-responsive crystallites are obtained by complexing the model proteins with cationic azobenzene dyes. The crystalline state is readily switched to a dispersed phase under ultraviolet light and restored by subsequent visible-light illumination. The switching can be reversibly repeated for multiple cycles without noticeable structure deterioration. Importantly, the photo-treatment not only significantly increases the crystallinity, but creates crystallites at conditions where no ordered lattices are observed upon directly mixing the components. Further control over the azobenzene isomerization kinetics produces protein single crystals of up to ≈50 μm. This approach offers an intriguing method to fabricate metamaterials and study optically controlled crystallization.     

Peruvian Food Chain Jenga: Learning Ecosystems with an Interactive Model

A pilot study was conducted on a multimodal educational tool, Peruvian Food Chain Jenga (PFCJ), with 5th‐grade students (N = 54) at a public charter school. The goal was to compare the effectiveness of the multimodal tool to a more traditional presentation of the same materials (food chain) using an experimental/control design. Data collection included a pretest/posttest and a “What I Did/What I Learned” response sheet. Quantitative analysis of pretest/posttest results showed both groups improved from pretest to posttest; however, there was no statistically significant difference between posttest results of experimental and control groups. Qualitative analysis of student open‐ended responses indicated a difference between students who used the PFCJ and students in the control. The most striking difference occurred in how the students perceived the connectedness of species and the awareness of human impact. Our findings suggest that using a model such as PFCJ as a means of teaching and connecting scientific content with practices related to ecosystems is an effective method of engaging students in intelligent discussions about these topics.     

In Vitro Effects of Papaverine on Cell Proliferation,Reactive Oxygen Species,and Cell Cycle Progression in Cancer Cells

Papaverine (PPV) is an alkaloid isolated from the Papaver somniferum. Research has shown that PPV inhibits proliferation. However, several questions remain regarding the effects of PPV in tumorigenic cells. In this study, the influence of PPV was investigated on the proliferation (spectrophotometry), morphology (light microscopy), oxidative stress (fluorescent microscopy), and cell cycle progression (flow cytometry) in MDA-MB-231, A549, and DU145 cell lines. Exposure to 150 μM PPV resulted in time- and dose-dependent antiproliferative activity with reduced cell growth to 56%, 53%, and 64% in the MDA-MB-231, A549, and DU145 cell lines, respectively. Light microscopy revealed that PPV exposure increased cellular protrusions in MDA-MB-231 and A549 cells to 34% and 23%. Hydrogen peroxide production increased to 1.04-, 1.02-, and 1.44-fold in PPV-treated MDA-MB-231, A549, and DU145 cells, respectively, compared to cells propagated in growth medium. Furthermore, exposure to PPV resulted in an increase of cells in the sub-G₁ phase by 46% and endoreduplication by 10% compared to cells propagated in growth medium that presented with 2.8% cells in the sub-G₁ phase and less than 1% in endoreduplication. The results of this study contribute to understanding of effects of PPV on cancer cell lines.     

Axial solvent coordination in "base-fff" cob(II)alamin and related co(II)-corrinates revealed by 2D-EPR

Detailed information on the structure of cobalt(II) corrinates is of interest in the context of studies on the coenzyme B(12) catalyzed enzymatic reactions, where cob(II)alamin has been identified as a reaction intermediate. Cob(II)ester (heptamethyl cobyrinate perchlorate) is found to be soluble in both polar and nonpolar solvents and is therefore very suitable to study solvent effects on Co(II) corrinates. In the literature, Co(II) corrinates in solution are often addressed as four-coordinated Co(II) corrins. However, using a combination of continuous-wave (CW) and pulse electron paramagnetic resonance (EPR) and pulse ENDOR (electron nuclear double resonance) at different microwave frequencies we clearly prove axial ligation for Cob(II)ester and the base-off form of cob(II)alamin (B(12r)) in different solvents. This goal is achieved by the analysis of the g values, and the hyperfine couplings of cobalt, some corrin nitrogens and hydrogens, and solvent protons. These parameters are shown to be very sensitive to changes in the solvent ligation. Density functional computations (DFT) facilitate largely the interpretation of the EPR data. In the CW-EPR spectrum of Cob(II)ester in methanol, a second component appears below 100 K. Different cooling experiments suggest that this observation is related to the phase transition of methanol from the alpha-phase to the glassy state. A detailed analysis of the EPR parameters indicates that this transition induces a change from a five-coordinated (above 100 K) to a six-coordinated (below 100 K) Co(II) corrin. In a CH(3)OH:H(2)O mixture the phase-transition properties alter and only the five-coordinated form is detected for Cob(II)ester and for base-off B(12r) at all temperatures. Our study thus shows that the characteristics of the solvent can have a large influence on the structure of Co(II) corrinates and that comparison with the protein-embedded cofactor requires some caution. Finally, the spectral similarities between Cob(II)ester and base-off B(12r) prove the analogies in their electronic structure.     

Double electron electron resonance as a method for characterization of micelles

Double electron electron resonance (DEER) is an experimental technique used to determine distance between electron spins. In this work, we show that it can be used to study the properties of micelles in solution, specifically their volume and the aggregation number. The feasibility of the method is tested on micelles of Pluronic block copolymers, PEO(x)-PPO(y)-PEO(x), built from chains of poly(ethylene oxide) (PEO), comprising the more hydrophilic corona, and a poly(propylene oxide) (PPO) block constituting the hydrophobic core. In this work, the dimensions of the hydrophobic core of micelles of Pluronic L64 (x = 13, y = 30), P123 (x = 20, y = 70), and F127 (x = 106, y = 70) and their aggregation number were studied. This was done using the spin-probe 4-hydroxy-tempo-benzoate (4HTB), which is hydrophobic and is localized in the hydrophobic core of the micelles and does not dissolve in aqueous solution. The measurements were carried out on frozen solutions, freeze quenched after equilibration at 50 degrees C. It was found that the hydrophobic core radii occupied by 4HTB in 7.5 wt % F127 and 6 wt % L64 are 4.0 +/- 0.05 and 3.8 +/- 0.1 nm, respectively, and the corresponding aggregation numbers are 57 +/- 2 and 206 +/- 14. The micelles of 6 wt % P123 were found to have a rod shape, and the addition of 4HTB at concentrations higher than 0.7 mM resulted in a phase transitioned to spherical micelles. Finally, this study also showed that the micelle structure is preserved upon rapid freezing.     

Expedient synthesis of β,β-disubstituted α-methylenepropionates

Baylis-Hillman alcohols are excellent sources of the allylic halides ArCHCH(CH₂X)(CO₂R) (X=Br, Cl; R¹=Me, Et, Bu^t). The Z double bond isomers are attained in high isomeric purity (>14:1, Z/E). The halides are chemo- and regiospecifically transformed into the acrylates (ArCHR²)C(CH₂)(CO₂R¹) on treatment with Zn(R²)₂ (R²=Me, Et, CH₂TMS, CH₂SiMe₂OMe) or PrZnBr in the presence of catalytic amounts of copper(I) salts (0.5-20 mol%) in high yield.     

Electron-mediating Cu(A) centers in proteins: a comparative high field (1)H ENDOR study

High field (W-band, 95 GHz) pulsed electron-nuclear double resonance (ENDOR) measurements were carried out on a number of proteins that contain the mixed-valence, binuclear electron-mediating Cu(A) center. These include nitrous oxide reductase (N(2)OR), the recombinant water-soluble fragment of subunit II of Thermus thermophilus cytochrome c oxidase (COX) ba(3) (M160T9), its M160QT0 mutant, where the weak axial methionine ligand has been replaced by a glutamine, and the engineered "purple" azurin (purpAz). The three-dimensional (3-D) structures of these proteins, apart from the mutant, are known. The EPR spectra of all samples showed the presence of a mononuclear Cu(II) impurity with EPR characteristics of a type II copper. At W-band, the g( perpendicular) features of this center and of Cu(A) are well resolved, thus allowing us to obtain a clean Cu(A) ENDOR spectrum. The latter consists of two types of ENDOR signals. The first includes the signals of the four strongly coupled cysteine beta-protons, with isotropic hyperfine couplings, A(iso), in the 7-15 MHz range. The second group consists of weakly coupled protons with a primarily anisotropic character with A(zz) < 3 MHz. Orientation selective ENDOR spectra were collected for N(2)OR, M160QT0, and purpAz, and simulations of the cysteine beta-protons signals provided their isotropic and anisotropic hyperfine interactions. A linear correlation with a negative slope was found between the maximum A(iso) value of the beta-protons and the copper hyperfine interaction. Comparison of the best-fit anisotropic hyperfine parameters with those calculated from dipolar interactions extracted from the available 3-D structures sets limit to the sulfur spin densities. Similarly, the small coupling spectral region was simulated on the basis of the 3-D structures and compared with the experimental spectra. It was found that the width of the powder patterns of the weakly coupled protons recorded at g(perpendicular) is mainly determined by the histidine H(epsilon)(1) protons. Furthermore, the splitting in the outer wings of these powder patterns indicates differences in the positions of the imidazole rings relative to the Cu(2)S(2) core. Comparison of the spectral features of the weakly coupled protons of M160QT0 with those of the other investigated proteins shows that they are very similar to those of purpAz, where the Cu(A) center is the most symmetric, but the copper spin density and the H(epsilon)(1)-Cu distances are somewhat smaller. All proteins show the presence of a proton with a significantly negative A(iso) value which is assigned to an amide proton of one of the cysteines. The simulations of both strongly and weakly coupled protons, along with the known copper hyperfine couplings, were used to estimate and compare the spin density distribution in the various Cu(A) centers. The largest sulfur spin density was found in M160T9, and the lowest was found in purpAz. In addition, using the relation between the A(iso) values of the four cysteine beta-protons and the H-C-S-S dihedral angles, the relative contribution of the hyperconjugation mechanism to A(iso) was determined. The largest contribution was found for M160T9, and the lowest was found for purpAz. Possible correlations between the spin density distribution, structural features, and electron-transfer functionality are finally suggested.