The Impact of pH on Catalytically Critical Protein Conformational Changes: The Case of the Urease,a Nickel Enzyme

Urease uses a cluster of two Ni^II ions to activate a water molecule for urea hydrolysis. The key to this unsurpassed enzyme is a change in the conformation of a flexible structural motif, the mobile flap, which must be able to move from an open to a closed conformation to stabilize the chelating interaction of urea with the Ni^II cluster. This conformational change brings the imidazole side chain functionality of a critical histidine residue, αHis323, in close proximity to the site that holds the transition state structure of the reaction, facilitating its evolution to the products. Herein, we describe the influence of the solution pH in modulating the conformation of the mobile flap. High-resolution crystal structures of urease inhibited in the presence of N-(n-butyl)phosphoric triamide (NBPTO) at pH 6.5 and pH 7.5 are described and compared to the analogous structure obtained at pH 7.0. The kinetics of urease in the absence and presence of NBPTO are investigated by a calorimetric assay in the pH 6.0–8.0 range. The results indicate that pH modulates the protonation state of αHis323, which was revealed to have pK_a=6.6, and consequently the conformation of the mobile flap. Two additional residues (αAsp224 and αArg339) are shown to be key factors for the conformational change. The role of pH in modulating the catalysis of urea hydrolysis is clarified through the molecular and structural details of the interplay between protein conformation and solution acidity in the paradigmatic case of a metalloenzyme.     

A Note on Fick’s Law with Phase Transitions

Journal of Statistical Physics - We characterize the non equilibrium stationary states in two classes of systems where phase transitions are present. We prove that the interface in the limit is a...     

Access to Enantiopure Advanced Intermediates en Route to Madangamines

The synthesis of enantiopure ABCE and ABCD tetracyclic advanced intermediates en route to madangamine alkaloids and studies for the construction of the triunsaturated 15-membered D ring of madangamine B and the saturated 13-membered D ring of madangamine E are reported.     

Exploring the Phase-Selective,Green, Hydrothermal Synthesis of Upconverting Doped Sodium Yttrium Fluoride: Effects of Temperature,Time, and Precursors

The aim of this work was i) to develop a hydrothermal, low-temperature synthesis protocol affording the upconverting hexagonal phase NaYF₄ with suitable dopants while adhering to the “green chemistry” standards and ii) to explore the effect that different parameters have on the products. In optimizing the synthesis protocol, short reaction times and low temperatures (below 150 °C) were considered. Yb³⁺ and Er³⁺ ions were chosen as dopants for the NaYF₄ material. Within the context of the second goal, parameters including nature of the precursors, treatment temperature, and treatment time were investigated to afford a pure hexagonal crystalline phase, both in the doped and undoped materials. To fully explore the synthesis results, the prepared materials were characterized from a structural (XRD), compositional (XPS, ICP-MS), and morphological (SEM) point of view. The upconverting properties of the compounds were confirmed by photoluminescence measurements.     

Coarsening Dynamics in a Simplified DNLS Model

We investigate the coarsening evolution occurring in a simplified stochastic model of the Discrete NonLinear Schrödinger (DNLS) equation in the so-called negative-temperature region. We provide an explanation of the coarsening exponent n=1/3, by invoking an analogy with a suitable exclusion process. In spite of the equivalence with the exponent observed in other known universality classes, this model is certainly different, in that it refers to a dynamics with two conservation laws.     

Single‐Walled Carbon Nanotubes in Highly Viscous Media: A Comparison between the Dispersive Agents [BMIM][BF4], L121, and Triton X‐100

Dispersions of single‐walled carbon nanotubes (SWNTs) have been prepared by using the room‐temperature ionic liquid [BMIM][BF₄] (1‐butyl‐3‐methylimidazolium tetrafluoroborate), the triblock copolymer Pluronic L121 [poly(ethylene oxide)₅‐poly(propylene oxide)₆₈‐poly(ethylene oxide)₅] and the non‐ionic surfactant Triton X‐100 (TX100) in the pure state. The size of the SWNTs aggregates and the dispersion degree in the three viscous systems depend on the sonication time, as highlighted by UV/Vis/NIR spectroscopy and optical microscopy analysis. A nonlinear increase in conductivity can be observed as a function of the SWNTs loading, as suggested by electrochemical impedance spectroscopy. The generation of a three‐dimensional network of SWNTs showing a viscoelastic gel‐like behavior above a critical percolation concentration has been found at 25 °C in all the investigated systems by oscillatory rheology measurements.     

Molecular signal suppression by in situ microextraction in nuclear magnetic resonance spectroscopy

The detailed characterization of complex mixtures by NMR is often hampered by the presence of signals from uninformative compounds, the resonances of which overlap with those of the molecules of interest. We provide here a proof of principle for an approach to NMR signal suppression in complex samples using Molecularly Imprinted Polymers (MIPS). Addition of a few milligrams of polymer to a solution traps the target molecule in typical micromolar to millimolar concentration, thus achieving in situ signal suppression, without altering any other spectral features. This method minimized any manipulation or perturbation of the spectrum and was applied to a complex mixture of known compounds and to a plant extract, in both cases spiked with a compound (bisphenol A), which was subsequently removed by selective binding to a complementary MIP. What is described in this report is comparable with microextraction and may in due course be applied to a large number of analytical challenges. Copyright © 2014 John Wiley & Sons, Ltd.     

Degeneracy of the Antithrombin Binding Sequence in Heparin: 2-O-Sulfated Iduronic Acid Can Replace the Critical Glucuronic Acid

Heparin binds to and activates antithrombin (AT) through a specific pentasaccharide sequence, in which a trisaccharide subsite, containing glucuronic acid (GlcA), has been considered as the initiator in the recognition of the polysaccharide by the protein. Recently it was suggested that sulfated iduronic acid (IdoA2S) could replace this “canonical” GlcA. Indeed, a heparin octasaccharidic sequence obtained by chemoenzymatic synthesis, in which GlcA is replaced with IdoA2S, has been found to similarly bind to and activate antithrombin. By using saturation-transfer-difference (STD) NMR, NOEs, transferred NOEs (tr-NOEs) NMR and molecular dynamics, we show that, upon binding to AT, this IdoA2S unit develops comparable interactions with AT as GlcA. Interestingly, two IdoA2S units, both present in a ¹C₄-²S₀ equilibrium in the unbound saccharide, shift to full ²S₀ and full ¹C₄ upon binding to antithrombin, providing the best illustration of the critical role of iduronic acid conformational flexibility in biological systems.     

Fractional powers of the noncommutative Fourier's law by the S‐spectrum approach

Let e_?, for ? = 1,2,3, be orthogonal unit vectors in and let be a bounded open set with smooth boundary ?Ω. Denoting by a point in Ω, the heat equation, for nonhomogeneous materials, is obtained replacing the Fourier law, given by the following: into the conservation of energy law, here a, b, are given functions. With the S‐spectrum approach to fractional diffusion processes we determine, in a suitable way, the fractional powers of T. Then, roughly speaking, we replace the fractional powers of T into the conservation of energy law to obtain the fractional evolution equation. This method is important for nonhomogeneous materials where the Fourier law is not simply the negative gradient. In this paper, we determine under which conditions on the coefficients a, b, the fractional powers of T exist in the sense of the S‐spectrum approach. More in general, this theory allows to compute the fractional powers of vector operators that arise in different fields of science and technology. This paper is devoted to researchers working in fractional diffusion and fractional evolution problems, partial differential equations, and noncommutative operator theory.