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 unified theory for brittle and ductile shear mode fracture

A unified theory captures both brittle and ductile fracture. The fracture toughness is proportional to the applied stress squared and the length of the crack. For purely brittle solids, this criterion is equivalent to Griffith's theory. In other cases, it provides a theoretical basis for the Irwin-Orowan formula. For purely ductile solids, the theory makes direct contact with the Bilby-Cottrell-Swinden model. The toughness is highest in ductile materials because the shielding dislocations in the plastic zone provide additional resistance to crack growth. This resistance is the force opposing dislocation motion, and the Peach-Koehler force overcomes it. A dislocation-free zone separates the plastic zone from and the tip of the crack. The dislocation-free zone is finite because molecular forces responsible for the cohesion of the surfaces near the crack tip are not negligible. At the point of crack growth, the length of the dislocation-free zone is constant and the shielding dislocations advance in concert. As in Griffith's theory, the crack is in unstable equilibrium. The theory shows that a dimensionless variable controls the elastoplastic behaviour. A relationship for the size of the dislocation-free zone is derived in terms of the macroscopic and microscopic parameters that govern the fracture.     

X-ray and UV photoelectron spectroscopy of Ag nanoclusters

The main purpose of the present work is to analyze a series of Ag nanoparticles (NPs) with different size or ligand functionalization by using X-ray photoelectron spectroscopy (XPS) and to identify the differences in the band-shape and energy peak position of photoemission spectra due to the particle dimension. A transmission electron microscopy characterization was performed, to verify the consistency of the results. Three types of samples were prepared starting from AgNO₃ water solution and adding different capping agents. In the first two cases, the formation of NPs was promoted by the reduction of silver ions Ag⁺¹ to metallic Ag⁰ through the addition of sodium borohydride, whereas in the last case, it was triggered by the exposure to UV light. Depending on the size of the NPs, a different physical behavior can be recognized. NPs with diameter of about 5 nm are characterized by the phenomenon of localized surface plasmon resonance (LSPR). The other type of samples having a diameter of about 1.5 nm presents discrete energy levels instead of electronic bands, and in this case, a typical fluorescence phenomenon can be observed. In the latter case, we can refer to such systems as nanoclusters. The XPS analyses were focused on the Ag 3D spectra looking for the possible shifts of the Ag doublet as a function of the particles size. The ultraviolet photoelectron spectroscopy with He II source was used for the investigation of possible changes in the valence band.     

Solid-State Dynamics and High-Pressure Studies of a Supramolecular Spiral Gear

The structures and solid-state dynamics of the supramolecular salts of the general formula [(12-crown-4)₂ ⋅ DABCOH₂](X)₂ (where DABCO=1,4-diazabicyclo[2.2.2]octane, X=BF₄, ClO₄) have been investigated as a function of temperature (from 100 to 360 K) and pressure (up to 3.4 GPa), through the combination of variable-temperature and variable-pressure XRD techniques and variable-temperature solid-state NMR spectroscopy. The two salts are isomorphous and crystallize in the enantiomeric space groups P3₂2₁ and P3₁2₁. All building blocks composing the supramolecular complex display dynamic processes at ambient temperature and pressure. It has been demonstrated that the motion of the crown ethers is maintained on lowering the temperature (down to 100 K) or on increasing the pressure (up to 1.5 GPa) thanks to the correlation between neighboring molecules, which mesh and rotate in a concerted manner similar to spiral gears. Above 1.55 GPa, a collapse-type transition to a lower-symmetry ordered structure, not attainable at a temperature of 100 K, takes place, proving, thus, that the pressure acts as the means to couple and decouple the gears. The relationship between temperature and pressure effects on molecular motion in the solid state has also been discussed.     

A Journey from Thermally Tunable Synthesis to Spectroscopy of Phenylmethanimine in Gas Phase and Solution

Phenylmethanimine is an aromatic imine with a twofold relevance in chemistry: organic synthesis and astrochemistry. To tackle both aspects, a multidisciplinary strategy has been exploited and a new, easily accessible synthetic approach to generate stable imine-intermediates in the gas phase and in solution has been introduced. The combination of this formation pathway, based on the thermal decomposition of hydrobenzamide, with a state-of-the-art computational characterization of phenylmethanimine laid the foundation for its first laboratory observation by means of rotational electric resonance spectroscopy. Both E and Z isomers have been accurately characterized, thus providing a reliable basis to guide future astronomical observations. A further characterization has been carried out by nuclear magnetic resonance spectroscopy, showing the feasibility of this synthetic approach in solution. The temperature dependence as well as possible mechanisms of the thermolysis process have been examined.     

Word problems and ceers

This note addresses the issue as to which ceers can be realized by word problems of computably enumerable (or, simply, c.e.) structures (such as c.e. semigroups, groups, and rings), where being realized means to fall in the same reducibility degree (under the notion of reducibility for equivalence relations usually called “computable reducibility”), or in the same isomorphism type (with the isomorphism induced by a computable function), or in the same strong isomorphism type (with the isomorphism induced by a computable permutation of the natural numbers). We observe, e.g., that every ceer is isomorphic to the word problem of some c.e. semigroup, but (answering a question of Gao and Gerdes) not every ceer is in the same reducibility degree of the word problem of some finitely presented semigroup, nor is it in the same reducibility degree of some non-periodic semigroup. We also show that the ceer provided by provable equivalence of Peano Arithmetic is in the same strong isomorphism type as the word problem of some non-commutative and non-Boolean c.e. ring.     

Electronic Transitions in Different Redox States of Trinuclear 5,6,11,12,17,18-Hexaazatrinaphthylene-Bridged Titanium Complexes: Spectroelectrochemistry and Quantum Chemistry

Multinuclear transition metal complexes bridged by ligands with extended π-electronic systems show a variety of complex electronic transitions and electron transfer reactions. While a systematic understanding of the photochemistry and electrochemistry has been attained for binuclear complexes, much less is known about trinuclear complexes such as hexaphenyl-5,6,11,12,17,18-hexaazatrinaphthylene-tristitanocene [(Cp₂Ti)₃HATN(Ph)₆]. The voltammogram of [(Cp₂Ti)₃HATN(Ph)₆] shows six oxidation and three reduction waves. Solution spectra of [(Cp₂Ti)₃HATN(Ph)₆] and of the electrochemically formed oxidation products show electronic transitions in the UV, visible and the NIR ranges. Density functional theory (DFT) and linear response time-dependent DFT show that the three formally titanium(II) centers transfer an electron to the HATN ligand in the ground state. The optically excited transitions occur exclusively between ligand-centered orbitals. The charged titanium centers only provide an electrostatic frame to the extended π-electronic system. Complete active self-consistent field (CASSCF) calculation on a structurally simplified model compound, which considers the multi-reference character imposed by the three titanium centers, can provide an interpretation of the experimentally observed temperature-dependent magnetic behavior of the different redox states of the title compound in full consistency with the interpretation of the electronic spectra.     

Sub‐ and Supramolecular X‐Ray Characterization of Engineered Tissues from Equine Tendon,Bovine Dermis,and Fish Skin Type‐I Collagen

Collagen represents one of the most widely used biomaterial for scaffolds fabrication in tissue engineering as it represents the mechanical support of natural tissues. It also provides physical scaffolding for cells and it influences their attachment, growth, and tissue regeneration. Among all fibrillary collagens, type I is considered one of the gold standard for scaffolds fabrication, thanks to its high biocompatibility, biodegradability, and hemostatic properties. It can be extracted by chemical and enzymatic protocols from several collagen‐rich tissues, such as tendon and skin, of different animal species. Both the extraction processes and the manufacturing protocols for scaffolds fabrication provide structural and mechanical changes that can be tuned in order to deeply impact the properties of the final biomaterial. The aim of this review is to discuss the role of X‐rays to study structural changes of type I collagen from fresh collagen‐rich tissues (bovine, equine, fish) to the final scaffolds, with the aim to screen across available collagen sources and scaffolds fabrication protocols to be used in tissue regeneration.     

estimates for overdetermined Radon transforms

We prove several variations on the results of F. Ricci and G. Travaglini (2001), concerning bounds for convolution with all rotations of arc length measure on a fixed convex curve in . Estimates are obtained for averages over higher-dimensional convex (nonsmooth) hypersurfaces, smooth -dimensional surfaces, and nontranslation-invariant families of surfaces. We compare Ricci and Travaglini's approach, based on average decay of the Fourier transform, with an approach based on boundedness of Fourier integral operators, and show that essentially the same geometric condition arises in proofs using the two techniques.