The Effects of the Metal Ion Substitution into the Active Site of Metalloenzymes: A Theoretical Insight on Some Selected Cases

A large number of enzymes need a metal ion to express their catalytic activity. Among the different roles that metal ions can play in the catalytic event, the most common are their ability to orient the substrate correctly for the reaction, to exchange electrons in redox reactions, to stabilize negative charges. In many reactions catalyzed by metal ions, they behave like the proton, essentially as Lewis acids but are often more effective than the proton because they can be present at high concentrations at neutral pH. In an attempt to adapt to drastic environmental conditions, enzymes can take advantage of the presence of many metal species in addition to those defined as native and still be active. In fact, today we know enzymes that contain essential bulk, trace, and ultra-trace elements. In this work, we report theoretical results obtained for three different enzymes each of which contains different metal ions, trying to highlight any differences in their working mechanism as a function of the replacement of the metal center at the active site

On the Inhibition Mechanism of Glutathione Transferase P1 by Piperlongumine. Insight From Theory

Piperlongumine (PL) is an anticancer compound whose activity is related to the inhibition of human glutathione transferase of pi class (GSTP1) overexpressed in cancerous tumors and implicated in the metabolism of electrophilic compounds. In the present work, the inhibition mechanism of hydrolyzed piperlongumine (hPL) has been investigated employing QM and QM/MM levels of theory. The potential energy surfaces (PESs) underline the contributions of Tyr residue close to G site in the catalytic pocket of the enzyme. The proposed mechanism occurs through a one-step process represented by the nucleophilic addition of the glutathione thiol to electrophilic species giving rise to the simultaneous C-S and H-C bonds formation. Both the used methods give barrier heights (19.8 and 21.5 kcal mol−1 at QM/MM and QM, respectively) close to that experimentally measured for the C-S bond formations (23.8 kcal mol−1)

QM Cluster or QM/MM in Computational Enzymology: The Test Case of LigW-Decarboxylase

The catalytic mechanism of the decarboxylation of 5-carboxyvanillate by LigW producing vanillic acid has been studied by using QM cluster and hybrid QM/MM methodologies. In the QM cluster model, the environment of a small QM model is treated with a bulky potential while two QM/MM models studies include partial and full protein with and without explicitly treated water solvent. The studied reaction involves two sequential steps: the protonation of the carbon of the 5-carboxy-vanillate substrate and the decarboxylation of the intermediate from which results deprotonated vanillic acid as product. The structures and energetics obtained by using three structural models and two density functionals are quite consistent to each other. This indicates that the small QM cluster model of the presently considered enzymatic reaction is appropriate enough and the reaction is mainly influenced by the active site

Participation of the nucleobases in the regioselective backbone fragmentation of nucleic acids. A molecular dynamics and tandem mass spectrometric investigation on a model dinucleoside phosphotriester

The anions (I–III) obtained from O-methyl 5′-O-(5′-deoxythymidine) 3′-O-(2′,3′-dideoxyuridine) phosphate by the competitive removal of the 3-N-H protons of the nucleobases and of the methyl group from the phosphotriester bond, assume in the gas phase stable conformations as a function of their charge site. The mass-analyzed ion kinetic energy (MIKE) spectra of I and III show that the regioselective backbone cleavage of the internucleotidic linkage is controlled by the 2′-H proton transfer to the nucleobase within the 5′-end nucleoside. Similar pathways are taken by species II when the nucleobase is eliminated as neutral from the 5′-end nucleoside

Use of an "Intelligent Knife" (iknife), Based on the Rapid Evaporative Ionization Mass Spectrometry Technology, for Authenticity Assessment of Pistachio Samples

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Influence of lifestyle habits, nutritional status and insulin resistance in NAFLD

Non alcoholic fatty liver disease (NAFLD) is associated with obesity, diabetes and insulin resistance (IR). The aim of our study was to assess the relationship between IR, anthropometry, lifestyle habits, resting energy expenditure (REE) and degree of fatty liver at ultrasound in 48 overweight patients with NAFLD as compared to 24 controls without fatty liver, matched for age. Nutritional status, alcohol intake and physical activity were assessed by skinfold thickness measurements, a 7-day diary, and SenseWear armband (SWA). REE was assessed by both SWA (REE-SWA) and a Vmax metabolic cart (REE-Vmax). Fatty liver was measured by US and the Doppler Power Index was calculated. IR was assessed using the HOMA index. There was significant correlation between waist circumference, HOMA, Doppler power index and fatty liver grade at US. Multivariate analysis showed that alteration of waist circumference, Doppler power index, and HOMA were the major significant predictors of fatty liver. Our data demonstrated a significant association between NAFLD and central adiposity and IR

The integration of triggered drug delivery with real time quantification using FRET; creating a super ‘smart’ drug delivery system

The ability to control drug release at a specific physiological target enables the possibility of an enhanced therapeutic effect with reduced off-target toxic side effects. The discipline of controlled drug release has grown to include most areas of medicine with examples in the literature of targeted drug delivery to the majority of organs within the human body. In addition, a variety of external stimuli used to meditate the drug release process have also been investigated. Nonetheless, the concurrent real time monitoring of drug release has not been widely studied. In this manuscript, we present a novel micellar drug delivery system that is not only capable of releasing its cargo when stimulated by light but also provides a real time analysis of the amount of cargo remaining. Controlled drug release from the delivery system was mediated by physicochemical changes of a spiropyran-merocyanine photochromic dyad, while drug quantification was enabled using a Förster Resonance Energy Transfer (FRET) relationship between the photochrome and a co-encapsulated BODIPY fluorophore. The percentage of drug released from the delivery system was significantly greater (24%) when exposed to light irradiation compared to an analogous control maintained in the dark (5%). Furthermore, the fluorescence read-out capability also enabled the drug-release process to be followed in living cells with a significantly reduced fluorescence emission observed for those cells incubated with the delivery system and exposed to light irradiation compared to control cells maintained in the dark. Combined, these results highlight the utility of this approach to theranostic drug delivery with the potential of light-triggered released together with a fluorescence read-out to enable quantification of the drug release process. [Display omitted

MIDDLE JURASSIC - EARLY CRETACEOUS INTEGRATED BIOSTRATIGRAPHY (AMMONITES, CALCAREOUS NANNOFOSSILS AND CALPIONELLIDS) OF THE CONTRADA DIESI SECTION (SOUTH-WESTERN SICILY, ITALY)

Facies and biostratigraphic analyses of the Contrada Diesi succession, cropping out along the northern slope of Mt. Magaggiaro (Sciacca, SW Sicily), provided new data on the Middle Jurassic-Early Cretaceous pelagic sedimentation in the Saccense domain. The richness in ammonites allowed the identification of Bathonian-Kimmeridgian Biozones and Subzones, while the Tithonian-Valanginian interval was defined mainly by calpionellids and calcareous nannofossils. Facies and microbiofacies analyses of the Jurassic-Cretaceous pelagic sediments of the area, together with ammonite, calpionellid and calcareous nannofossil integrated biostratigraphy, were very effective tools for comparison of biostratigraphic events. Many gaps in sedimentation were recognized, the most important spanning the middle and late Berriasian and part of the early Berriasian. The Contrada Diesi succession provides new litho-biostratigraphic data on the Saccense Domain. It suggests a high degree of internal variability tied to the irregular paleotopography of the carbonate platform substrate (Inici Fm.), derived from Early Jurassic tectonics. Gaps in sedimentation in the Contrada Diesi sections indicate that the environment of the Saccense Domain was characterized by a variable rate of sedimentation and energy changes

MIDDLE JURASSIC - EARLY CRETACEOUS INTEGRATED BIOSTRATIGRAPHY (AMMONITES, CALCAREOUS NANNOFOSSILS AND CALPIONELLIDS) OF THE CONTRADA DIESI SECTION (SOUTH-WESTERN SICILY, ITALY)

Facies and biostratigraphic analyses of the Contrada Diesi succession, cropping out along the northern slope of Mt. Magaggiaro (Sciacca, SW Sicily), provided new data on the Middle Jurassic-Early Cretaceous pelagic sedimentation in the Saccense domain. The richness in ammonites allowed the identification of Bathonian-Kimmeridgian Biozones and Subzones, while the Tithonian-Valanginian interval was defined mainly by calpionellids and calcareous nannofossils. Facies and microbiofacies analyses of the Jurassic-Cretaceous pelagic sediments of the area, together with ammonite, calpionellid and calcareous nannofossil integrated biostratigraphy, were very effective tools for comparison of biostratigraphic events. Many gaps in sedimentation were recognized, the most important spanning the middle and late Berriasian and part of the early Berriasian. The Contrada Diesi succession provides new litho-biostratigraphic data on the Saccense Domain. It suggests a high degree of internal variability tied to the irregular paleotopography of the carbonate platform substrate (Inici Fm.), derived from Early Jurassic tectonics. Gaps in sedimentation in the Contrada Diesi sections indicate that the environment of the Saccense Domain was characterized by a variable rate of sedimentation and energy changes