The catalytic activity of proline racemase: a quantum mechanical/molecular mechanical study

The enzyme proline racemase from the eukaryotic parasite Trypanosoma cruzi (responsible for endemic Chagas disease) catalyzes the reversible stereoinversion of chiral Calpha in proline. We employed a new combined quantum mechanical and molecular mechanical (QM/MM) potential to study the reaction mechanism of the enzyme. Three critical points were found: two almost isoenergetic minima (M1a and M2a), in which the enzyme is bound to L- and D-Pro, respectively, and a transition state (TSCa), unveiling a highly asynchronous concerted process. A systematic analysis was performed on the optimized geometries to point out the key role played by some residues in stabilizing the transition state.     

Kinetic modeling of charge-transfer quenching in the CP29 minor complex

We performed transient absorption (TA) measurements on CP29 minor light-harvesting complexes that were reconstituted in vitro with either violaxanthin (Vio) or zeaxanthin (Zea) and demonstrate that the Zea-bound CP29 complexes exhibit charge-transfer (CT) quenching that has been correlated with the energy-dependent quenching (qE) in higher plants. Simulations of the difference TA kinetics reveal two-phase kinetics for intracomplex energy transfer to the CT quenching site in CP29 complexes, with a fast <500 fs component and a approximately 6 ps component. Specific chlorophyll sites within CP29 are identified as likely locations for CT quenching. We also construct a kinetic model for CT quenching during qE in an intact system that incorporates CP29 as a CT trap and show that the model is consistent with previous in vivo measurements on spinach thylakoid membranes. Finally, we compare simulations of CT quenching in thylakoids with those of the individual CP29 complexes and propose that CP29 rather than LHCII is a site of CT quenching.     

Ocimum campechianum Mill. from Amazonian Ecuador: Chemical Composition and Biological Activities of Extracts and Their Main Constituents (Eugenol and Rosmarinic Acid)

The essential oil (EO), the methanolic (MeOH), and the 70% ethanolic (70% EtOH) extracts obtained from the aerial parts of Ocimum campechianum Mill. (Ecuador) were chemically characterized through gas-chromatography coupled to mass spectrometry detector (GC-MS), high-performance liquid chromatography coupled to diode array-mass spectrometry detectors (HPLC-DAD-MS) and studied for their in vitro biological activity. The radical scavenger activity, performed by spectrophotometric 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) assays, highlighted significant IC₅₀ values for the EO, extracts and their main constituents (eugenol and rosmarinic acid). EO (and eugenol) showed noteworthy activity against Pseudomonas syringae pv. syringae and a moderate effect against clinical Candida strains, with possible synergism in association to fluconazole against the latter microorganisms. The extracts and pure molecules exhibited weak cytotoxic activity against the HaCat cell line and no mutagenicity against Salmonella typhimurium TA98 and TA100 strains, giving indication of safety. Instead, EO showed a weak activity against adenocarcinomic human alveolar basal epithelial cells (A549). The above-mentioned evidence leads us to suggest a potential use of the crude drug, extracts, and EO in cosmetic formulation and food supplements as antioxidant agents. In addition, EO may also have a possible application in plant protection and anti-Candida formulations.     

Correlations and aggregate statistics in granular packs

We study how the aggregate statistical properties for density fluctuations in granular aggregates scale with the sample size and how such a scaling is associated with the correlations between grains. Correlations are studied both between grain positions and between Vorono? cell volumes, showing distinct behaviors and properties. A non-linear scaling in the aggregate volume fluctuations as function of the sample size is discovered and the connection between such anomalous scaling and correlations is explained. It emerges that volume fluctuations might be described by means of a single universal equation for all samples at all cluster sizes.     

Mechanical stabilization effect of water on a membrane-like system

The penetration resistance of a prototypical model-membrane system (HS-(CH2)11-OH self-assembled monolayer (SAM) on Au(111)) to the tip of an atomic force microscope (AFM) is investigated in the presence of different solvents. The compressibility (i.e., height vs tip load) of the HS-(CH2)11-OH SAM is studied differentially, with respect to a reference structure. The reference consists of hydrophobic alkylthiol molecules (HS-(CH2)17-CH3) embedded as nanosized patches into the hydrophilic SAM by nanografting, an AFM-assisted nanolithography technique. We find that the penetration resistance of the hydrophilic SAM depends on the nature of the solvent and is much higher in the presence of water than in 2-butanol. In contrast, no solvent-dependent effect is observed in the case of hydrophobic SAMs. We argue that the mechanical resistance of the hydroxyl-terminated SAM is a consequence of the structural order of the solvent-SAM interface, as suggested by our molecular dynamics simulations. The simulations show that in the presence of 2-butanol the polar head groups of the HS-(CH2)11-OH SAM, which bind only weakly to the solvent molecules, try to bind to each other, disrupting the local order at the interface. On the contrary, in the presence of water the polar head groups bind preferentially to the solvent that, in turn, mediates the release of the surface strain, leading to a more ordered interface. We suggest that the mechanical stabilization effect induced by water may be responsible for the stability of even more complex, real membrane systems.     

‘Gate effect’ in templated polyacrylamide membranes influences the electrotransport of proteins and finds applications in proteome analysis

Templating is an effective way for the structural modifications of a material and hence for altering its functional properties. Here protein imprinting was exploited to alter polymeric polyacrylamide (PAA) membranes. The sieving properties and selection abilities of the material formed were evaluated by studying the electrically driven transport of various proteins across templated PAA membranes. The sieving properties correlated with the templating process and depended on the quantity of template used during the polymerisation. For 1 mg/mL protein-templated membranes a ‘gate effect’ was shown, which induced a preferential migration of the template and of similar-size proteins. Such template preferential electrotransport was exploited for the selective removal of certain proteins in biological fluids prior to proteome analysis (depletion of albumin from human serum); the efficiency of the removal was demonstrated by analysing the serum proteome by two-dimensional electrophoresis experiments. Figure PAA templeted membrane for the electroremoval of serum albumin before proteome analysis     

Intramolecular vibrational force fields for linear carbon chains through an adaptative linear scaling scheme

In this work, the vibrational force fields of hydrogen-capped oligoynes of increasing chain lengths are investigated by means of density functional theory calculations. It is shown that the interaction force constants between CC stretching coordinates decrease slowly with the distance between the two bonds considered. The consequence for the frequency dispersion of longitudinal optical (LO) phonons of an infinite polyyne chain is discussed and related to the observed behavior of the spectra of finite-size molecules. Effects of the exchange-correlation functional and of the basis set on the vibrational force constants are also investigated and the need for a scaling procedure is pointed out. Accordingly, new force fields which allow predictions in very good quantitative agreement with the available experimental data for oligoynes have been obtained, providing a sound assignment of alpha and beta lines.     

Exploring nanoscale electrical and electronic properties of organic and polymeric functional materials by atomic force microscopy based approaches

Beyond imaging, atomic force microscopy (AFM) based methodologies enable the quantitative investigation of a variety of physico-chemical properties of (multicomponent) materials with a spatial resolution of a few nanometers. This Feature Article is focused on two AFM modes, i.e. conducting and Kelvin probe force microscopies, which allow the study of electrical and electronic properties of organic thin films, respectively. These nanotools provide a wealth of information on (dynamic) characteristics of tailor-made functional architectures, opening pathways towards their technological application in electronics, catalysis and medicine.     

The Ni2+ binding properties of Helicobacter pylori NikR

The binding constants between Ni2+ and Helicobacterpylori NikR have been determined using isothermal titration microcalorimetry in order to rationalize the role of this protein as a nickel-dependent biological sensor.