Phylogenetic analysis and homology modelling of <Emphasis Type="Italic">Paracentrotus lividus</Emphasis> nectin

The extracellular matrix protein Pl-nectin, a 210-kDa homodimer originally purified from sea urchin eggs, plays a crucial role in cell adhesion and embryonic morphogenesis. The compiled cDNA sequence, obtained by RT-PCR primer walking and 3′ RACE, identified a 984aa product containing a 23aa signal peptide and including all six internal peptides identified by protein microsequencing. The protein is a new member of the galactose-binding protein superfamily as it consists of six 151–156aa-long tandemly repeated domains (D1–D6), homologous to the discoidin-like domains, also known as F5/8-type C domains. Based on homology modelling, we present a three-dimensional structure (3D) for D5, identified as the prototype domain. The molecular modelling of the assembled Pl-nectin homodimer accounts for a Pl-nectin quaternary structure composed of two 105-kDa C-shaped monomers linked by a S–S bridge. The presence of an LDT motif between the first and the second exposed loops of the D2 domain suggests the binding of Pl-nectin to an integrin receptor. Altogether, the in silico analysis described here is consistent with previous biochemical reports and offers a basis for predictions to be experimentally tested.     

Unexpected Behavior of Diastereomeric Ions in the GasPhase: A Stimulus for Pondering on ee Measurements by ESI-MS

The most common protocols for the quantitative determination of the enantiomeric excess (ee) of raw mixtures by ESI-MS reveal inadequate in cases where the distribution of diastereomeric derivatives diverges from the ee of original solutions. This phenomenon is attributable to a matrix effect, i.e., to the stereospecific formation of high order noncovalent adducts in the ESI droplets, which alters the actual availability of the diastereomeric species under MS analysis. In this frame, the assumption of classic protocols that the ionization correction factor q is independent on the composition of the mixture submitted to analysis is questionable. An alternative methodology is presented in this paper, which is aimed at circumventing the problem by excluding any chemical derivatization of the original raw mixture. It is based on the measurement of the actual distribution of ESI-formed proton-bound diastereomeric complexes from the enantiomeric mixture through a careful analysis of their reaction kinetics with a suitable reactant.      

Direct Synthesis of 3-Aryl Substituted Isocoumarins and Phthalides through Palladium Acetate Catalyzed C(sp2)−H Activation in Ionic Liquids

A novel Pd-catalysed oxidative coupling between benzoic acids and vinylarenes or acrylates to furnish isocoumarins and phthalides is reported. The reaction proceeds smoothly in molten tetrabutylammonium acetate via a selective C−H bond activation, with very low percentage of ligand-free palladium acetate as the catalyst, under atmospheric pressure of oxygen. Sub-stoichiometric amount of copper acetate is also required as a reoxidant for the palladium.     

A Functional Equation Whose Unknown is \mathcal{P}([0,1]) Valued

We study a functional equation whose unknown maps a Euclidean space into the space of probability distributions on [0,1]. We prove existence and uniqueness of its solution under suitable regularity and boundary conditions, we show that it depends continuously on the boundary datum, and we characterize solutions that are diffuse on [0,1]. A canonical solution is obtained by means of a Randomly Reinforced Urn with different reinforcement distributions having equal means. The general solution to the functional equation defines a new parametric collection of distributions on [0,1] generalizing the Beta family.     

On the chromatic polynomial of a graph

Let P(G,λ) be the chromatic polynomial of a graph G with n vertices, independence number α and clique number ω. We show that for every λ≥n, ()^α≤≤ () ^{n −ω}. We characterize the graphs that yield the lower bound or the upper bound.?These results give new bounds on the mean colour number μ(G) of G: n− (n−ω)() ^{n −ω}≤μ(G)≤n−α() ^α. Received: December 12, 2000 / Accepted: October 18, 2001?Published online February 14, 2002     

Modelling pedestrian dynamics into a metro station by thermostatted kinetic theory methods

This paper deals with the modelling of pedestrian dynamics at the entry of a metro station by means of the thermostatted kinetic theory framework. Specifically, the model depicts the time evolution of the pedestrian dynamics at the turnstiles under no panic conditions. The modelling of the microscopic interactions is based on the stochastic game theory and reflects the decision dynamics of the turnstiles pursued by pedestrians. A qualitative analysis is addressed to the equilibrium solutions by means of the classical stability theory of perturbations. Numerical simulations aim at showing the emerging behaviours captured by the model. In particular the model validation is obtained by performing a sensitivity analysis on the parameters and on the initial conditions. Further refinements and research perspective, including the modelling under panic conditions, are discussed in the last section of the paper.     

Investigation of anthropic effects connected with metal ions concentration, organic matter and grain size in Bormida river sediments

An investigation on the sediment composition and grain size was carried out along the Bormida river (Piedmont, Northern Italy). The samples were taken both in the riverbed and on its banks. Multivariate statistical exploratory methods permitted to identify possible sources of primary pollution. In particular, principal component analysis (PCA) showed that there are probably at least three anthropogenic main causes of pollution, one connected with Cr, Ni and Sn, the second with cadmium and the last one with mercury. Some correlations were found between heavy metal ion concentrations and organic matter and/or the sediment grain size. Differences between the samples collected in the riverbed and on the banks were identified and the relationships between the principal components and the distance of the samples from the riverbed and from the hot spot represented by the ACNA industrial site were also analyzed.     

Effect of ortho-SR groups on O-H bond strength and H-atom donating ability of phenols: a possible role for the Tyr-Cys link in galactose oxidase active site?

Rotation about the Ar-S bond in ortho-(alkylthio)phenols strongly affects the bond dissociation enthalpy (BDE) and the reactivity of the OH group. Newly synthesized sulfur containing heterocycles 3 and 4, where the -SR group is almost coplanar with the phenolic ring, are characterized by unusually low BDE(O-H) values (79.6 and 79.2 kcal/mol, respectively) and by much higher reactivities toward peroxyl radicals than the ortho-methylthio derivative 1 (82.0 kcal/mol). The importance of the intramolecular hydrogen bond (IHB) in determining the BDE(O-H) was demonstrated by FT-IR experiments, which showed that in heterocycles 3 and 4 the IHB between the phenolic OH group and the S atom is much weaker than that present in 1. Since the IHB can be formed only if the -SR group adopts an out-of-plane geometry, this interaction is possible only in the methylthio derivative 1 and not in 3 and 4. The additive contribution to the phenolic BDE(O-H) of the -SR substituent therefore varies from -3.1 to +2.8 kcal/mol for the in-plane and out-of-plane conformations, respectively. These results may be relevant to understanding the role of the tyrosine-cysteine link in the active site of galactose oxidase, an important enzyme that catalyzes the two-electron aerobic oxidation of primary alcohols to aldehydes. The switching of the ortho -SR substituent between perpendicular and planar conformations may account for the catalytic efficiency of this enzyme.     

Classification of water molecules in protein binding sites

Water molecules play a crucial role in mediating the interaction between a ligand and a macromolecular receptor. An understanding of the nature and role of each water molecule in the active site of a protein could greatly increase the efficiency of rational drug design approaches: if the propensity of a water molecule for displacement can be determined, then synthetic effort may be most profitably applied to the design of specific ligands with the displacement of this water molecule in mind. In this paper, a thermodynamic analysis of water molecules in the binding sites of six proteins, each complexed with a number of inhibitors, is presented. Two classes of water molecules were identified: those conserved and not displaced by any of the ligands, and those that are displaced by some ligands. The absolute binding free energies of 54 water molecules were calculated using the double decoupling method, with replica exchange thermodynamic integration in Monte Carlo simulations. It was found that conserved water molecules are on average more tightly bound than displaced water molecules. In addition, Bayesian statistics is used to calculate the probability that a particular water molecule may be displaced by an appropriately designed ligand, given the calculated binding free energy of the water molecule. This approach therefore allows the numerical assessment of whether or not a given water molecule should be targeted for displacement as part of a rational drug design strategy.