On the possibility of extending the Nore-Frenkel generalized law of correspondent states to non-isotropic patchy interactions

Colloidal systems (and protein solutions) are often characterized by attractive interactions whose range is much smaller than the particle size. When this is the case and the interaction is spherical, systems obey a generalized law of correspondent states (GLCS), first proposed by Noro and Frenkel [ J.Chem.Phys. 113, 2941 (2000) ]. The thermodynamic properties become insensitive to the details of the potential, depending only on the value of the second virial coefficient B_2 and the density $\rho$. The GLCS does not generically hold for the case of non-spherical potentials. In this Letter we suggest that when particles interact via short-ranged small-angular amplitude patchy interactions (so that the condition of only one bond per patch is fulfilled) it is still possible to generalize the GLCS close to the liquid-gas critical point. Keywords: Colloids, Second Virial Coefficient, Proteins interactions, Short-ranged attractive attractions.Comment: 11 pages, 3 figures. Accepted for publication on J. Phys. Chem.

Noro-Frenkel scaling in short-range square well: A Potential Energy Landscape study

We study the statistical properties of the potential energy landscape of a system of particles interacting via a very short-range square-well potential (of depth $-u_0$), as a function of the range of attraction $\Delta$ to provide thermodynamic insights of the Noro and Frenkel [ M.G. Noro and D. Frenkel, J.Chem.Phys. {\bf 113}, 2941 (2000)] scaling. We exactly evaluate the basin free energy and show that it can be separated into a {\it vibrational} ($\Delta$-dependent) and a {\it floppy} ($\Delta$-independent) component. We also show that the partition function is a function of $\Delta e^{\beta u_o}$, explaining the equivalence of the thermodynamics for systems characterized by the same second virial coefficient. An outcome of our approach is the possibility of counting the number of floppy modes (and their entropy).Comment: 4 pages, 4 figures accepted for publication on PR

Nuevas tendencias en las políticas de inmigración italianas: “cambiar algo para que nada cambie”

Este ARI examina los recientes cambios en la política de inmigración italiana llevados a cabo en 2008 por el gobierno conservador de Silvio Berlusconi. Las medidas contra la migración irregular aprobadas en 2008 han suscitado una oleada de críticas en toda la UE. El gobierno italiano de Silvio Berlusconi ha sido acusado de racismo mientras que el ministro de Interior italiano insistía en que solo se trataba de formas razonables de ocuparse de la inmigración irregular y de garantizar la seguridad de los ciudadanos italianos. Este ARI sostiene que las nuevas normas, a pesar de ser más ambiguas de lo que parecen a primera vista (y a veces bastante desagradables), no resuelven la contradicción existente en la política de inmigración italiana, donde existe una demanda creciente de mano de obra extranjera que choca con la tendencia hacia medidas más restrictivas. El principal objeto de este ARI es mostrar que la reforma propuesta por el gobierno italiano difícilmente logrará reducir el flujo de inmigrantes irregulares en Italia

New Trends in Italian Immigration Policies: 'To change everything in order to keep everything the same'

This ARI looks at the recent developments in Italian immigration policies carried out in 2008 by the conservative government of Silvio Berlusconi. The measures against irregular migration approved in 2008 have given rise to a wave of criticism across the EU. The Italian government of Silvio Berlusoni has been accused of racism while the Italian Minister of the Interior insists that his measures are simply reasonable ways of dealing with irregular immigration and guaranteeing the safety of Italian citizens. This paper argues that the new rules, although more uncertain than they seem at first glance (and sometimes thoroughly unpleasant), do not solve the contradictory logic of Italy’s immigration policies, with an increasing demand for foreign labour conflicting with the trend towards more restrictive measures. The main object of this paper is to show that the reform proposed by the Italian government is unlikely to reduce the rate of irregular migrants in Italy

The binding modes of VIVO2+ions in blood proteins and enzymes

The binding modes of VIVO2+ ions to hemoglobin (Hb), human serum transferrin (hTf), immunoglobulin G (IgG), vanadium bromoperoxidase (VBrPO) and VIVO2+-substituted imidazoleglycerol-phosphatase dehydratase (IGPD) were determined by a combined approach of full DFT and MM techniques. These results reproduce and explain the experimental spectroscopic (EPR and ESEEM) data

È possibile misurare l’integrazione degli immigrati? Lo stato dell’arte

Da diversi decenni, l’immigrazione è un tema caldo per l’opinione pubblica dei paesi europei (e non). Vi è una diffusa insoddisfazione per la capacità delle politiche adottate di favorire effettivamente l’«integrazione» dei segmenti di popolazione straniera residenti sul territorio. In che misura questa insoddisfazione coglie una difficoltà reale? Per saperlo, bisognerebbe essere in grado di definire con esattezza cosa debba intendersi per «integrazione», come essa andrebbe misurata e, last but not least, come valutare se le politiche messe in atto dai governi occidentali producono o meno gli effetti desiderati. Su ognuno di questi punti, esiste un ricco dibattito scientifico spesso poco conosciuto. In questo lavoro viene condotta una rassegna critica della letteratura scientifica sul tema, volta ad evidenziare le risorse già disponibili e i problemi ancora aperti

Rationalizing the Decavanadate(V) and Oxidovanadium(IV) Binding to G-Actin and the Competition with Decaniobate(V) and ATP

The experimental data collected over the past 15 years on the interaction of decavanadate(V) (V10O286-; V10), a polyoxometalate (POM) with promising anticancer and antibacterial action, with G-actin, were rationalized by using several computational approaches (docking, density functional theory (DFT), and molecular dynamics (MD)). Moreover, a comparison with the isostructural and more stable decaniobate(V) (Nb10O286-; Nb10) was carried out. Four binding sites were identified, named α, β, γ, and δ, the site α being the catalytic nucleotide site located in the cleft of the enzyme at the interface of the subdomains II and IV. It was observed that the site α is preferred by V10, whereas Nb10 is more stable at the site β; this indicates that, differently from other proteins, G-actin could contemporaneously bind the two POMs, whose action would be synergistic. Both decavanadate and decaniobate induce conformational rearrangements in G-actin, larger for V10 than Nb10. Moreover, the binding mode of oxidovanadium(IV) ion, VIVO2+, formed upon the reduction of decavanadate(V) by the -SH groups of accessible cysteine residues, is also found in the catalytic site α with (His161, Asp154) coordination; this adduct overlaps significantly with the region where ATP is bound, accounting for the competition between V10 and its reduction product VIVO2+ with ATP, as previously observed by EPR spectroscopy. Finally, the competition with ATP was rationalized: since decavanadate prefers the nucleotide site α, Ca2+-ATP displaces V10 from this site, while the competition is less important for Nb10 because this POM shows a higher affinity for β than for site α. A relevant consequence of this paper is that other metallodrug-protein systems, in the absence or presence of eventual inhibitors and/or competition with molecules of the organism, could be studied with the same approach, suggesting important elements for an explanation of the biological data and a rational drug design

DFT Protocol for EPR prediction of paramagnetic Cu(II) complexes and application to protein binding sites

With the aim to provide a general protocol to interpret electron paramagnetic resonance (EPR) spectra of paramagnetic copper(II) coordination compounds, density functional theory (DFT) calculations of spin Hamiltonian parameters g and A for fourteen Cu(II) complexes with different charges, donor sets, and geometry were carried out using ORCA software. The performance of eleven functionals was tested, and on the basis of the mean absolute percent deviation (MAPD) and standard deviation (SD), the ranking of the functionals for Az is: B3LYP > B3PW91 ~ B3P86 > PBE0 > CAM-B3LYP > TPSSh > BH and HLYP > B2PLYP > MPW1PW91 > ω-B97x-D » M06; and for gz is: PBE0 > BH and HLYP > B2PLYP > ω-B97x-D > B3PW91~B3LYP~B3P86 > CAM-B3LYP > TPSSh~MPW1PW91 » M06. With B3LYP the MAPD with respect to A exp tl z is 8.6% with a SD of 4.2%, while with PBE0 the MAPD with respect to g exp tl z is 2.9% with a SD of 1.1%. The results of the validation confirm the fundamental role of the second order spin-orbit contribution to Az. The computational procedure was applied to predict the values of gz and Az of the adducts formed by Cu(II) with albumin and two fragments of prion protein, 106-126 and 180-193

Exploring Repetitiveness Measures for Two-Dimensional Strings

Detecting and measuring repetitiveness of strings is a problem that has been extensively studied in data compression and text indexing. However, when the data are structured in a non-linear way, like in the context of two-dimensional strings, inherent redundancy offers a rich source for compression, yet systematic studies on repetitiveness measures are still lacking. In the paper we introduce extensions of repetitiveness measures to general two-dimensional strings. In particular, we propose a new extension of the measures $\delta$ and $\gamma$, diverging from previous square based definitions proposed in [Carfagna and Manzini, SPIRE 2023]. We further consider generalizations of macro schemes and straight line programs for the 2D setting and show that, in contrast to what happens on strings, 2D macro schemes and 2D SLPs can be both asymptotically smaller than $\delta$ and $\gamma$. The results of the paper can be easily extended to $d$-dimensional strings with $d > 2$

Validation and Applications of Protein-Ligand Docking Approaches Improved for Metalloligands with Multiple Vacant Sites

Altres ajuts: COST Action CM1306Decoding the interaction between coordination compounds and proteins is of fundamental importance in biology, pharmacy, and medicine. In this context, protein-ligand docking represents a particularly interesting asset to predict how small compounds could interact with biomolecules, but to date, very little information is available to adapt these methodologies to metal-containing ligands. Here, we assessed the predictive capability of a metal-compatible parameter set for the docking program GOLD for metalloligands with multiple vacant sites and different geometries. The study first presents a benchmark of 25 well-characterized X-ray metalloligand-protein adducts. In 100% of the cases, the docking solutions are superimposable to the X-ray determination, and in 92% the value of the root-mean-square deviation between the experimental and calculated structures is lower than 1.5 Å. After the validation step, we applied these methods to five case studies for the prediction of the binding of pharmacological active metal species to proteins: (i) the anticancer copper(II) complex [Cu II (Br)(2-hydroxy-1-naphthaldehyde benzoyl hydrazine)(indazole)] to human serum albumin (HSA); (ii) one of the active species of antidiabetic and antitumor vanadium compounds, V IV O 2+ ion, to carboxypeptidase; (iii) the antiarthritic species [Au I (PEt 3 )] + to HSA; (iv) the antitumor oxaliplatin to ubiquitin; (v) the antitumor ruthenium(II) compound RAPTA-PentaOH to cathepsin B. The calculations suggested that the binding modes are in good agreement with the partial information retrieved from spectroscopic and spectrometric analysis and allowed us, in certain cases, to propose additional hypotheses. This method is an important update in protein-metalloligand docking, which could have a wide field of application, from biology and inorganic biochemistry to medicinal chemistry and pharmacology