Protein structure prediction and biomolecular recognition: from protein sequence to peptidomimetic design with the human beta3 integrin

Computational tools can bridge the gap between sequence and protein 3D structure based on the notion that information is to be retrieved from the databases and that knowledge-based methods can help in approaching a solution of the protein-folding problem. To this aim our group has implemented neural network-based predictors capable of performing with some success in different tasks, including predictions of the secondary structure of globular and membrane proteins, the topology of membrane proteins and porins and stable alpha-helical segments suited for protein design. Moreover we have developed methods for predicting contact maps in proteins and the probability of finding a cysteine in a disulfide bridge, tools which can contribute to the goal of predicting the 3D structure starting from the sequence (the so called ab initio prediction). All our predictors take advantage of evolution information derived from the structural alignments of homologous (evolutionary related) proteins and taken from the sequence and structure databases. When it is necessary to build models for proteins of unknown spatial structure, which have very little homology with other proteins of known structure, non-standard techniques need to be developed and the tools for protein structure predictions may help in protein modeling. The results of a recent simulation performed in our lab highlights the role of high performing computing technology and of tools of computational biology in protein modeling and peptidomimetic design.     

First identification of excited states in 59Zn

Excited states in ⁵⁹Zn were observed for the first time following the fusion-evaporation reaction ²⁴Mg + ⁴⁰Ca at a beam energy of 60 MeV. The GASP array in conjunction with the ISIS Silicon ball and the NeutronRing allowed for the detection of γ-rays in coincidence with evaporated light particles. The mirror symmetry of ⁵⁹Zn and ⁵⁹Cu is discussed. Received: 28 May 2002 / Accepted: 10 July 2002 / Published online: 3 December 2002 RID="a" ID="a"Present address: Oliver Lodge Laboratory, University of Liverpool, P.O. Box 147, Liverpool, L69 7ZE, United Kingdom; e-mail: ca@ns.ph.liv.ac.uk. RID="b" ID="b"Present address: Physik-Departament, Technische Universit?t München, D-85748 Garching, Germany. Communicated by W. Henning     

Gas-phase reactions of nitronium ions with acetylene and ethylene: an experimental and theoretical study

A comparative study of the gas-phase reactions of NO2+ with acetylene and ethylene was performed by using FT-ICR, MIKE, CAD, and NfR/ CA mass spectrometric techniques, in conjunction with ab initio calculations at the MP2/6-31+G* level of theory. Both reactions proceed according to the same mechanism, that is, 1,3-dipolar cycloaddition, but yield products of different stability. The C2H2NO2+ adduct from acetylene has an aromatic character and hence is highly stabilized with respect to the C2H4NO2+ adduct from ethylene. Both cycloadducts tend to isomerize into O-nitroso derivatives, that is, nitrosated ketene and nitrosated acetaldehyde, which represent the thermodynamically most stable products from the addition of NO2+ to acetylene and ethylene, respectively. As prototypal examples of the reactivity of free nitronium ions with most simple pi systems, the reactions investigated are useful starting points to model the mechanism of aromatic nitration.     

3H‐1,2‐Dithiole‐3‐thione derivatives as novel solvatochromic dyes

The UV–Vis spectrum of 5‐(1‐butylthio)‐3H‐1,2‐dithiole‐3‐thione (1a) and that of the chromium pentacarbonyl complex of 5‐methyl‐3H‐1,2‐dithiole‐3‐thione (3) present significant changes with the solvent polarity. The two absorption bands shown by the compounds in the region above 300 nm were identified by theoretical calculations. For Compound 1a these are n→π^* and →π^* transitions and for Compound 3 the longest wavelength absorption corresponds to a charge transfer band and shows a remarkably negative solvatochromism. Not only has the wavelength of maximum absorption changed with the solvent but also the ratio of the absorbances at the two wavelengths. The effect of solvents was correlated with solvatochromic parameters such as π^* and α. The spectrum of 5‐(1‐butylthio)‐3H‐1,2‐dithiole‐3‐one ( 2 ) was also measured in different solvents but in this case the changes observed are less significant than for the other two compounds. The spectra of 1a and 3 were also determined in the presence of anionic (SDS), cationic (CTAB), and neutral surfactants (Brig‐35) and it is shown that these compounds can be used as probes for the polarity of the binding sites of organized assemblies. Copyright © 2008 John Wiley & Sons, Ltd.     

Soft Constraint Logic Programming and Generalized Shortest Path Problems

In this paper we study the relationship between Constraint Programming (CP) and Shortest Path (SP) problems. In particular, we show that classical, multicriteria, partially ordered, and modality-based SP problems can be naturally modeled and solved within the Soft Constraint Logic Programming (SCLP) framework, where logic programming is coupled with soft constraints. In this way we provide this large class of SP problems with a high-level and declarative linguistic support whose semantics takes care of both finding the cost of the shortest path(s) and also of actually finding the path(s). On the other hand, some efficient algorithms for certain classes of SP problems can be exploited to provide some classes of SCLP programs with an efficient way to compute their semantics.     

Excitation of stable transverse wavepackets with quadratic and cubic susceptibilities

We have identified a family of (2+1)D spatial solitary waves which can stably propagate in bulk media in the presence of coexisting diffraction, self-focusing Kerr and quadratic nonlinearities. In a conspicuous range of excitation conditions close to the stationary solutions, the emerging wavepackets are immune to the detrimental occurrence of filamentation and collapse, typical of pure Kerr media. The presence of a second-order contribution to the cubic nonlinear response is, therefore, able to prevent optical damage in applications relying on self-guidance. We show that the cross-phase modulation plays an important effect on stability. Our estimate shows that the effects of the cubic susceptibility cannot be neglected below a certain beam size in realistic crystals (e.g. KTP or similar).     

Theory of power coupling between multimode optical fibres

In this paper power coupling between two multimode optical fibres is investigated. A formalism (based on a geometrical approach) suitable for analysing any coupling configuration between fibres with any index profile and any radiance distribution is presented. The model is applied to obtain coupling losses both in uniformly excited parabolic- and step-index fibres, in the presence of all kinds of coupling errors. Numerical results of extensive utility are shown and useful asymptotic expressions of coupling efficiency, valid for small values of coupling error parameters, are derived together with some practical rules for error combination. Mention is also made of some experimental results we have obtained, which corroborate some previous assertions. The work can supply a useful tool in the design of joints and connectors between single fibres or optical cables.