Exploitation of proteomics strategies in protein structure-function studies

Mass spectrometry plays a central role in structural proteomics, particularly in highly intensive structural genomics projects. This review paper reports some examples taken from recent work from the authors' laboratory and is aimed at showing that modem proteomics strategies are instrumental in the integration of structural genomic projects in fields such as: (i) protein-protein interactions, (ii) protein-DNA interactions, (iii) protein-ligand interactions, and (iv) protein-folding intermediates

Bidimensional Tandem Mass Spectrometry for Selective Identification of Nitration Sites in Proteins.

Nitration of protein tyrosine residues is very often regarded as a molecular signal of peroxynitrite formation during development, oxidative stress, and aging. However, protein nitration might also have biological functions comparable to protein phosphorylation, mainly in redox signaling and in signal transduction. The major challenge in the proteomic analysis of nitroproteins is the need to discriminate modified proteins, usually occurring at substoichiometric levels from the large amount of nonmodified proteins. Moreover, precise localization of the nitration site is often required to fully describe the biological process. Existing methodologies essentially rely on immunochemical techniques either using 2D-PAGE fractionation in combination with western blot analyses or exploiting immunoaffinity procedures to selectively capture nitrated proteins. Here we report a totally new approach involving dansyl chloride labeling of the nitration sites that rely on the enormous potential of MSn analysis. The tryptic digest from the entire protein mixture is directly analyzed by MS on a linear ion trap mass spectrometer. Discrimination between nitro- and unmodified peptide is based on two selectivity criteria obtained by combining a precursor ion scan and an MS3 analysis. This new procedure was successfully applied to the identification of 3-nitrotyrosine residues in complex protein mixtures

Deamidation at Asparagine and Glutamine As a Major Modification upon Deterioration/Aging of Proteinaceous Binders in MuralPaintings

Proteomic strategies are herein proved to be a complementary approach to the well established amino acid composition analysis for the characterization of the aging and deterioration phenomena occurring to proteinaceous materials in works-of-art. Amino acid analyses on several samples demonstrated that proteins in the frescoes from the Camposanto Monumentale in Pisa are deteriorated as revealed by the decrease in Met, Lys, and Tyr content and by the presence in all the samples of amino malonic acid as a result of Ser, Phe, and Cys oxidation. Proteomic analysis identified deamidation at Asn and Gln as a further major event occurred. This work paves the way to the exploitation of proteomic strategies for the investigation of the molecular effects of aging and deterioration in historical objects. Results show that proteomic searches for deamidation by liquid chromatography-tandem mass spectrometry (LC-MS/MS) could constitute a routine analysis for paintings or any artistic and historic objects where proteins are present. Peptides that can be used as molecular markers when casein is present were identified

Measurement of the ratio of branching fractions B(Bs -> Ds K)/B(Bs -> Ds pi) at CDF II

The CP violation has played a central role in particle physics since 1964, year of its discovery in the kaon system. The large asymmetries predicted, and later observed, in the B meson system have confirmed the Cabibbo-Kobayashi-Maskawa (CKM) picture, but opened further questions and stimulated an increase of precision of the measurements in the search for new physics sources of CP violation. While the CKM scheme can accommodate a certain amount of CP violation, it does not require it, nor it provides any fundamental motivation for its existence. In fact, the "cosmological question" of the dominance of matter over antimatter in our universe is a strong hint for the presence of CP-violating effects of a much larger strength than the standard CKM mechanism. Experimental measurements allow to determine the angles and the sides of the so-called "unitarity triangle", formed by the CKM matrix parameters. Today a good level of precision has been reached for two of the angles, but the resolution on the third one (angle gamma) is still rather poor. One of the most important decay to probe such a field is the Cabibbo-suppressed mode Bs -> Ds K, which can have a large CP-violating interference via Bs mixing. Isolating a clean sample of such decays is a crucial step toward a precise measurement of gamma and this thesis deals this challenge. Selecting an enriched sample of Bs -> Ds K decays, keeping high the signal efficiency and rejecting the huge amount of background, which overwhelms the signal of interest by several order of magnitude, is a crucial ingredient. It also essential to disentangle Bs -> Ds K decays from kinematically similar decays, which lay down in the same mass region of the signal. In particular the thesis describes the analysis of the Bs->Ds K decays collected by CDF II experiment at the Tevatron collider. The thesis uses the full data sample of the CDF II corresponding to about 10/fb of integrate luminosity. To improve the signal to background ratio the selection of the Bs -> Ds K decays is optimized using an Artificial Neural Network, allowing an optimal use of the multidimensional information contained in the input variables. As far as the presence of similar and larger physics backgrounds a careful determination of the backgrounds features and a precision calibration, using real data, of the particle identification observables is done. Thus all information, coming from kinematics and particle identification of the final state particles, is combined in an unbinned maximum likelihood fit to disentangle relative fractions of all contributions. As a result, we measure the branching ratio B(Bs -> Ds K)/B(Bs -> Ds pi) decay

Composable partial multiparty session types for open systems

Session types are a well-established framework for the specification of interactions between components of a distributed systems. An important issue is how to determine the type for an open system, i.e., obtained by assembling subcomponents, some of which could be missing. To this end, we introduce partial sessions and partial (multiparty) session types. Partial sessions can be composed, and the type of the resulting system is derived from those of its components without knowing any suitable global type nor the types of missing parts. To deal with this incomplete information, partial session types represent the subjective views of the interactions from participants’ perspectives; when sessions are composed, different partial views can be merged if compatible, yielding a unified view of the session. Incompatible types, due to, e.g., miscommunications or deadlocks, are detected at the merging phase. In fact, in this theory the distinction between global and local types vanishes. We apply these types to a process calculus for which we prove subject reduction and progress, so that well-typed systems never violate the prescribed constraints. In particular, we introduce a generalization of the progress property, in order to accommodate the case when a partial session cannot progress not due to a deadlock, but because some participants are still missing. Therefore, partial session types support the development of systems by incremental assembling of components

A rapid and selective mass spectrometric method for the identification of nitrated proteins.

The nitration of protein tyrosine residues represents an important posttranslational modification during development, oxidative stress, and biological aging. The major challenge in the proteomic analysis of nitroproteins is the need to discriminate modified proteins, usually occurring at substoichiometric levels, from the large amount of nonmodified proteins. Moreover, precise localization of the nitration site is often required to fully describe the biological process. Identification of the specific targets of protein oxidation was previously accomplished using immunoprecipitation techniques followed by immunochemical detection. Here, we report a totally new approach involving dansyl chloride labeling of the nitration sites which relies on the enormous potential of MSn analysis. The tryptic digest from the entire protein mixture is directly analyzed by MS on a linear ion trap mass spectrometer. Discrimination between nitro- and unmodified peptide is based on two selectivity criteria obtained by combining a precursor ion scan and a MS3 analysis. The novel labeling procedure was successfully applied to the identification of 3-nitrotyrosine residues in complex protein mixture

Rehabilitation and seismic upgrading of the masonry arch bridge over the Magra river in Villafranca

The paper deals with the rehabilitation of an historical masonry bridge crossing the Magra river and connecting the small towns of Mulazzo and Villafranca in the northern part of Tuscany (I).The masonry arch bridge, characterized by eight arches spanning 19 m around each and by around 12 m height intermediate masonry piers on shallow foundations, was built in 1874. Since the original carriageway width was not sufficient to allow two lanes, in 1961 it was widened by means of two lateral prestressed concrete beams, supported by the piers, so hiding the arches and modifying severely the original aspect of the bridge itself. In 2011, during the Magra flooding, two arches on the Mulazzo side collapsed due to scour of the extreme pier. The reconstruction the collapsed arches and rehabilitation and the strengthening of the bridge, which has been completed last year, is discussed and the execution of the interventions, which has performed without erection of temporary support in the riverbed, is also illustrated. Particular attention is devoted to the original solutions which have been adopted for the full seismic upgrading of the bridge according to the Italian Building Code currently in force, recovering the original architectural aspect of the bridge and widening the carriageway as well

The Italian public finances in the period 1998-2007: temporary factors, medium-term trends and discretionary measures

The paper examines the development of Italy’s public finances after the consolidation period 1992-97, which secured participation in the European Monetary Union from the outset. The “structural” developments in the main budgetary components are assessed, excluding the effects of the economic cycle and of temporary measures. The analysis shows a rapid deterioration in the years 1998-2003, whose roots can be traced back to the consolidation of the early 1990s, achieved primarily by means of tax increases and cuts in capital expenditure. Since 2004 there has been a structural improvement, initially modest but substantial in 2006 and 2007. Sustaining this adjustment and making further progress may again prove difficult, as the fiscal correction is similar in nature to the previous consolidation effort. Looking at the whole period 1998-2007, the deterioration of the public finances seems attributable to the difficulty to restrain the growth of current primary expenditure.structural budget, business cycle, temporary measures, public finances

Environmental Pollution and Peripheral Artery Disease

Peripheral artery disease (PAD) of the lower limbs represents one of the most important clinical conditions among vascular disease and can negatively impact quality of life of affected patients, representing also an important socioeconomic burden. Several risk factors predispose to PAD and its complications. Nevertheless, the role of pollution in this context has not been fully evaluated and this article explored the most updated information on epidemiology and environmental pollution in order to hypothesize the possible contribution of air pollution in the onset of PAD. Pollution is an important problem for the global community and has harmful effects on human health and cardiovascular system, and, specifically, particulate matter 10 (PM10) was found significantly associated with PAD