Gas-phase chemistry of the negative ions of fully-protected peptides by high-resolution electrospray ionization tandem mass spectrometry

Fully-protected C-terminal free peptides can be conveniently analyzed by high-resolution electrospray tandem mass spectrometry (ESI-MS/MS) in a quadrupole quadrupole time-of-flight tandem hybrid mass spectrometer, operated in the negative (-) ionizaionization mode. The unusual choice of negative ions in mass spectrometry applications to peptide analysis was needed to obtain exhaustive sequence and structural data. The low-energy collision-induced dissociation (CID) experiments provided, in fact, tandem mass spectra displaying highly diagnostic fragments with a good signal-to-noise ratio. The method is applied to segments of porcine calcitonin (Cal), Cal (1016, 1), Cal (1724, 2) and Cal (2528, 3) whose [M H]- deprotonated molecular ions provided low-energy CID mass spectra which allow the evaluation either of the primary structure of the peptide and of the location of the side-chain protective groups. ESI (+) MS can be conveniently used, in the high resolution mode, to achieve precise information on the elemental composition of the examined peptides.     

Identification and assay of wild-type and modified nucleoside mixtures by turbo ionspray ionization tandem mass spectrometry

A method is presented which allows the identification and assay of a nucleoside in the presence of other analogues and homologues. The method is based on the conventional multiple reaction monitoring approach performed on the [M + H]+ ions of wild-type and modified nucleosides produced by the turbo ionspray ionization method on a triple-quadrupole mass spectrometer. The accuracy of the quantitative determination relies on the evaluation of a response factor rho, which takes into account the kinetics of dissociation of the parent ions into the protonated [B + 2H]+ nucleobase ions. The evaluation of the absolute concentration of each analyte in the examined mixture does not require any previous chromatographic separation.     

Clustering of financial time series

This paper addresses the topic of classifying financial time series in a fuzzy framework proposing two fuzzy clustering models both based on GARCH models. In general clustering of financial time series, due to their peculiar features, needs the definition of suitable distance measures. At this aim, the first fuzzy clustering model exploits the autoregressive representation of GARCH models and employs, in the framework of a partitioning around medoids algorithm, the classical autoregressive metric. The second fuzzy clustering model, also based on partitioning around medoids algorithm, uses the Caiado distance, a Mahalanobis-like distance, based on estimated GARCH parameters and covariances that takes into account the information about the volatility structure of time series. In order to illustrate the merits of the proposed fuzzy approaches an application to the problem of classifying 29 time series of Euro exchange rates against international currencies is presented and discussed, also comparing the fuzzy models with their crisp version.     

An investigation on the nature of the peptide at m/z 904, overexpressed in plasma of patients with colorectal cancer and familial adenomatous polyposis

In an investigation devoted to the search for plasma markers for colorectal cancer (CRC), carried out by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry, a series of overexpressed peptides were identified in the plasma of patients. Among them the peptide with molecular weight 903 Da was the most abundant one, with a mean +/- (SD) relative abundance of 37 +/- 17% and a frequency over 60%. Interestingly, also in plasma samples of ten subjects affected by familial adenomatous polyposis (FAP), the peptide with molecular weight 903 was overexpressed. In this investigation, MALDI/MS/MS experiments were carried out on the ion at m/z 904 detected in the MALDI mass spectra of CRC and FAP patients. The data analysis by SwissProt.2007.01.09 indicates that this peptide is due to the sequence RPPGFSPF, found in the kininogen-1 precursor, which is an alpha-2-thiol proteinase inhibitor. In the case of subjects affected by a particular FAP syndrome, the MALDI/MS/MS spectra were quite different from those obtained from CRC and FAP patients. In fact, two sequences have been evidenced: RPPGFSPF belonging to kininogen-1 precursor, and PRKSSSSR belonging to Forkhead box protein 01A.     

Simulation of the Interactions of Arginine with Wild-Type GALT Enzyme and the Classic Galactosemia-Related Mutant p.Q188R by a Computational Approach

Classic galactosemia is an inborn error of metabolism associated with mutations that impair the activity and the stability of galactose-1-phosphate uridylyltransferase (GALT), catalyzing the third step in galactose metabolism. To date, no treatments (including dietary galactose deprivation) are able to prevent or alleviate the long-term complications affecting galactosemic patients. Evidence that arginine is able to improve the activity of the human enzyme expressed in a prokaryotic model of classic galactosemia has induced researchers to suppose that this amino acid could act as a pharmacochaperone, but no effects were detected in four galactosemic patients treated with this amino acid. Given that no molecular characterizations of the possible effects of arginine on GALT have been performed, and given that the samples of patients treated with arginine are extremely limited for drawing definitive conclusions at the clinical level, we performed computational simulations in order to predict the interactions (if any) between this amino acid and the enzyme. Our results do not support the possibility that arginine could function as a pharmacochaperone for GALT, but information obtained by this study could be useful for identifying, in the future, possible pharmacochaperones for this enzyme.     

Proteomics of bovine myelin sheath: Characterization of a truncated form of P0 by MALDI-TOF/TOF mass spectrometry

The glycoprotein P0, the major structural protein of the peripheral nerve myelin, plays a critical role in holding myelin lamellae together via interaction of both extracellular and cytoplasmic domains. Mutations in the human P0 gene give rise to severe and progressive forms of dominantly inherited peripheral neuropathies like CMT1B. Here we report on the characterization of a bovine P0-derived protein of nearly 26 kD that corresponds to the P0 protein truncated in its cytoplasmic domain. Matrix assisted laser desorption ionization (MALDI)-time-of-flight/time-of-flight (TOF/TOF) mass spectrometry (MS) analysis on its tryptic digest has provided a peptide mapping, the main difference of which from the normal P0 analog was represented by the absence of the cluster of peaks at m/z 1513.7501, 1530.7701, and 1546.7651. The latter corresponds to the P0 fragment QTPVLYAMLDHSR and to its pyroglutamic and methionine-oxidized derivatives. The species at 1530.7701 covering the sequence 186-198 of P0 is not an artifact and might have a functional role in the myelin architecture.     

Free vibrations of spatial Timoshenko arches

This paper addresses the evaluation of the exact natural frequencies and vibration modes of structures obtained by assemblage of plane circular arched Timoshenko beams. The exact dynamic stiffness matrix of the single circular arch, in which both the in-plane and out-of-plane motions are taken into account, is derived in an useful dimensionless form by revisiting the mathematical approach already adopted by Howson and Jemah (1999 [18]), for the in plane and the out-of-plan natural frequencies of curved Timoshenko beams. The knowledge of the exact dynamic stiffness matrix of the single arch makes the direct evaluation of the exact global dynamic stiffness matrix of spatial arch structures possible. Furthermore, it allows the exact evaluation of the frequencies and the corresponding vibration modes, for the distributed parameter model, through the application of the Wittrick and Williams algorithm. Consistently with the dimensionless form proposed in the derivation of the equations of motion and the dynamic stiffness matrix, an original and extensive parametric analysis on the in-plane and out-of-plane dynamic behaviour of the single arch, for a wide range of structural and geometrical dimensionless parameters, has been performed. Moreover, some numerical applications, relative to the evaluation of exact frequencies and the corresponding mode shapes in spatial arched structures, are reported. The exact solution has been numerically validated by comparing the results with those obtained by a refined finite element simulation.     

Interactions of a water-soluble calix[4]arene with spermine: solution and solid-state characterisation

Abstract

The octaanionic 5,11,17,23-tetrasulfonato-25,26,27,28-tetrakis(hydroxycarbonylmethoxy)-calix[4]arene (cone conformation) (C₄TsTc) was investigated as a sensor for the biogenic tetracationic polyamine, spermine _.(H₄Spe⁴⁺). Fluorescence titration experiments of the water-soluble calixarene with spermine showed the formation of the 2:1 and 1:1 calixarene:spermine complexes in solution. The single crystal X-ray diffraction analysis of [(NaC₄TsTc)₄·(H₄Spe)₇] confirmed the formation of 2:1 and 1:1 calixarene:spermine species and showed that the water-soluble calixarene binds the spermine either by partially hosting it in the inner cavity or through the carboxylate groups on the lower rim. In order to investigate the effect of multivalent systems, supramolecular assemblies of octaanionic calixarene molecules templated by meso-tetrakis(4-N-methylpyridyl)porphyrin (H₂T₄) in different stoichiometric porphyrin:calixarene ratios (1:4 and 3:4) were also tested for spermine binding in solution. Fluorescence titration experiments with the 1:4 and 3:4 H₂T₄:C₄TsTc supramolecular complexes showed that the multivalent assemblies are more sensitive to the presence of spermine than the calixarene alone.