Catarina F. Correia

Vibrational signatures of protonated, phosphorylated amino acids in the gas phase.

Structural characterization of protonated phosphorylated serine, threonine, and tyrosine was performed using mid-infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations. The ions were generated and analyzed by an external electrospray source coupled to a Paul ion-trap type mass spectrometer. Their fragmentation was induced by the resonant absorption of multiple photons from a tunable free electron laser (FEL) beam. IRMPD spectra were recorded in the 900-1850 cm(-1) energy range and compared to the corresponding computed IR spectra. On the basis of the frequency and intensity of two independent bands in the 900-1400 cm(-1) energy range, it is possible to identify the phosphorylated residue. IRMPD spectra for a 12-residue fragment of stathmin in its phosphorylated and nonphosphorylated forms were also recorded in the 800-1400 cm(-1) energy range. The lack of spectral congestion in the 900-1300 cm(-1) region makes their distinction facile. Our results show that IRMPD spectroscopy may became a valuable tool for structural characterization of small phosphorylated peptides.

Structure of Sodiated Octa-Glycine: IRMPD Spectroscopy and Molecular Modeling

The structure of the sodiated peptide GGGGGGGG-Na+ or G8-Na+ was investigated by infrared multiple photon dissociation (IRMPD) spectroscopy and a combination of theoretical methods. IRMPD was carried out in both the fingerprint and N—H/O—H stretching regions. Modeling used the polarizable force field AMOEBA in conjunction with the replica-exchange molecular dynamics (REMD) method, allowing an efficient exploration of the potential energy surface. Geometries and energetics were further refined at B3LYP-D and MP2 quantum chemical levels. The IRMPD spectra indicate that there is no free C-terminus OH and that several N—Hs are free of hydrogen bonding, while several others are bound, however not very strongly. The structure must then be either of the charge solvation (CS) type with a hydrogen-bound acidic OH, or a salt bridge (SB). Extensive REMD searches generated several low-energy structures of both types. The most stable structures of each type are computed to be very close in energy. The computed energy barrier separating these structures is small enough that G8-Na+ is likely fluxional with easy proton transfer between the two peptide termini. There is, however, good agreement between experiment and computations in the entire spectral range for the CS isomer only, which thus appears to be the most likely structure of G8-Na+ at room temperature.

Structural Characterization by IRMPD Spectroscopy and DFT Calculations of Deprotonated Phosphorylated Amino Acids in the Gas Phase

Gas-phase infrared spectra of deprotonated phosphorylated amino acids ([pAA-H](-))-phosphoserine ([pSer-H](-)), phosphothreonine ([pThr-H](-)), and phosphotyrosine ([pTyr-H](-))-and of the dihydrogen phosphate anion H(2)PO(4)(-) have been recorded in the mid-IR region (650-2000 cm(-1)) under tandem mass spectrometry conditions. The experimental setup involved a Paul ion trap equipped with an electrospray ionization source coupled with a tunable free electron laser (FEL). Spectral assignment of the observed IRMPD bands and identification of the vibrational signatures of the phosphorylation have been performed by comparison with DFT calculations. The H(2)PO(4)(-) anion has been used as a simple model of a free deprotonated phosphate group, helping the identification of the IR signatures of phosphorylation. Our results show that deprotonation occurs on the phosphate group for the three amino acids. A comparison between the deprotonated and protonated phosphorylated amino acids is reported for the most important vibrational features.

IRMPD Spectroscopy of a Protonated, Phosphorylated Dipeptide†

The protonated, phosphorylated dipeptide [GpY+H](+) is characterized by mid-infrared multiple-photon dissociation (IRMPD) spectroscopy and quantum-chemical calculations. The ions are generated in an external electrospray source and analyzed in a Fourier transform ion cyclotron resonance mass spectrometer, and their fragmentation is induced by resonant absorption of multiple photons emitted by a tunable free-electron laser. The IRMPD spectra are recorded in the 900-1730 cm(-1) range and compared to the absorption spectra computed for the lowest energy structures. A detailed calibration of computational levels, including B3LYP-D and coupled cluster, is carried out to obtain reliable relative energies of the low-energy conformers. It turns out that a single structure can be invoked to assign the IRMPD spectrum. Protonation at the N terminus leads to the formation of a strong ionic hydrogen bond with the phosphate P=O group in all low-energy structures. This leads to a P=O stretching frequency for [GpY+H](+) that is closer to that of [pS+H](+) than to that of [pY+H](+) and thus demonstrates the sensitivity of this mode to the phosphate environment. The COP phosphate ester stretching mode is confirmed to be an intrinsic diagnostic for identification of which type of amino acid is phosphorylated.

O-H bond dissociation enthalpies in hydroxyphenols. A time-resolved photoacoustic calorimetry and quantum chemistry study

Time-resolved photoacoustic calorimetry (TR-PAC) was used to investigate the energetics of O–H bonds of phenol, catechol, pyrogallol, and phloroglucinol. Values of −27.1 ± 3.9, −44.1 ± 4.4 and −1.6 ± 3.8 kJ mol−1, respectively, were obtained for the solution-phase (acetonitrile) O–H bond dissociation enthalpies of the last three compounds relative to the O–H bond dissociation enthalpy in phenol, ΔDHosln(ArO–H) = DHosln(ArO–H) − DHosln(PhO–H). A value of 388.7 ± 3.7 kJ mol−1 was determined for the PhO–H bond dissociation enthalpy in acetonitrile. Density functional theory (MPW1PW91/aug-cc-pVDZ) calculations and complete basis set (CBS-4M) calculations were carried out to analyse intramolecular hydrogen bonding and to predict gas-phase O–H bond dissociation enthalpies, DHo(ArO–H). A microsolvation model, based on the DFT calculations, was used to study the differential solvation of the phenols and their radicals in acetonitrile and to bridge solution- and gas-phase data. The results strongly suggest that ΔDHosln(ArO–H) ≈ ΔDHo(ArO–H). Hence, to calculate absolute gas-phase O–H bond dissociation enthalpies in substituted phenols from the corresponding solution-phase values, the solvation enthalpies of the substituted phenols and their radicals are not required.

Identification and quantitative analysis of human transthyretin variants in human serum by Fourier transform ion-cyclotron resonance mass spectrometry

Transthyretin (TTR) is a homotetrameric protein involved in thyroid hormone transport in blood and in retinol binding in the central nervous system. More than 80 point mutations in this protein are known to be associated with the formation of amyloid deposits and systemic amyloidotic pathologies. Age at onset varies according to the mutation but considerable variations also occur for subjects carrying the same mutation. Moreover, wild-type TTR forms amyloid deposits in systemic senile amyloidosis, a geriatric disorder. An accurate diagnostic and the choice of therapeutic options depend on the identification of the specific mutation. Previous characterization of TTR variants by mass spectrometry required the use of antibodies for sample enrichment. We developed a novel assay based on ultra high-resolution mass spectrometry to identify human TTR variants. The method, requiring a very low sample amount, is based on SDS-PAGE fractionation of human serum, followed by peptide mass fingerprinting by MALDI-FTICR-MS (matrix assisted laser desorption ionization coupled to Fourier transform ion cyclotron resonance mass spectrometry). Moreover, it is possible to perform a relative quantification of wild type and mutant TTR forms by mass spectrometry. The method was tested and validated with the V30M mutant, involved in familial amyloidotic neuropathy of Portuguese type.

Protein Interaction Networks Reveal Novel Autism Risk Genes within GWAS Statistical Noise

Genome-wide association studies (GWAS) for Autism Spectrum Disorder (ASD) thus far met limited success in the identification of common risk variants, consistent with the notion that variants with small individual effects cannot be detected individually in single SNP analysis. To further capture disease risk gene information from ASD association studies, we applied a network-based strategy to the Autism Genome Project (AGP) and the Autism Genetics Resource Exchange GWAS datasets, combining family-based association data with Human Protein-Protein interaction (PPI) data. Our analysis showed that autism-associated proteins at higher than conventional levels of significance (P<0.1) directly interact more than random expectation and are involved in a limited number of interconnected biological processes, indicating that they are functionally related. The functionally coherent networks generated by this approach contain ASD-relevant disease biology, as demonstrated by an improved positive predictive value and sensitivity in retrieving known ASD candidate genes relative to the top associated genes from either GWAS, as well as a higher gene overlap between the two ASD datasets. Analysis of the intersection between the networks obtained from the two ASD GWAS and six unrelated disease datasets identified fourteen genes exclusively present in the ASD networks. These are mostly novel genes involved in abnormal nervous system phenotypes in animal models, and in fundamental biological processes previously implicated in ASD, such as axon guidance, cell adhesion or cytoskeleton organization. Overall, our results highlighted novel susceptibility genes previously hidden within GWAS statistical “noise” that warrant further analysis for causal variants.

A non-invasive method based on saliva to characterize transthyretin in familial amyloidotic polyneuropathy patients using FT-ICR high-resolution MS

Purpose: To identify, characterize and perform a relative quantification of human transthyretin (TTR) variants in human saliva.

The control and data acquisition system of a laser in-vessel viewing system

This paper presents the dedicated control and data acquisition system (CADAS) of a new laser in-vessel viewing system that has been developed for inspection purposes in fusion experiments. CADAS is based on a MC68060 microprocessor and on-site developed VME instrumentation. Its main aims are to simultaneously control the laser alignment system as well as the laser beam deflection for in-vessel scanning, acquire a high-resolution image and support real-time data flow rates up to 2 Mbyte/s from the acquisition modules to the hard disk and network. The hardware (modules for control and alignment acquisition, scanning acquisition and monitoring) as well as the three levels of software are described.

Pharmacogenetics of risperidone response and induced side effects

Risperidone is an atypical antipsychotic that has been effectively used to treat several psychiatric diseases. Atypical antipsychotics present some advantages over conventional antipsychotics, primarily because they offer effective treatment alternatives that are relatively free of extrapyramidal symptoms. However, as with all antipsychotics, there are wide individual differences in response to risperidone, both regarding therapeutic effects and adverse effects, imposing some limitations with respect to the therapeutic use of the drug. Genetic factors are thought to play an important role in determining the variability to drug response. A growing number of studies are investigating how genetic polymorphisms of enzymes involved in drug metabolism or of receptors targeted by antipsychotic agents influence drug treatment of several neuropsychiatric diseases. In this article we will review the genetic variability in both the pharmacokinetics of risperidone action and in pharmacodynamic structures mediating risperidone effects, as well as the pharmacogenetic studies performed for these genes.