Parent Fragment Research Articles

Efficient Modeling of MS/MS Data for Metabolic Flux Analysis.

Metabolic flux analysis (MFA) is a widely used method for quantifying intracellular metabolic fluxes. It works by feeding cells with isotopic labeled nutrients, measuring metabolite isotopic labeling, and computationally interpreting the measured labeling data to estimate flux. Tandem mass-spectrometry (MS/MS) has been shown to be useful for MFA, providing positional isotopic labeling data. Specifically, MS/MS enables the measurement of a metabolite tandem mass-isotopomer distribution, representing the abundance in which certain parent and product fragments of a metabolite have different number of labeled atoms. However, a major limitation in using MFA with MS/MS data is the lack of a computationally efficient method for simulating such isotopic labeling data. Here, we describe the tandemer approach for efficiently computing metabolite tandem mass-isotopomer distributions in a metabolic network, given an estimation of metabolic fluxes. This approach can be used by MFA to find optimal metabolic fluxes, whose induced metabolite labeling patterns match tandem mass-isotopomer distributions measured by MS/MS. The tandemer approach is applied to simulate MS/MS data in a small-scale metabolic network model of mammalian methionine metabolism and in a large-scale metabolic network model of E. coli. It is shown to significantly improve the running time by between two to three orders of magnitude compared to the state-of-the-art, cumomers approach. We expect the tandemer approach to promote broader usage of MS/MS technology in metabolic flux analysis. Implementation is freely available at www.cs.technion.ac.il/~tomersh/methods.html

Coulomb-explosion imaging using a pixel-imaging mass-spectrometry camera

Femtosecond laser-induced Coulomb-explosion imaging of 3,5-dibromo-$3{}^{\ensuremath{'}},5{}^{\ensuremath{'}}$-difluoro-$4{}^{\ensuremath{'}}$-cyanobiphenyl molecules prealigned in space is explored using a pixel-imaging mass-spectrometry (PImMS) camera. The fast-event-triggered camera allows the concurrent detection of the correlated two-dimensional momentum images, or covariance maps, of all the ionic fragments resulting from fragmentation of multiple molecules in each acquisition cycle. Detailed simulation of the covariance maps reveals that they provide rich information about the parent molecular structure and fragmentation dynamics. Future opportunities for imaging the real-time dynamics of intramolecular processes are considered.

Development of a Large Animal Model of Osteochondritis Dissecans of the Knee: A Pilot Study.

Background:Treatment of osteochondritis dissecans (OCD) of the knee is challenging, and evidence for stage-dependent treatment options is lacking. Basic science approaches utilizing animal models have provided insight into the etiology of OCD but have yet to produce a reliable and reproducible large animal model of the disease on which to test new surgical strategies.Purpose/Hypotheses:The purpose of this study was to develop an animal model featuring an OCD-like lesion in terms of size, location, and International Cartilage Repair Society (ICRS) grading. The hypothesis was that surgical creation of an osteochondral defect followed by placement of a barrier between parent bone and progeny fragment would generate a reproducible OCD-like lesion.Study Design:Controlled laboratory study.Methods:Bilateral osteochondral lesions were created in the medial femoral condyles of 9 Yucatan minipigs. After lesion creation, a biodegradable membrane was interposed between the progeny and parent bone. Five different treatment groups were evaluated at 2 weeks: a control with no membrane (ctrl group; n = 4), a slowly degrading nanofibrous poly(∊-caprolactone) membrane (PCL group; n = 4), a fenestrated PCL membrane with 1.5-mm holes covering 25% of surface area (fenPCL group; n = 4), a collagen membrane (Bio-Gide) (CM group; n = 3), and a fenestrated CM (fenCM group; n = 3). Five unperturbed lateral condyles (1 from each treatment group) served as sham controls. After euthanasia on day 14, the lesion was evaluated by gross inspection, fluoroscopy, micro–computed tomography (micro-CT), and histology. To quantify changes between groups, a scoring system based on gross appearance (0-2), fluoroscopy (0-2), and micro-CT (0-6) was established. Micro-CT was used to quantify bone volume per total volume (BV/TV) in a defined region surrounding and inclusive of the defect.Results:The no scaffold group showed healing of the subchondral bone at 2 weeks, with continuity of subchondral bone elements. Conversely, condyles treated with PCL or CM showed substantial remodeling, with loss of bone in both the progeny fragment and surrounding parent bone. When these membranes were fenestrated (fenPCL and fenCM groups), bone loss was less severe. Histological analysis showed no integration in the cartilage layer in any treatment group, while fibrous tissue formed between the parent and progeny fragments. Micro-CT showed significant differences in mean BV/TV between the PCL (27.4% ± 2.3%) and the sham (47.7% ± 1.4%) or no scaffold (54.9% ± 15.1%) groups (P < .01 and P < .05, respectively). In addition, a significant difference in bone loss was evident between the PCL and fenPCL groups (mean BV/TV, 46.6% ± 15.2%; P < .05), as well as between the PCL and fenCM (mean BV/TV, 50.9% ± 3.5%) and fenPCL groups (P < .01). Grading by 6 blinded reviewers using an OCD scoring system with 3 subcategories showed a significant difference between control and PCL groups.Conclusion:This study successfully developed a large animal model of OCD-like lesions in the knee joint of Yucatan minipigs. The lesions generated matched characteristics of an ICRS grade 3 OCD lesion in humans. These findings set the stage for ongoing model refinement as well as exploration of novel interventional therapies to restore function and bone and cartilage patency in individuals affected by this rare but significant disease.Clinical Relevance:This developed model will serve as a platform on which to further investigate the natural course as well as emerging treatment options for OCD.

Gas-phase conformations of small polyprolines and their fragment ions by IRMPD spectroscopy

Infrared multiple-photon dissociation (IRMPD) spectroscopy has been used to examine the gas-phase conformations of a series of short protonated polyproline ions (Pro3–Pro6), their CID/IRMPD fragmentation pathways, and the associated fragment identities. Consistent with previous findings, and in combination with density functional theory (DFT) and MM/MD methods, a series of conformers for the protonated parent ions having their first peptide bond in the cis conformation has been identified. This conformation maximizes the solvation of the protonated N-terminus and stabilizes these compact globular-type conformations. This is in contrast to the PPI and PPII polyproline-type helices reported for larger polyproline peptides in solution. As well, this conformation leads to a unique fragmentation pattern upon collisional or multiple-photon activation. We report observation of the uncommon, but thermodynamically favored, diketopiperazine-type b2+ fragment ion. Formation of b2+ ions along the diketopiperazine pathway is in line with a cis configuration of the first amide linkage in the protonated parent ion. Additionally, the parent ion conformations, fragmentation pathways, and proton affinities of the resulting fragments have been related to the observed proline-effect in CID mass spectra.

π-Electron ring-currents and bond-currents in some conjugated altan-structures.

Ring-currents and bond-currents calculated using the Hückel-London-Pople-McWeeny (HLPM) method are reported for a series of altan-structures recently explored by Monaco et al. and to which these authors have applied the ab initio ipso-centric formalism in order to calculate the structures' π-electron current-density maps. Two aspects of the conclusions of their ab initio study are confirmed by means of the much more simplistic HLPM formalism adopted here: namely (a) that the inner core in these altan-structures generally displays similar current patterns to those previously reported for the parent fragments, and (b) that the unexpected diamagnetic circulation in the outer [4n]-perimeter of altan-kekulene reported by Monaco et al. is not an artifact of their method but appears to be confirmed. Attention is drawn to the conceptual advantages of discussing bond currents rather than just (equivalent) ring currents.

Covariance imaging experiments using a pixel-imaging mass-spectrometry camera

The ``pixel imaging mass spectrometry'' camera is used to perform femtosecond laser-induced Coulomb explosion imaging of 3,5-dibromo-3${}^{\ensuremath{'}}$,5${}^{\ensuremath{'}}$-difluoro-4${}^{\ensuremath{'}}$-cyanobiphenyl molecules prealigned in space. The experiment allows the concurrent detection of the correlated two-dimensional momentum images of all the ionic fragments resulting from fragmentation of multiple molecules in each acquisition cycle. The Coulomb explosion studies provide rich information about the parent molecular structure and fragmentation dynamics, and open new opportunities for real-time imaging of intramolecular processes.

Investigations of dissociative photoionization of isooctane by synchrotron radiation

Using vacuum ultraviolet photons produced by synchrotron radiation and reflection time-of-flight mass spectrometer, dissociative photoionization of isooctane was measured in the photon energy region of 9.7–15.6eV under ultrasonic molecular beam. Then the dissociative ionization products at different photon energies were obtained. By measuring the photoionization efficiency curves, the appearance potentials of the dominative ion fragments and the vertical ionization energy of isooctane were determined. In addition, combining with G3 calculations we obtained the structure and energy of the parent, neutral and ion fragments. By comparing the experimental measurements with the theoretical calculations, the dissociative photoionization channels of isooctane were elucidated, and formation enthalpies of the fragmented ions and the dissociation energy of the parent ion were obtained.

Rapid genomic and transcriptomic alterations induced by wide hybridization: Chrysanthemum nankingense × Tanacetum vulgare and C. crassum × Crossostephium chinense (Asteraceae)

BackgroundHybridization is a major driver of evolution in plants. In a number of plant species, the process of hybridization has been revealed to be accompanied by wide-ranging genetic and epigenetic alterations, some of which have consequences on gene transcripts. The Asteraceae family includes a number of polyploid species, and wide crossing is seen as a viable means of genetically improving ornamental species such as Chrysanthemum spp. However, the consequences of hybridization in this taxon have yet to be characterized.ResultsAmplified fragment length polymorphism (AFLP), methylation sensitive amplification polymorphism (MSAP) and cDNA-AFLP profiling of the two intergeneric hybrids C. nankingense × Tanacetum vulgare and C. crassum × Crossostephium chinense were employed to characterize, respectively, the genomic, epigenomic and transcriptomic changes induced by the hybridization event. The hybrids’ AFLP profiles included both the loss of specific parental fragments and the gain of fragments not present in either parent’s profile. About 10% of the paternal fragments were not inherited by the hybrid, while the corresponding rate for the maternal parent fragments was around 4–5%. The novel fragments detected may have arisen either due to heterozygosity in one or other parent, or as a result of a deletion event following the hybridization. Around one half of the cDNA-AFLP fragments were common to both parents, about 30% were specific to the female parent, and somewhat under 20% specific to the male parent; the remainder (2.9-4.7%) of the hybrids’ fragments were not present in either parent’s profile. The MSAP fingerprinting demonstrated that the hybridization event also reduced the amount of global cytosine methylation, since > 50% of the parental fragments were methylated, while the corresponding frequencies for the two hybrids were 48.5% and 50.4%.ConclusionsCombining two different Asteraceae genomes via hybridization clearly induced a range of genomic and epigenomic alterations, some of which had an effect on the transcriptome. The rapid genomic and transcriptomic alterations induced by hybridization may accelerate the evolutionary process among progenies.

Atmospheric pressure chemical ionisation mass spectrometry analysis linked with chemometrics for food classification – A case study: Geographical provenance and cultivar classification of monovarietal clarified apple juices

In the present work, we have evaluated for first time the feasibility of APCI-MS volatile compound fingerprinting in conjunction with chemometrics (PLS-DA) as a new strategy for rapid and non-destructive food classification. For this purpose 202 clarified monovarietal juices extracted from apples differing in their botanical and geographical origin were used for evaluation of the performance of APCI-MS as a classification tool. For an independent test set PLS-DA analyses of pre-treated spectral data gave 100% and 94.2% correct classification rate for the classification by cultivar and geographical origin, respectively. Moreover, PLS-DA analysis of APCI-MS in conjunction with GC–MS data revealed that masses within the spectral ACPI-MS data set were related with parent ions or fragments of alkyesters, carbonyl compounds (hexanal, trans-2-hexenal) and alcohols (1-hexanol, 1-butanol, cis-3-hexenol) and had significant discriminating power both in terms of cultivar and geographical origin.

Comparative Proteomic Analysis of Normal and Collagen IX Null Mouse Cartilage Reveals Altered Extracellular Matrix Composition and Novel Components of the Collagen IX Interactome

Collagen IX is an integral cartilage extracellular matrix component important in skeletal development and joint function. Proteomic analysis and validation studies revealed novel alterations in collagen IX null cartilage. Matrilin-4, collagen XII, thrombospondin-4, fibronectin, βig-h3, and epiphycan are components of the in vivo collagen IX interactome. We applied a proteomics approach to advance our understanding of collagen IX ablation in cartilage. The cartilage extracellular matrix is essential for endochondral bone development and joint function. In addition to the major aggrecan/collagen II framework, the interacting complex of collagen IX, matrilin-3, and cartilage oligomeric matrix protein (COMP) is essential for cartilage matrix stability, as mutations in Col9a1, Col9a2, Col9a3, Comp, and Matn3 genes cause multiple epiphyseal dysplasia, in which patients develop early onset osteoarthritis. In mice, collagen IX ablation results in severely disturbed growth plate organization, hypocellular regions, and abnormal chondrocyte shape. This abnormal differentiation is likely to involve altered cell-matrix interactions but the mechanism is not known. To investigate the molecular basis of the collagen IX null phenotype we analyzed global differences in protein abundance between wild-type and knock-out femoral head cartilage by capillary HPLC tandem mass spectrometry. We identified 297 proteins in 3-day cartilage and 397 proteins in 21-day cartilage. Components that were differentially abundant between wild-type and collagen IX-deficient cartilage included 15 extracellular matrix proteins. Collagen IX ablation was associated with dramatically reduced COMP and matrilin-3, consistent with known interactions. Matrilin-1, matrilin-4, epiphycan, and thrombospondin-4 levels were reduced in collagen IX null cartilage, providing the first in vivo evidence for these proteins belonging to the collagen IX interactome. Thrombospondin-4 expression was reduced at the mRNA level, whereas matrilin-4 was verified as a novel collagen IX-binding protein. Furthermore, changes in TGFβ-induced protein βig-h3 and fibronectin abundance were found in the collagen IX knock-out but not associated with COMP ablation, indicating specific involvement in the abnormal collagen IX null cartilage. In addition, the more widespread expression of collagen XII in the collagen IX-deficient cartilage suggests an attempted compensatory response to the absence of collagen IX. Our differential proteomic analysis of cartilage is a novel approach to identify candidate matrix protein interactions in vivo, underpinning further analysis of mutant cartilage lacking other matrix components or harboring disease-causing mutations.

A SILAC-based Approach Identifies Substrates of Caspase-dependent Cleavage upon TRAIL-induced Apoptosis

The extracellular ligand-induced extrinsic pathway of apoptosis is executed via caspase protease cascades that activate downstream effectors by means of site-directed proteolysis. Here we identify proteome changes upon the induction of apoptosis by the cytokine tumor necrosis factor–related apoptosis-inducing ligand (TRAIL) in a Jurkat T cell line. We detected caspase-dependent cleavage substrates by quantifying protein intensities before and after TRAIL induction in SDS gel slices. Apoptotic protein cleavage events are identified by a characteristic stable isotope labeling with amino acids in cell culture (SILAC) ratio pattern across gel slices that results from differential migration of the cleaved and uncleaved proteins. We applied a statistical test to define apoptotic substrates in the proteome. Our approach identified more than 650 of these cleaved proteins in response to TRAIL-induced apoptosis, including many previously unknown substrates and cleavage sites. Inhibitor treatment combined with triple SILAC demonstrated that the detected cleavage events were caspase dependent. Proteins located in the lumina of organelles such as mitochondria and endoplasmic reticulum were significantly underrepresented in the substrate population. Interestingly, caspase cleavage is generally observed in not only one but several members of stable complexes, but often with lower stoichiometry. For instance, all five proteins of the condensin I complex were cleaved upon TRAIL treatment. The apoptotic substrate proteome data can be accessed and visualized in the MaxQB database and might prove useful for basic and clinical research into TRAIL-induced apoptosis. The technology described here is extensible to a wide range of other proteolytic cleavage events.

Can mitochondrial dysfunction be initiated by dissociative electron attachment to xenobiotics?

Resonance attachment of low-energy electrons to xenobiotic molecules, 2,4-dichlorophenoxyacetic acid (2,4-D), dichlorodiphenyltrichloroethane (DDT) and dichlorodiphenyldichloroethylene (DDE), was investigated under gas-phase conditions by means of complementary experimental techniques. Electron transmission spectroscopy (ETS) and dissociative electron attachment spectroscopy (DEAS), in the 0-6 eV and 0-15 eV energy range, respectively, were applied with the aim of modeling the behavior of these pesticide molecules under reductive conditions in vivo. Formation of long-lived parent molecular anions and fragment negative ions was observed at incident electron energies very close to zero, in agreement with the results of density functional theory calculations. The gas-phase DEA process, analogous to dissociative electron transfer in solution, was considered as a model for the initial step which occurs in the intermembrane space of mitochondria when a xenobiotic molecule captures an electron "leaked" from the respiratory chain. A possible involvement of the fragments produced by DEA to the pesticides under investigation into cellular processes is discussed. It is concluded that the free radicals and potential DNA adducts formed by DEA are expected to be dangerous for mitochondrial functionalities, while several of the products observed could act as messenger molecules, thus interfering with the normal cellular signaling pathways.

Resolving the microcosmos of complex samples: UPLC/travelling wave ion mobility separation high resolution mass spectrometry for the analysis of in vivo drug metabolism studies

In vivo drug metabolism studies with low concentrations of analytes and high matrix burden are challenging. Of special interest are ‘first-in-man’ studies in early stages of pharmaceutical development that do not use 14C labeled drug candidates. Beside conventional MS-fishing techniques which are biased towards known/expected metabolites and mass defect filtration procedures, this paper focuses on the untargeted/unbiased analysis of drug related compounds in complex matrices using two orthogonal separation techniques: UPLC and TWIMS. Standard sample material after oral administration of a drug compound to rats was investigated by UPLC/TWIMS in MSE acquisition mode using interlaced collision energies for the parallel detection of [M+H]+ parent ions and fragments. Due to the fragmentation after ion mobility separation in the transfer region of the Synapt G2-triwave device, [M+H]+ ion species are aligned with their related fragments by virtue of possessing the same retention time and drift time profile. Four dimensional data analysis of the continuum raw data was performed by automated peak picking and alignment within the MSE viewer software. As result, completely purified MS- and MS/MS-data of metabolites were extracted from raw mass data with high matrix burden and were used without compromise for structure elucidation. This analytical methodology is universally applicable for the unbiased/untargeted and robust analysis of any analyte of interest in complex matrices, including small molecules, peptides and proteins. The high quality data files can be used as data repositories for the purpose of retrospective analysis which is of particular interest for the long term process in drug development.

Investigations of human platelet-type 12-lipoxygenase: role of lipoxygenase products in platelet activation

Human platelet-type 12-lipoxygenase (12-LOX) has recently been shown to play an important role in regulation of human platelet function by reacting with arachidonic acid (AA). However, a number of other fatty acids are present on the platelet surface that, when cleaved from the phospholipid, can be oxidized by 12-LOX. We sought to characterize the substrate specificity of 12-LOX against six essential fatty acids: AA, dihomo-γ-linolenic acid (DGLA), eicosapentaenoic acid (EPA), α-linolenic acid (ALA), eicosadienoic acid (EDA), and linoleic acid (LA). Three fatty acids were comparable substrates (AA, DGLA, and EPA), one was 5-fold slower (ALA), and two showed no reactivity with 12-LOX (EDA and LA). The bioactive lipid products resulting from 12-LOX oxidation of DGLA, 12-(S)-hydroperoxy-8Z,10E,14Z-eicosatrienoic acid [12(S)-HPETrE], and its reduced product, 12(S)-HETrE, resulted in significant attenuation of agonist-mediated platelet aggregation, granule secretion, αIIbβ3 activation, Rap1 activation, and clot retraction. Treatment with DGLA similarly inhibited PAR1-mediated platelet activation as well as platelet clot retraction. These observations are in surprising contrast to our recent work showing 12(S)-HETE is a prothrombotic bioactive lipid and support our hypothesis that the overall effect of 12-LOX oxidation of fatty acids in the platelet is dependent on the fatty acid substrates available at the platelet membrane.

Phytosterols in pumpkin seed oil extracted by organic solvents and supercritical CO2

AbstractPhytosterols in Cucurbita pepo convar. citrullina seed oil were analyzed by GC–MS after extraction by the organic solvents, hexane and petroleum ether, and by supercritical carbon dioxide at 400 bar and 40°C. Desmosterol, campesterol, stigmasterol, β‐sitosterol, spinasterol, Δ7,22,25‐stigmastatrienol, Δ7‐stigmastenol, Δ7,25‐stigmastadienol, and Δ7‐avenasterol were identified mass spectrometrically via detection of the parent molecular ions and fragmentation patterns of corresponding trimethylsilyl derivatives. The used derivatizing agents N‐methyl‐N‐(trimethylsilyl)trifluoroacetamide (MSTFA) and N,O‐bis(trimethylsilyl)trifluoroacetamide (BSTFA) are equally effective for phytosterol content determination. As expected, the predominant phytosterols were Δ7‐sterols that ranged from 91.0 to 94.2% of the total phytosterol content given as sum of free sterols and steryl esters. Comparison of extraction methods revealed that, although the oil yields obtained by extraction with hexane, petroleum ether and supercritical CO2 were 43.37, 44.65, and 36.17%, respectively, the total phytosterol content in supercritical CO2 extract (294 mg/100 g oil, for both MSTFA and BSTFA) was about 30% higher than in hexane and about 20% higher than in petroleum ether extract.Practical applications: Extraction with the application of fluids in supercritical state opens a new approach to the production of edible vegetable oils. Many economical, health, and environmental aspects are interlaced in this modern approach. By applying the supercritical extraction, the selectivity of the extraction can be significantly improved compared to traditional methods of extraction. Thus, depending on the operating conditions of supercritical CO2 extraction higher total phytosterol content can be achieved resulting in improved nutritional value of the pumpkin seed oil.

Quantitative Statistical Analysis of Standard and Human Blood Proteins from Liquid Chromatography, Electrospray Ionization, and Tandem Mass Spectrometry

It will be important to determine if the parent and fragment ion intensity results of liquid chromatography, electrospray ionization and tandem mass spectrometry (LC-ESI-MS/MS) experiments have been randomly and independently sampled from a normal population for the purpose of statistical analysis by general linear models and ANOVA. The tryptic parent peptide and fragment ion m/z and intensity data in the mascot generic files from LC-ESI-MS/MS of purified standard proteins, and human blood protein fractionated by partition chromatography, were parsed into a Structured Query Language (SQL) database and were matched with protein and peptide sequences provided by the X!TANDEM algorithm. The many parent and/or fragment ion intensity values were log transformed, tested for normality, and analyzed using the generic Statistical Analysis System (SAS). Transformation of both parent and fragment intensity values by logarithmic functions yielded intensity distributions that closely approximate the log-normal distribution. ANOVA models of the transformed parent and fragment intensity values showed significant effects of treatments, proteins, and peptides, as well as parent versus fragment ion types, with a low probability of false positive results. Transformed parent and fragment intensity values were compared over all sample treatments, proteins or peptides by the Tukey-Kramer Honestly Significant Difference (HSD) test. The approach provided a complete and quantitative statistical analysis of LC-ESI-MS/MS data from human blood.

α-Secretase-derived Fragment of Cellular Prion, N1, Protects against Monomeric and Oligomeric Amyloid β (Aβ)-associated Cell Death

In physiological conditions, both β-amyloid precursor protein (βAPP) and cellular prion (PrP(c)) undergo similar disintegrin-mediated α-secretase cleavage yielding N-terminal secreted products referred to as soluble amyloid precursor protein-α (sAPPα) and N1, respectively. We recently demonstrated that N1 displays neuroprotective properties by reducing p53-dependent cell death both in vitro and in vivo. In this study, we examined the potential of N1 as a neuroprotector against amyloid β (Aβ)-mediated toxicity. We first show that both recombinant sAPPα and N1, but not its inactive parent fragment N2, reduce staurosporine-stimulated caspase-3 activation and TUNEL-positive cell death by lowering p53 promoter transactivation and activity in human cells. We demonstrate that N1 also lowers toxicity, cell death, and p53 pathway exacerbation triggered by Swedish mutated βAPP overexpression in human cells. We designed a CHO cell line overexpressing the London mutated βAPP (APP(LDN)) that yields Aβ oligomers. N1 protected primary cultured neurons against toxicity and cell death triggered by oligomer-enriched APP(LDN)-derived conditioned medium. Finally, we establish that N1 also protects neurons against oligomers extracted from Alzheimer disease-affected brain tissues. Overall, our data indicate that a cellular prion catabolite could interfere with Aβ-associated toxicity and that its production could be seen as a cellular protective mechanism aimed at compensating for an sAPPα deficit taking place at the early asymptomatic phase of Alzheimer disease.

Ultrafast Predissociation Dynamics of Excited State of Acrylic Acid

The ultrafast predissociation dynamics of acrylic acid after excitation to the second electronically excited state (S-2) with a 200 nm pump pulse were studied using a femtosecond pump-probe technique combined with time-of-flight mass spectroscopy (TOF-MS). The time-resolved mass spectra signals of the parent ion and fragment ions were collected. By using the kinetic equations to fit and analyze the time-resolved mass spectra ion signals, the existence of the predissociation channel was revealed. The excited molecule populated in the S-2 state decayed to the first electronically excited state (S-1) through a fast internal conversion process over a period of 210 fs. The excited molecule populated on the S-1 state then decayed to the vibrationally hot ground state (S-0) through another internal conversion process over a period of 1.49 ps. Finally, on the vibrationally hot ground state surface, the molecule dissociated to the neutral fragments, H2C=CH and HOCO, H2C=CHCO and OH via C - C bond fission and C - O bond fission, respectively. The corresponding predissociation time constants were determined to be approximately 4 and 3 ps, respectively. The generation of fragment ions can occur in two ways, both from the dissociation of the parent ion and the ionization of the neutral fragments on the vibrationally hot ground state surface.

LIAD-fs scheme for studies of ultrafast laser interactions with gas phase biomolecules

Laser induced acoustic desorption (LIAD) has been used for the first time to study the parent ion production and fragmentation mechanisms of a biological molecule in an intense femtosecond (fs) laser field. The photoacoustic shock wave generated in the analyte substrate (thin Ta foil) has been simulated using the hydrodynamic HYADES code, and the full LIAD process has been experimentally characterised as a function of the desorption UV-laser pulse parameters. Observed neutral plumes of densities >10(9) cm(-3) which are free from solvent or matrix contamination demonstrate the suitability and potential of the source for studying ultrafast dynamics in the gas phase using fs laser pulses. Results obtained with phenylalanine show that through manipulation of fundamental femtosecond laser parameters (such as pulse length, intensity and wavelength), energy deposition within the molecule can be controlled to allow enhancement of parent ion production or generation of characteristic fragmentation patterns. In particular by reducing the pulse length to a timescale equivalent to the fastest vibrational periods in the molecule, we demonstrate how fragmentation of the molecule can be minimised whilst maintaining a high ionisation efficiency.

Urolithin as a Converging Scaffold Linking Ellagic acid and Coumarin Analogues: Design of Potent Protein Kinase CK2 Inhibitors

Casein kinase 2 (CK2) is a ubiquitous, essential, and highly pleiotropic protein kinase; its abnormally high constitutive activity is suspected to underlie its pathogenic potential in neoplasia and other relevant diseases. Previously, using different in silico screening approaches, two potent and selective CK2 inhibitors were identified by our group: ellagic acid, a naturally occurring tannic acid derivative (K(i)=20 nM) and 3,8-dibromo-7-hydroxy-4-methylchromen-2-one (DBC, K(i)=60 nM). Comparing the crystallographic binding modes of both ellagic acid and DBC, an X-ray structure-driven merging approach was taken to design novel CK2 inhibitors with improved target affinity. A urolithin moiety is proposed as a possible bridging scaffold between the two known CK2 inhibitors, ellagic acid and DBC. Optimization of urolithin A as the bridging moiety led to the identification of 4-bromo-3,8-dihydroxy-benzo[c]chromen-6-one as a novel, potent and selective CK2 inhibitor, which shows a K(i) value of 7 nM against the protein kinase, representing a significant improvement in affinity for the target compared with the two parent fragments.