Sequence Determination (sequence + determination)

Distribution by Scientific Domains


Selected Abstracts


Identification of proteins directly from tissue: in situ tryptic digestions coupled with imaging mass spectrometry

JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 2 2007
M. Reid Groseclose
Abstract A novel method for on-tissue identification of proteins in spatially discrete regions is described using tryptic digestion followed by matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) with MS/MS analysis. IMS is first used to reveal the protein and peptide spatial distribution in a tissue section and then a serial section is robotically spotted with small volumes of trypsin solution to carry out in situ protease digestion. After hydrolysis, 2,5-Dihydroxybenzoic acid (DHB) matrix solution is applied to the digested spots, with subsequent analysis by IMS to reveal the spatial distribution of the various tryptic fragments. Sequence determination of the tryptic fragments is performed using on-tissue MALDI MS/MS analysis directly from the individual digest spots. This protocol enables protein identification directly from tissue while preserving the spatial integrity of the tissue sample. The procedure is demonstrated with the identification of several proteins in the coronal sections of a rat brain. Copyright © 2007 John Wiley & Sons, Ltd. [source]


The vanG glycopeptide resistance operon from Enterococcus faecalis revisited

MOLECULAR MICROBIOLOGY, Issue 3 2003
Florence Depardieu
Summary Acquired VanG-type resistance to vancomycin (MIC = 16 µg ml,1) but susceptibility to teicoplanin in Enterococcus faecalis BM4518 and WCH9 is due to the inducible synthesis of peptidoglycan precursors ending in d -alanine- d -serine. The vanG cluster, assigned to a chromosomal location, was composed of genes recruited from various van operons. The 3, end encoded VanG, a d -Ala:d -Ser ligase, VanXYG, a putative bifunctional d,d -peptidase and VanTG, a serine racemase: VanG and VanTG were implicated in the synthesis of d -Ala:d -Ser as in VanC- and VanE-type strains. Upstream from the structural genes for these proteins were vanWG with unknown function and vanYG containing a frameshift mutation which resulted in premature termination of the encoded protein and accounted for the lack of UDP-MurNAc-tetrapeptide in the cytoplasm. Without the frameshift mutation, VanYG had homology with Zn2+ dependent d,d -carboxypeptidases. The 5, end of the gene cluster contained three genes vanUG, vanRG and vanSG encoding a putative regulatory system, which were co-transcribed constitutively from the PYG promoter, whereas transcription of vanYG,WG,G,XYG,TG was inducible and initiated from the PYG promoter. Transfer of VanG-type glycopeptide resistance to E. faecalis JH2-2 was associated with the movement, from chromosome to chromosome, of genetic elements of c. 240 kb carrying also ermB -encoded erythromycin resistance. Sequence determination of the flanking regions of the vanG cluster in donor and transconjugants revealed the same 4 bp direct repeats and 22 bp imperfect inverted repeats that delineated the large element. [source]


Membrane associated nonmuscle myosin II functions as a motor for actin-based vesicle transport in clam oocyte extracts

CYTOSKELETON, Issue 10 2007
Ana S. DePina
Abstract Nonmuscle myosin II (Myo2) has been shown to associate with membranes of the trans -Golgi network and to be involved in Golgi to ER retrograde protein transport. Here, we provide evidence that Myo2 not only associates with membranes but functions to transport vesicles on actin filaments (AFs). We used extracts from unactivated clam oocytes for these studies. AFs assembled spontaneously in these extracts and myosin-dependent vesicle transport was observed upon activation. In addition, actin bundles formed and moved relative to each other at an average speed of ,0.30 ,m/s. Motion analysis revealed that vesicles moved on the spontaneously assembled AFs at speeds greater than 1 ,m/s. The motor on these vesicles was identified as a member of the nonmuscle Myo2 family based on sequence determination by Edman chemistry. Vesicles in these extracts were purified by sucrose gradient centrifugation and movement was reconstituted in vitro using skeletal muscle actin coated coverslips. When peripheral membrane proteins of vesicles including Myo2 were removed by salt stripping or when extracts were treated with an antibody specific to clam oocyte nonmuscle Myo2, vesicle movement was inhibited. Blebbistatin, a Myo2 specific inhibitor, also blocked vesicle movement. Myo2 light chain kinase activity was found to be essential for vesicle movement and sliding of actin bundles. Together, our data provide direct evidence that nonmuscle Myo2 is involved in actin-dependent vesicle transport in clam oocytes. Cell Motil. Cytoskeleton 2007. © 2007 Wiley-Liss, Inc. [source]


Germ-line transformation of pink bollworm (Lepidoptera: Gelechiidae) mediated by the piggyBac transposable element

INSECT MOLECULAR BIOLOGY, Issue 3 2000
J. J. Peloquin
Abstract The pink bollworm, Pectinophora gossypiella, is a world-wide pest of cultivated cotton. In certain growing regions populations are suppressed by a sterile release strategy. Efforts to improve the sterile insect technique as well as our understanding of lepidopteran biology could benefit greatly from a germ-line transformation system. We report transformation of pink bollworm with a piggyBac transposable element carrying the enhanced green flourescent protein (EGFP) marker gene. This vector,marker system resulted in recovery of transgenics at a rate of approximately 3.5%. Integration of the transforming construct that was typical of piggyBac was demonstrated by Southern analysis and sequence determination of transposon flanks. Expression of the EGFP marker was visualized by fluorescent microscopy and Western Blot analysis. Maintenance of transformed strains indicates that the transgene segregates in a Mendelian fashion and has been stable over fourteen generations to date. [source]


A fast, reproducible and low-cost method for sequence deconvolution of ,on-bead' peptides via ,on-target' maldi-TOF/TOF mass spectrometry

JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 3 2010
Giulio A. Amadei
Abstract A novel approach to high-throughput sequence deconvolution of on-bead small peptides (MW < 2000 Da) using on-target MALDI-TOF/TOF instrumentation is presented. Short peptides of pentamer and octamer length, covalently attached to TentaGel polystyrene beads through a photolabile linker, were placed onto the MALDI target, apportioned with suitable matrix (2,5-dihydroxybenzoic acid) and then hit with the instrument laser (Nd : YAG, 355 nm). This induced easy and highly reproducible photochemical cleavage, desorption (MS mode) and fragmentation (MS/MS mode). Peptide fragments were identified with a mass accuracy of 0.1 Da of the expected values. This technique significantly accelerates the sequence determination of positive peptide hits obtained from random combinatorial libraries when screening against biological targets, paving the way for a rapid and efficient method to identify molecular imaging ligands specific to pathological targets in cancer and other diseases. Copyright © 2009 John Wiley & Sons, Ltd. [source]


Compositional and configurational sequence determination of methyl methacrylate/ethyl acrylate copolymers by one- and two-dimensional nuclear magnetic resonance spectroscopy

JOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 2 2003
A. S. Brar
Abstract Ethyl acrylate (E)/methyl methacrylate (M) copolymers of different compositions were prepared, and their compositions were determined with 1H NMR spectra. The complete spectral assignments, in terms of the compositional and configurational sequences of these copolymers, were made with the help of distortionless enhancement by polarization transfer and two-dimensional heteronuclear single quantum coherence spectroscopy. The ,-(CH3)M, CH (E), CH2, and ,CO carbons of both M and E units were found to be sensitive to various compositional and configurational sequences. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 313,326, 2003 [source]


GAG Mimetic Libraries: Sulphated Peptide as Heparin-like Glycosaminoglycan Mimics in Their Interaction with FGF-1

MOLECULAR INFORMATICS, Issue 8 2005
Socorro Vázquez-Campos
Abstract Heparin and heparan sulphate (HS) are heterogenous, linear, polysulphated polysaccharides that are important in the regulation of a wide variety of biological processes including blood coagulation, in cell differentiation, adhesion, invasion, migration and development, and in tumor-related cellular events such as growth regulation and metastasis. In general, heparin/HS interacts with proteins mainly through ionic interactions between its negatively charged groups and positively charged groups on the proteins. From a mechanistic or therapeutic standpoint, it is attractive to design less complex charged molecules, other than oligosaccharides, as mimics of heparin. In an attempt to improve the accessibility of heparin mimics, it was assumed, provided that the correct charge topography could be achieved, that sulphated peptides might also act as mimics. Therefore, sulphated peptide combinatorial libraries were generated on solid support to identify novel polyanionic structures that mimic the role of heparin/HS in its binding to fibroblast growth factors (FGFs). Libraries were synthesised by direct sulphation of the peptide on solid phase or by using O- sulphonated building blocks during peptide synthesis. Quantitative solid-phase O -sulphonation of hydroxy amino acid residues in a peptide chain was effected by sulphur trioxide pyridine (SO3 -Pyr) complex in anhydrous pyridine at 65,°C for 4,h. O- Sulphonated building blocks were successfully synthesised in solution and, after stabilisation of the sulphate group by complexion with tetrabutyl ammonium ions, were employed in the synthesis of sulphated peptide libraries, similar to those generated by direct O- sulphonation on solid supports. The libraries were incubated with fluorescent-labelled FGF-1, and analysis and sequence determination of active compounds was carried out using Edman degradation. Selected sulphated peptides from the screening were resynthesised and their affinity for FGF-1 (acidic FGF) was studied in solution competition assays using surface plasmon resonance. These studies showed that sulphated decapeptides do bind to FGF-1 and inhibit its binding to immobilised heparin in the low micromolar concentration range. [source]


A mass spectrometry-based strategy for detecting and characterizing endogenous proteinase activities in complex biological samples

PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 3 2008
Sarah Robinson
Abstract Endogenous proteinases in biological fluids such as human saliva produce a rich peptide repertoire that reflects a unique combination of enzymes, substrates, and inhibitors/activators. Accordingly, this subproteome is an interesting source of biomarkers for disease processes that either directly or indirectly involve proteolysis. However, the relevant proteinases, typically very low abundance molecules, are difficult to classify and identify. We hypothesized that a sensitive technique for monitoring accumulated peptide products in an unbiased, global manner would be very useful for detecting and profiling proteolytic activities in complex biological samples. Building on the longstanding use of 18O isotope-based approaches for the classification of proteolytic and other enzymatic processes we devised a new method for evaluating endogenous proteinases. Specifically, we showed that upon ex vivo incubation endogenous proteinases in human parotid saliva introduced 18O from isotopically enriched water into the C-terminal carboxylic groups of their peptide products. Subsequent peptide sequence determination and inhibitor profiling enabled the detection of discrete subsets of proteolytic products that were generated by different enzymes. As a proof-of-principle we used one of these fingerprints to identify the relevant activity as tissue kallikrein. We termed this technique PALeO. Our results suggest that PALeO is a rapid and highly sensitive method for globally assessing proteinase activities in complex biological samples. [source]


Primary structural determination of N-terminally blocked peptides from the bark of Eucommia ulmoides Oliv by mass spectrometric analysis

RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 9 2003
Ren-Huai Huang
Sequencing of N-terminally blocked proteins/peptides is a challenge since these molecules inhibit processing by Edman degradation. By using high accuracy Fourier transform ion cyclotron resonance (FTICR) tandem mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS), the primary structures of two novel N-terminally blocked antifungal peptides (EAFP1 and EAFP2), purified from the bark of Eucommia ulmoides Oliv, have been determined. The results show that the high mass accuracy provided by FTICR mass spectrometry is effective to determine the N-terminally blocking group, and can simplify the task of spectral interpretation and improve the precision of sequence determination. The combination of MALDI-TOFMS with carboxyl peptidase Y digestion was used to determine the C-terminal 36- and 27-residue sequences of EAFP1 and EAFP2, respectively, to provide the sequence linkage information for tryptic fragments. Compared with traditional peptide chemistry the advantage of mass spectrometric techniques is their simplicity, speed and sensitivity. Copyright © 2003 John Wiley & Sons, Ltd. [source]


Automatic function switching and its usefulness in peptide and protein analysis using direct infusion microspray quadrupole time-of-flight mass spectrometry

RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 19 2001
Emmy Hoyes
Automatic function switching has been investigated for high-throughput protein identification and sequencing of peptides using direct infusion of tryptic digests on a quadrupole time-of-flight instrument. The increase in speed and the high quality of data make it a favourable technique for tandem mass spectrometry when compared to manual selection of each precursor ion; these advantages are not restricted to combined LC/MS/MS analyses for which the automatic function-switching mode was originally developed. This mode was compared to analyses performed using a slow scan of the quadrupole analyzer with repeated recording of product ion spectra. For the specific purpose of generating product ion data for sequence determination (as opposed to surveying all precursors of a selected product ion), the automatic function-switching mode was, as expected, markedly superior with respect to speed of analysis and quality of data. Furthermore, the automatic function-switching mode provides greater versatility with respect to selection of optimal collision energies. Copyright © 2001 John Wiley & Sons, Ltd. [source]


Recent Advances and Future Prospects in Peptaibiotics, Hydrophobin, and Mycotoxin Research, and Their Importance for Chemotaxonomy of Trichoderma and Hypocrea

CHEMISTRY & BIODIVERSITY, Issue 5 2008
Thomas Degenkolb
Abstract Fungi of the genus Trichoderma with teleomorphs in Hypocrea are abundant producers of a group of amphiphilic, non-ribosomal peptide antibiotics, which are rich in the non-proteinogenic amino acid Aib (, -aminoisobutyric acid). They are referred to as peptaibiotics, or peptaibols, if a 1,2-amino alcohol is present at the C-terminus. Trichoderma/Hypocrea, like other ascomycetous fungi, also produce hydrophobins, a class of small, cysteine-rich proteins. Advanced soft ionization mass spectrometric techniques such as LC-CID-MS, LC-ESI-MSn, and IC-MALDI-TOF-MS enabled the high-throughput analysis, simultaneous detection and sequence determination of peptaibiotics and hydrophobins from minute quantities of fungal materials. Some Trichoderma species have been recognized to produce peptaibiotics as well as simple mycotoxins of the trichothecene group. The combination of sequence data of both groups of peptides with the pattern of low-molecular-weight secondary metabolites, including trichothecene-type mycotoxins, independently confirmed the results of morphological, molecular, and phylogenetic analyses. This approach established a new lineage in Trichoderma/Hypocrea, the Brevicompactum clade, comprising four new and one redescribed species. Notably, commercial preparations of single or mixed cultures of Trichoderma species, in particular T. harzianum, and T. koningii, are registered as biocontrol agents for soil and plant pathogens. In this context, it is emphasized that the four mycotoxin-producing species of the recently established Brevicompactum clade (T. brevicompactum, T. arundinaceum, T. turrialbense, and T. protrudens) are not closely related to any of the Trichoderma species currently used as biocontrol agents. Furthermore, possible health concerns about release of peptaibiotics in the biosphere are discussed with respect to their bioactivities and their use as drugs in human and veterinary medicine. Finally, future prospects regarding novel bioactivities and further research needs, including interdisciplinary taxonomic approaches, are outlined. [source]