Biomedical subjects

A Loboda

Publications and source records attributed to A Loboda.

13 recordsLinked to original sources

PubMed2005

Heme oxygenase-1-dependent and -independent regulation of angiogenic genes expression: effect of cobalt protoporphyrin and cobalt chloride on VEGF and IL-8 synthesis in human microvascular endothelial cells.

Induction of heme oxygenase-1 (HO-1) expression can be achieved by stimulation with cobalt protoporphyrin (CoPPIX) or cobalt chloride (CoCl2). HO-1 has been recently implicated in regulation of angiogenesis and CoCl2 is known to potently activate hypoxia inducible factor-1 (HIF-1) transcription factor, a key regulator of angiogenic response in hypoxia. Here we determined the effect of CoPPIX and CoCl2 on the expression of vascular endothelial growth factor (VEGF) and interleukin-8 (IL-8), the two major angiogenic mediators, in human microvascular endothelial cells (HMEC-1). CoPPIX induced HO-1 expression and strongly enhanced VEGF and IL-8 synthesis, through the activation of VEGF and IL-8 promoters. Inhibition of HO activity by SnPPIX decreased VEGF production, while, interestingly, it did not affect IL-8. CoCl2 activated hypoxia-responsive element (HRE) and consequently VEGF generation via the enhancement of production of reactive oxygen species (ROS). On the other hand, CoCl2 did not influence IL-8 expression, while CoPPIX did not induce ROS elevation neither it affected HRE activity in VEGF promoter. Our data show that although both CoCl2 and CoPPIX induce HO-1, the influence of CoCl2 on VEGF does not involve HO-1 and is HIF-1-dependent, while the effect of CoPPIX does not involve HIF-1 but relies on HO-1.

Cells, Cultured↗

PubMed2001

Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching.

MALDI-quadrupole time-of-flight mass spectrometry was applied to identify proteins from organisms whose genomes are still unknown. The identification was carried out by successively searching a sequence database-first with a peptide mass fingerprint, then with a packet of noninterpreted MS/MS spectra, and finally with peptide sequences obtained by automated interpretation of the MS/MS spectra. A "MS BLAST" homology searching protocol was developed to overcome specific limitations imposed by mass spectrometric data, such as the limited accuracy of de novo sequence predictions. This approach was tested in a small-scale proteomic project involving the identification of 15 bands of gel-separated proteins from the methylotrophic yeast Pichia pastoris, whose genome has not yet been sequenced and which is only distantly related to other fungi.

Algorithms↗

PubMed2001

Determination of the complete amino acid sequence for the coat protein of brome mosaic virus by time-of-flight mass spectrometry. Evidence for mutations associated with change of propagation host.

Time-of-flight mass spectrometry (TOFMS) has been applied to determine the complete coat protein amino acid sequences of a number of distinct brome mosaic virus (BMV) isolates. Ionization was carried out by both electrospray ionization and matrix-assisted laser desorption/ionization (MALDI). After determining overall coat protein masses, the proteins were digested with trypsin or Lys-C proteinases, and the digestion products were analyzed in a MALDI QqTOF mass spectrometer. The N terminus of the coat protein was found to be acetylated in each BMV isolate analyzed. In one isolate (BMV-Valverde), the amino acid sequence was identical to that predicted from the cDNA sequence of the "type" isolate, but deviations from the predicted amino acid sequence were observed for all the other isolates analyzed. When isolates were propagated in different host taxa, modified coat protein sequences were observed in some cases, along with the original sequence. Sequencing by TOFMS may therefore provide a basis for monitoring the effects of host passaging on a virus at the molecular level. Such TOFMS-based analyses assess the complete profiles of coat protein sequences actually present in infected tissues. They are therefore not subject to the selection biases inherent in deducing such sequences from reverse-transcribed viral RNA and cloning the resulting cDNA.

Amino Acid Sequence↗

PubMed2001

Quantitative proteomic analysis using a MALDI quadrupole time-of-flight mass spectrometer.

We describe an approach to the quantitative analysis of complex protein mixtures using a MALDI quadrupole time-of-flight (MALDI QqTOF) mass spectrometer and isotope coded affinity tag reagents (Gygi, S. P.; et al. Nat. Biotechnol. 1999, 17, 994-9.). Proteins in mixtures are first labeled on cysteinyl residues using an isotope coded affinity tag reagent, the proteins are enzymatically digested, and the labeled peptides are purified using a multidimensional separation procedure, with the last step being the elution of the labeled peptides from a microcapillary reversed-phase liquid chromatography column directly onto a MALDI sample target. After addition of matrix, the sample spots are analyzed using a MALDI QqTOF mass spectrometer, by first obtaining a mass spectrum of the peptides in each sample spot in order to quantify the ratio of abundance of pairs of isotopically tagged peptides, followed by tandem mass spectrometric analysis to ascertain the sequence of selected peptides for protein identification. The effectiveness of this approach is demonstrated in the quantification and identification of peptides from a control mixture of proteins of known relative concentrations and also in the comparative analysis of protein expression in Saccharomyces cerevisiae grown on two different carbon sources.

Fungal Proteins↗

PubMed2001

Archived polyacrylamide gels as a resource for proteome characterization by mass spectrometry.

Mass spectrometry was applied to identify protein spots excised from an archived two-dimensional polyacrylamide gel that had been dried and stored for eight years at room temperature. All proteins were successfully identified. Detailed characterization of protein digests by matrix-assisted laser desorption/ionization (MALDI) peptide mapping, nanoelectrospray tandem mass spectrometry and MALDI-quadrupole time-of-flight mass spectrometry revealed no evidence of protein degradation or modifications that could hamper identification of proteins in a sequence database. The experiment with a model protein demonstrated that the pattern of tryptic peptides and the yield of individual peptides were not noticeably changed in the in-gel digest of the archived protein spot compared to the digest of the spot excised from a fresh gel. Thus, the characterization of "archived proteomes" has the potential to advance proteomic research without repeating "wet" biochemistry experiments, that had been perfected in the laboratory years ago.

Acrylic Resins↗

PubMed2001

Matrix-assisted laser desorption/ionization quadrupole time-of-flight mass spectrometry: an elegant tool for peptidomics.

A Matrix-assisted laser desorption/ionization hybrid quadrupole orthogonal acceleration time-of-flight mass spectrometer was employed to acquire neuropeptide mass spectra, directly from neuropeptide secreting tissue deposited on the sample target, in the presence of dihydroxybenzoic acid as matrix. The cockroach corpus cardiacum served as model neuroendocrine tissue. Twelve neuropeptide ion peaks, with mass-to-charge ratio values ranging between 800 and 3,000 Da were selected for tandem mass spectrometry. All peptides below 1,600 Da could be fully sequenced; tandem mass spectrometry analysis of the remaining (three) largest peptides resulted in (limited) sequence tags, which, also due to unavailability of an appropriate neuropeptide structure database, did not allow complete structure elucidation.

Amino Acid Sequence↗

PubMed2001

A model for 4-aminopyridine action on K channels: similarities to tetraethylammonium ion action.

We present a model for the action of 4-aminopyridine (4AP) on K channels. The model is closely based on the gating current studies of the preceding paper and has been extended to account for ionic current data in the literature. We propose that 4AP, like tetraethylammonium ion and other quaternary ammonium ions, enters and leaves the channel only when the activation gate is open, a proposal that is strongly supported by the literature. Once in the open channel, 4AP's major action is to bias the activation gate toward the closed conformation by approximately the energy of a hydrogen bond. S4 segment movement, as reflected in gating currents, is almost normal for a 4AP-occupied channel; only the final opening transition is affected. The model is qualitatively the same as the one used for many years to explain the action of quaternary ammonium ions.

4-Aminopyridine↗

PubMed2001

Resolving the gating charge movement associated with late transitions in K channel activation.

We examined the late transitions in the activation sequence of potassium channels by analyzing gating currents of mutant Shaker IR channels and using the potassium channel blocker 4-aminopyridine (4AP). Gating currents were recorded from a double mutant of Shaker that was nonconducting (W434F mutation) and had the late gating transitions shifted to the right on the voltage axis (L382C mutation), thus separating the late transitions from the early ones. 4AP applied to the double mutant blocked the final transition and made possible novel observations of the isolated intermediate transitions, the ones that immediately precede the final opening of the channel. These transitions, which have not been well characterized previously, produce a distinct fast component in the gating current tails. Two intermediate transitions contribute to the fast component and carry 23% of the total gating charge. The effect of 4AP is well modeled as a selective block of the final gating transition, which opens the channel. The final transition contributes approximately 5% of the total gating charge.

4-Aminopyridine↗

PubMed2001

Dilated and defunct K channels in the absence of K+.

Potassium ions are vital for maintaining functionality of K channels. In their absence, many K channel types enter a long-lasting defunct condition characterized by absence of conductance and drastic changes in gating current. We show that channels pass through a dilated condition with altered selectivity as they are becoming defunct. To characterize these abnormalities we examined gating and ionic currents generated by Shaker IR and by three nonconducting mutants, W434F, D447N, and Y445A, in 0 K+. On entering the dilated condition, Shaker IR becomes permeable to Na+ and tetramethylammonium-positive (TMA+), signaling deformation of the selectivity filter. When dilated, nearly normal closing is possible at -140 mV. At -80 mV, however, closing is very slow and channels stray from the dilated into the defunct condition. Restoration from defunct to dilated condition requires tens of seconds at 0 mV and can occur in the absence of K+. W434F and D447N are similar to Shaker IR, showing Na+ and TMA+ permeability when dilated. The defunct gating currents are similar in Shaker IR and these two mutants and are reminiscent of the early transitions of normal gating. Y445A does not become defunct and shows Na+ but not TMA+ permeability on K+ removal.

Amino Acid Substitution↗

PubMed2000

Modulation of the activities of catalase-peroxidase HPI of Escherichia coli by site-directed mutagenesis.

Catalase-peroxidases have a predominant catalatic activity but differ from monofunctional catalases in exhibiting a substantial peroxidatic reaction which has been implicated in the activation of the antitubercular drug isoniazid in Mycobacterium tuberculosis. Hydroperoxidase I of Escherichia coli encoded by katG is a catalase-peroxidase, and residues in its putative active site have been the target of a site directed-mutagenesis study. Variants of residues R102 and H106, on the distal side of the heme, and H267, the proximal side ligand, were constructed, all of which substantially reduced the catalatic activity and, to a lesser extent, the peroxidatic activity. In addition, the heme content of the variants was reduced relative to the wild-type enzyme. The relative ease of heme loss from HPI and a mixture of tetrameric enzymes with 2, 3, and 4 hemes was revealed by mass spectrometry analysis. Conversion of W105 to either an aromatic (F) or aliphatic (I) residue caused a 4-5-fold increase in peroxidatic activity, coupled with a >99% inhibition of catalatic activity. The peroxidatic-to-catalatic ratio of the W105F variant was increased 2800-fold such that compound I could be identified by both electronic and EPR spectroscopy as being similar to the porphyrin cation radical formed in other catalases and peroxidases. Compound I, when generated by a single addition of H(2)O(2), decayed back to the native or resting state within 1 min. When H(2)O(2) was generated enzymatically in situ at low levels, active compound I was evident for up to 2 h. However, such prolonged treatment resulted in conversion of compound I to a reversibly inactivated and, eventually, to an irreversibly inactivated species, both of which were spectrally similar to compound I.

Amino Acid Substitution↗

PubMed2000

MALDI quadrupole time-of-flight mass spectrometry: a powerful tool for proteomic research.

A MALDI QqTOF mass spectrometer has been used to identify proteins separated by one-dimensional or two-dimensional gel electrophoresis at the femtomole level. The high mass resolution and the high mass accuracy of this instrument in both MS and MS/MS modes allow identification of a protein either by peptide mass fingerprinting of the protein digest or from tandem mass spectra acquired by collision-induced dissociation of individual peptide precursors. A peptide mass map of the digest and tandem mass spectra of multiple peptide precursor ions can be acquired from the same sample in the course of a single experiment. Database searching and acquisition of MS and MS/MS spectra can be combined in an interactive fashion, increasing the information value of the analytical data. The approach has demonstrated its usefulness in the comprehensive characterization of protein in-gel digests, in the dissection of complex protein mixtures, and in sequencing of a low molecular weight integral membrane protein. Proteins can be identified in all types of sequence databases, including an EST database. Thus, MALDI QqTOF mass spectrometry promises to have remarkable potential for advancing proteomic research.

Amino Acid Sequence↗

PubMed1998

Loss of shaker K channel conductance in 0 K+ solutions: role of the voltage sensor.

In potassium-free solutions some types of K channels enter a long-lasting nonconducting or "defunct" state. It is known that Shaker K channels must open in K+-free solutions to become defunct. Gating current studies presented here indicate an abnormal conformation in the defunct state that restricts S4 movement and alters its kinetics. Thus an abnormality initiated in the P region spreads to the gating apparatus. We find that channels most readily become defunct on repolarization to an intermediate voltage, thus prolonging occupancy of one of the several intermediate closed states. The state dependence of becoming defunct was further dissected by using the gating mutant L382A. Simply closing this channel at 0 mV (reversing the last activation step) does not make the mutant channel defunct. Instead, it is necessary to move further left (more fully closed) in the activation sequence. This was confirmed with ShIR experiments showing that channels become defunct only if there is inward gating charge movement. Rapid transit through the intermediate states, achieved at very negative voltage, is relatively ineffective at making channels defunct. Several mutations that removed C-type inactivation also made the channels resistant to becoming defunct. Our results show that normal gating current cannot be stably recorded in the absence of K+.

Amino Acid Substitution↗

PubMed1997

A new technique for decomposition of selected ions in molecule ion reactor coupled with ortho-time-of-flight mass spectrometry.

A molecule ion reactor (MIR), i.e. a gas filled radio-frequency only quadrupole with a longitudinal electrical field (RFQLEF), is used as an atmospheric pressure ionization interface for an orthogonal time-of-flight mass spectrometer (O-TOFMS). A new phenomenon of selective ion 'heating' in a MIR near Mathieu's instability threshold was found and confirmed by computer simulation. The 'heating' in collisions with buffer gas molecules leads to ion decomposition. In the case of multicharged ions, fragments with an m/z value higher than that of the parent ion have a stable motion and can be analysed by an O-TOFMS. Fragmentation of bradykinin and beta-endorphin molecular ions having a selected charge state is demonstrated. The spectra show clear 'ladder' structure. The phenomenon may be used as an alternative to tandem mass spectrometry (MS/MS) for molecule structure analysis.

Amino Acid Sequence↗