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PubMed1983

Analysis of cyclic enzyme reaction schemes by the graph-theoretic method.

The development of the graph-theoretic method is proposed particularly for the analysis of closed cycles of elementary stages in enzyme reaction schemes. Some simplifications of the graph structure may be based on the application of Kirchhoff's laws to enzyme reaction graphs in the steady-state. The importance of the cyclic processes for enzyme regulations and a principle non-equilibrium of this phenomenon are emphasized. As an example of the regulatory role of cycles "the liberation" from substrate inhibition by substrate analogues is considered. The modification of the graph-theoretic method in the pre-steady-state kinetics for arbitrary initial conditions (for pre-mixing procedures) is also discussed. The necessary and sufficient conditions for damped oscillations in the pre-steady state are formulated which are the equality conditions for some of the rate constants along the cycle (both for reversible and irreversible stages).

Enzyme Inhibitors↗
PubMed2004

Toward an HDAC6 inhibitor: synthesis and conformational analysis of cyclic hexapeptide hydroxamic acid designed from alpha-tubulin sequence.

A cyclic hexapeptide hydroxamic acid inhibitor for HDAC6 has been designed and synthesized on the basis of the facts that alpha-tubulin is the substrate of HDAC6 and of the excellent inhibitory activity of cyclic tetrapeptide hydroxamic acids (CHAPs) for HDACs. Unexpectedly, cyclic hexapeptide hydroxamic acid showed very low HDAC inhibitory activity. To explain the low activity, we have carried out conformation analysis and compared it to the crystal structure of alpha-tubulin. The conformation around the acetylated lysine of the cyclic hexapeptide substrate or the aminosuberate hydroxamic acid [Asu(NHOH)] of cyclic hexapeptide inhibitor is different from that around alpha-tubulin's lysine-40. The difference in the conformation seems to cause some steric hindrance at the capping site resulting in poor binding capacity.

Acetylation↗
PubMed2006

Repetitive determination of chemical oxygen demand by cyclic flow injection analysis using on-line regeneration of consumed permanganate.

A cyclic flow injection analysis (cyclic FIA) for the repetitive determination of chemical oxygen demand (COD) was developed. The acidic KMnO4 method was carried out by adopting a single-line circulating flow system. The oxidant (KMnO4) consumed by the oxidation of organic substances was regenerated and reused repeatedly, resulting in an extreme reduction of hazardous wastes. Only 50 ml of the reagent carrier solution containing 0.2 mM KMnO4 and 1 mM HIO4 in 0.8 M H2SO4 solution was continuously circulated through the system. The KMnO4 could play two roles: acting as an oxidant of the organic substances and/or a spectrophotometric reagent. The co-existing HIO4 acted as a regenerator of KMnO4, which made it possible to recycle the system repeatedly. Under two different digestions (70 and 130 degrees C), 50 repetitive determinations of standard sodium oxalate (6.5 mg COD L(-1)) and D-glucose (7.2 mg COD L(-1)) were skillfully carried out with a slightly decreased baseline. The analytical frequency was 30 samples per hour for COD determination. The proposed method saved consumption of the used reagents, KMnO4 and H2SO4, and thus these wastes were extremely reduced. The obtained COD values with the proposed method were co-related with those provided by the manual standard method, but were fairly low owing to the insufficient digestion step.

Flow Injection Analysis↗
PubMed2004

Ion mobility-mass spectrometry applied to cyclic peptide analysis: conformational preferences of gramicidin S and linear analogs in the gas phase.

In this paper, we present an investigation of the gas-phase structural differences between cyclic and linear peptide ions by matrix-assisted laser desorption ionization-ion mobility-mass spectrometry. Specifically, data is shown for gramicidin S (cyclo-VOLFPVOLFP where phenylalanines are D rather than L-type amino acids and the O designates the non-standard amino acid ornithine) and five linear gramicidin S analogues. Results are interpreted as evidence for a beta-sheet (or beta-hairpin) conformational preference in both linear-protonated and sodiated-cyclic gramicidin S gas-phase peptides, and a preference for the protonated-cyclic peptide to adopt a collapsed, random coil-type conformation. A comparison with solution-phase circular dichroism measurements is performed, and structures similar to those observed in the gas phase appear to be favored in low-dielectric solvents such as 2,2,2-triflouroethanol. The utility of ion mobility-mass spectrometry (IM-MS) as a means of rapidly distinguishing between linear and cyclic peptide forms in also discussed.

Amino Acid Sequence↗
PubMed1989

Spectral analysis of cyclic symptoms in late luteal phase dysphoric disorder.

Fifty-eight subjects self-referred for premenstrual difficulty were evaluated for late luteal phase dysphoric disorder through a spectral analysis technique applied to prospective symptom ratings. Data from the Schedule for Affective Disorders and Schizophrenia--Life-time Version were used to group the subjects according to the absence or presence of past or present psychiatric disorders. The two psychiatric groups were compared with regard to both patterns of significant symptom change and premenstrual symptom severity. Differences between the groups are used to discuss issues regarding the reliable identification of late luteal phase dysphoric disorder and the impact of other psychiatric disorders on this syndrome.

Adult↗
PubMed1999

Kinetic analysis of cyclic CMP-specific and multifunctional phosphodiesterases by quantitative positive-ion fast-atom bombardment mass spectrometry.

Two enzymes, cyclic CMP-specific phosphodiesterase and multifunctional phosphodiesterase, are responsible for the hydrolysis of cytidine 3',5'-cyclic monophosphate in living cells. Quantitation of both enzymes has been carried out by positive-ion fast-atom bombardment mass spectrometric analysis of the enzyme incubates after termination of the reaction. The kinetic data obtained are in close agreement with parallel data obtained by the conventional radiometric assay. The extra facility of the mass spectrometry based assay to monitor several incubation components simultaneously has been exploited to study the concurrent hydrolysis of alternate cyclic nucleotide substrates and provides kinetic parameters of significance in interpreting substrate-enzyme interactions. This is extended by the use of collisionally-induced dissociation of the protonated molecules of the liberated products to identify the mononucleotide isomers resulting from the cyclic nucleotide hydrolysis.

2',3'-Cyclic Nucleotide 3'-Phosphodiesterase↗
PubMed1983

Quantitative analysis of cyclic AMP waves mediating aggregation in Dictyostelium discoideum.

We have previously reported the detection of cAMP waves within monolayers of aggregating Dictyostelium discoideum cells (K. J. Tomchik and P.N. Devreotes, 1981, Science 212, 443-446). The computer-assisted analysis presented here of the fluorographic images of the cAMP waves reveals (1) all the waves have a consistent width and height; (2) cAMP concentrations within centers of concentric aggregation territories oscillate periodically while at spiral centers the concentration builds up to a plateau value within 2 mm; (3) cells within the region of intersection of two oppositely directed cAMP waves are stimulated to produce more cAMP than those responding to a single wave; (4) cells start to move when the cAMP level begins to increase and cease movement when the peak cAMP concentration reaches the cell.

Computers↗
PubMed1996

Spectral analysis of cyclic fluctuations in haemodynamic parameters in critically ill patients.

In critically ill patients haemodynamic parameters are being routinely monitored. All of the fluctuations in blood pressures cannot be visualised since on most monitors the time window is too short and trend curves do not have a sufficient time resolution. Therefore, frequency analysis was applied to an 800-second window. Systemic artery pressure, central venous pressure and pulmonary artery pressure curves of 6 patients were sampled with a frequency of 40 Hz. The signals were transformed into the frequency domain by the Fast Fourier Transform method. Bispectral analysis was applied to determine the origin of higher frequencies. There were three main frequencies present: heart stroke rate, respiratory frequency and a slow frequency (< 0.05 Hz), which was equal to the used infusion rate (2-10 ml/h) of vaso-active drugs. Continuous infusion of short-acting vaso-active drugs delivered by pulsatile diaphragm pumps to produce slow significant fluctuations in especially the arterial blood pressures (range: 5-40 mmHg). The periodicity of these slow fluctuations is not visualised during routine monitoring, so the observer may misinterpret the cause of changes in blood pressure and make inappropriate clinical decisions. A solution for detection of such slow waves is Fast Fourier Transform combined with bispectral analysis.

Blood Pressure Determination↗
PubMed2002

Four-dimensional analysis of cyclic changes in coronary artery shape.

The objective of this study was to derive a method for quantifying the dynamic geometry of coronary arteries. Coronary artery geometry plays an important role in atherosclerosis. Coronary artery geometry also influences the performance of coronary interventions. Conversely, implantation of stents may alter coronary artery geometry. Clinical tools to define vessel shape have not been readily available. Using a Frenet-Serret curvature analysis applied to 3D reconstruction data derived from standard coronary angiograms, 21 coronary arteries were analyzed at end-diastole (ED) and end-systole (ES). Vessels were divided anatomically: type 1 consisted of vessels lying in the AV groove (left circumflex, right coronary) and type 2 consisted of vessels overlying actively contracting myocardium (left anterior descending, diagonal, obtuse marginal, right ventricular marginal, posterior descending, posterolateral). Vessel segments were analyzed by assessing the changes in curvature, torsion, and discrete flexion points (FPs), areas of systolic bending in the arterial contour. The curvature from ED to ES of type 1 vessels was unchanged (-0.02 +/- 0.03 cm(-1)), while the curvature change of type 2 vessels showed a 38% increase (0.33 +/- 0.04 cm(-1); P < 0.001). Type 1 vessels had fewer FPs per vessel than type 2 vessels (0.38 +/- 0.18 and 2.40 +/- 0.23 FP/vessel, respectively; P < 0.001). FPs were more common in distal segments and branch vessels. A method to quantify cyclic changes in coronary artery shape was applied to 3D data sets derived from standard coronary angiograms. Coronary arteries undergo a cyclic change in shape resulting in changes in overall curvature as well as formation of discrete flexion points. These changes in vessel shape are asymmetrically distributed in coronary arteries.

Coronary Angiography↗
PubMed1978

Direct gas chromatographic analysis of cyclic N-nitrosamines.

A rapid gas chromatographic technique has been developed for quantitative estimation of cyclic N-nitrosamines. Cumbersome clean-up procedures are unnecessary and quantitative estimation can be done by injecting hexane extract without further pretreatment. The detection limit for the procedures is ca. 0.5 ng.

Chromatography, Gas↗
PubMed2002

Modified solvent accessibility free energy prediction analysis of cyclic urea inhibitors binding to the HIV-1 protease.

One of the most successful drug targets against AIDS in the last decade has been the HIV-1 protease (HIV-1 PR), an enzyme that processes the polyprotein gene products into active replicative viral proteins. In our quest for a wide-ranging, binding free energy function we have extended the solvent accessibility free energy predictor (SAFE_p) method, recently developed for peptidic HIV-1 PR inhibitors, to the study of the binding of cyclic urea (CU) HIV-1 PR inhibitors. Our results show that there is a need for a specific term depicting polar contacts to be added to the original SAFE_p analytical expression, an outcome not seen in our studies of HIV-1 PR peptidic inhibitors. Nevertheless, despite the higher profile of the electrostatic interactions in the binding of the CU inhibitors, our analysis indicates that CU inhibitor binding is still driven by the hydrophobic entropic contribution, as much as for the peptidic inhibitors.

Binding Sites↗
PubMed1992

Quantitative analysis of cyclic beta-turn models.

The beta-turn is a frequently found structural unit in the conformation of globular proteins. Although the circular dichroism (CD) spectra of the alpha-helix and beta-pleated sheet are well defined, there remains some ambiguity concerning the pure component CD spectra of the different types of beta-turns. Recently, it has been reported (Hollósi, M., Kövér, K.E., Holly, S., Radics, L., & Fasman, G.D., 1987, Biopolymers 26, 1527-1572; Perczel, A., Hollósi, M., Foxman, B.M., & Fasman, G.D., 1991a, J. Am. Chem. Soc. 113, 9772-9784) that some pseudohexapeptides (e.g., the cyclo[(delta)Ava-Gly-Pro-Aaa-Gly] where Aaa = Ser, Ser(OtBu), or Gly) in many solvents adopt a conformational mixture of type I and the type II beta-turns, although the X-ray-determined conformation was an ideal type I beta-turn. In addition to these pseudohexapeptides, conformational analysis was also carried out on three pseudotetrapeptides and three pseudooctapeptides. The target of the conformation analysis reported herein was to determine whether the ring stress of the above beta-turn models has an influence on their conformational properties. Quantitative nuclear Overhauser effect (NOE) measurements yielded interproton distances. The conformational average distances so obtained were interpreted utilizing molecular dynamics (MD) simulations to yield the conformational percentages. These conformational ratios were correlated with the conformational weights obtained by quantitative CD analysis of the same compounds. The pure component CD curves of type I and type II beta-turns were also obtained, using a recently developed algorithm (Perczel, A., Tusnády, G., Hollósi, M., & Fasman, G.D., 1991b, Protein Eng. 4(6), 669-679). For the first time the results of a CD deconvolution, based on the CD spectra of 14 beta-turn models, were assigned by quantitative NOE results. The NOE experiments confirmed the ratios of the component curves found for the two major beta-turns by CD analysis. These results can now be used to enhance the conformational determination of globular proteins on the basis of their CD spectra.

Amino Acid Sequence↗
PubMedDate not supplied

HPLC analysis of cyclic adenosine diphosphate ribose and adenosine diphosphate ribose: determination of NAD+ metabolites in hippocampal membranes.

Cyclic adenosine diphosphate-ribose (cADPR) and ADPR were separated by high-performance liquid chromatography (HPLC) on a CarboPac PA-1 column at strong basic pH and quantitated by a pulsed amperometric detector. Although this HPLC method was quite sensitive and highly reproducible, it did not allow the separation of cADPR from guanosine monophosphate (GMP) which, when present, could be removed by ion-affinity chromatography, using gel-immobilized Fe3+ columns. Crude synaptic membranes from rat hippocampi were incubated with nicotinamide adenine dinucleotide (NAD) and acidic extracts were subject to HPLC analysis after neutralization. Incubation led to a time-dependent formation of ADPR, which was amplified when membranes were incubated in the presence of guanosine trisphosphate (GTP), guanosine-5'-0-(3-thiotrisphosphate) (GTP-gamma-S) or AlF3. cADPR did not accumulate in detectable amounts and only a minimal proportion (< 5%) of radioactivity originating from [3H]NAD co-eluted with authentic cADPR in extracts from hippocampal membranes. The simultaneous detection of cADPR and ADPR we have described may help the search for inhibitors of cADPR metabolism, which will allow to measure the cADPR that accumulates under basal conditions or in response to extracellular signals.

Adenosine Diphosphate Ribose↗
PubMed2004

Motility of a biflagellate sperm: waveform analysis and cyclic nucleotide activation.

The sperm of the freshwater clam Corbicula fluminea are unusual in that they have two flagella, both of which are capable of beating. When Corbicula sperm are removed from the gonad and placed into freshwater, most remain immotile. Video microscopy was used to assess signaling molecules capable of activating Corbicula sperm motility. Experiments using the cAMP analogs dbcAMP or 8-Br-cAMP show that elevating cAMP activates flagellar motility. Treatments with 8-Br-cGMP activated motility in similar numbers of sperm. Treatments with the selective cAMP-dependent protein kinase (PKA) inhibitor H-89 block activation by 8-Br-cAMP but not by 8-Br-cGMP. Similar treatments with the cGMP-dependent protein kinase (PKG) inhibitor Rp-8-pCPT-cGMPS block activation by 8-Br-cGMP but not by 8-Br-cAMP. These results suggest that cAMP and cGMP each work through their specific kinase to activate flagellar motility. Analysis of spontaneously activated freely swimming sperm shows that the two flagella beat with different parameters. The A flagellum beats with a shorter wavelength and a higher frequency than the B flagellum. The observed differences in flagellar waveform indicate that the flagella are differentially controlled.

Animals↗