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PubMed2005

Structure determination and conformation analysis of symmetrical dimers.

Conformational and stereochemical analysis of six new symmetrical dimers was performed using proton-proton vicinal coupling measured from (1)H NMR and (13)C satellites of (1)H NMR signals, natural abundance (13)C-edited nuclear overhauser effect (NOE) experiments, comprehensive NOE analysis and molecular modeling. The (13)C satellite analysis and (13)C-edited NOE experiments were carried out to extract spectral information between equivalent protons. Molecular modeling was applied for estimations of three-dimensional parameters of the studied dimers, which were subsequently used to generate a set of theoretical NOE for each possible conformation. The J-coupling, (13)C-edited NOE and quantitative NOE analyses showed the predominance of gauche conformation for three dimers, whereas a mixture of gauche and anti conformations (45:55) for three other dimers was established by quantitative NOE analysis. X-ray crystallographic study confirmed the stereochemistry of one of the dimers and revealed a discrepancy in conformation stability between liquid and solid states.

Carbon Isotopes↗

PubMed1993

Validation of volumetric flow measurements by means of a Doppler-tipped coronary angioplasty guide wire.

We used an in vitro model to validate volumetric flow measurements obtained with an 0.018-inch angioplasty guidewire with a 12 MHz transducer mounted on its tip. By using a modified two-head roller pump device, flow was adjusted incrementally from a minimum of 90 ml/min to a maximum of 550 ml/min. Flow was measured with the Doppler guide wire in tubing ranging from 1.9 mm to 6.0 mm internal diameter, as the product of the spectral Doppler velocity integral and the cross-sectional area of the tubing, over a 1-minute period. It was an excellent correlation between the Doppler calculated flow rates and actual flow, regardless of tubing diameter (r = 0.99). These results suggest that the Doppler spectral output of this device might be accurately applied to estimates of volumetric flow in human coronary arteries.

Angioplasty, Balloon, Coronary↗

PubMed1990

ESR of spin-labeled bacteriophage M13 coat protein in mixed phospholipid bilayers.

Bacteriophage M13 major coat protein was spin-labeled with a nitroxide derivative of iodoacetamide, preferentially at the single methionine that is located in the hydrophobic region of the protein. The spin-labeled protein was incorporated at different lipid-to-protein ratios in phospholipid bilayers composed of dimyristoylphosphatidylglycerol (DMPG), dimyristoylphosphatidylcholine (DMPC), or the 1:1 molar mixture of these lipids. Both conventional and saturation transfer (ST) ESR studies were performed to investigate the rotational motions of the protein over a large dynamic range. The conventional ESR spectra indicate that the mobility of the spin labelled protein in the lipid gel phase decreases in the order: DMPG greater than DMPC/DMPG (1:1) greater than DMPC. In the liquid crystalline phase, the largest mobility is found in DMPC/DMPG (1:1, mol/mol) mixtures, but the mobility is still greater in DMPG than in DMPC. The results are interpreted in terms of different degrees of protein aggregation in the different lipids. Segmental motion with rotational correlation times on the order of tens of nanoseconds, motional anisotropy, and spectral overlap complicate the analysis of the STESR spectra. An estimate of the size of the protein aggregates is found to be in the region of 85 monomer units. Removing the polar tails from the protein by proteolytic digestion results in an enhanced aggregation in the gel phase. In the liquid crystalline phase, the segmental wobbling mobility of the protein is increased relative to the native protein, whereas the overall rotational diffusion is not changed greatly.

Capsid↗

PubMed1975

Quantitative assessment of the electroencephalogram in renal disease.

EEGs wre recorded from renal patients to determine if there are quantifiable characteristic changes in the EEG was quantified by calculating the percentage of spectral power in the bandwidth 3-7 c/sec referrred to a frequency range of 3-13 c/sec and by computing the mean frequency of the dominant rhythm in the EEG. Blood urea nitrogen and creatinine concentrations, as well as a self-assessment of the patient's clinical condition, were recorded. The general finding of this research is that EEG slowing, as evaluated by power spectral techniques, is correlated with uremia-associated variables. 1. In a non-dialyzed patient population with renal failure, slowing in the EEG was found to be directly corelated with increased creatinine concentrations. 2. Quantitative measures of slow wave activity computed using power spectral techniques were found to be highly corelated with an estimate of slowing made by an electroencephalographer. 3. Compared with undialyzed azotemic patients, malignant hypertensive patients with comparable serum creatinine concentrations typically displayed increased slow wave activity, while slowing was generally reduced in the dialyzed patient population. 4. A series of EEGs recorded from one patient during the first three dialyses of her life revealed that slow wave activity decreased during each successive dialysis. In another patient, all quantified EEG values recorded prior to renal transplantation significantly improved after transplantation...

Adolescent↗

PubMed2006

The effect of hypobaric hypoxia on multichannel EEG signal complexity.

OBJECTIVE: The objective of this study was the development and evaluation of nonlinear electroencephalography parameters which assess hypoxia-induced EEG alterations, and describe the temporal characteristics of different hypoxic levels' residual effect upon the brain electrical activity. METHODS: Multichannel EEG, pO2, pCO2, ECG, and respiration measurements were recorded from 10 subjects exposed to three experimental conditions (100% oxygen, hypoxia, recovery) at three-levels of reduced barometric pressure. The mean spectral power of EEG under each session and altitude were estimated for the standard bands. Approximate Entropy (ApEn) of EEG segments was calculated, and the ApEn's time-courses were smoothed by a moving average filter. On the smoothed diagrams, parameters were defined. RESULTS: A significant increase in total power and power of theta and alpha bands was observed during hypoxia. Visual interpretation of ApEn time-courses revealed a characteristic pattern (decreasing during hypoxia and recovering after oxygen re-administration). The introduced qEEG parameters S1 and K1 distinguished successfully the three hypoxic conditions. CONCLUSIONS: The introduced parameters based on ApEn time-courses are assessing reliably and effectively the different hypoxic levels. ApEn decrease may be explained by neurons' functional isolation due to hypoxia since decreased complexity corresponds to greater autonomy of components, although this interpretation should be further supported by electrocorticographic animal studies. SIGNIFICANCE: The introduced qEEG parameters seem to be appropriate for assessing the hypoxia-related neurophysiological state of patients in the hyperbaric chambers in the treatment of decompression sickness, carbon dioxide poisoning, and mountaineering.

Adult↗

PubMed2006

Computational modeling of biologically active molecules using NMR spectra.

The molecular structure and NMR chemical shift information of a compound can be combined to form powerful models of biological activity. NMR spectral data and structure information can be combined on a structural template analogous to 3D-QSAR methodology or orientation independently in spectral space. Surprisingly, quantitative spectrometric data-activity relationship (QSDAR) models built on structure templates are inferior to multi-dimensional QSDAR models built in spectral space. 3D-QSDAR modeling could be useful for estimating chemical toxicity, risk assessment of environmental contaminants and drug lead-compound identifications.

Anti-Bacterial Agents↗

PubMed2006

Expression, purification and characterization of calcium-triggered luciferin-binding protein of Renilla reniformis.

The Ca2+-triggered luciferin-binding protein of Renilla reniformis (RLBP) is a non-covalent complex of apoprotein (apoRLBP) and coelenterazine (luciferin). The gene encoding apoRLBP with 552 nucleotides has been synthesized by assembly PCR methods with synthetic oligonucleotides, and the histidine-tagged apoRLBP expressed as a soluble form in the periplasmic space of Escherichia coli cells. The apoRLBP was purified by nickel chelate chromatography and the procedure yielded 18.2mg of recombinant apoRLBP from 80 ml of cultured cells with purity greater than 95%. The purified apoRLBP was converted to RLBP by incubation with coelenterazine in the presence of dithiothreitol and the purity of recombinant RLBP was estimated to be over 95% by comparison with the absorption spectral data of native RLBP. When RLBP mixed with Ca2+, coelenterazine was dissociated from RLBP and was utilized for the luminescence reaction of Renilla luciferase. Also semi-synthetic RLBPs with h-, e-, and Bis-coelenterazines were prepared and characterized.

Aequorin↗

PubMed2006

An adaptive clutter rejection method based on AR model in color flow imaging.

The ultrasound Doppler signal scattered from blood is heavily corrupted by the clutter signal reflected from slowly moving muscular tissue. The Doppler frequency shift of blood flow and clutter in different parts of human body greatly changes. Therefore, if a fixed wall filter is selected, the optimal filtering effect can not be attained. An adaptive clutter rejection method is proposed in this paper, which consists of a weak clutter rejector and a 2-order AR estimator. The clutter and blood power thresholds were preliminary defined in the weak clutter rejector. The echo power is compared with the two pre-defined thresholds, and the result was used to select an appropriate wall filter. The output of the weak clutter rejector is estimated by a 2-order AR estimator and two poles are acquired. The low frequency pole denotes the clutter signal and the high frequency pole denotes the blood signal. Before the AR estimation, a static signal is added to avoid producing split spectral peaks. It is illustrated in the simulation that the proposed method can detect the slower blood flow with smaller variance compared with the traditional wall filtering method.

Algorithms↗

PubMed1976

Specific ion-exchange chromatography and fluorimetric assay for urinary 3-O-methyldopamine.

A technique for the selective extraction of 3-O-methyldopamine, normetanephrine and metanephrine from a single urine sample has been investigated. After hydrolysis of the conjugates, the diluted mixture is passed through a Dowex 50W-X2 column and the methoxylated amines are eluted by means of concentrated ammonia. The eluate, containing metanephrine, normetanephrine and 3-O-methyldopamine is evaporated, and a solution of the residue in borate buffer is fractionated under strictly controlled conditions on an Amberlite CG-50 column. The three amines so separated are estimated by specific fluorimetric methods. The extraction recovery is 80 +/- 3% for pure solutions and 78 +/- 4% for 3-O-methyldopamine added to urine. The fluorimetric procedure, carried out under well-defined conditions, allows the estimation of 10 ng of 3-O-methethyldopamine. The spectral characteristics of the fluorescent derivative are similar to those obtained with dopamine, so that it can be assumed that iodine oxidation of 3-O-methyldopamine demethylates this compound and oxidises the resulting dopamine to the dopamine fluorophore (5,6-dihydroxy-indole). Of the compounds that might interfere in the fluorimetric procedure, dopamine, DOPA and alpha-methyl-DOPA are destroyed by the ammoniacal elution from the Dowex column and 3-O-methyl-DOPA is eliminated in the effluent from the Amberlite column. The elimination of interfering compounds and the improved separation on Amberlite ensure high specificity for this procedure. We have applied the method to normal urine and to pathological urines from patients with adrenergic tumours or untreated and treated parkinsonian subjects; vital information has been obtained on the prognosis of adrenergic tumours. The presence of large amounts of dopamine, normetanephrine and/or metanephrine does not affect the assay for 3-O-methyldopamine. The method is also applicable to rat and dog urine, and can be applied to tissue extracts with little modification.

Adrenal Gland Neoplasms↗

PubMed1999

Phospholipids stabilize the secondary structure of the sodium-coupled branched-chain amino acid carrier of Pseudomonas aeruginosa.

For functional reconstitution of bacterial cotransporters (carriers or permeases) including the sodium-coupled branched-chain amino acid carrier (LIV-II carrier) of Pseudomonas aeruginosa, the presence of phospholipid is required through the process of solubilization and purification of the transporters from the bacterial membranes, suggesting the possibility that phospholipid may stabilize the structure of the cotransporter proteins to be in a functional form. In this study, this possibility was examined by studying the effect of denaturant on the secondary structure of the LIV-II carrier purified in the absence and presence of phospholipid using circular dichroism (CD) spectroscopy. CD spectra of the purified LIV-II carrier solubilized in n-octyl-beta-D-glucopyranoside (OG), OG/dioleoylphosphatidylethanolamine (DOPE)/dioleoylphosphatidylglycerol (DOPG) mixture, and dispersed into DOPE/DOPG small unilamellar vesicles were measured in the absence of denaturant. The three spectra were very similar and had a trough at 222 nm with mean residue molar ellipticity of -23000 deg.cm(2)/dmol and a shoulder at 208 nm. CD spectral analyses with three different methods (S.W. Provencher, J. Glöckner, Estimation of globular protein secondary structure from circular dichroism, Biochemistry 20 (1981) 33-37; J.Y. Yang, C.-S.C. Wu, H.Z. Martinez, Calculation of protein conformation from circular dichroism, Methods Enzymol. 130 (1986) 208-269; N. Sreerama, R.W. Woody, A self-consistent method for the analysis of protein secondary structure from circular dichroism, Anal. Biochem. 209 (1993) 32-44) revealed that the LIV-II carrier solubilized in OG/DOPE/DOPG mixture contained 69-75% alpha-helix and 0-9% beta-sheet. Addition of 6 M guanidine hydrochloride decreased 48% of the amplitude at 222 nm of the CD spectrum of the carrier solubilized in OG alone and 9-14% of the CD amplitude of the carrier solubilized in OG/DOPE/DOPG or OG/dioleoylphosphatidylcholine mixture and dispersed in liposomes composed of DOPE/DOPG. These results show that the ordered secondary structure of the LIV-II carrier is partially unfolded in OG without phospholipid by denaturant but is greatly stabilized with phospholipids with oleoyl chains independently of their polar head group composition and suggest that the alpha-helical structure of the carrier is mainly embedded in the lipid environment.

Bacterial Proteins↗

PubMed2000

Study of relaxation rates of stable paramagnetic centers in gamma-irradiated alanine.

The stable L-alanine radical induced by gamma-irradiation was examined by electron paramagnetic resonance (EPR), transfer saturation EPR and electron nuclear double resonance (ENDOR) in the temperature region of fast motion of the methyl group (180-320 K). From the obtained spectral line broadening and spectral intensity the correlation time for the methyl rotation was estimated. The complex processes determining the relaxation rate were examined in the same temperature interval. It was shown that important contributions to the relaxation rate arise from non-secular and pseudo-secular types of contributions. The non-secular contribution involves intramolecular dynamics while the pseudo-secular contribution originates from intermolecular motions. The obtained values for the dynamical parameters have been compared with those obtained by pulse EPR methods and by proton nuclear magnetic resonance (NMR) on undamaged crystals.

Alanine↗

PubMed1998

Helix packing in the lactose permease determined by metal-nitroxide interaction.

The magnetic dipolar interaction between site-directed metal-nitroxide pairs can be exploited to measure distances within proteins [Voss, J., Salwinski, L., Kaback, H. R., and Hubbell, W. L. (1995) Proc. Natl. Acad. Sci. U.S.A. 92, 12295-12299; Voss, J., Hubbell, W. L., and Kaback, H. R. (1995) Proc. Natl. Acad. Sci. U.S. A. 92, 12300-12303], and the approach is utilized here to measure helix proximities in the lactose permease of Escherichia coli. A high-affinity divalent metal binding site was created by replacing Arg302 (helix IX) and Glu325 (helix X) with His residues in permease mutants containing single Cys residues in helices II, V, or VII and a biotin acceptor domain to facilitate purification. Mutant proteins were purified by avidin affinity chromatography, labeled specifically with a nitroxide free radical and investigated by electron paramagnetic resonance spectroscopy in the absence or presence of Cu(II). Spectral broadening due to bound Cu(II) was used to estimate distances between the metal center and the spin-labeled side chains. For each of the transmembrane domains probed, the variation in interspin distance with sequence position is consistent with an alpha-helical structure. The measured distances were also used to construct a model that is in good agreement with packing data obtained from other approaches.

Bacterial Proteins↗

PubMed1999

Inhibition of factor Xa by a peptidyl-alpha-ketothiazole involves two steps. Evidence for a stabilizing conformational change.

Recently, peptidylketothiazoles have been shown to be potent inhibitors of proteases, but the details of the interaction have not yet been studied. In the work presented here, the interaction of factor Xa, a coagulation protease, with the transition state inhibitor BnSO(2)-D-Arg-Gly-Arg-ketothiazole (C921-78) is characterized. C921-78 is a tight and selective inhibitor of the coagulation protease factor Xa (K(d) = 14 pM). The hydrolytic activity of factor Xa was inhibited by C921-78 in a time-dependent manner. The rate-limiting step of the bimolecular combination of inhibitor and enzyme was competitive with the substrate. Conversely, the inhibitor could be displaced from the active site of the enzyme after exposure of the preformed complex to an excess of substrate or to the active site inhibitor dansyl-Glu-Gly-Arg-chloromethyl ketone (DEGR-CMK) in a slow reaction. The formation of the C921-78-factor Xa complex resulted in a 60% increase in the magnitude of the fluorescence emission spectrum. Rapid mixing of the enzyme and inhibitor produces a monophasic fluorescence increase, compatible with spectral transition in a single step. The rate constant for this reaction increased hyperbolically with the concentration of C921-78, but the amplitude remained constant. These results are consistent with the initial formation of an enzyme-inhibitor complex (EI), followed by a unimolecular conversion of EI to EI linked to a spectral transition. The rate constants of the isomerization provide an estimate of 300000-fold stabilization. Thus, the inhibition of factor Xa by C921-78 follows a mechanism similar to that described classically for slow tight binding inhibitors. However, the two steps of the reaction cannot be kinetically separated by the rapid equilibrium assumption, and therefore, the formation of EI is partially rate-limiting, too. The driving energy for the unusually fast isomerization step may result from the highly favorable interactions of the inhibitor in the primary binding site.

Amino Acid Sequence↗

PubMed1981

The influence of concanavalin A on glutamate-induced current fluctuations in locust muscle fibres.

1. The influence of the plant lectin Concanavalin A (ConA) on the properties of membrane channels opened by 25-200 microM-L-glutamate in voltage-clamped locust muscle fibres has been studied. Power spectral density plots of membrane current fluctuations were used to estimate the mean lifetime and conductance of glutamate-induced channels. 2. Exposure to ConA (10 micrograms/ml.) increased the amplitude of the mean current evoked by 200 microM-glutamate from 7.7 +/- 4.7 nA (mean +/- S.D.) to 81 +/- 57 nA (membrane potential -60 mV, temperature 16 degrees C). The mean conductance of glutamate-induced channels (65 +/- 16.8 pS at 16 degrees C) was negligibly affected by the lectin. 3. In normal saline the mean lifetime of glutamate-induced channels tau noise decreased on membrane hyperpolarization. After treatment with ConA (70 micrograms/ml.), tau noise become totally independent of membrane voltage when studied at potentials in the range -60 to -120 mV. The value of tau noise at the resting potential was little altered by the lectin.

Animals↗

PubMed1990

Perceptual linear predictive (PLP) analysis of speech.

A new technique for the analysis of speech, the perceptual linear predictive (PLP) technique, is presented and examined. This technique uses three concepts from the psychophysics of hearing to derive an estimate of the auditory spectrum: (1) the critical-band spectral resolution, (2) the equal-loudness curve, and (3) the intensity-loudness power law. The auditory spectrum is then approximated by an autoregressive all-pole model. A 5th-order all-pole model is effective in suppressing speaker-dependent details of the auditory spectrum. In comparison with conventional linear predictive (LP) analysis, PLP analysis is more consistent with human hearing. The effective second formant F2' and the 3.5-Bark spectral-peak integration theories of vowel perception are well accounted for. PLP analysis is computationally efficient and yields a low-dimensional representation of speech. These properties are found to be useful in speaker-independent automatic-speech recognition.

Adult↗

PubMed1993

Doppler effect for sound emitted by a moving airborne source and received by acoustic sensors located above and below the sea surface.

The acoustic emissions from a propeller-driven aircraft are received by a microphone mounted just above ground level and then by a hydrophone located below the sea surface. The dominant feature in the output spectrum of each acoustic sensor is the spectral line corresponding to the propeller blade rate. A frequency estimation technique is applied to the acoustic data from each sensor so that the Doppler shift in the blade rate can be observed at short time intervals during the aircraft's transit overhead. For each acoustic sensor, the observed variation with time of the Doppler-shifted blade rate is compared with the variation predicted by a simple ray-theory model that assumes the atmosphere and the sea are distinct isospeed sound propagation media separated by a plane boundary. The results of the comparison are shown for an aircraft flying with a speed of about 250 kn at altitudes of 500, 700, and 1000 ft.

Acoustics↗

PubMed1995

The perception of amplified speech by listeners with hearing loss: acoustic correlates.

Audibility-based approaches to hearing-aid selection generally have focused on the long-term average speech spectrum (LTASS). Advances in amplification technology (e.g., multiband signal processing, level-dependent frequency shaping, full dynamic range compression, adaptive compression) make it difficult to predict the audibility of short-term components of speech from the amplified LTASS. This study was designed to quantify the audibility of a specific phonemes as processed by two different hearing-aid circuits (linear and full dynamic range compression), and to investigate the relation between audibility and performance on a nonsense syllable recognition task. Data were obtained from three subjects with moderate sensorineural hearing loss. Nine unvoiced consonants were presented in two vowel contexts (/i/ and /a/) in both the pre- and post-vocalic position at three intensities. While the performance on selected conditions appeared to vary by hearing-aid type, only one subject showed a statistically significant difference between the two hearing-aid systems. Acoustic analyses revealed a variety of spectral and temporal changes to the speech signal following processing. Estimates of audibility were based upon each subject's thresholds and an acoustic analysis of the amplified signal that varied across phonemes and consonant position. A signal detection approach was used to predict performance from a simple measure of audibility.

Amplifiers, Electronic↗

PubMed1990

Purification and characterization of the reduced-nicotinamide-dependent 2,2'-dithiodiethanesulfonate reductase from Methanobacterium thermoautotrophicum delta H.

A novel reduced nicotinamide-dependent disulfide reductase, the 2,2'-dithiodiethanesulfonate [(S-CoM)2] reductase (CoMDSR) of Methanobacterium thermoautotrophicum was purified 405-fold to electrophoretic homogeneity. Both NADPH and NADH functioned as electron donors, although rates with NADPH were three times higher. Reduced factor F420, the deazaflavin electron carrier characteristic of methanogenic bacteria, was not a substrate for the enzyme. The enzyme was most active with (S-CoM)2 but could also reduce L-cystine at 23% the (S-CoM)2 rate. Results of sodium dodecyl sulfate polyacrylamide gel electrophoresis indicated that the enzyme was monomeric with an Mr of about 64,000; spectral analysis showed that it was a flavoprotein with an estimated composition of one molecule of flavin per polypeptide. Maximal activity occurred at 64 degrees C, and the pH optimum was 8.5. The apparent Km for both NADPH and (S-CoM)2 was 80 microM. The enzyme was completely inactivated by oxygen in crude cell extracts but was oxygen stable in the homogeneous state. The low activity of the CoMDSR in cell extracts as well as its relatively low rate of reducing CoM-S-S-HTP (the heterodisulfide of the two thiol cofactors involved in the last step of methanogenesis) make it unlikely that it plays a role in the methylreductase system. It may be involved in the redox balance of the cell, such as the NADPH-dependent bis-gamma-glutamylcystine reductase with which it shows physical similarity in another archaebacterium, Halobacterium halobium (A. R. Sundquist and R. C. Fahey, J. Bacteriol. 170:3459-3467, 1988). The CoMDSR might also be involved in regenerating the coenzyme M trapped as its homodisulfide, a nonutilizable form of the cofactor.

Chromatography, Affinity↗