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At least 1,243 records · Page 69Linked to original sources
PubMed2005

Tools for building a comprehensive modeling system for virtual screening under real biological conditions: The Computational Titration algorithm.

Computational tools utilizing a unique empirical modeling system based on the hydrophobic effect and the measurement of logP(o/w) (the partition coefficient for solvent transfer between 1-octanol and water) are described. The associated force field, Hydropathic INTeractions (HINT), contains much rich information about non-covalent interactions in the biological environment because of its basis in an experiment that measures interactions in solution. HINT is shown to be the core of an evolving virtual screening system that is capable of taking into account a number of factors often ignored such as entropy, effects of solvent molecules at the active site, and the ionization states of acidic and basic residues and ligand functional groups. The outline of a comprehensive modeling system for virtual screening that incorporates these features is described. In addition, a detailed description of the Computational Titration algorithm is provided. As an example, three complexes of dihydrofolate reductase (DHFR) are analyzed with our system and these results are compared with the experimental free energies of binding.

1-Octanol↗
PubMed2006

Isothermal titration calorimetry study of epicatechin binding to serum albumin.

The interaction of epicatechin with bovine serum albumin (BSA) was studied by isothermal titration calorimetry. The binding constant (K) and associated thermodynamic binding parameters (n, DeltaH) were determined for the interaction at three solution concentrations of BSA using a binding model assuming independent binding sites. These data show weak non-covalent binding of epicatechin to BSA. The interaction energetics varied with BSA concentration in the calorimeter cell, suggesting that the binding of epicatechin induced BSA aggregation. The free energy (DeltaG) remained constant within a range of 2 kJ mol(-1) and negative entropy was observed, indicating an enthalpy driven exothermic interaction. It is concluded that the non-covalent epicatechin-BSA complex is formed by hydrogen bonding.

Algorithms↗
PubMed2006

Uncertainty evaluation in the chloroquine phosphate potentiometric titration: application of three different approaches.

A measurement result cannot be properly interpreted if not accompanied by its uncertainty. Several methods to estimate uncertainty have been developed. From those methods three in particular were chosen in this work to estimate the uncertainty of the Eu. Ph. chloroquine phosphate assay, a potentiometric titration commonly used in medicinal control laboratories. The famous error-budget approach (also called bottom-up or step-by-step) described by the ISO Guide to the expression of Uncertainty in Measurement (GUM) was the first method chosen. It is based on the combination of uncertainty contributions that have to be directly derived from the measurement process. The second method employed was the Analytical Method Committee top-down which estimates uncertainty through reproducibility obtained during inter-laboratory studies. Data for its application were collected in a proficiency testing study carried out by over 50 laboratories throughout Europe. The last method chosen was the one proposed by Barwick and Ellison. It uses a combination of precision, trueness and ruggedness data to estimate uncertainty. These data were collected from a validation process specifically designed for uncertainty estimation. All the three approaches presented a distinctive set of advantages and drawbacks in their implementation. An expanded uncertainty of about 1% was assessed for the assay investigated.

Chloroquine↗
PubMed2004

Real-time quantitative PCR-based serum neutralization test for detection and titration of neutralizing antibodies to chicken anemia virus.

Detection and titration of chicken anemia virus (CAV)-neutralizing antibodies has relied on tedious, time-consuming passaging of infected cells, or subjective recognition of cytopathic effect in individual cells, because CAV replicates in culture only in lymphoblastoid cell lines, and thus generates no plaques. This paper describes a rapid method, in which CAV genomes in infected cells are quantitated by qPCR 3-4 days postinfection (p.i.), without passaging cells. Three sera, weakly positive with a commercial CAV ELISA kit, from broiler chickens immunized with a commercial CAV vaccine, were used to develop the assay. Virus neutralization titers of these sera were determined using two different CAV-susceptible cell lines (MDCC-MSB1 and MDCC-CU147) by the conventional method of passaging cells infected with 10,000 TCID(50) CAV per well, and by qPCR-based methods using cells infected with 100 or 10,000 TCID(50) per well in 24-well or 96-well plates. The method was also adapted to conventional PCR. The positive sera exhibited virus neutralization activity at dilutions ranging from 1:10 to 1:320 by the various assays. Although virus neutralization titers differed somewhat depending on the assay conditions used, the relative order of the titers of the three positive sera was the same for all assays. The qPCR-based assays are as sensitive and more rapid for detection of neutralizing antibody than the conventional assay based on passaging infected cells, and more sensitive for detection of low-level CAV antibodies than a commercial blocking ELISA.

Animals↗
PubMed2005

Quantitative real-time PCR for titration of infectious recombinant AAV-2 particles.

In this report, we present a fast, reliable and easy to perform method to quantify infectious titers of recombinant AAV-2 (rAAV-2) particles using the LightCycler technology, which is independent from the therapeutic transgene and without the presence of a marker gene. The method is based on the life cycle of AAV-2: after infection of the host cell, the single stranded (ss) AAV-2 genome is converted into a double stranded (ds) form. Following infection with rAAV-2, HeLa cells were lysed and ssDNA of transcriptionally inactive particles were efficiently removed by ssDNA-specific S1 nuclease digestion. The remaining viral dsDNA can be quantified by quantitative real-time PCR (qPCR). For validation of the new method, rAAV-2 preparations were analyzed by two other standard methods for titration of infectious particles in parallel, i.e. the infectious center assay (ICA) as well as flow cytometry using GFP as a marker. Comparing the infectious titers of 40 different AAV-2 fractions assessed by qPCR with the titers determined by FACS analysis a significant correlation (r=0.87, p<0.001) with a mean ratio of the titers assessed by qPCR and FACS of 1.92 (S.D.+/-1.59) was found. Further, the titers of seven rAAV-2 fractions using qPCR and ICA covering 5 log ranges were compared and a significant correlation was found between the results (r=0.80, p<0.001) with a mean ratio of 3.38 (S.D.+/-1.79), respectively.

Cell Line↗
PubMed2004

A randomized trial of auto-titrating CPAP and fixed CPAP in the treatment of obstructive sleep apnea-hypopnea.

BACKGROUND: Continuous positive airway pressure (CPAP) remains the treatment of choice for obstructive sleep apnea hypopnea (OSAH). Auto-titrating CPAP (APAP) devices automatically adjust pressure and may improve treatment compliance compared to fixed CPAP (F-CPAP). METHODS: Randomized, prospective, single-blind, crossover trial to compare efficacy, side effects, compliance, patient satisfaction and preference between APAP and F-CPAP therapy in patients with moderate to severe OSAH. There were two treatment periods of 4 weeks each (APAP and F-CPAP), separated by a 2-week washout period. RESULTS: Ten CPAP-naive OSAH patients (9 males) completed the study. They had Mean +/- SD age of 44.9 +/- 9.7 years; body mass index of 35.9 +/- 12.9 kg/m2 and apnea/hypopnea index (AHI) of 47.2 +/- 35.6. Both forms of therapy were equally effective in improving the symptoms and in reducing the AHI. Both forms of therapy were associated with frequent side effects and had similar patient compliance. At the end of the study, more patients (6-1) preferred F-CPAP to A-CPAP therapy. CONCLUSION: A-PAP was as effective as F-CPAP in the treatment of OSAH but was not associated with fewer side effects, better compliance, better satisfaction or increased patient preference.

Adult↗
PubMed2005

Thermodynamics study of the dimerization equilibria of rhodamine B and 6G in different ionic strengths by photometric titration and chemometrics method.

The dimerization constants of rhodamine B and 6G have been determined by studying the dependence of their absorption spectra on the temperature in the range 20-80 degrees C at different total concentrations of rhodamine B (5.89 x 10(-6) to 2.36 x 10(-4)M) and rhodamine 6G (2.34 x 10(-5) to 5.89 x 10(-4)M) and in different concentrations of LiCl, NaCl and KCl salts as supporting electrolytes. The monomer-dimer equilibrium of rhodamine B and 6G have been determined by chemometrics refinement of the absorption spectra obtained by thermometric titrations performed at different ionic strengths. The quantitative analysis of the data of undefined mixtures, was carried out by simultaneous resolution of the overlapping spectral bands in the whole set of absorption spectra. The dimerization constants are varied by changing the ionic strength and the degree of dimerization are decreased by increasing of the ionic strength of the medium. The enthalpy and entropy of the dimerization reactions were determined from the dependence of the equilibrium constants on the temperature (van't Hoff equation). From the thermodynamic results the TDeltaS degrees -DeltaH degrees plot was sketched. It shows a fairly good positive correlation which indicates the enthalpy-entropy compensation in the dimerization reactions (compensation effect).

Computers↗
PubMed2006

Study on the inclusion behavior of p-sulphonatocalix[4]arene with 9-amino-acridine by spectrofluorometric titrations.

Spectrofluorometric titrations have been performed to investigate the inclusion behavior of p-sulphonatocalix[4]arene (SC4A) and 9-amino-acridine (AA) in citrate buffer solution (pH 5.92). It was found that the fluorescence intensity of AA quenched regularly upon the addition of SC4A. The proposed interaction mechanism between SC4A and AA indicates that AA partially goes into the cavity of SC4A with the help of strong electrostatic interaction and hydrogen bonding, which formed by the protonated N atom and the amino groups of AA bonding with sulphonyl groups of SC4A, respectively. The inclusion ratio was 1:1 and the inclusion constant was 1.84 x 10(5) L mol(-1) at 25.0 degrees C.

Aminacrine↗
PubMed2005

Historical article: Titration studies and the structure of DNA.

During the period of 1946-1956 ideas on the structure of the nucleic acids, especially DNA, were profoundly influenced by physico-chemical studies and, in particular, by electrometric titration studies pioneered by J. Masson Gulland and D.O. Jordan. It was eventually conclusively inferred when such studies had been sufficiently refined that: in DNA, the only hydrogen bonding that occurred was between the 1:6 amino groups of adenine and cytosine, and the -NH-CO "enolic" groups of thymine and guanine; the polynucleotide chains of DNA were not branched (or interrupted); and the internally hydrogen-bonded double-helical structure was stable both in aqueous solution and in the fibrous state.

DNA↗
PubMed2005

A modified critical test and its use in two dose titration trials to assess efficacy of praziquantel for Anoplocephala perfoliata in equids.

Aims of this study with 43 equids naturally infected with Anoplocephala perfoliata in two dose titration trials were to document (i) the usefulness of a critical test with a 48 h treatment to necropsy period, (ii) efficacy of an oral paste of 0.5-2.0 mg praziquantel/kg body weight, and (iii) when after treatment would fecal egg counts provide best estimates of the tapeworm's prevalence in a herd. All feces passed by an equid after treatment and collected in successive 12 h batches were examined for tapeworms. At necropsy, tapeworms were identified as attached to the mucosa or unattached. Tapeworms were examined with a stereoscope and identified as normal or abnormal. Fecal samples were taken for egg counts at treatment and at 6 h intervals thereafter. In 32 of 36 treated equids, efficacy was 100% and mean efficacies for 0.5, 1.0, 1.5 and 2.0 mg praziquantel/kg body weight were 85.5, 99.7, 100 and 100%, respectively. Two equids treated with 0.5 mg praziquantel/kg body weight had low efficacies (5.4 and 38.1%) and normal tapeworms were found attached in the ventral colon and in one equid also in the dorsal colon. In seven untreated equids, tapeworms were primarily in the cecum with 21.3% detached. "Major fragments" or worms without a scolex but otherwise nearly a complete worm were 20.5% of the number of intact worms; they were not included in the efficacy analysis but should be. If the two equids with low efficacy were eliminated and if the number of all tapeworms and major fragments are combined less than 0.5% were in feces within 12 h of treatment, about 20% were in the 12-24 h period, 42% in 24-36h, 24% in 36-48 h and 13.5% in the equids at necropsy. One horse passed all its tapeworms in 24 h. This 48 h test when compared with a 24 h one with no examination of feces was more efficient in use of trial animals and reduced underestimation and overestimation of efficacy. However, a protocol similar to the 48 h test but with a 24 or 36 h post-treatment period should be investigated. The mean egg count peaked 18-24 h after treatment and samples taken at that time would provide the best estimate of prevalence. The Cornell-Wisconsin centrifugal flotation technique had a specificity of 100% and at 18 and 24 h its sensitivity was 94%. A brief discussion on critical and controlled tests for assessing efficacy of an anthelmintic for A. perfoliata is presented.

Administration, Oral↗
PubMed2005

The activity of wild-type and mutant phenylalanine hydroxylase and its regulation by phenylalanine and tetrahydrobiopterin at physiological and pathological concentrations: an isothermal titration calorimetry study.

The activity of phenylalanine hydroxylase (PAH) is regulated by the levels of both the substrate (L-Phe) and the natural cofactor (6R)-tetrahydrobiopterin (BH4). It has recently been observed that many PAH mutants associated with BH4-responsive phenylketonuria display abnormal kinetic and regulatory properties as shown by standard kinetic analyses. In this work, we have developed a high-sensitive and high-throughput activity assay based on isothermal titration calorimetry (ITC) in order to study the kinetic properties of wild-type PAH (wt-PAH) and the BH4-responsive c.204A>T (p.R68S) mutant at physiological and superphysiological concentrations of L-Phe and BH4. Compared to wt-PAH, the p.R68S mutant showed reduced apparent and equilibrium binding affinity for the natural cofactor and increased affinity and non-cooperative response for L-Phe, together with a strong substrate inhibition that is alleviated at high BH4 concentrations. For both wt-PAH and mutant, the apparent affinity for BH4 decreases at increasing L-Phe concentrations, and the affinity for the substrate also depends on the cofactor concentration. Our results indicate that the activity landscape for wt and mutant enzymes is more complex than expected from standard kinetic analyses and highlight the applicability of this ITC-based assay to characterize the activity and regulation of PAH at a wide range of substrate and cofactor concentrations. Moreover, the results aid to understand the activity dynamics of wild-type and mutant PAH under physiological and pathological conditions, as well as BH4-responsiveness in certain PKU mutations.

Animals↗
PubMed2000

Beta-blocker titration failure is independent of severity of heart failure.

In the present study, predictors of complicated initiation of beta blockade in patients with idiopathic dilated cardiomyopathy was studied. We found that generally accepted measures of severity of heart failure are not predictable, whereas low systolic blood pressure (< or =120 mm Hg) was the strongest predictor for problematic (up)titration.

Adolescent↗
PubMed1999

Association of ethanol with lipid membranes containing cholesterol, sphingomyelin and ganglioside: a titration calorimetry study.

The association of ethanol at physiologically relevant concentrations with lipid bilayers of different lipid composition has been investigated by use of isothermal titration calorimetry (ITC). The liposomes examined were composed of combinations of lipids commonly found in neural cell membranes: dimyristoyl phosphatidylcholine (DMPC), ganglioside (GM(1)), sphingomyelin and cholesterol. The calorimetric results show that the interaction of ethanol with fluid lipid bilayers is endothermic and strongly dependent on the lipid composition of the liposomes. The data have been used to estimate partitioning coefficients for ethanol into the fluid lipid bilayer phase and the results are discussed in terms of the thermodynamics of partitioning. The presence of 10 mol% sphingomyelin or ganglioside in DMPC liposomes enhances the partitioning coefficient by a factor of 3. Correspondingly, cholesterol (30 mol%) reduces the partitioning coefficient by a factor of 3. This connection between lipid composition and partitioning coefficient correlates with in vivo observations. Comparison of the data with the molecular structure of the lipid molecules suggests that ethanol partitioning is highly sensitive to changes in the lipid backbone (glycerol or ceramide) while it appears much less sensitive to the nature of the head group.

Anesthetics↗
PubMed2003

An isothermal titration calorimetry study on the binding of four volatile general anesthetics to the hydrophobic core of a four-alpha-helix bundle protein.

A molecular understanding of volatile anesthetic mechanisms of action will require structural descriptions of anesthetic-protein complexes. Previous work has demonstrated that the halogenated alkane volatile anesthetics halothane and chloroform bind to the hydrophobic core of the four-alpha-helix bundle (Aalpha(2)-L38M)(2) (Johansson et al., 2000, 2003). This study shows that the halogenated ether anesthetics isoflurane, sevoflurane, and enflurane are also bound to the hydrophobic core of the four-alpha-helix bundle, using isothermal titration calorimetry. Isoflurane and sevoflurane both bound to the four-alpha-helix bundle with K(d) values of 140 +/- 10 micro M, whereas enflurane bound with a K(d) value of 240 +/- 10 micro M. The DeltaH degrees values associated with isoflurane, sevoflurane, and enflurane binding were -7.7 +/- 0.1 kcal/mol, -8.2 +/- 0.2 kcal/mol, and -7.2 +/- 0.1 kcal/mol, respectively. The DeltaS degrees values accompanying isoflurane, sevoflurane, and enflurane binding were -8.5 cal/mol K, -10.4 cal/mol K, and -8.0 cal/mol K, respectively. The results indicate that the hydrophobic core of (Aalpha(2)-L38M)(2) is able to accommodate three modern ether anesthetics with K(d) values that approximate their clinical EC(50) values. The DeltaH degrees values point to the importance of polar interactions for volatile general anesthetic binding, and suggest that hydrogen bonding to the ether oxygens may be operative.

Anesthetics, General↗
PubMed1979

K+ conductance modified by a titratable group accessible to protons from the intracellular side of the squid axon membrane.

In the range of pH examined (5.2-10), variations of internal pH from high to low values result in a reversible decrease of the conductance of the open K channels, without significantly affecting the kinetics parameters. A linear plot of the conductance versus internal pH suggests the existence of a titratable group that has an apparent pKa of about 6.9, and that is accessible to protons only from the intracellular side of the membrane.

Animals↗
PubMed1993

Multigrid solution of the nonlinear Poisson-Boltzmann equation and calculation of titration curves.

Although knowledge of the pKa values and charge states of individual residues is critical to understanding the role of electrostatic effects in protein structure and function, calculating these quantities is challenging because of the sensitivity of these parameters to the position and distribution of charges. Values for many different proteins which agree well with experimental results have been obtained with modified Tanford-Kirkwood theory in which the protein is modeled as a sphere (reviewed in Ref. 1); however, convergence is more difficult to achieve with finite difference methods, in which the protein is mapped onto a grid and derivatives of the potential function are calculated as differences between the values of the function at grid points (reviewed in Ref. 6). Multigrid methods, in which the size of the grid is varied from fine to coarse in several cycles, decrease computational time, increase rates of convergence, and improve agreement with experiment. Both the accuracy and computational advantage of the multigrid approach increase with grid size, because the time required to achieve a solution increases slowly with grid size. We have implemented a multigrid procedure for solving the nonlinear Poisson-Boltzmann equation, and, using lysozyme as a test case, compared calculations for several crystal forms, different refinement procedures, and different charge assignment schemes. The root mean square difference between calculated and experimental pKa values for the crystal structure which yields best agreement with experiment (1LZT) is 1.1 pH units, with the differences in calculated and experimental pK values being less than 0.6 pH units for 16 out of 21 residues. The calculated titration curves of several residues are biphasic.

Algorithms↗
PubMed1994

Near infrared spectral changes of cytochrome aa3 during potentiometric titrations.

Singular value decomposition (SVD) was used to deconvolute the spectral changes occurring in the near infrared region during potentiometric titrations of cytochrome aa3. Overall oxidized minus reduced difference spectra revealed a broad absorbance feature centered near 830 nm with an apparent Em near 250 mV. However, SVD did not isolate any spectral species with an absorbance centered near 830 nm. It was found that the spectral changes occurring in the wavelength region from 650 to 950 nm were associated mainly with cytochromes a and a3. It was concluded that the absorbance at 830 nm should not be used as an independent measure of the concentration of CuA in cytochrome aa3.

Animals↗
PubMed1996

Evaluation of linked protonation effects in protein binding reactions using isothermal titration calorimetry.

A theoretical development in the evaluation of proton linkage in protein binding reactions by isothermal titration calorimetry (ITC) is presented. For a system in which binding is linked to protonation of an ionizable group on a protein, we show that by performing experiments as a function of pH in buffers with varying ionization enthalpy, one can determine the pK(a)'s of the group responsible for the proton linkage in the free and the liganded states, the protonation enthalpy for this group in these states, as well as the intrinsic energetics for ligand binding (delta H(o), delta S(o), and delta C(p)). Determination of intrinsic energetics in this fashion allows for comparison with energetics calculated empirically from structural information. It is shown that in addition to variation of the ligand binding constant with pH, the observed binding enthalpy and heat capacity change can undergo extreme deviations from their intrinsic values, depending upon pH and buffer conditions.

Calorimetry↗