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PubMed1980

On the interaction of caffeine with nucleic acids. IV. Studies of the caffeine-DNA interaction by infrared and ultraviolet linear dichroism, proton and deuteron nuclear magnetic resonance.

The DNA-caffeine interaction at high concentration of caffeine (Cf) leads to an arrangement of Cf molecules outside of the DNA double helix with an orientation parallel to the bases both in the A and B form as demonstrated by infrared linear dichroism. Addition of DNA broadens the 1H NMR lines of Cf in aqueous solution indicating a specific binding. Intercalation is not the predominant mechanism, the deuterium relaxation time T1 = (38 +/- 7) ms and the estimated reorientation correlation time tau cb = 0.17 ns of caffeine-8[2H] in the Cf-DNA complex suggest an outside stacking of the ligand. According to the results a model on the DNA-Cf complex at high Cf concentration (binding process II) is suggested including the caffeine-induced reorientation of the hydration shell of DNA.

Caffeine↗

PubMed1979

Androgen-uterine interactions: an assessment of androgen interaction with the testosterone- and estrogen-receptor systems and stimulation of uterine growth and progesterone-receptor synthesis.

This study investigates growth and the induction of progesterone-receptor synthesis in the immature (day 20--23) rat uterus after injection of different doses of 5 alpha-dihydrotestosterone (DHT) and testosterone (T) in long- and short acting injection vehicles. Moderate doses of T (300 microgram/day in saline for 3 days) elicit uterine growth (ca. 250% of control) that is abolished by concomitant injections of antiandrogen (1 mg flutamide/day or 8 mg DIMP/day) but is unaffected by injections of antiestrogens (60 microgram CI-628 or U11,100A/day). Uterine growth evoked by 17 beta-estradiol (3 microgram/day for 3 days) is, however, only antagonized with the antiestrogens but not antiandrogens. Experiments employing whole uteri in vitro indicate that the specific nuclear uptake of 10(-8) M [3H]T is markedly inhibited by the antiandrogens DIMP, flutamide, and the hydroxylated flutamide metabolite (LACT) [LACT greater than DIMP greater than FLUT] while the antiestrogens CI-628 and U11,100A are ineffective. In contrast, the specific nuclear uptake of 10(-8) M [3H]-estradiol is inhibited by only the antiestrogens and not antiandrogens. When very high (5 or 10 mg) doses of DHT Are administered in an oil-containing injection vehicle, nuclear translocation and cytoplasmic depletion of the estrogen receptor does occur and a uterotrophic response is elicited which is resistant to antagonism by antiandrogen. Likewise, the DHT-stimulated increase in progesterone-receptor content is not decreased by concomitant antiandrogen. Similar 5 or 10 mg doses of DHT, administered in a water-soluble dimethylsulfoxide vehicle, show little estrogen-receptor movement and the DHT-induced uterine growth and induction of progesterone-receptor synthesis is almost completely eliminated with antiandrogen. Regardless of the degree of uterine growth stimulation, however, the androgens are poor stimulators of uterine progesterone-receptor synthesis compared with estradiol. These results indicate that androgens may interact with both the androgen- and estrogen-receptor systems in the uterus in inducing uterine growth and that the nature of the cellular mechanism, i.e., whether the androgen- and/or estrogen-receptor system is involved, is dependent critically upon the in vivo dose of androgen and the mode of hormone administration.

Androgen Antagonists↗

PubMed2004

Microbial-gut interactions in health and disease. Interactions between dendritic cells and bacteria in the regulation of intestinal immunity.

Dendritic cells (DCs) are immunoregulatory antigen-presenting cells. DCs can be potent activators of naïve T cells and influence the generation and homing of effector lymphocytes; they can also induce regulatory mechanisms and maintain non-responsiveness. In part, these different outcomes are influenced by exposure of the DC to microbial products. The regulatory role of DCs is of particular importance at mucosal surfaces such as the intestine, where the immune system exists in intimate association with the external antigenic environment. Much of what we know about DCs has come from studies on the cells outside the gastrointestinal tract but information about gut DCs and their contribution to the specialized immune environment of the gut is now emerging. Here, we review current knowledge on gut DCs, suggest models for interactions between DCs and the commensal microflora in health and disease, and discuss gut DCs as targets for probiotic therapies.

Dendritic Cells↗

PubMed2005

A simplified model to predict P-glycoprotein interacting drugs from 3D molecular interaction field.

A new two components partial least squares discriminant analysis (PLS) model for the prediction of P-glycoprotein-associated ATPase activity of drugs by using VolSurf compute theoretical molecular descriptors derived from 3D molecular interaction field was reported in the present study. By using 27 diverse drugs from literature, two models were constructed (R(2)=0.9003, 0.8150; Q(2)=0.7165, 0.7630) in this paper, which were similar to models that utilized MolSurf parametrization (R(2)=0.7760, 0.7180; Q(2)=0.7420, 0.6950) by using 22 drugs reported in the same literature. The results investigated VolSurf software was superior to MolSurf in its simplicity. Properties associated with the volume, polarizability, and hydrogen bond could have important impact on the P-glycoprotein-associated ATPase activity.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2005

Evaluating user interactions with clinical information systems: a model based on human-computer interaction models.

OBJECTIVES: This article proposes a model for dimensions involved in user evaluation of clinical information systems (CIS). The model links the dimensions in traditional CIS evaluation and the dimensions from the human-computer interaction (HCI) perspective. PROPOSED METHOD: In this article, variables are defined as the properties measured in an evaluation, and dimensions are defined as the factors contributing to the values of the measured variables. The proposed model is based on a two-step methodology with: (1) a general review of information systems (IS) evaluations to highlight studied variables, existing models and frameworks, and (2) a review of HCI literature to provide the theoretical basis to key dimensions of user evaluation. RESULTS: The review of literature led to the identification of eight key variables, among which satisfaction, acceptance, and success were found to be the most referenced. DISCUSSION: Among those variables, IS acceptance is a relevant candidate to reflect user evaluation of CIS. While their goals are similar, the fields of traditional CIS evaluation, and HCI are not closely connected. Combining those two fields allows for the development of an integrated model which provides a model for summative and comprehensive user evaluation of CIS. All dimensions identified in existing studies can be linked to this model and such an integrated model could provide a new perspective to compare investigations of different CIS systems.

Attitude to Computers↗

PubMed2004

Identification of a novel gene, DZIP (DAZ-interacting protein), that encodes a protein that interacts with DAZ (deleted in azoospermia) and is expressed in embryonic stem cells and germ cells.

Evidence from diverse organisms, including humans, suggests that the DAZ (Deleted in Azoospermia) gene and a closely related homolog, DAZL (DAZ-like), are required early in germ cell development to maintain initial germ cell populations. Here we report the identification and characterization of the DZIP (DAZ-Interacting Protein) gene, which encodes at least three different protein isoforms that contain a C2H2 zinc-finger domain. The DZIP gene is expressed predominantly in human embryonic stem cells and fetal and adult germ cells; moreover, two DZIP protein isoforms colocalize with DAZ and/or DAZL proteins in these tissues. Finally, we provide evidence indicating that DZIP may associate with DAZ and its other cofactors in an RNA-binding protein complex that functions in both ES cells and germ cells.

Adaptor Proteins, Signal Transducing↗

PubMed2003

Interaction between artificial membranes and enflurane, a general volatile anesthetic: DPPC-enflurane interaction.

The structural modifications of the dipalmitoylphosphatidylcholine (DPPC) organization induced by increasing concentration of the volatile anesthetic enflurane have been studied by differential scanning calorimetry, small-angle, and wide-angle x-ray scattering. The interaction of enflurane with DPPC depends on at least two factors: the enflurane-to-lipid concentration ratio and the initial organization of the lipids. At 25 degrees C (gel state), the penetration of enflurane within the lipids induces the apparition of two different mixed lipid phases. At low anesthetic-to-lipid molar ratio, the smectic distance increases whereas the direction of the chain tilt changes from a tilt toward next-neighbors to a tilt between next-neighbors creating a new gel phase called L(beta')(2NNN). At high ratio, the smectic distance is much smaller than for the pure L(beta') DPPC phase, i.e., 50 A compared to 65 A, the aliphatic chains are perpendicular to the membrane and the fusion temperature of the phase is 33 degrees C. The electron profile of this phase that has been called L(beta)(i), indicates that the lipids are fully interdigitated. At 45 degrees C (fluid state), a new melted phase, called L(alpha)(2), was found, in which the smectic distance decreased compared to the initial pure L(alpha)(1) DPPC phase. The thermotropic behavior of the mixed phases has also been characterized by simultaneous x-ray scattering and differential scanning calorimetry measurements using the Microcalix calorimeter of our own. Finally, titration curves of enflurane effect in the mixed lipidic phase has been obtained by using the fluorescent lipid probe Laurdan. Measurements as a function of temperature or at constant temperature, i.e., 25 degrees C and 45 degrees C give, for the maximal effect, an enflurane-to-lipid ratio (M/M), within the membrane, of 1 and 2 for the L(alpha)(2) and the L(beta)(i) lamellar phase respectively. All the results taken together allowed to draw a pseudo-binary phase diagram of enflurane-dipalmitoylphosphatidylcholine in excess water.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed1996

Avidin-biotin interactions at vesicle surfaces: adsorption and binding, cross-bridge formation, and lateral interactions.

Densely packed domains of membrane proteins are important structures in cellular processes that involve ligand-receptor binding, receptor-mediated adhesion, and macromolecule aggregation. We have used the biotin-avidin interaction at lipid vesicle surfaces to mimic these processes, including the influence of a surface grafted polymer, polyethyleneglycol (PEG). Single vesicles were manipulated by micropipette in solutions of fluorescently labeled avidin to measure the rate and give an estimate of the amount of avidin binding to a biotinylated vesicle as a function of surface biotin concentration and surface-grafted PEG as PEG-lipid. The rate of avidin adsorption was found to be four times less with 2 mol% PEG750 than for the unmodified surface, and 10 mol% PEG completely inhibited binding of avidin to biotin for a 2-min incubation. Using two micropipettes, an avidin-coated vesicle was presented to a biotinylated vesicle. In this vesicle-vesicle adhesion test, the accumulation of avidin in the contact zone was observed, again by using fluorescent avidin. More importantly, by controlling the vesicle membrane tension, this adhesion test provided a direct measure of the spreading pressure of the biotin-avidin-biotin cross-bridges confined in the contact zone. Assuming ideality, this spreading pressure gives the concentration of avidin cross-bridges in the contact zone. The rate of cross-bridge accumulation was consistent with the diffusion of the lipid-linked "receptors" into the contact zone. Once adherent, the membranes failed in tension before they could be peeled apart. PEG750 did not influence the mechanical equilibrium because it was not compressed in the contact zone, but it did perform an important function by eliminating all nonspecific adhesion. This vesicle-vesicle adhesion experiment, with a lower tension limit of 0.01 dyn/cm, now provides a new and useful method with which to measure the spreading pressures and therefore colligative properties of a range of membrane-bound macromolecules.

Adsorption↗

PubMed1996

VASP interaction with vinculin: a recurring theme of interactions with proline-rich motifs.

VASP (vasodilator-stimulated phosphoprotein), a protein associated with microfilaments at cellular contact sites, has been identified as a ligand for profilin and zyxin, two proteins also involved in microfilament dynamics and organization at these regions. Here, we report that VASP also directly binds to vinculin, another component of adherens junctions. Competition experiments with a vinculin-derived peptide showed that a proline-rich motif, located in the hinge region that connects vinculin's head and tail domains, is involved in VASP binding. The same motif is present in zyxin but the interactions of VASP with vinculin and zyxin differ in detail. Hence, this motif may be recognized by VASP in different ways when presented in distinct cellular sites.

Amino Acid Sequence↗

PubMed1997

PLATIN (plant-atmosphere interaction) I: A model of plant-atmosphere interaction for estimating absorbed doses of gaseous air pollutants.

A PLant-ATmosphere INteraction model (PLATIN) was developed for estimating air pollutant absorbed doses under ambient conditions. PLATIN is based on the canopy energy balance combined with a gas transport submodel. The model has three major resistance components: (1) a turbulent atmospheric resistance Rah(zm) that describes the atmospheric transport properties between a measurement height above the canopy and the conceptual height z=d+z0m which represents the sink for momentum according to the big-leaf concept; (2) a quasilaminar layer resistance R(b,A) that quantifies the way in which the transfer of sensible heat and matter (e.g. latent heat, ozone) differs from momentum transfer; (3) a canopy or surface resistance R(c,A) that describes the influences of the plant/soil system on the exchange processes. Soil water content is simulated by a Force-Restore model. By a simple interception submodel precipitation and dew are partitioned into intercepted water and water reaching the soil surface. PLATIN can be run in a prognostic or a diagnostic mode. It is also intended for on-line use in air quality monitoring networks.

Journal Article↗

PubMed2002

The Roter interaction analysis system (RIAS): utility and flexibility for analysis of medical interactions.

The Roter interaction analysis system (RIAS), a method for coding medical dialogue, is widely used in the US and Europe and has been applied to medical exchanges in Asia, Africa, and Latin America. Contributing to its rapid dissemination and adoption is the system's ability to provide reasonable depth, sensitivity, and breadth while maintaining practicality, functional specificity, flexibility, reliability, and predictive validity to a variety of patient and provider outcomes. The purpose of this essay is two-fold. First, to broadly overview the RIAS and to present key capabilities and coding conventions, and secondly to address the extent to which the RIAS is consistent with, or complementary to, linguistic-based techniques of communication analysis.

Communication↗

PubMed1999

Health care providers and purchasers and evaluation of interactive health communication applications. Science Panel on Interactive Communication and Health.

Health care providers and purchasers of health services have an opportunity to improve patient care and potentially save costs through the wise purchase of interactive health communication applications for patients and employees. Purchasing decisions based on evaluation and evidence should drive the design and development of new systems. The cycle of evaluation includes a needs assessment before system development, usability testing during development, and studies of use and outcomes in natural settings. This type of evidence is critical to our understanding of how best to provide health information and decision assistance to patients, employees, and others.

Community Participation↗

PubMed2001

Model membrane/substrate interactions: ethanol and procaine interactions.

The ability of ethanol to lower the surface tension of water plays a major role in its ability to affect membrane lipids. Typical lipids will show little expansion on exposure to ethanol substrates and may even show condensations. At the same time, the overall stability of the lipid phase is significantly reduced. Previously, we reported experimental and theoretical studies of the stearic acid (SA)/procaine (PR) system. PR substrate concentrations were examined in the 10(-4)-10(-2) M range as Gibbs monolayers, in order to establish the surface activity of both charged and uncharged species, and to estimate the orientation of the PR species at the air/water interface. SA interactions with PR substrates were studied by compressing films of the former and recording the surface pressure/area per molecule isotherms at both pH 2 and 8, so that the SA was in an uncharged and charged state, respectively. More recently, we have carried out similar studies with L-alpha-dipalmitoyl phosphatidylcholine (DPPC), maintaining the substrate pH at between 5 and 6, at PR concentrations of 10(-6)-10(-2)M. We also carried out studies of the DPPC/PR system using fluorescence microscopy in order to examine the effects of PR on the biphasic liquid expanded/liquid condensed (LE/LC) transition region. In the absence of any lipid film, PR species appear to be horizontally oriented at the air/water interface, while the surface activity of PR species increases in the order PRH(2+)<PRH(+)<PR, with the neutral species being the most surface active. "Penetration" of a lipid film appears to be predominately due to the insertion of the lipophilic portion of the PR species, though some deeper penetration may occur. Penetration also appears to be greater when the film is charged, thus, SA films show greater expansion at pH 8 than they do at pH 2. For both SA and DPPC the penetration of PR species may be reversed by increasing surface pressure and the penetration goes through a maximum value which is dependent on both the substrate PR concentration and the nature of the lipid film. This phenomenon may be related to that of pressure anesthesia reversal. For DPPC, the maximum penetration occurs where the film is undergoing a LE/LC transition and it appears that PRH(+) penetrates DPPC more easily than SA. Fluorescence microscopy indicates that the presence of PR species creates much smaller LC domains, while maintaining the total amount of that phase. This is interpreted in terms of a reduction of the line tension between the LE and LC phases due to a line activity of the PR species. Thus, PR will preferentially locate at interfaces within the membrane and this observation should also apply to the lipid-protein interface.

Journal Article↗

PubMedDate not supplied

Electrochemical investigations of the interaction of metal chelates with DNA. 3. Electrogenerated chemiluminescent investigation of the interaction of tris(1,10-phenanthroline)ruthenium(II) with DNA.

The electrogenerated chemiluminescence (ECL) that results from the oxidation of tris(1,10-phenanthroline)ruthenium(II), at a gold electrode in the presence of oxalate, was used to investigate the interaction of the Ru(II) chelate with calf thymus DNA. The decrease in ECL emission from the excited state, Ru(phen)3(2+*), in the presence of DNA, is ascribed to binding to binding of the chelate to the DNA strand. An ECL titration of the metal complex with DNA allowed determination of the equilibrium constant (K) and binding-site size (s) for association of Ru(phen)3(2+), under the assumption that only the free metal complex contributes to the observed emission. In 25 mM Na2C2O4, 2 mM phosphate buffer, pH 5, 0.05% Tween-20, 0.05% Triton X-100, regression based on the McGhee/von Hippel model, which accounts for free base pair gaps between binding sites, yielded K = 8.1 (+/- 0.2) x 10(3) M-1 and s = 4 bp.

Animals↗

PubMed1991

Subsite interactions of ribonuclease T1: Asn36 and Asn98 accelerate GpN transesterification through interactions with the leaving nucleoside N.

We previously presented evidence that ribonuclease T1 (RNase T1; EC 3.1.27.3) contains a subsite that, by interacting with the leaving nucleoside N of GpN dinucleoside phosphate substrates, contributes to catalysis. The kcat values for transphosphorylation follow the order GpC greater than GpA greater than GpU whereas the equilibrium dissociation constants for these substrates are very similar [Steyaert, J., Wyns, L., & Stanssens, P. (1991) Biochemistry (preceding paper in this issue)]. Consistent with this notion, we find that the rate of transesterification of the synthetic substrate GpMe, in which the leaving nucleoside is replaced by a methanol group, is at least 3 orders of magnitude lower than that of GpN substrates. The enzyme's affinity for GpMe is very similar to that for the various GpN substrates, indicating that the apparent contribution of the leaving nucleoside to ground-state binding is minimal. To identify the side chains that belong to the RNase T1 subsite, we searched for amino acid substitutions that differentially affect the transesterification kinetics of GpNs versus GpMe. The Asn36Ala, Tyr38Phe, His92Gln, and Asn98Ala mutants have been analyzed. Of these, the Asn36Ala and Asn98Ala substitutions reduce the transphosphorylation rate of the different GpNs considerably whereas they have virtually no effect on the rate of GpMe transphosphorylation. This observation shows that the Asn36 and Asn98 amide functions are part of the RNase T1 subsite. The sum of the contributions of the two residues accounts quite precisely for the differences in turnover rates among GpC, GpA, and GpU.

Amino Acid Sequence↗

PubMed2001

The acetylation state of human fetal hemoglobin modulates the strength of its subunit interactions: long-range effects and implications for histone interactions in the nucleosome.

The source of the 70-fold increased tetramer strength of liganded fetal hemoglobin relative to that of adult hemoglobin between pH 6.0 and 7.5 reported earlier [Dumoulin et al. (1997) J. Biol. Chem. 272, 31326] has been identified as the N-terminal Gly residue of the gamma-chain, which is replaced by Val in adult hemoglobin. This was revealed by extending the study of the pH dependence of the tetramer-dimer equilibrium of these hemoglobins into the alkaline range as far as pH 9. From pH 7.5 to 9.0, the 70-fold difference in the association equilibrium constant between hemoglobins F and A lessened progressively. This behavior was attributed to the difference in the pK(a) 8.1 of Gly-1(gamma) compared to the pK(a) 7.1 value of Val-1(beta) of hemoglobins F and A, respectively. Evidence for this conclusion was obtained by demonstrating that natural hemoglobin F(1), which is specifically acetylated at Gly-1(gamma) and hence unable to be protonated, behaves like HbA and not HbF in its tetramer-dimer association properties over the pH range studied. An increased degree of protonation of the gamma-chain N-terminus of hemoglobin F from pH 9.0 to 8.0 is therefore suggested as responsible for its increased tetramer strength representing an example of transmission of a signal from its positively charged N-terminal tail to the distant subunit allosteric interface where the equilibrium constant is measured. An analogy is made between the effects of acetylation of the fetal hemoglobin tetramer on the strength of its subunit interactions and acetylation of some internal Lys residues within the N-terminal segments of the histone octamer around which DNA is wrapped in the nucleosome.

Acetylation↗

PubMed1982

Studies on interaction of anthracycline antibiotics and deoxyribonucleic acid: equilibrium binding studies on interaction of daunomycin with deoxyribonucleic acid.

We have used equilibrium dialysis and fluorescence and absorbance titration to study the interaction of daunomycin with DNA. Our data at 200 mM Na+ are best fit by the neighbor exclusion model, with K = 7.0 x 10(5) M-1 and an exclusion parameter of three to four base pairs. The binding is dependent on ionic strength, with d log K/d log [Na+] = -0.84, from which we may estimate quantitatively ion release and the binding free energy corrected for the free energy of counterion release. From the temperature dependence of the binding constant, we find the binding to be exothermic, with a van't Hoff enthalpy of -12.8 kcal/mol. Competition dialysis experiments show that G+C base pairs are slightly preferred as binding sites for the drug and suggest that daunomycin binds preferentially to G+C pairs at low r. Cesium chloride density gradient sedimentation experiments provide an experimental demonstration of this preference. Daunomycin increases the Tm for DNA melting by some 30 degrees C as binding approaches saturation, with biphasic melting at low drug/base pair ratios. The data from these equilibrium studies are consistent with intercalative binding of daunomycin and provide a solid foundation for further structural and kinetic studies.

Base Composition↗

PubMed1985

Interactions between the oligomycin sensitivity conferring protein (OSCP) and beef heart mitochondrial F1-ATPase. 2. Identification of the interacting F1 subunits by cross-linking.

Interactions between oligomycin sensitivity conferring protein (OSCP) and subunits of beef heart mitochondrial F1-ATPase have been explored by cross-linking at an OSCP/F1 molar ratio close to 1 to ensure specific high-affinity binding of OSCP to F1 [see Dupuis et al. [Dupuis, A., Issartel, J.-P., Lunardi, J., Satre, M., & Vignais, P.V. (1985) Biochemistry (preceding paper in this issue)]]. Cross-links between F1 subunits and OSCP were established by means of two zero length cross-linkers, 1-[3-(dimethylamino)propyl]-3-ethylcarbodiimide and N-(ethoxycarbonyl)-2-ethoxydihydroquinoline. The cross-linked products were separated by sodium dodecyl suflate-polyacrylamide gel electrophoresis. Coomassie blue staining revealed two cross-linked products of Mr 75 000 and 80 000 which could result from the binding of OSCP to the alpha and beta subunits of F1. Definite identification of the cross-linked products was achieved by chemical labeling with specific radiolabeled reagents and by blotting on nitrocellulose filters followed by immunocharacterization with anti-alpha, anti-beta, and anti-OSCP antibodies. OSCP was found to cross-link with the alpha and beta subunits of F1.

Adenosine Triphosphatases↗