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At least 865 records · Page 48Linked to original sources
PubMed1999

Applications of amorphous track models in radiation biology.

The average or amorphous track model uses the response of a system to gamma-rays and the radial distribution of dose about an ion's path to describe survival and other cellular endpoints from proton, heavy ion, and neutron irradiation. This model has been used for over 30 years to successfully fit many radiobiology data sets. We review several extensions of this approach that address objections to the original model, and consider applications of interest in radiobiology and space radiation risk assessment. In the light of present views of important cellular targets, the role of target size as manifested through the relative contributions from ion-kill (intra-track) and gamma-kill (inter-track) remains a critical question in understanding the success of the amorphous track model. Several variations of the amorphous model are discussed, including ones that consider the radial distribution of event-sizes rather than average electron dose, damage clusters rather than multiple targets, and a role for repair or damage processing.

Animals↗
PubMed2005

A flexible approach to the calculation of resonance energy transfer efficiency between multiple donors and acceptors in complex geometries.

Resonance energy transfer provides a practical way to measure distances in the range of 10-100 A between sites in biological molecules. Although the relationship between the efficiency of energy transfer and the distance between sites is well described for a single pair of fluorophores, the situation is more difficult when more than two fluorophores are present. Using a Monte Carlo calculation scheme, we demonstrate how resonance energy transfer can be used to measure distances between fluorophores in complex geometries. We demonstrate the versatility of the approach by calculating the efficiency of energy transfer for individual fluorophores randomly distributed in two and three dimensions, for linked pairs of donors and acceptors and pentameric structures of five linked fluorophores. This approach can be used to relate the efficiency of energy transfer to the distances between fluorophores, R0, molecular concentrations, laser power, and donor/acceptor ratios in ensembles of molecules or when many fluorophores are attached to a single molecule such as in multimeric proteins.

Algorithms↗
PubMed2001

Modeling the effect of solvation on solute retention in reversed-phase liquid chromatography.

The retention of a homologous series of alkylbenzenes was determined on octyl and octadecyl reversed-phase columns in several polar organic liquids. Free energies of transfer were calculated by the SM5.0R classical solvation model for each organic liquid tested and for several alkanes. The relationships between the measured retention factors and the calculated free energies of transfer were then investigated. Although the natural logarithms of the retention factor and the calculated free energies of transfer were linearly correlated, the obtained free energies of transfer of the solutes did not completely explain the retention behavior of the solutes. Nonetheless, even in these pure organic liquids, the energetics of RPLC retention behaved very similarly to those of partitioning.

Chromatography, High Pressure Liquid↗
PubMed2003

Application of Brønsted-type LFER in the study of the phospholipase C mechanism.

Phosphatidylinositol-specific phospholipase C cleaves the phosphodiester bond of phosphatidylinositol to form inositol 1,2-cyclic phosphate and diacylglycerol. This enzyme also accepts a variety of alkyl and aryl inositol phosphates as substrates, making it a suitable model enzyme for studying mechanism of phosphoryl transfer by probing the linear free-energy relationship (LFER). In this work, we conducted a study of Brønsted-type relationship (log k = beta(lg) pK(a) + C) to compare mechanisms of enzymatic and nonenzymatic reactions, confirm the earlier proposed mechanism, and assess further the role of hydrophobicity in the leaving group as a general acid-enabling factor. The observation of the high negative Brønsted coefficients for both nonenzymatic (beta(lg) = -0.65 to -0.73) and enzymatic cleavage of aryl and nonhydrophobic alkyl inositol phosphates (beta(lg) = -0.58) indicates that these reactions involve only weak general acid catalysis. In contrast, the enzymatic cleavage of hydrophobic alkyl inositol phosphates showed low negative Brønsted coefficient (beta(lg) = -0.12), indicating a small amount of the negative charge on the leaving group and efficient general acid catalysis. Overall, our results firmly support the previously postulated mechanism where hydrophobic interactions between the enzyme and remote parts of the leaving group induce an unprecedented negative-charge stabilization on the leaving group in the transition state.

Catalysis↗
PubMedDate not supplied

Chemical reactivity as a tool to study carcinogenicity: reaction between estradiol and estrone 3,4-quinones ultimate carcinogens and guanine.

In this article we study the chemical reactions between guanine and two ultimate carcinogens, the 3,4-quinone forms of the estrogens estrone (E1) and estradiol (E2). DNA was truncated to guanine, i.e. no deoxyribose moiety was included. Due to a complex reaction that involves proton transfer via water molecules we applied linear free energy relationships rather than computation of the transition state and activation energies. The minima corresponding to reactants and products were obtained on the B3LYP/6-31G(d) level. The effects of hydration were considered using the solvent reaction field of Tomasi and co-workers and the Langevin dipoles model of Florian and Warshel. No significant difference in reaction free energy for the reaction involving estrone and estradiol metabolites was found, despite the fact that for the two substances different carcinogenic activities were reported. Differences in carcinogenicity may be therefore attributed to other types of interactions or reactions such as (i) specific interactions of the carbonyl or hydroxyl group with DNA giving rise to different activation free energies for the reactions, (ii) the reaction of depurination and subsequent effects on the DNA, (iii) enzymatic or nonenzymatic oxidation steps (P450, aromatase, peroxidases, O2) and detoxification reactions (catechol-O-methyl transferase, S-transferase), or (iv) binding of the hormone to its nuclear receptors.

Carcinogens↗
PubMed1987

Chlorophyll-protein complexes of barley photosystem I.

Photosystem I (PSI) preparations with a chlorophyll a/b ratio of 6.0 were isolated from barley thylakoids using two different methods. The high-molecular-mass complex (CP1a) which is resolved by non-denaturing gel electrophoresis had the same properties as a PSI preparation (PSI-200) isolated by Triton X-100 solubilisation of thylakoids followed by sucrose gradient ultracentrifugation. This material had a chlorophyll:P700 ratio of 208:1 and was composed of three different chlorophyll-protein complexes which could be separated from each other by solubilising the PSI preparation in dodecyl maltoside followed by sucrose gradient ultracentrifugation. Approximately half of the chlorophyll, including all the chlorophyll b, was located in two antenna complexes designated LHCI-680 and LHCI-730, which were identified by their characteristic low-temperature fluorescence emission spectra. The rest of the chlorophyll a was associated with the PSI reaction centre, P700 Chla-P1, which fluoresced at 720 nm. Each chlorophyll-protein complex had a unique polypeptide composition and characteristic circular dichroic and absorption spectra. The use of dodecyl maltoside instead of dodecyl sulphate resulted in a less denatured form of LHCI-680, which fluoresced at 690 nm at 77 K. One of the sucrose gradient fractions contained a complex consisting of only LHCI-730 and P700 Chla-P1 which fluoresced at 731 nm, indicating that LHCI-730 is structurally associated with P700 Chla-P1 and quenches its fluorescence. Approximately three-quarters of the light-harvesting antenna chlorophyll was in LHCI-730, but only about one-quarter of the normal complement of LHCI-730 was required to quench the reaction centre. By reducing the amount of Triton relative to the chlorophyll concentration, a PSI preparation (chlorophyll a/b ratio of 3.5) with a chlorophyll:P700 ratio of 300:1 was isolated. It contained no photosystem II, but a significant amount of LHCII which was functionally connected to the PSI reaction centre. Reconstitution studies demonstrated that excitation energy transfer from LHCII to PSI requires the presence of LHCI-680, and we propose that, in PSI, the following linear excitation energy transfer sequence occurs: LHCII----LHCI-680----LHCI-730----P700 Chla-P1.

Centrifugation, Density Gradient↗
PubMed1995

Fluorescence energy transfer in one dimension: frequency-domain fluorescence study of DNA-fluorophore complexes.

Fluorescence resonance energy transfer among linear DNA bound fluorophores was carried out to study the process in one dimension. The donor fluorescence intensity decays in the case of energy transfer in one dimension are stretched exponential and show exp[-(t/tau)1/6] time dependence, which results in an initial more rapid decay and subsequent slower decay at long times when compared to those in higher dimensions. DNA-bound 4',6'-diamidino-2-phenyl indole (DAPI), acridine orange (AO), and ethidium bromide (EB) were used as donors. The acceptors were in the case of DAPI AO and EB; in the case of AO nile blue (NB), methylene blue (MB), and crystal violet (CV); and NB, MB, and oxazine 750 in the case of EB. As expected, the donor intensity decays became highly heterogeneous upon energy transfer and were characterized by the simultaneous presence of both highly and marginally quenched donors. The intensity decays for all three donors in the presence of various acceptors are satisfactorily described by the Förster model of energy transfer in one dimension. The intensity decays also allow for clear rejection of a two- or three-dimensional model. The experimentally recovered critical Förster distances (R0) ranged between 37 A in the case of DAPI and EB to 70 A in the case of AO and CV donor-acceptor pairs. These recovered R0 values compare reasonably with those calculated from spectral properties if we use values of 1.25 for k2, and 1.5 for the refractive index of DNA. The k2 value will be even higher, between 1.5 and 2.0, if the consensus DNA refractive index of 1.75 is used. These k2 values strongly suggest that the dipoles of the acceptor chromophores when bound to DNA are not randomly oriented but are aligned preferentially in plane.

Acridine Orange↗
PubMed2006

Intramolecular and intermolecular energy transfers in donor-acceptor linear porphyrin arrays.

We present highly time-resolved spontaneous fluorescence spectra of a porphyrin array system that consists of an energy donor and an acceptor linked by a phenyl group. The donors are meso-meso directly linked zinc(II) porphyrin arrays and the acceptor is a zinc(II) 5,15-di(phenylethynyl)porphyrin. The spectra over the entire Q (S1) emission band following the excitation of the donor B (S2) state have been measured directly without the conventional spectral reconstruction method. The time-resolved fluorescence spectra revealed detailed energy relaxation processes within the donor and subsequent energy transfer to the acceptor. The observed energy transfer rates to the acceptor are consistent with the Forster energy transfer rates calculated on the assumption that the energy is localized in the Q state of each porphyrin unit of the donor prior to the energy transfer. The passage of the energy deposited initially on one porphyrin unit of the donor to the acceptor illustrates a sequence of energy delocalization and localization processes before it finally reaches the acceptor.

Journal Article↗
PubMed2006

Efficient light harvesting in dye-endcapped conjugated polymers probed by single molecule spectroscopy.

The development of sophisticated microscopic models of energy transfer in linear multichromophoric systems such as conjugated polymers is rarely matched by suitable experimental studies on the microscopic level. To assess the roles of structural, temporal, and energetic disorder in energy transfer, single molecule spectroscopic investigations of the elementary processes leading to energetic relaxation in conjugated polymers are desirable. We present a detailed study of energy transfer processes occurring in dye-endcapped conjugated polymer molecules on the single molecule level. These processes are mostly masked in ensemble investigations. Highly efficient intramolecular energy transfer along a single polyindenofluorene chain to a perylene endcap occurs in many instances and is resolved in real time. We further consider the spectral emission characteristics of the single molecule, the polarization anisotropy which reveals the chain conformation, the fluorescence intermittency, and the temperature dependence and conclude that the efficiency of energy transfer in the ensemble is controlled by the statistics of the individual molecules. The weak thermal activation of energy transfer indicates the involvement of vibrational modes in interchromophoric coupling. Whereas backbone-endcap coupling is strong, the rate-limiting step for intramolecular energy transfer is the migration along the backbone. The results are particularly relevant to understanding undesired exciton trapping on fluorenone defects in polyfluorenes.

Journal Article↗
PubMed2003

Theoretical cross sections for electron collisions in water: structure of electron tracks.

To understand what happens when biological matter is irradiated needs a detailed knowledge of the microscopic distribution of interactions and especially of the energy deposited in irradiated matter. Monte Carlo event-by-event simulations are particularly suitable for this task. However, the development of these track-structure codes necessitates accurate interaction cross sections for all the electronic processes: ionization, excitation and elastic scattering. In these conditions, we have recently developed a Monte Carlo code for electrons in water, this latter being commonly used to simulate the biological medium. All the electronic processes are studied in detail via theoretical differential and total cross-section calculations. The purpose of this work is to make an inter-comparison of our cross sections with those used in the electron track-structure codes developed in the literature, and to compare macroscopic quantities such as stopping powers and mean energy transfer distributions to available experimental data and/or to theoretical predictions in liquid water.

Algorithms↗
PubMed2005

Binding of wogonin to human gammaglobulin.

The binding of wogonin to HGG was studied by spectroscopic method including circular dichroism (CD), fourier transformation infrared spectra (FT-IR), fluorescence spectra. The binding parameters and the thermodynamic parameters for the reaction have been calculated according to Sips method and Gibbs-Helmholtz equation, respectively, at different temperatures. AutoDock3.05 program was used to calculate the interaction modes between the drug and HGG. The Sips plots indicated that the binding of HGG to wogonin at 297, 304, 310 and 317 K is characterized by two binding sites with the average affinity constant Ko at 2.102x10(4), 2.078x10(4), 1.956x10(4) and 1.931x10(4), respectively. The binding process was exothermic, spontaneous and entropy driven, as indicated by the thermodynamic analyses, and the major part of binding energy is electrostatic interaction accompanied by hydrophobic interaction and hydrogen bond. The secondary structure compositions of free HGG and its wogonin complexes were estimated by the FT-IR spectra and the curve-fitted results of amide I band, which are in good agreement with the analyses of CD spectra. Furthermore, the average binding distance between wogonin and HGG (5.60 nm) was obtained on the basis of the theory of Förster energy transfer.

Binding Sites↗
PubMed1989

Interactions of the dimethyldiazaperopyrenium dication with nucleic acids. 2. Binding to double-stranded polynucleotides.

The interactions of dimethyldiazaperopyrenium dication (1) with DNA have been studied by spectroscopic methods: absorption, static and dynamic fluorescence, and linear dichroism. 1 binds strongly to DNA at 250 mM NaCl, with a higher affinity for G-C pairs as compared to A-T pairs. The dye fluorescence is enhanced when it is bound to A-T pairs, whereas the emission is quenched in the vicinity of G-C pairs. Evidence for intercalation has been obtained via energy transfer and linear dichroism measurements.

Base Composition↗
PubMed1994

Measurements of trapped protons and cosmic rays from recent Shuttle flights.

Two new charged particle detectors have been flown in five recent Shuttle flights. The tissue-equivalent proportional counter measures the lineal energy spectrum of space radiation in the 0.26-300 keV micrometer-1 range. The charged particle spectrometer is a double dE/dx x E and dE/dx x Chrenekov detector system which provides a measurement of the differential energy spectrum of protons from 13 to 350 MeV and dose rate in silicon. In this paper the dose rate, equivalent dose rate, and radiation, quality factor for trapped protons and cosmic radiation are reported on separately. A comparison of the integral LET spectra with recent transport code calculations shows significant disagreement. Using the calculated dose rate from the omnidirectional AP8MAX model with IGRF reference magnetic field epoch 1970, and observed dose rate as a function of geographic latitude and longitude, the westward drift of the south Atlantic anomaly has been determined. The east-west effect has also been studied and a 'second' radiation belt observed. A comparison of the galactic cosmic radiation (GCR) lineal energy transfer spectra with model calculations shows disagreement comparable with those of the trapped protons.

Atlantic Ocean↗
PubMed2004

Do electrostatic interactions with positively charged active site groups tighten the transition state for enzymatic phosphoryl transfer?

The effect of electrostatic interactions on the transition-state character for enzymatic phosphoryl transfer has been a subject of much debate. In this work, we investigate the transition state for alkaline phosphatase (AP) using linear free-energy relationships (LFERs). We determined k(cat)/K(M) for a series of aryl sulfate ester monoanions to obtain the Brønsted coefficient, beta(lg), and compared the value to that obtained previously for a series of aryl phosphorothioate ester dianion substrates. Despite the difference in substrate charge, the observed Brønsted coefficients for AP-catalyzed aryl sulfate and aryl phosphorothioate hydrolysis (-0.76 +/- 0.14 and -0.77 +/- 0.10, respectively) are strikingly similar, with steric effects being responsible for the uncertainties in these values. Aryl sulfates and aryl phosphates react via similar loose transition states in solution. These observations suggest an apparent equivalency of the transition states for phosphorothioate and sulfate hydrolysis reactions at the AP active site and, thus, negligible effects of active site electrostatic interactions on charge distribution in the transition state.

Alkaline Phosphatase↗
PubMed2004

Distances between tropomyosin sites across the muscle thin filament using luminescence resonance energy transfer: evidence for tropomyosin flexibility.

To obtain information about the interaction of tropomyosin (Tm) with actin associated with the regulatory states of the muscle thin filament, we used luminescence resonance energy transfer (LRET) between Tb(3+) as a donor and rhodamine as an acceptor. A novel Tb(3+) chelator, S-(2-nitro-5-thiobenzoate)cysteaminyl-DTPA-Cs124, was synthesized, which specifically labels Cys groups in proteins. With the Tb chelate as the donor and tetramethylrhodamine-5-maleimide as the acceptor, both bound to specific Cys groups of Tm, we obtained 67 A as the distance between Tm's across the actin filament, a much shorter value than that obtained from structural studies (72-86 A). The difference appears to be due to submillisecond motion associated with Tm flexibility, which brings the probes closer during the millisecond lifetime of the donor. Ca(2+) did not change the energy transfer with the reconstituted thin filament, but myosin subfragment 1 decreased the transfer, consistent with either a 5-6 A increase in distance or, more likely, a decrease in flexibility.

Actin Cytoskeleton↗
PubMed1992

Enhancement of carotenoid-to-chlorophyll singlet energy transfer by carotenoid-carotenoid interaction.

The apparent quantum yield of singlet-singlet spirilloxanthin-to-bacteriochlorophyll a energy transfer increases linearly with the residual spirilloxanthin content in Rhodospirillum rubrum membrane vesicles from which this carotenoid has been partially removed. Since it has been previously shown that carotenoid-carotenoid interaction is a linear function of the residual spirilloxanthin level in the major pigment-protein complex of those vesicles (Zurdo, J., R. M. Lozano, C. Fernandez-Cabrera, and J. M. Ramirez. 1991. Biochem. J. 274:881-884), it appears that such degenerate interaction enhances singlet energy transfer. Part of the enhancement may be explained if the energy donor is the spirilloxanthin 1Bu----1Ag (S2----S0) transition, because exciton coupling probably brings its energy closer to that of the Qx (S2----S0) transition of bacteriochlorophyll. In contrast, it seems that the possible stabilization of the spirilloxanthin 2Ag (S1) state would hardly improve energy transfer, because this hidden state probably lies below the S1 bacteriochlorophyll state. In any case, the stabilizing effects of carotenoid-carotenoid interactions seem insufficient to explain the enhancement of energy transfer. Direct or indirect effects of carotenoid dimerization on the three-dimensional structure of the pigment cluster appear to be required to account for such enhancement.

Bacteriochlorophylls↗
PubMed2004

Millisecond pulsed radio frequency glow discharge time of flight mass spectrometry: temporal and spatial variations in molecular energetics.

The internal energy distributions, P(epsilon), of a millisecond pulsed radio frequency glow discharge plasma were investigated using tungsten hexcarbonyl W(CO)(6) as a "thermometer molecule". Vapor of the probe molecule, W(CO)(6), was introduced into the plasma and subjected to various ionization and excitation processes therein. The resultant molecular and fragment ions were monitored using a Time-of-Flight mass spectrometer. Ion abundance data were utilized in combination with the known energetics of W(CO)(6) to construct the P(epsilon) plots. The P(epsilon) of W(CO)(6) exhibited strong temporal dependence over the pulse cycle: Distinct internal energy distributions were found at the discharge breakdown period (prepeak), the steady state period (plateau), and the post-pulse period (afterpeak). Spatial variation in P(epsilon) was also observed, especially during the plateau regime. The observations suggest that this pulsed glow discharge affords excellent energy tunability that can be used to perform selective ionization and fragmentation for molecular, structural, and elemental information. Parametric studies were performed to evaluate the effects of discharge pressure and operating power on P(epsilon). These studies also provided insight into the correlation of the observed P(epsilon)s with the fundamental ionization and excitation mechanisms in the plasma. The temporal and spatial variations in P(epsilon) were hence attributed to changes in the dominant energy transfer processes at specific times in specific regions of the plasma. These data will be useful in future efforts to optimize the analytical performance of this source for chemical speciation.

Air Ionization↗