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At least 145 records · Page 8Linked to original sources
PubMed1998

Analysis of protein self-association at constant concentration by fluorescence-energy transfer.

Fluorescence-resonance-energy transfer from subunits labelled with a fluorescence donor group to subunits labelled with a fluorescence acceptor group can be used for quantitative analysis of protein self-association. The present approach evaluates fluorescence measurements on mixtures of equimolar solutions of donor-labelled and acceptor-labelled protein composed by systematic variation of the volume ratio. Its attractive feature is that it allows the determination of equilibrium constants at fixed total concentration. Problems encountered by most other methods, which require the equilibria to be followed to high dilution, are avoided. Conditions to be fulfilled are that a reactive site is available on the protein for specific introduction of the labels and that labelling neither affects the conformation nor interferes with the intermolecular interactions. It is desirable that the Forster distance of the donor/acceptor pair complies with its separation. While dimerisation constants can be determined exclusively by fluorescence measurements, the analysis of more complex cases of self-association depends on additional independent information. This communication reports on an application of the approach to the association/dissociation equilibrium between insulin monomers and dimers. Labelling of insulin at the epsilon-amino group of LysB29 does not disturb the conformation nor does it affect dimerisation. 2-Aminobenzoyl and 3-nitrotyrosyl residues served as the donor/acceptor pairs. Because they are less bulky than most other fluorescence labels and are of balanced polarity they do not alter the chemical nature of the protein. Their Forster distance of 29 A matches their 32-A separation in the insulin dimer. Energy transfer was measured as a function of the molar fractions of donor-insulin and acceptor-insulin at constant total concentration. Evaluation of this dependence resulted in a dimerisation constant, K12, of 0.72x10(5) M(-1). Its agreement with values obtained with other methods demonstrates that the present approach is a reliable alternative.

Circular Dichroism↗
PubMed2004

Intra- and intermolecular energy transfer in highly excited ozone complexes.

The energy transfer of highly excited ozone molecules is investigated by means of classical trajectories. Both intramolecular energy redistribution and the intermolecular energy transfer in collisions with argon atoms are considered. The sign and magnitude of the intramolecular energy flow between the vibrational and the rotational degrees of freedom crucially depend on the projection K(a) of the total angular momentum of ozone on the body-fixed a axis. The intermolecular energy transfer in single collisions between O(3) and Ar is dominated by transfer of the rotational energy. In accordance with previous theoretical predictions, the direct vibrational de-excitation is exceedingly small. Vibration-rotation relaxation in multiple Ar+O(3) collisions is also studied. It is found that the relaxation proceeds in two clearly distinguishable steps: (1) During the time between collisions, the vibrational degrees of freedom are "cooled" by transfer of energy to rotation; even at low pressure equilibration of the internal energy is slow compared to the time between collisions. (2) In collisions, mainly the rotational modes are "cool" by energy transfer to argon.

Journal Article↗
PubMed2006

Energy transfer among chlorophylls in trimeric light-harvesting complex II of Bryopsis corticulans.

A study on energy transfer among chlorophylls (Chls) in the trimeric unit of the major light-harvesting complex II (LHC II) from Bryopsis corriculan, was carried out using time-correlated single photon counting. In the chlorophyll Q region of LHC II, six molecules characterized as Chlb628, Chlb646, Chlb652(654,657), Chla664(666), Chla674(677,680) and Chla682(683) were discriminated according to their absorption spectrum and fluorescence emission spectrum. Then, excited by pulsed light of 628 nm, fluorescence kinetics spectra in the chlorophyll Q region were measured. In accordance with the principles of fluorescence kinetics, these kinetics data were analyzed with a multi-exponential model. Time constants on energy transfer were obtained. An overwhelming percentage of energy transfer among chlorophylls undergoes a process longer than 97 picoseconds (ps), which shows that, before transferring energy to another Chl, the excited Chl might convert energy to vibrations of a lower state with different multiplicity (intersystem crossing). Energy transfer at the level of approximately 10 ps was also obtained, which was interpreted as the excited Chls may go through internal conversion before transferring energy to another Chl. Although with a higher standard deviation, time constants at the femtosecond level can not be entirely excluded, which can be attributed to the ultrafast process of direct energy transfer. Owing to the arrangement and direction of the dipole moment of Chls in LHC II, the probability of these processes is different. The fluorescence lifetimes of Chlb652(654,657), Chla664(666), Chla674(677,680) and Chla682(683) were determined to be 1.44 ns, 1.43 ns, 636 ps and 713 ps, respectively. The percentages of energy dissipation in the pathway of fluorescence emission were no more than 40% in the trimeric unit of LHC II. These results are important for a better understanding of the relationship between the structure and function of LHC II.

Chlorophyll↗
PubMed2005

Intramolecular energy transfer in pyrene-bodipy molecular dyads and triads.

Molecules bearing a 4,4-difluoro-8-(aryl)-1,3,5,7-tetramethyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene (bodipy) core and 1-pyrenyl-1-phenyl-4-(1-ethynylpyrene), or 1-phenyl-4-[1-ethynyl-(6-ethynylpyrene)pyrene] units were constructed in a step-by-step procedure based on palladium(0)-promoted cross-coupling reactions with the required preconstructed modules. X-ray structures of single crystals reveal a twisted arrangement of the two chromophores. In one case, an almost perfect orthogonal arrangement is found. These dyes are strongly luminescent in solution and display rich electrochemistry in which all redox processes of the bodipy and pyrene fragments are clearly resolved. The absorption spectra indicate that the bodipy and pyrene chromophores are spectrally isolated, thereby inducing a large "virtual" Stokes shift. The latter is realised by efficient transfer of intramolecular excitation energy by the Förster dipole-dipole mechanism. The rate of energy transfer depends on the structure of the dual-dye system and decreases as the centre-to-centre separation increases. The energy transfer efficiency, however, exceeds 90 % in all cases. The linkage of two pyrene residues by an ethyne group leads to a decrease in the energy-transfer efficiency, with the two polycycles acting as a single chromophore. The directly linked bodipy-pyrene dual dye binds to DNA and operates as an efficient solar concentrator when dispersed in plastic.

Boron Compounds↗
PubMed2000

Förster energy transfer in an optical microcavity.

By studying the transfer of excitation energy between dye molecules confined within an optical microcavity, we demonstrate experimentally that Förster energy transfer is influenced by the local photonic mode density. Locating donor and acceptor molecules at well-defined positions allows the transfer rate to be determined as a function of both mutual separation and cavity length. The results show that the Förster transfer rate depends linearly on the donor emission rate and hence photonic mode density, providing the potential to control energy transfer by modification of the optical environment.

Journal Article↗
PubMed2005

A new algorithm for predicting triplet-triplet energy-transfer activated complex coordinate in terms of accurate potential-energy surfaces.

The new algorithm presented here allows, for the first time, the determination of the optimal geometrical distortions that an acceptor molecule in the triplet-triplet energy-transfer process undergoes, as well as the dependence of the activation energy of the process on the triplet energy difference of donor and acceptor molecules. This algorithm makes use of the complete potential-energy surfaces (singlet and triplet states), and contrasts with the first-order approximation already published [L. M. Frutos, O. Castano, J. L. Andres, M. Merchan, and A. U. Acuna, J. Chem. Phys. 120, 1208 (2004)] in which an expansion of the potential-energy surfaces was used. This algorithm is gradient based and finds the best trajectory for the acceptor molecule, starting from S(0) ground-state equilibrium geometry, to achieve the maximum variation of the singlet-triplet energy gap with the minimum energy of activation on S(0). Therefore, the algorithm allows the determination of a "reaction path" for the triplet-triplet energy-transfer processes. Also, the algorithm could also serve eventually to find minimum-energy crossing (singlet-triplet) points on the potential-energy surface, which can play an important role in the intersystem crossing process for the acceptor molecules to recover their initial capacity as acceptors. Also addressed is the misleading use of minimum-energy paths in T(1) to describe the energy-transfer process by comparing these results with those obtained using the new algorithm. The implementation of the algorithm is illustrated with different potential-energy surface models and it is discussed in the frame of nonvertical behavior.

Journal Article↗
PubMed2001

Quantitative distance information on protein-DNA complexes determined in polyacrylamide gels by fluorescence resonance energy transfer.

In polyacrylamide gels, we have quantitatively determined Forster transfer (fluorescense resonance energy transfer, FRET) between two fluorescent dyes attached to DNA in protein-DNA complexes. The donor-dye fluorescein labeled to DNA retains its free mobility in the polyacrylamide gel, however, its fluorescence properties change. The different quantum yield of fluorescein in the gel is found to be independent of the gel concentration and can thus be quantitatively taken into account by a reduced Forster distance R0 of 46 A compared to 50 A in solution. We have determined global structural properties of two proteins binding to double-labeled DNA using a novel gel-based fluorescence resonance energy transfer assay. In polyacrylamide gels we have analyzed the binding of integration host factor (IHF) and the high mobility group protein NHP6a to their substrate DNA. The measured Forster transfer efficiency allows us to deduce information on the overall shape and the DNA bending angle in the complex.

Acrylic Resins↗
PubMed1988

Brownian dynamics simulations of intramolecular energy transfer.

A novel technique for modelling intramolecular energy transfer is presented. Brownian dynamics calculations are used to compute the trajectories of donor and acceptor species, and the instantaneous orientation factor is calculated during each temporal iteration. In this work, several model systems are considered. Trajectories were computed for energy transfer between a flexible donor and a rigidly fixed acceptor. We have considered configurations where the donor is, (1) tethered to a fixed point in space, but free to diffuse rotationally, and (2) constrained to wobble in a cone. The luminescence decay of the donor is 'measured', and a non-single-exponential decay is observed for configurations of efficient energy transfer. Luminescence anisotropy measurements of constrained and unconstrained donors reflect the contribution of both energy transfer and rotational diffusion to the shape of the anisotropy decay curve.

Chemical Phenomena↗
PubMed2003

Dimerization and inter-chromophore distance of Cph1 phytochrome from Synechocystis, as monitored by fluorescence homo and hetero energy transfer.

We investigated the dimerization of phytochrome Cph1 from the cyanobacterium Synechocystis by fluorescence resonance energy transfer (FRET). As donor we used the chromophore analogue phycoerythrobilin (PEB) and as acceptor either the natural chromophore phycocyanobilin (PCB; hetero transfer) or PEB (homo transfer). Both chromophores bind in a 1:1 stoichiometry to apo-monomers expressed in Escherichia coli. Energy transfer was characterized by time-resolved fluorescence intensity and anisotropy decay after excitation of PEB by picosecond pulses from a tunable Ti-sapphire laser system. ApoCph1 was first assembled with PEB at a low stoichiometry of 0.1. The remaining sites were then sequentially titrated with PCB. In the course of this titration, the mean lifetime of PEB decreased from 3.33 to 1.25 ns in the P(r) form of Cph1, whereas the anisotropy decay was unaffected. In the P(fr)/P(r) photoequilibrium (about 65% P(fr)), the mean lifetime decreased significantly less, to 1.67 ns. These observations provide strong support for inter-chromophore hetero energy transfer in mixed PEB/PCB dimers. The reduced energy transfer in P(fr) may be due to a structural difference but is at least in part due to the difference in spectral overlap, which was 4.1 x 10(-13) and 1.6 x 10(-13) cm(3) M(-1) in P(r) and P(fr), respectively. From the changes in the mean lifetime, rates of hetero energy transfer of 0.68 and 0.37 ns(-1) were calculated for the P(r) form and the P(fr)/P(r) photoequilibrium, respectively. Sequential titration of apo Cph1 with PEB alone to full occupancy did not affect the intensity decay but led to a substantial increase in depolarization. This is the experimental signature of homo energy transfer. Values for the rate of energy transfer k(HT) (0.47 ns(-1)) and the angle 2theta between the transition dipole moment directions (2theta = 45 +/- 5 degrees) were determined from an analysis of the concentration dependence of the anisotropy at five different PEB/Cph1 stoichiometries. The independently determined rates of hetero and homo energy transfer are thus of comparable magnitude and consistent with the energy transfer interpretation. Using these results and exploiting the 2-fold symmetry of the dimer, the chromophore-chromophore distance R(DA) was calculated and found to be in the range 49 A < R(DA) < 63 A. Further evidence for energy transfer in Cph1 dimers was obtained from dilution experiments with PEB/PEB dimers: the lifetime was unchanged, but the anisotropy increased as the dimers dissociated with increasing dilution. These experiments allowed a rough estimate of 5 +/- 3 microM for the dimer dissociation constant. With the deletion mutant Cph1Delta2 that lacks the carboxy terminal histidine kinase domain less energy transfer was observed suggesting that in this mutant dimerization is much weaker. The carboxy terminal domain of Cph1 that is involved in intersubunit trans-phosphorylation and signal transduction thus plays a dominant role in the dimerization. The FRET method provides a sensitive assay to monitor the association of Cph1 monomers.

Bacterial Proteins↗
PubMed2000

Development of a ubiquitin transfer assay for high throughput screening by fluorescence resonance energy transfer.

An assay based on fluorescence resonance energy transfer (FRET) has been developed to screen for ubiquitination inhibitors. The assay measures the transfer of ubiquitin from Ubc4 to HECT protein Rsc 1083. Secondary reagents (streptavidin and antibody to glutathione-S-transferase [GST]), pre-labeled with fluorophores (europium chelate, Eu(3+), and allophycocyanin [APC]), are noncovalently attached via tags (biotin and GST) to the reactants (ubiquitin and Rsc). When Rsc is ubiquitinated, Eu(3+) and APC are brought into close proximity, permitting energy transfer between the two fluorescent labels. FRET was measured as time-resolved fluorescence at the emission wavelength of APC, almost entirely free of nonspecific fluorescence from Eu(3+) and APC. The FRET assay generated a lower ratio of signal to background (8 vs. 31) than an assay for the same ubiquitination step that was developed as a dissociation-enhanced lanthanide fluoroimmunoassay (DELFIA). However, compared to the DELFIA method, use of FRET resulted in higher precision (4% vs. 11% intraplate coefficient of variation). Quenching of fluorescence was minimal when compounds were screened at 10 microg/ml using FRET. Employing a quick and simple homogeneous method, the FRET assay for ubiquitin transfer is ideally suited for high throughput screening.

Dimethyl Sulfoxide↗
PubMed1998

Import of radiation phenomena of electrons and therapeutic low-level laser in regard to the mitochondrial energy transfer.

OBJECTIVE: The authors describe a consistent theoretical model of the cellular energy transfer (respiratory chain) by taking into consideration the radiation phenomena of electrons and therapeutic low level laser. SUMMARY BACKGROUND DATA: Biochemical models of the cellular energy transfer regard the classical corpuscular aspect of electrons as the responsible energy carriers, thereby ignoring the wave-particle dualism of the electrons and the import of radiation energy in this process. METHODS: The authors show the influence of radiation phenomena on the cellular energy transfer, explaining consistently some of the intermediate steps of this complex process. RESULTS: Because of the inherent wave-particle dualism of the electrons, it is appropriate to regard radiation phenomena to explain the cellular energy transfer. The classical biochemical models use only the particle part of the electrons as energy carriers. The connection between energy transport by radiation and the order in structures may be understood if, for instance, structurally bound energy is released during the dissolution of structures (oxidation of foodstuffs) or is again manifested (final reduction of oxygen to water). With a attention to the energy values relevant for the respiratory chain, the import of electromagnetic radiation of characteristic ranges of wavelengths on the cellular energy transfer becomes evident. Depending on its wavelength, electromagnetic radiation in the form of light can stimulate macromolecules and can initiate conformation changes in proteins or can transfer energy to electrons. Low level laser from the red and the near infrared region corresponds well with the characteristic energy and absorption levels of the relevant components of the respiratory chain. This laser stimulation vitalizes the cell by increasing the mitochondrial ATP(adenosine-tri-phosphate)-production. CONCLUSIONS: With regard to radiation phenomena and its inhanced electron flow in the cellular energy transfer (respiratory chain), it is possible to explain the experimentally found increase of ATP-production by means of low-level laser light on a cellular level. Intense research for this biostimulative effect is still necessary.

Adenosine Triphosphate↗
PubMed1987

Flow cytometric measurements of fluorescence energy transfer using single laser excitation.

Flow cytometric energy transfer (FCET) measurements between labeled specific sites of cell surface elements (Szöllosi et al., Cytometry, 5:210-216, 1984) have been extended in a simplified form using a flow cytometer equipped with single excitation beam. This versatile and easily applicable method has several advantages over any nonflow cytometric (i.e., spectrofluorimetric) energy transfer measurements on cell surfaces: The labeled ligands can be applied in excess, without washing, thereby enabling the investigation of relatively labile receptor-ligand complexes. Contributions of signals from cell debris, from cell aggregates, or from nonviable cells can be avoided by gating the data collection on the light scatter signal. The heterogeneity of the cell population with respect to the proximity of the labeled binding sites can be studied. In the cases of homologous ligands or of ligands binding to the same molecule but at different epitopes, the determination of fluorescence resonance energy transfer efficiency values can be carried out on a cell-by-cell basis, offering data on intramolecular conformational changes. This modified FCET method enabled us to demonstrate the uniform density of glycoproteins, specific for Con A binding, in the plasma membrane of normal and Gross virus leukemic mouse cells of different sizes. The utility of this procedure has also been demonstrated by using the mean fluorescence intensities of the distribution curves in the calculation of the fluorescence energy transfer efficiency.

Antigens, Surface↗
PubMed2006

Singlet energy transfer in porphyrin-based donor-bridge-acceptor systems: interaction between bridge length and bridge energy.

Singlet excitation energy transfer is governed by two donor-acceptor interactions, the Coulombic and exchange interactions giving rise to the Förster and Dexter mechanisms, respectively, for singlet energy transfer. In transfer between colliding molecules or between a donor (D) and acceptor (A) connected in donor-bridge-acceptor (D-B-A) system by an inert spacer (B), the distinction between these two mechanisms is quite clear. However, in D-B-A systems connected by a pi-conjugated bridge, the exchange interaction between the donor and acceptor is mediated by the virtual low-lying excited states (unoccupied orbitals) of that bridge and, as a consequence, becomes much more long-range in character. Thus, the clear distinction to the Coulombic mechanism is lost. This so-called superexchange mechanism for singlet energy transfer has been shown to make a significant contribution to the energy transfer rates in several D-B-A systems, and its D-A distance as well as D-B energy gap dependencies have been studied. We here demonstrate that in a series of oligo-p-phenyleneethynylene (OPE) bridged porphyrin-based D-B-A systems with varying D-A distances the Förster and through-bond (superexchange) mechanisms both make considerable contributions to the observed singlet energy transfer rates. The donor is either a zinc porphyrin or a zinc porphyrin with a pyridine ligand, and the acceptor is a free base porphyrin. By comparison to a homologous series where only the D-B energy gaps varies, a separation between the two energy transfer mechanisms was possible and, moreover, an interplay between distance and energy gap dependencies was noted. The distance dependence was shown to be approximately exponential with an attenuation factor beta=0.20 A-1. If the effect of the varying D-B energy gaps in the OPE series was taken into account, a slightly higher beta-value was obtained. Ground-state absorption, steady-state, and time-resolved emission spectroscopy were used. The experimental study is accompanied by time-dependent density functional theory (TD-DFT) calculations of the electronic coupling, and the experimental and theoretical results are in excellent qualitative agreement (same distance dependence).

Journal Article↗
PubMed1991

Structural interpretation of fluorescence resonance-energy transfer measurements.

Fluorescence resonance-energy transfer (FRET) has been widely used to determine distance information in macromolecular systems. However, little has been written about methods for combining FRET distances into coherent structural models. I argue that the methods used so far are inappropriate. This paper describes an algorithm specifically tailored for finding structures from FRET measurements. This algorithm finds structures which fit the experimentally measured parameter, the efficiency of energy transfer, rather than derived distances. The algorithm was implemented in Mathematica and applied to FRET distances obtained for the contractile protein actin. The approach used is applicable to other experimental techniques which measure distances between a relatively small number of loci.

Energy Transfer↗
PubMed1999

Architecture of a complex between the sigma70 subunit of Escherichia coli RNA polymerase and the nontemplate strand oligonucleotide. Luminescence resonance energy transfer study.

We used luminescence energy transfer measurements to determine the localization of 5'- and 3'-ends of a 12-nucleotide nontemplate strand oligonucleotide bound to sigma70 holoenzyme. Five single reactive cysteine mutants of sigma70 (cysteine residues at positions 1, 59, 366, 442, and 596) were labeled with a europium chelate fluorochrome (donor). The oligonucleotide was modified at the 5'- or at the 3'-end with Cy5 fluorochrome (acceptor). The energy transfer was observed upon complex formation between the donor-labeled sigma70 holoenzyme and the acceptor-labeled nontemplate strand oligonucleotide, whereas no interaction was observed with the template strand oligonucleotide. The oligonucleotide was bound in one preferred orientation. This observation together with the sequence specificity of single-stranded oligonucleotide interaction suggests that two mechanisms of discrimination between the template and nontemplate strand are used by sigma70: sequence specificity and strand polarity specificity. The bound oligonucleotide was found to be close to residue 442, confirming that the single-stranded DNA binding site of sigma70 is located in an alpha-helix containing residue 442. The 5'-end of the oligonucleotide was oriented toward the COOH terminus of the helix.

Base Sequence↗
PubMed2005

Shell-to-shell energy transfer in magnetohydrodynamics. I. Steady state turbulence.

We investigate the transfer of energy from large scales to small scales in fully developed forced three-dimensional magnetohydrodynamics (MHD) turbulence by analyzing the results of direct numerical simulations in the absence of an externally imposed uniform magnetic field. Our results show that the transfer of kinetic energy from large scales to kinetic energy at smaller scales and the transfer of magnetic energy from large scales to magnetic energy at smaller scales are local, as is also found in the case of neutral fluids and in a way that is compatible with the Kolmogorov theory of turbulence. However, the transfer of energy from the velocity field to the magnetic field is a highly nonlocal process in Fourier space. Energy from the velocity field at large scales can be transferred directly into small-scale magnetic fields without the participation of intermediate scales. Some implications of our results to MHD turbulence modeling are also discussed.

Journal Article↗
PubMed2005

Using fluorescence resonance energy transfer to measure distances along individual DNA molecules: corrections due to nonideal transfer.

Single molecule fluorescence resonance energy transfer has been extensively used to measure distance changes and kinetics in various biomolecular systems. However, due to complications involving multiple de-excitation pathways of the dyes, the absolute inter-dye distance information has seldom been recovered. To circumvent this we directly probe the relative variations in the quantum yield of individual fluorophores. B-DNA was used as a scaffold to position the donor (Cy3 or TMR) at precise distances from the acceptor (Cy5) within the Forster radius. We found that the variation in the Cy3 quantum yield is approximately 5 times larger than that of TMR. By taking into account the molecule-to-molecule variability in the acceptor/donor quantum yield ratio, the apparent fluorescence resonance energy transfer efficiencies were scaled to yield the theoretical values. We obtained very good agreement with a physical model that predicts distances along B-DNA.

Carbocyanines↗
PubMed2004

Detection of tryptophan to tryptophan energy transfer in proteins.

Förster resonance energy transfer (FRET) studies usually involve observation of intensity or lifetime changes in the donor or acceptor molecule and usually these donor and acceptor molecules differ (heterotransfer). The use of polarization to monitor FRET is far less common, although it was one of the first methods utilized. In 1960, Weber demonstrated that homotransfer between tryptophan molecules contributes to depolarization. He also discovered that the efficiency of homotransfer becomes much less effective upon excitation near the red-edge of the absorption. This "red-edge effect" was shown to be a general phenomenon of homotransfer. We have utilized Weber's red-edge effect to study tryptophan homotransfer in proteins. Specifically, we determined the polarization of the tryptophan fluorescence upon excitation at 295 nm and 310 nm (near the red-edge). Rotational diffusion leads to depolarization of the emission excited at either 295 nm or 310 nm, but homotransfer only contributes to depolarization upon excitation at 295 nm. Hence, the 310/295 polarization ratio gives an indication of tryptophan to tryptophan energy transfer. In single tryptophan systems, the 310/295 ratios are generally below 2 whereas in multi-tryptophan systems, the 310/295 ratios can be greater than 3.

Animals↗