Location and orientation of the chromophore in bacteriorhodopsin: Analysis by fluorescence energy transfer

The spatial location and orientation of the retinal chromophore in bacteriorhodopsin were estimated from a fluorescence energy transfer study. The energy donor used in this study was a fluorescent retinal derivative, which was obtained by partial reduction of the purple membrane with sodium borohydride, and the energy acceptor was the native chromophore remaining in the same membrane. Since bacteriorhodopsin forms a two-dimensional crystal with P₃ symmetry in the purple membrane, and the membrane structure is maintained after the reduction, the rate of energy transfer from a donor to any acceptor existing in the same membrane can be calculated as a function of the location and orientation of the chromophores in the unit cell. Quantitative analyses of the fluorescence decay curve and the quantum yield, with various extents of reduction, enabled us to determine the most probable location and orientation. The result suggested that the chromophore was situated near the centre of the protein in such an orientation that the dipole-dipole interaction with neighbouring chromophores was close to minimum.     

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.     

Letter: interpretation of intramolecular energy transfer experiments

The measurement of the efficiency of resonance energy transfer between two luminophores attached to the same macromolecular substrate is a promising tool for determining intramolecular distances if reasonable bounds can be placed upon the orientation factor k², To date, the analysis of such experiments has been based upon assumed average values of k². A critical review of this procedure is offered along with a method for estimating upper and lower limits for k² which derive from the freedom of motion of the luminophores as determined by polarized emission spectroscopy.     

An anomalous distance dependence of intraprotein chlorophyll-carotenoid triplet energy transfer

In the light-harvesting chlorophyll pigment-proteins of photosynthesis, a carotenoid is typically positioned within a distance of ~4 Å of individual chlorophylls or antenna arrays, allowing rapid triplet energy transfer from chlorophyll to the carotenoid. This triplet energy transfer prevents the formation of toxic singlet oxygen. In the cytochrome b₆f complex of oxygenic photosynthesis that contains a single chlorophyll a molecule, this chlorophyll is distant (14 Å) from the single β-carotene, as defined by x-ray structures from both a cyanobacterium and a green alga. Despite this separation, rapid (<8 ns) long-range triplet energy transfer from the chlorophyll a to β-carotene is documented in this study, in seeming violation of the existing theory for the distance dependence of such transfer. We infer that a third molecule, possibly oxygen trapped in an intraprotein channel connecting the chlorophyll a and β-carotene, can serve as a mediator in chlorophyll-carotenoid triplet energy transfer in the b₆f complex.     

Quenching of chlorophyll triplet states by carotenoids in algal light-harvesting complexes related to fucoxanthin-chlorophyll protein

Photosynthesis Research - We have used time-resolved absorption and fluorescence spectroscopy with nanosecond resolution to study triplet energy transfer from chlorophylls to carotenoids in a...     

Influence of end-to-end diffusion on intramolecular energy transfer as observed by frequency-domain fluorometry

We investigated the influence of end-to-end diffusion on intramolecular energy transfer between a naphthalene donor and dansyl acceptor linked by polymethylene chain. A range of viscosities from 0.6 to 200 cP were obtained using propylene glycol at different temperatures (0-80 degrees C) and methanol at 20 degrees C. The intensity decays of naphthalene were measured in the frequency domain. Several theoretical models, including distance distributions, were used to fit the data. The results indicate that end-to-end diffusion of flexible donor-acceptor pairs can be detected and quantified using frequency-domain fluorometry, even in the presence of a distribution of donor-to-acceptor distances.     

The balance between charge transfer and non-charge transfer pathways in the sensitization of singlet oxygen by pi pi* triplet states.

A charge transfer (CT) channel and a non-CT deactivation channel, both leading to formation of O(2)((1)Sigma (g)(+)), O(2)((1) Delta(g)) and O(2)((3)Sigma(g)(-)), compete in the quenching of triplet states by O(2). Recent studies by our group demonstrated that these channels are described by rather simple and general quantitative relations. In the present paper we use the detailed kinetic data on the quenching by O(2) of pi pi* triplet sensitizers of three homologous aromatic series in CCl(4) to derive a parameter, which describes the balance between CT and non-CT deactivation. This quantity, p(CT), is the relative contribution of CT mediated deactivation and is easily calculated for a sensitizer of known triplet energy from its quenching rate constant. The parameter p(CT) quantitatively describes the balance between both deactivation channels without requiring any knowledge of oxidation potentials. It is shown how the variation of p(CT) influences the efficiencies and the rate constants of O(2)((1)Sigma(g)(+)), O(2)((1)Delta(g)) and O(2)((3)Sigma(g)(-)) formation in the quenching process.     

Study of model protein-lipid systems by the energy transfer method

Complexes of ribonuclease, lysozyme, cytochrome c and hemoglobin with model phospholipid membranes composed of phosphatidylcholine and diphosphatidylglycerol (4:3, mol:mol) were investigated by the method of non-radiative fluorescence energy transfer. Evidence for the penetration of proteins in to the lipid bilayer interior was obtained. The size of the protein fragment incorporated into the polar membrane region was estimated.     

Energy transfer from enzymically generated triplet carbonyl compounds to the fluorescent state of flavins

Enzymically generated triplet carbonyl compounds transfer energy to the fluorescent state of flavins as shown by the suppression of the carbonyl chemiphosphorescence and concomitant appearance of the flavin fluorescence. A Stern-Volmer analysis including the effect of the collisional quenching by a diene indicates that the transfer occurs by a long range process.The present results open the way to “photobiology without light”.     

Phenothiazines and related compounds disrupt mitochondrial energy production by a calmodulin-independent reaction

Phenothiazines and related compounds bind to mitochondrial membranes in approximate proportion to their affinities for calmodulin. Penfluridol (16 microM), pimozide (20 microM), or trifluoperazine (66 microM) completely inhibit ADP-stimulated respiration in isolated rat liver mitochondria, but exert no effect on either uncoupler- or Ca2+-stimulated respiration. The inhibition of ADP-stimulated respiration results from inhibition of the oligomycin-sensitive ATPase. Inhibition of the ATPase does not involve interaction of phenothiazine with calmodulin. The addition of calmodulin with or without calcium to mitochondrial inner membrane preparations has no effect on ATPase activity. The addition of EGTA and the ionophore A23187 prior to the addition of phenothiazine does not prevent the phenothiazine-induced inhibiton of the ATPase. Measurements of inner membrane calmodulin content by gel electrophoresis or cyclic nucleotide phosphodiesterase activation are negative. Despite the absence of calmodulin in the inner membrane preparations, 12.5 nmol trifluoperazine bind per 100 microgram of membrane protein with an association constant, K, of 6.5 . 10(4) M-1. We conclude that calmodulin-binding neuroleptic agents, when added to whole cells, have the potential to disrupt mitochondrial energy production by a reaction which apparently does not involve a phenothiazine-calmodulin interaction.     

Quenching of fluorescence by triplet excited states in chloroplasts

The fluorescence quantum yield in spinach chloroplasts at room temperature has been studied utilizing a 0.5-4.0 mus duration dye laser flash of varying intensities as an excitation source. The yield (phi) and carotenoid triplet concentration were monitored both during and following the laser flash. The triplet concentration was monitored by transient absorption spectoscopy at 515 nm, while the yield phi following the laser was probed with a low intensity xenon flash. The fluorescence is quenched by factors of up to 10-12, depending on the intensity of the flash and the time interval following the onset of the flash. This quenching is attributed to a quencher Q whose concentration is denoted by Q. The relative instantaneous concentration of Q was calculated from phi utilizing the Stern-Volmer equation, and its buildup and decay kinetics were compared to those of carotenoid triplets. At high flash intensities (greater than 10(16) photon . cm-2) the decay kinetics of Q are slower than those of the carotenoid triplets, while at lower flash intensities they are similar. Q is sensitive to oxygen and it is proposed that Q, at the higher intensities, is a trapped chlorophyll triplet. This hypothesis accounts well for the continuing rise of the carotenoid triplet concentration for 1-2 mus after the cessation of the laser pulse by a slow detrapping mechanism, and the subsequent capture of the triplet energy by carotenoid molecules. At the maximum laser intensities, the carotenoid triplet concentration is about one per 100 chlorophyll molecules. The maximum chlorophyll ion concentration generated by the laser pulses was estimated to be below 0.8 ions/100 chlorophyll molecules. None of the observations described here were altered when a picosecond pulse laser train was substituted for the microsecond pulse. A simple kinetic model describing the generation of singlets and triplets (by intersystem crossing), and their subsequent interaction leading to fluorescence quenching, accounts well for the observations. The two coupled differential equations describing the time dependent evolution of singlet and triplet excited states are solved numerically. Using a single-triplet bimolecular rate constant of gammast = 10(-8) cm3 . s-1, the following observations can be accounted for: (1) the rapid initial drop in phi and its subsequent levelling off with increasing time during the laser pulse, (2) the buildup of the triplets during the pulse, and (3) the integrated yield of triplets per pulse as a function of the energy of the flash.     

Protease-sensitive signalling by chemically engineered intramolecular fluorescent resonance energy transfer mutants of green fluorescent protein

The native cysteine residues of green fluorescent protein (GFP) at positions 48 and 70 were replaced by non-thiolic amino acids, and new cysteine sites were introduced at specific, surface positions. Based on molecular modeling of the GFP structure, the sites chosen for mutagenesis to Cys were glutamic acid at position 6 and isoleucine at position 229. These new, unique cysteine sites provided reactive thiol groups suitable for site-specific chemical modification by eosin-based fluorescence labels. The new constructs were designed to serve as the basis of proof of principle for fluorescence resonance energy transfer (FRET) using an enzyme-activated (trypsin) intervening sequence between native and chemically conjugated fluorophores. These eosin moieties provided chemical FRET partners for the native GFP chromophore. On excitation, these GFP-eosin constructs exhibited strong intramolecular FRET, with quenching of the native GFP (511 nm) fluorophore emission and emission around 540 nm, corresponding to eosin. GFP mutants engineered with trypsin-sensitive sequences close to the eosin site, so that on trypsinolysis FRET was destroyed, the emission wavelength switching from that of the chemical FRET partner back to that of the native GFP fluorophore, providing efficient, ratio-based detection. This protein engineering provides the basis for novel bioprobes for enzymatic triggering using intramolecular FRET between GFP and carefully sited chemical labels.     

Simultaneous determination of intramolecular distance distributions and conformational dynamics by global analysis of energy transfer measurements.

Fluorescence energy transfer is widely used for determination of intramolecular distances in macromolecules. The time dependence of the rate of energy transfer is a function of the donor/acceptor distance distribution and fluctuations between the various conformations which may occur during the lifetime of the excited state. Previous attempts to recover both distance distributions and segmental diffusion from time-resolved experiments have been unsuccessful due to the extreme correlation between fitting parameters. A method has been developed, based on global analysis of both donor and acceptor fluorescence decay curves, which overcomes this extreme cross-correlation and allows the parameters of the equilibrium distance distributions and intramolecular diffusion constants to be recovered with high statistical significance and accuracy. Simulation studies of typical intramolecular energy transfer experiments reveal that both static and dynamic conformational distribution information can thus be obtained at a single temperature and viscosity.     

Hydration switch model for the proton transfer in the Schiff base region of bacteriorhodopsin

In a light-driven proton-pump protein, bacteriorhodopsin (BR), protonated Schiff base of the retinal chromophore and Asp85 form ion-pair state, which is stabilized by a bridged water molecule. After light absorption, all-trans to 13-cis photoisomerization takes place, followed by the primary proton transfer from the Schiff base to Asp85 that triggers sequential proton transfer reactions for the pump. Fourier transform infrared (FTIR) spectroscopy first observed O-H stretching vibrations of water during the photocycle of BR, and accurate spectral acquisition has extended the water stretching frequencies into the entire stretching frequency region in D(2)O. This enabled to capture the water molecules hydrating with negative charges, and we have identified the water O-D stretch at 2171 cm(-1) as the bridged water interacting with Asp85. We found that retinal isomerization weakens the hydrogen bond in the K intermediate, but not in the later intermediates such as L, M, and N. On the basis of the observation particularly on the M intermediate, we proposed a model for the mechanism of proton transfer from the Schiff base to Asp85. In the hydration switch model, hydration of a water molecule is switched in the M intermediate from Asp85 to Asp212. This will have raised the pK(a) of the proton acceptor, and the proton transfer is from the Schiff base to Asp85.