Linear-dichroism spectroscopy for the study of structural properties of proteins

This review gives an experiment directed survey of the application of linear-dichroism (LD) spectroscopy to the study of proteins. LD spectroscopy is a relatively simple technique that provides information on the orientation of chromophores in molecules, on molecular characteristies such as shape, size and electronic properties, and on binding parameters in molecular complexes. Since LD is only observed when the molecules are non-randomly oriented in the sample, particular attention is paid to various orientation techniques, viz. in electric and flow fields, in polymer films and gels, and by light induction (photoselection). Examples are given on bacteriorhodopsin and retinals, chlorosomes, lens crystallins, aspartate aminotransferase, and the interaction of gene32-and recA-protein with DNA.Abbreviations AAT aspartate aminotransferase - BR bacteriorhodopsin - CD circular dichroism - LD linear dichroism - PLP pyridoxal-5-phosphate - ss single stranded - TDM transition dipole moment     

Magnetic field-stimulated luminescence and a matrix model for energy transfer. A new method for determining the redox state of the first quinone acceptor in the reaction center of whole cells of Rhodospirillum rubrum

In whole cells of Rhodospirillum rubrum the light-induced absorbance difference spectrum of the reduction of the first quinone electron acceptor Q₁ was determined in order to relate the emission yield ф and the magnetic field-induced emission increase Δф to the redox state of Q₁. It was found that Δф/ф² is a linear function of the number of reaction centers, in which Q₁ is reduced, independent of the fraction of reaction centers in the oxidized state. The emission yield is a hyperbolic function of the fraction of reaction centers closed, either by reduction of the acceptor Q₁ or by oxidation of the primary electron donor P. Apparently, in whole cells of R. rubrum a matrix model for energy transfer between various photosynthetic units can be applied. A model is presented, which is a generalization of theoretical considerations reported before (Duysens, L.N.M. (1978) in Chlorophyll Organization and Energy Transfer in Photosynthesis, Ciba Found. Symp. 61 (New Series), pp. 323–340, Elsevier/North-Holland, Amsterdam) and which is in excellent agreement with the experiments. From simultaneous measurements of Δф and ф the redox state of the reaction center can relatively easily be determined. So far, this is the only method for simultaneously measuring the fractions P⁺ and Q⁻₁ in intact cells under steady-state conditions.     

Function and properties of a soluble c-type cytochrome c-551 in secondary photosynthetic electron transport in whole cells of Chromatium vinosum as studied with flash spectroscopy

Changes in the absorption spectrum induced by 10-μs flashes and continuous light of various intensities were studied in whole cells of Chromatium vinosum.This paper describes the role and function of a soluble c-type cytochrome, c-551, which was surprisingly found to act in many ways similar to the cytochrome c-420 in Rhodospirillum rubrum, described in a previous paper [1].After the photooxidation of the membrane bound high potential cytochrome c-555 by a 10-μs flash, (the low potential cytochrome c-552 was kept permanently in the oxidized state) the oxidation of c-551 is observed ($\text{t}{}_{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}\text{= 0.3}\text{ms}$). From a careful analysis of the absorbance difference spectrum and the kinetics it is concluded that there is approximately 0.6–0.7 c-551 per reaction center and that essentially all the c⁺-555 is reduced via the cytochrome c-551. The oxidized-reduced difference spectrum of c-551 shows peaks at 551 and 421.5 nm. The reduction of c⁺-551 following the flash-induced oxidation is strongly inhibited by HOQNO, but only slightly by antimycin A.Cytochrome c-551 reduces only the oxidized high potential cytochrome c-555, which is probably located on the outside of the membrane, on the opposite side of the primary acceptor. The low potential cytochrome c-552 does not show any detectable interaction with cytochrome c-551. After the cells have been sonicated, no c-551 is photooxidized and at least part of the cytochrome occurs in the solution.Analysis of the reduction kinetics of c⁺-551 in the absence and presence of external donors suggests that c⁺-551 is partly reduced via a cyclic pathway, which is blocked by addition of o-phenanthroline, and partly via a non-cyclic pathway. The non-cyclic reduction rate of c⁺-551 (k = 6 s^?1) is increased approximately 5–10 times upon thiosulphate addition, suggesting a role for c-551 between the final donor pool and the oxidized membrane bound c-type cytochromes.     

On the magnetic field dependence of the yield of the triplet state in reaction centers of photosynthetic bacteria

The yield of the triplet state in reaction centers of Rhodopseudomonas sphaeroides is dependent on the strength of an applied magnetic field. Reaction centers of the wild type that lack a functional iron complexed to the primary acceptor ubiquinone show a dependence similar to that of reaction centers of the mutant R-26 in which the iron-ubiquinone complex is intact. Apparently, the iron of the iron-ubiquinone complex is not essential to the effect, but it does exert an influence on its extent. In chromatophores, the effect is about 2-fold decreased; the value of the magnetic field at which half the effect is found is about 500 G, in contrast to this value for reaction centers, which is 50–100 G. The magnetodependence of the triplet yield is discussed in terms of the Chemically Induced Dynamic Electron Polarization mechanism (CIDEP).     

Study of the binding of single-stranded DNA-binding protein to DNA and poly(rA) using electric field induced birefringence and circular dichroism spectroscopy

Binding of the single-stranded DNA-binding protein (SSB) of Escherichia coli to single-stranded (ss) polynucleotides produces characteristic changes in the absorbance (OD) and circular dichroism (CD) spectra of the polynucleotides. By use of these techniques, complexes of SSB protein and poly(rA) were shown to display two of the binding modes reported by Lohman and Overman [Lohman, T.M., & Overman, L. (1985) J. Biol. Chem. 260, 3594-3603]. The circular dichroism spectra of the "low salt" (10 mM NaCl) and "high salt" (greater than 50 mM NaCl) binding mode are similar in shape, but not in intensity. SSB binding to poly(rA) yields a complexed CD spectrum that shares several characteristics with the spectra obtained for the binding of AdDBP, GP32, and gene V protein to poly(rA). We therefore propose that the local structure of the SSB-poly(rA) complex is comparable to the structures proposed for the complexes of these three-stranded DNA-binding proteins with DNA (and RNA) and independent of the SSB-binding mode. Electric field induced birefringence experiments were used to show that the projected base-base distance of the complex is about 0.23 nm, in agreement with electron microscopy results. Nevertheless, the local distance between the successive bases in the complex will be quite large, due to the coiling of the DNA around the SSB tetramer, thus partly explaining the observed CD changes induced upon complexation with single-stranded DNA and RNA.     

Peridinin chlorophyll a protein: relating structure and steady-state spectroscopy

Peridinin chlorophyll a protein (PCP) from Amphidinium carterae has been studied using absorbance (OD), linear dichroism (LD), circular dichroism (CD), fluorescence emission, fluorescence anisotropy, fluorescence line narrowing (FLN), and triplet-minus-singlet spectroscopy (T-S) at different temperatures (4-293 K). Monomeric PCP binds eight peridinins and two Chls a. The trimeric structure of PCP, resolved at 2 A [Hofmann et al. (1996) Science 27, 1788-1791], allows modeling of the Chl a-protein and Chl a-Chl a interactions. The FLN spectrum shows that Chl a is not or is very weakly hydrogen-bonded and that the central magnesium of the emitting Chl a is monoligated. Simulation of the temperature dependence of the absorption spectra indicates that the Huang-Rhys factor, characterizing the electron-phonon coupling strength, has a value of approximately 1. The width of the inhomogeneous distribution function is estimated to be 160 cm(-)(1). LD experiments show that the two Chls a in PCP are essentially isoenergetic at room temperature and that a substantial amount of PCP is in a trimeric form. From a comparison of the measured and simulated CD, it is concluded that the interaction energy between the two Chls a within one monomer is very weak, <10 cm(-)(1). In contrast, the Chls a appear to be strongly coupled to the peridinins. The 65 cm(-)(1) band that is visible in the low-frequency region of the FLN spectrum might indicate a Chl a-peridinin vibrational mode. The efficiency of Chl a to peridinin triplet excitation energy transfer is approximately 100%. On the basis of T-S, CD, LD, and OD spectra, a tentative assignment of the peridinin absorption bands has been made.     

Spectroscopic Characterization of the Excitation Energy Transfer in the Fucoxanthin–Chlorophyll Protein of Diatoms

We characterized the energy transfer pathways in the fucoxanthin–chlorophyll protein (FCP) complex of the diatom Cyclotella meneghiniana by conducting ultrafast transient absorption measurements. This light harvesting antenna has a distinct pigment composition and binds chlorophyll a (Chl-a), fucoxanthin and chlorophyll c (Chl-c) molecules in a 4:4:1 ratio. We find that upon excitation of fucoxanthin to its S₂ state, a significant amount of excitation energy is transferred rapidly to Chl-a. The ensuing dynamics illustrate the presence of a complex energy transfer network that also involves energy transfer from the unrelaxed or ‘hot’ intermediates. Chl-c to Chl-a energy transfer occurs on a timescale of a 100 fs. We observe no significant spectral evolution in the Chl-a region of the spectrum. We have applied global and target analysis to model the measured excited state dynamics and estimate the spectra of the states involved; the energy transfer network is discussed in relation to the pigment organization of the FCP complex.     

Origin of the F685 and F695 fluorescence in Photosystem II

The emission spectra of CP47-RC and core complexes of Photosystem II (PS II) were measured at different temperatures and excitation wavelengths in order to establish the origin of the emission and the role of the core antenna in the energy transfer and charge separation processes in PS II. Both types of particles reveal strong dependences of spectral shape and yield on temperature. The results indicate that the well-known F-695 emission at 77 K arises from excitations that are trapped on a red-absorbing CP47 chlorophyll, whereas the F-685 nm emission at 77 K arises from excitations that are transferred slowly from 683 nm states in CP47 and CP43 to the RC, where they are trapped by charge separation. We conclude that F-695 at 77 K originates from the low-energy part of the inhomogeneous distribution of the 690 nm absorbing chlorophyll of CP47, while at 4 K the fluorescence originates from the complete distribution of the 690 nm chlorophyll of CP47 and from the low-energy part of the inhomogeneous distribution of one or more CP43 chlorophylls.     

Excitation energy trapping in photosystem I complexes depleted in Lhca1 and Lhca4

We report a time-resolved fluorescence spectroscopy characterization of photosystem I (PSI) particles prepared from Arabidopsis lines with knock-out mutations against the peripheral antenna proteins of Lhca1 or Lhca4. The first mutant retains Lhca2 and Lhca3 while the second retains one other light-harvesting protein of photosystem I (Lhca) protein, probably Lhca5. The results indicate that Lhca2/3 and Lhca1/4 each provides about equally effective energy transfer routes to the PSI core complex, and that Lhca5 provides a less effective energy transfer route. We suggest that the specific location of each Lhca protein within the PSI-LHCI supercomplex is more important than the presence of so-called red chlorophylls in the Lhca proteins.     

Energy transfer in the peridinin chlorophyll-a protein of Amphidinium carterae studied by polarized transient absorption and target analysis

The peridinin chlorophyll-a protein (PCP) of dinoflagellates differs from the well-studied light-harvesting complexes of purple bacteria and green plants in its large (4:1) carotenoid to chlorophyll ratio and the unusual properties of its primary pigment, the carotenoid peridinin. We utilized ultrafast polarized transient absorption spectroscopy to examine the flow of energy in PCP after initial excitation into the strongly allowed peridinin S2 state. Global and target analysis of the isotropic and anisotropic decays reveals that significant excitation (25-50%) is transferred to chlorophyll-a directly from the peridinin S2 state. Because of overlapping positive and negative features, this pathway was unseen in earlier single-wavelength experiments. In addition, the anisotropy remains constant and high in the peridinin population, indicating that energy transfer from peridinin to peridinin represents a minor or negligible pathway. The carotenoids are also coupled directly to chlorophyll-a via a low-lying singlet state S1 or the recently identified SCT. We model this energy transfer time scale as 2.3 +/- 0.2 ps, driven by a coupling of approximately 47 cm(-1). This coupling strength allows us to estimate that the peridinin S1/SCT donor state transition moment is approximately 3 D.