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Richard J Cogdell

Publications and source records attributed to Richard J Cogdell.

At least 19 recordsLinked to original sources

Self-assembled monolayer of light-harvesting core complexes of photosynthetic bacteria on an amino-terminated ITO electrode.

Light-harvesting antenna core (LH1-RC) complexes isolated from Rhodospirillum rubrum and Rhodopseudomonas palustris were successfully self-assembled on an ITO electrode modified with 3-aminopropyltriethoxysilane. Near infra-red (NIR) absorption, fluorescence, and IR spectra of these LH1-RC complexes indicated that these LH1-RC complexes on the electrode were stable on the electrode. An efficient energy transfer and photocurrent responses of these LH1-RC complexes on the electrode were observed upon illumination of the LH1 complex at 880 nm.

Bacterial Proteins↗

The architecture and function of the light-harvesting apparatus of purple bacteria: from single molecules to in vivo membranes.

This review describes the structures of the two major integral membrane pigment complexes, the RC-LH1 'core' and LH2 complexes, which together make up the light-harvesting system present in typical purple photosynthetic bacteria. The antenna complexes serve to absorb incident solar radiation and to transfer it to the reaction centres, where it is used to 'power' the photosynthetic redox reaction and ultimately leads to the synthesis of ATP. Our current understanding of the biosynthesis and assembly of the LH and RC complexes is described, with special emphasis on the roles of the newly described bacteriophytochromes. Using both the structural information and that obtained from a wide variety of biophysical techniques, the details of each of the different energy-transfer reactions that occur, between the absorption of a photon and the charge separation in the RC, are described. Special emphasis is given to show how the use of single-molecule spectroscopy has provided a more detailed understanding of the molecular mechanisms involved in the energy-transfer processes. We have tried, with the help of an Appendix, to make the details of the quantum mechanics that are required to appreciate these molecular mechanisms, accessible to mathematically illiterate biologists. The elegance of the purple bacterial light-harvesting system lies in the way in which it has cleverly exploited quantum mechanics.

Amino Acid Sequence↗

Probing the electronic structure and conformational flexibility of individual light-harvesting 3 complexes by optical single-molecule spectroscopy.

We present fluorescence-excitation spectra of individual light-harvesting 3 (LH3 or B800-820) complexes of Rhodopseudomonas acidophila at 1.2 K. The optical single-molecule studies were employed to investigate the electronic structure as well as the conformational flexibility of the individual pigment-protein complexes. The optical spectra resemble those of individual light-harvesting 2 (LH2) complexes, in agreement with the structural similarity of both types of complexes. Although variations among the LH3 spectra are large, there is a distinct difference in the spectral features of the 800 and 820 nm region that appears in all the complexes studied. In the B800 region 4-6 narrow bands are present whereas in the B820 region a limited number of relatively broad bands are observed. These observations can generally be interpreted in terms of localized excitations in the 800 nm region and delocalized excitations in the 820 nm region. The observed heterogeneous spectral behavior, especially in the B820 band, indicates that the B820 pigments of LH3 are sensitive to light-induced local conformational changes. It is suggested that a rotation of the C(3)-acetyl chain of a BChl a pigment bound to the beta-subunit of the light-harvesting complex is the origin of the conformational flexibility and affects the optical properties of the whole pigment-protein complex.

Biophysics↗

Two-dimensional electronic spectroscopy of the B800-B820 light-harvesting complex.

Emerging nonlinear optical spectroscopies enable deeper insight into the intricate world of interactions and dynamics of complex molecular systems. 2D electronic spectroscopy appears to be especially well suited for studying multichromophoric complexes such as light-harvesting complexes of photosynthetic organisms as it allows direct observation of couplings between the pigments and charts dynamics of energy flow on a 2D frequency map. Here, we demonstrate that a single 2D experiment combined with self-consistent theoretical modeling can determine spectroscopic parameters dictating excitation energy dynamics in the bacterial B800-B820 light-harvesting complex, which contains 27 bacteriochlorophyll molecules. Ultrafast sub-50-fs dynamics dominated by coherent intraband processes and population transfer dynamics on a picosecond time scale were measured and modeled with one consistent set of parameters. Theoretical 2D spectra were calculated by using a Frenkel exciton model and modified Förster/Redfield theory for the calculation of dynamics. They match the main features of experimental spectra at all population times well, implying that the energy level structure and transition dipole strengths are modeled correctly in addition to the energy transfer dynamics of the system.

Bacterial Proteins↗

Lipidic sponge phase crystallization of membrane proteins.

Bicontinuous lipidic cubic phases can be used as a host for growing crystals of membrane proteins. Since the cubic phase is stiff, handling is difficult and time-consuming. Moreover, the conventional cubic phase may interfere with the hydrophilic domains of membrane proteins due to the limited size of the aqueous pores. Here, we introduce a new crystallization method that makes use of a liquid analogue of the cubic phase, the sponge phase. This phase facilitates a considerable increase in the allowed size of aqueous domains of membrane proteins, and is easily generalised to a conventional vapour diffusion crystallisation experiment, including the use of nanoliter drop crystallization robots. The appearance of the sponge phase was confirmed by visual inspection, small-angle X-ray scattering and NMR spectroscopy. Crystals of the reaction centre from Rhodobacter sphaeroides were obtained by a conventional hanging-drop experiment, were harvested directly without the addition of lipase or cryoprotectant, and the structure was refined to 2.2 Angstroms resolution. In contrast to our earlier lipidic cubic phase reaction centre structure, the mobile ubiquinone could be built and refined. The practical advantages of the sponge phase make it a potent tool for crystallization of membrane proteins.

Binding Sites↗

Carotenoid stoichiometry in the LH2 crystal: no spectral evidence for the presence of the second molecule in the alpha/beta-apoprotein dimer.

In this work we have investigated the carotenoid-protein interactions in LH2 complexes of Rhodopseudomonas acidophila both in "free in solution" mixed-micelles and in three-dimensional crystals by Raman spectroscopy in resonance with the carotenoid (Car) molecules. We show that the Car molecules when bound to their binding pockets show no significant differences when the complexes are "free in solution" or packed in crystalline arrays. Furthermore, there is no significant wavelength dependence in the Raman spectrum of the Car molecules of LH2. This indicates that there is only one Car configuration in LH2 and thus only one molecule per alpha/beta-heterodimer.

Apoproteins↗

Lateral organization of a membrane protein in a supported binary lipid domain: direct observation of the organization of bacterial light-harvesting complex 2 by total internal reflection fluorescence microscopy.

A unique method is described for directly observing the lateral organization of a membrane protein (bacterial light-harvesting complex LH2) in a supported lipid bilayer using total internal reflection fluorescence (TIRF) microscopy. The supported lipid bilayer consisted of anionic 1,2-dioleoyl-sn-glycero-3-[phospho-rac-(1'-glycerol)] (DOPG) and 1,2-distearoly-sn-3-[phospho-rac-(1'-glycerol)] (DSPG) and was formed through the rupture of a giant vesicle on a positively charged coverslip. TIRF microscopy revealed that the bilayer was composed of phase-separated domains. When a suspension of cationic phospholipid (1,2-dioleoyl-sn-glycero-3-ethylphosphocholine: EDOPC) vesicles (approximately 400 nm in diameter), containing LH2 complexes (EDOPC/LH2 = 1000/1), was put into contact with the supported lipid bilayer, the cationic vesicles immediately began to fuse and did so specifically with the fluid phase (DOPG-rich domain) of the supported bilayer. Fluorescence from the incorporated LH2 complexes gradually (over approximately 20 min) spread from the domain boundary into the gel domain (DSPG-rich domain). Similar diffusion into the domain-structured supported lipid membrane was observed when the fluorescent lipid (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-lissamine-rhodamine B sulfonyl: N-Rh-DOPE) was incorporated into the vesicles instead of LH2. These results indicate that vesicles containing LH2 and lipids preferentially fuse with the fluid domain, after which they laterally diffuse into the gel domain. This report describes for first time the lateral organization of a membrane protein, LH2, via vesicle fusion and subsequent lateral diffusion of the LH2 from the fluid to the gel domains in the supported lipid bilayer. The biological implications and applications of the present study are briefly discussed.

Bacterial Proteins↗

Excited-state dynamics of carotenoids in light-harvesting complexes. 1. Exploring the relationship between the S1 and S* states.

Dispersed transient absorption spectra collected at variable excitation intensities in combination with time-resolved signals were used to explore the underlying connectivity of the electronic excited-state manifold of the carotenoid rhodopin glucoside in the light-harvesting 2 complex isolated from Rhodopseudomonas acidophila. We find that the S state, which was recently identified as an excited state in carotenoids bound in bacterial light-harvesting complexes, exhibits a different response to the increase of excitation intensity than the S(1) state, which suggests that the models used so far to describe the excited states of carotenoids are incomplete. We propose two new models that can describe both the time-resolved and the intensity-dependent data; the first postulates that S(1) and S* are not populated in parallel after the decay of the initially excited S(2) state but instead result from the excitation of distinct ground-state subpopulations. The second model introduces a resonantly enhanced light-induced transition during excitation, which promotes population to higher-lying excited states that favors the formation of S* over S(1). Multiwavelength target analysis of the time-resolved and excitation-intensity dependence measurements were used to characterize the involved states and their responses. We show that both proposed models adequately fit the measured data, although it is not possible to determine which model is most apt. The physical origins and implications of both models are explored.

Antioxidants↗

Excited-state dynamics of carotenoids in light-harvesting complexes. 2. Dissecting pulse structures from optimal control experiments.

Dispersed multipump-probe (PPP) spectroscopy was used to explore the role of saturation, annihilation, and structured pulses in recent coherent control experiments on the light-harvesting 2 complex from Rhodopseudomonas acidophila (Herek et al. Nature 2002, 417, 533). We discuss the complimentary aspects between the PPP technique and coherent control studies, in particular the ability to dissect complicated pulse structures and the utility in exploring incoherent mechanisms. With the aid of a simple multistate model involving only population dynamics, we illustrate how the optimized structured pulses may be explained in terms of an interplay between excited-state populations, saturation, and annihilation. Furthermore, we discuss the experimental conditions that are required for incoherent effects to contribute to control experimental signals, with particular emphasis on pulse intensities, and show that the optimization of a ratio of conservative signals (i.e., not modulated by external dynamics) is required to exclude saturation effects from coherent control studies.

Carotenoids↗

Conformational relaxation of single bacterial light-harvesting complexes.

We have employed the technique of single-molecule fluorescence microspectroscopy to investigate the spontaneous conformational evolution of individual peripheral LH2 complexes from the purple bacterium Rhodopseudomonas acidophila. Fluorescence microscopy is a sensitive tool, which allows the spectral changes of single complexes to be monitored on a time scale from 0.1 s to many minutes. Here we have investigated "natural" (occurring in the absence of excitation) spectral diffusion after a spectral jump has occurred. In a quarter of all the observed spectral jumps recorded with the LH2 complexes, a further spontaneous evolution occurs, in the absence of illumination, that results in the formation of a different spectroscopic state. We suggest that this is due to a natural conformational development of the pigment-protein complex, which so far has not been observed for this type of complex at the single-molecule level. The functional significance of such structural rearrangements is not yet clear but may be associated with the necessity for the light-harvesting complexes to adjust their shape in the densely packed photosynthetic membrane.

Bacterial Proteins↗

Carotenoid-bacteriochlorophyll energy transfer in LH2 complexes studied with 10-fs time resolution.

In this report, we present a study of carotenoid-bacteriochlorophyll energy transfer processes in two peripheral light-harvesting complexes (known as LH2) from purple bacteria. We use transient absorption spectroscopy with approximately 10 fs temporal resolution, which is necessary to observe the very fast energy relaxation processes. By comparing excited-state dynamics of the carotenoids in organic solvents and inside the LH2 complexes, it has been possible to directly evaluate their energy transfer efficiency to the bacteriochlorophylls. In the case of okenone in the LH2 complex from Chromatium purpuratum, we obtained an energy transfer efficiency of etaET2=63+/-2.5% from the optically active excited state (S2) and etaET1=61+/-2% from the optically dark state (S1); for rhodopin glucoside contained in the LH2 complex from Rhodopseudomonas acidophila these values become etaET2=49.5+/-3.5% and etaET1=5.1+/-1%. The measurements also enabled us to observe vibrational energy relaxation in the carotenoids' S1 state and real-time collective vibrational coherence initiated by the ultrashort pump pulses. Our results are important for understanding the dynamics of early events of photosynthesis and relating it to the structural arrangement of the chromophores.

Bacterial Chromatophores↗

The structural basis of non-photochemical quenching is revealed?

Light-harvesting complex II (LHCII, the major plant light-harvesting pigment-protein complex, efficiently harvests light-energy. However, if the incident light intensity is too high and photosynthesis becomes saturated, LHCII can switch into a quenching state that prevents photodamage. This important process is called non-photochemical quenching, or NPQ, and represents feedback control. Andrew Pascal et al. have recently proposed a detailed model of NPQ based upon the crystal structure of LHCII from spinach.

Crystallography↗

Comparative study of spectral flexibilities of bacterial light-harvesting complexes: structural implications.

This work presents a comparative study of the frequencies of spectral jumping of individual light-harvesting complexes of six different types: LH2 of Rhodopseudomonas acidophila, Rhodobacter sphaeroides, and Rhodospirillum molischianum; LH1 of Rhodobacter sphaeroides; and two "domain swap mutants" of LH2 of Rhodobacter sphaeroides: PACLH1 and PACLH2mol, in which the alpha-polypeptide C-terminus is exchanged with the corresponding sequence from LH1 of Rhodobacter sphaeroides or LH2 of Rhodospirillum molischianum, respectively. The quasistable states of fluorescence peak wavelength that were previously observed for the LH2 of Rps. acidophila were confirmed for other species. We also observed occurrences of extremely blue-shifted spectra, which were associated with reversible bleaching of one of the chromophore rings. Different jumping behavior is observed for single complexes of different types investigated with the same equivalent excitation intensity. The differences in spectral diffusion are associated with subtle differences of the binding pocket of B850 pigments and the structural flexibility of the different types of complexes.

Bacterial Proteins↗

Spectral trends in the fluorescence of single bacterial light-harvesting complexes: experiments and modified redfield simulations.

In this work we present and discuss the single-molecule fluorescence spectra of a variety of species of light-harvesting complexes: LH2 of Rhodopseudomonas acidophila, Rhodobacter sphaeroides, and Rhodospirillum molischianum and LH1 of Rhodobacter sphaeroides. The emission spectrum of these complexes varies as a function of time as was described in earlier work. For each type of complex, we observe a pronounced and well-reproducible characteristic relationship between the fluorescence spectral parameters of the peak wavelength, width, and asymmetry. This dependence for the LH2 complexes can be quantitatively explained on the basis of a disordered exciton model by varying the static disorder and phonon coupling parameters. In addition, a correlation of the pigment site energies has to be assumed to interpret the behavior of the LH1 complex.

Bacterial Proteins↗

Sub-micro-second time-resolved absorption spectroscopy of a polar carotenoid analogue, 2-(all-trans-retinylidene)indan-1,3-dione; formation of the dication by direct triplet-excited sensitization.

Sub-micro-second time-resolved difference absorption spectra of a polar carotenoid analogue, 2-(all-trans-retinylidene)indan-1,3-dione (hereafter, we will call RetInd), were recorded in tetrahydrofuran at room temperature upon anthracene-sensitized triplet excitation. In addition to the typical Tn <-- T1 absorption spectrum of anthracene followed by that of RetInd, a novel transient species, which peaked at 670 nm, was detected. The lifetime and the population of the 670 nm species was not affected by the presence of oxygen but was quenched by the cation scavenger, triethylamine. Therefore, we have identified this species as a "cation". The transient 670 nm species was not generated by direct photoexcitation of RetInd in the absence of a triplet sensitizer. Therefore, this species was not generated via the T1 species of RetInd but rather via an "invisible state" of RetInd, which is generated by direct energy or electron transfer from T1 anthracene. This proposed pathway was confirmed by a singular-value decomposition followed by a global fitting analysis. The "cation" of RetInd shows vibrational structure in its absorption spectrum, and its lifetime was determined to be 15 micros. Chemical oxidation of RetInd in 2,2,2-trifluoroethanol (dichloromethane) produced a broad absorption band around 880 (1013) nm, which could be transformed into a shoulder around 640 (675) nm upon addition of increasing amounts of the oxidant, FeCl3. The former absorption band can be assigned to a radical cation, while the latter to a dication. Because of the spectral similarity, the 670 nm species can be assigned to the dication, and the "invisible state" is ascribed to the radical cation of RetInd. This is the first direct evidence for the production of a dication of a biological polyene moiety generated in non-halogenated solution following anthracene-sensitized excitation.

Journal Article↗

Selective chemical shift assignment of B800 and B850 bacteriochlorophylls in uniformly [13C,15N]-labeled light-harvesting complexes by solid-state NMR spectroscopy at ultra-high magnetic field.

The electronic ground states of the bacteriochlorophyll a type B800 and type B850 in the light-harvesting 2 complex of Rhodopseudomonas acidophila strain 10050 have been characterized by magic angle spinning (MAS) dipolar (13)C-(13)C correlation NMR spectroscopy. Uniformly [(13)C,(15)N] enriched light-harvesting 2 (LH2) complexes were prepared biosynthetically, while [(13)C,(15)N]-B800 LH2 complexes were obtained after reconstitution of apoprotein with uniformly [(13)C,(15)N]-enriched bacteriochlorophyll cofactors. Extensive sets of isotropic (13)C NMR chemical shifts were obtained for each bacteriochlorin ring species in the LH2 protein. (13)C isotropic shifts in the protein have been compared to the corresponding shifts of monomeric BChl a dissolved in acetone-d(6). Density functional theory calculations were performed to estimate ring current effects induced by adjacent cofactors. By correction for the ring current shifts, the (13)C shift effects due to the interactions with the protein matrix were resolved. The chemical shift changes provide a clear evidence for a global electronic effect on the B800 and B850 macrocycles, which is attributed to the dielectrics of the protein environment, in contrast with local effects due to interaction with specific amino acid residues. Considerable shifts of -6.2 < Deltasigma < +5.8 ppm are detected for (13)C nuclei in both the B800 and the B850 bacteriochlorin rings. Because the shift effects for the B800 and B850 are similar, the polarization of the electronic ground states induced by the protein environment is comparable for both cofactors and corresponds with a red shift of approximately 30 nm relative to the monomeric BChl dissolved in acetone-d(6). The electronic coupling between the B850 cofactors due to macrocycle overlap is the predominant mechanism behind the additional red shift in the B850.

Bacterial Proteins↗

Local electrostatic field induced by the carotenoid bound to the reaction center of the purple photosynthetic bacterium Rhodobacter sphaeroides.

Electroabsorption (EA) spectra were recorded in the region of the reaction center (RC) Qy absorption bands of bacteriochlorophyll (Bchl) and bacteriopheophytin, to investigate the effect of carotenoid (Car) on the electrostatic environment of the RCs of the purple bacterium Rhodobacter (Rb.) sphaeroides. Two different RCs were prepared from Rb. sphaeroides strain R26.1 (R26.1-RC); R26.1 RC lacking Car and a reconstituted RC (R26.1-RC+ Car) prepared by incorporating a synthetic Car (3,4-dihydrospheroidene). Although there were no detectable differences between these two RCs in their near infrared (NIR) absorption spectra at 79 and 293 K, or in their EA spectra at 79 K, significant differences were detected in their EA spectra at 293 K. Three nonlinear optical parameters of each RC were determined in order to evaluate quantitatively these differences; transition dipole-moment polarizability and hyperpolarizability (D factor), the change in polarizability upon photoexcitation (Deltaalpha), and the change in dipole-moment upon photoexcitation (Deltamu). The value of D or Deltaalpha determined for each absorption band of the two RC samples showed similar values at 77 or 293 K. However, the Deltamu values of the special pair Bchls (P) and the monomer Bchls absorption bands showed significant differences between the two RCs at 293 K. X-ray crystallography of the two RCs has revealed that a single molecule of the solubilizing detergent LDAO occupies part of the carotenoid binding site in the absence of a carotenoid. The difference in the value of Deltamu therefore represents the differential effect of the detergent LDAO and the carotenoid on P. The change of electrostatic field around P induced by the presence of Car was determined to be 1.7 x 10(5) [V/cm], corresponding to a approximately 10% change in the electrostatic field around P.

Carotenoids↗