Rapid-flow resonance Raman spectroscopy of bacterial photosynthetic reaction centers.

Rapid-flow resonance Raman vibrational spectra of bacterial photosynthetic reaction centers from the R-26 mutant of Rhodobacter sphaeroides have been obtained by using excitation wavelengths (810-910 nm) resonant with the lowest energy, photochemically active electronic absorption. The technique of shifted excitation Raman difference spectroscopy is used to identify genuine Raman scattering bands in the presence of a large fluorescence background. The comparison of spectra obtained from untreated reaction centers and from reaction centers treated with the oxidant K3Fe(CN)6 demonstrates that resonance enhancement is obtained from the special pair. Relatively strong Raman scattering is observed for special pair vibrations with frequencies of 36, 94, 127, 202, 730, and 898 cm-1; other modes are observed at 71, 337, and 685 cm-1. Qualitative Raman excitation profiles are reported for some of the strong modes, and resonance enhancement is observed to occur throughout the near-IR absorption band of the special pair. These Raman data determine which vibrations are coupled to the optical absorption in the special pair and, thus, probe the nuclear motion that occurs after electronic excitation. Implications for the interpretation of previous hole-burning experiments and for the excited-state dynamics and photochemistry of reaction centers are discussed.     

Initial electron donor and acceptor in isolated Photosystem II reaction centers identified with femtosecond mid-IR spectroscopy

Despite the apparent similarity between the plant Photosystem II reaction center (RC) and its purple bacterial counterpart, we show in this work that the mechanism of charge separation is very different for the two photosynthetic RCs. By using femtosecond visible-pump-mid-infrared probe spectroscopy in the region of the chlorophyll ester and keto modes, between 1,775 and 1,585 cm(-1), with 150-fs time resolution, we show that the reduction of pheophytin occurs on a 0.6- to 0.8-ps time scale, whereas P+, the precursor state for water oxidation, is formed after approximately 6 ps. We conclude therefore that in the Photosystem II RC the primary charge separation occurs between the "accessory chlorophyll" Chl(D1) and the pheophytin on the so-called active branch.     

Two-dimensional infrared spectroscopy of peptides by phase-controlled femtosecond vibrational photon echoes

Two-dimensional infrared spectra of peptides are introduced that are the direct analogues of two- and three-pulse multiple quantum NMR. Phase matching and heterodyning are used to isolate the phase and amplitudes of the electric fields of vibrational photon echoes as a function of multiple pulse delays. Structural information is made available on the time scale of a few picoseconds. Line narrowed spectra of acyl-proline-NH(2) and cross peaks implying the coupling between its amide-I modes are obtained, as are the phases of the various contributions to the signals. Solvent-sensitive structural differences are seen for the dipeptide. The methods show great promise to measure structure changes in biology on a wide range of time scales.     

Low frequency vibrational modes in proteins: Changes induced by point-mutations in the protein-cofactor matrix of bacterial reaction centers

As a step toward understanding their functional role, the low frequency vibrational motions (<300 cm⁻¹) that are coupled to optical excitation of the primary donor bacteriochlorophyll cofactors in the reaction center from Rhodobacter sphaeroides were investigated. The pattern of hydrogen-bonding interaction between these bacteriochlorophylls and the surrounding protein was altered in several ways by mutation of single amino acids. The spectrum of low frequency vibrational modes identified by femtosecond coherence spectroscopy varied strongly between the different reaction center complexes, including between different mutants where the pattern of hydrogen bonds was the same. It is argued that these variations are primarily due to changes in the nature of the individual modes, rather than to changes in the charge distribution in the electronic states involved in the optical excitation. Pronounced effects of point mutations on the low frequency vibrational modes active in a protein-cofactor system have not been reported previously. The changes in frequency observed indicate a strong involvement of the protein in these nuclear motions and demonstrate that the protein matrix can increase or decrease the fluctuations of the cofactor along specific directions.     

Coherent nuclear dynamics at room temperature in bacterial reaction centers.

A room-temperature study is reported of the femtosecond spectral evolution of the stimulated emission band of the primary electron-transfer precursor P* in bacterial photosynthesis. The study was performed with membranes of the antenna-deficient RCO1 mutant of Rhodobacter sphaeroides. A time-dependent red shift, reflecting nuclear motion out of the Franck-Condon region of the excited state, is resolved. Analysis of oscillatory features persisting for > 1 ps in the kinetics revealed main frequencies of the activated motions at 30, 84, 145, and 192 cm-1. The oscillations occur on the time scale of primary electron transfer. Our results set a lower limit for the vibrational dephasing time in P* that is not compatible with the usual assumption in theoretical treatments of complete vibrational relaxation prior to electron transfer, even at room temperature.     

Mechanism of the initial charge separation in bacterial photosynthetic reaction centers.

The initial electron transfer in reaction centers from Rhodobacter sphaeroides R26 was studied by a subpicosecond transient pump-probe technique. The measured kinetics at various wavelengths were analyzed and compared with several mechanisms for electron transfer. An unambiguous determination of the initial electron transfer mechanism in reaction centers cannot be made by studying the anion absorption region (640-690 nm), due to the spectral congestion in this region. However, correlations between the stimulated emission decay of the excited state of the special pair, P*, at 926 nm and bleaching of the bacteriopheophytin Qx absorption at 545 nm suggest that the electron transfer at 283 K is dominated by a two-step sequential mechanism, whereas one-step superexchange and the two-step sequential mechanism have about equal contributions at 22 K.     

Femtosecond coherent transient infrared spectroscopy of reaction centers from Rhodobacter sphaeroides.

Protein and cofactor vibrational dynamics associated with photoexcitation and charge separation in the photosynthetic reaction center were investigated with femto-second (300-400 fs) time-resolved infrared (1560-1960 cm-1) spectroscopy. The experiments are in the coherent transient limit where the quantum uncertainty principle governs the evolution of the protein vibrational changes. No significant protein relaxation accompanies charge separation, although the electric field resulting from charge separation modifies the polypeptide carbonyl spectra. The potential energy surfaces of the "special pair" P and the photoexcited singlet state P* and environmental perturbations on them are similar as judged from coherence transfer measurements. The vibrational dephasing time of P* modes in this region is 600 fs. A subpicosecond transient at 1665 cm-1 was found to have the kinetics expected for a sequential electron transfer process. Kinetic signatures of all other transient intermediates, P, P*, and P+, participating in the primary steps of photosynthesis were identified in the difference infrared spectra.     

Optical biopsy using tissue spectroscopy and optical coherence tomography.

'Optical biopsy' or 'optical diagnostics' is a technique whereby light energy is used to obtain information about the structure and function of tissues without disrupting them. In fluorescence spectroscopy, light energy (usually provided by a laser) is used to excite tissues and the resulting fluorescence provides information about the target tissue. Its major gastrointestinal application has been in the evaluation of colonic polyps, in which it can reliably distinguish malignant from benign lesions. Optical coherence tomography (OCT) has been used in the investigation of Barrett's epithelium (and dysplasia), although a variety of other applications are feasible. For example, OCT could assist in the identification and staging of mucosal and submucosal neoplasms, the grading of inflammation in the stomach and intestine, the diagnosis of biliary tumours and the assessment of villous architecture. OCT differs from endoscopic ultrasound, a complementary modality, in that it has a much higher resolution but lesser depth of penetration. The images correlate with the histopathological appearance of tissues, and the addition of Doppler methods may enable it to evaluate the vascularity of tumours and the amount of blood flow in varices. Refinements in these new optical techniques will likely make them valuable in clinical practice, although their specific roles have yet to be determined.     

Direct experimental observation of the low ionization potentials of guanine in free oligonucleotides by using photoelectron spectroscopy

Photodetachment photoelectron spectroscopy is used to probe the electronic structure of mono-, di-, and trinucleotide anions in the gas phase. A weak and well defined threshold band was observed in the photoelectron spectrum of 2'-deoxyguanosine 5'-monophosphate at a much lower ionization energy than the other three mononucleotides. Density function theory calculations revealed that this unique spectral feature is caused by electron-detachment from a pi orbital of the guanine base on 2'-deoxyguanosine 5'-monophosphate, whereas the lowest ionization channel for the other three mononucleotides takes place from the phosphate group. This low-energy feature was shown to be a "fingerprint" in all the spectra of dinucleotides and trinucleotides that contain the guanine base. The current experiment provides direct spectroscopic evidence that the guanine base is the site with the lowest ionization potential in oligonucleotides and DNA and is consistent with the fact that guanine is most susceptible to oxidation to give the guanine cation in DNA damage.     

Stark effect spectroscopy of Rhodobacter sphaeroides and Rhodopseudomonas viridis reaction centers

The nature of the initially excited state of the primary electron donor or special pair has been investigated by Stark effect spectroscopy for reaction centers from the photosynthetic bacteria Rhodopseudomonas viridis and Rhodobacter sphaeroides at 77 K. The data provide values for the magnitude of the difference in permanent dipole moment between the ground and excited state, [unk]Δμ[unk], and the angle [unk] between Δμ and the transition dipole moment for the electronic transition. [unk]Δμ[unk] and [unk] for the lowest-energy singlet electronic transition associated with the special pair primary electron donor were found to be very similar for the two species. [unk]Δμ[unk] for this transition is substantially larger than for the Q_y transitions of the monomeric pigments in the reaction center or for pure monomeric bacteriochlorophylls, for which Stark data are also reported. We conclude that the excited state of the special pair has substantial charge-transfer character, and we suggest that charge separation in bacterial photosynthesis is initiated immediately upon photoexcitation of the special pair. Data for Rhodobacter sphaeroides between 340 and 1340 nm are presented and discussed in the context of the detection of charge-transfer states by Stark effect spectroscopy.     

Femtosecond spectral evolution of the excited state of bacterial reaction centers at 10 K.

The femtosecond spectral evolution of reaction centers of Rhodobacter sphaeroides R-26 was studied at 10 K. Transient spectra in the near infrared region, obtained with 45-fs pulses (pump pulses centered at 870 nm and continuum probe pulses), were analyzed with associated kinetics at specific wavelengths. The t = 0-fs transient spectrum is very rich in structure; it contains separate induced bands at 807 and 796 nm and a bleaching near 760 nm, reflecting strong changes in interaction between all pigments upon formation of the excited state. A complex spectral evolution in the 800-nm region, most notably the bleaching of the 796-nm band, takes place within a few hundred femtosecond--i.e., on a time scale much faster than electron transfer from the primary donor P to the bacteriopheophytin acceptor HL. The remarkable initial spectral features and their evolution are presumably related to the presence of HL, as they were not observed in the DLL mutant of Rhodobacter capsulatus, which lacks this pigment. A simple linear reaction scheme with an intermediate state cannot account for our data; the initial spectral evolution must reflect relaxation processes within the excited state. The importance for primary photochemistry of long distance interactions in the reaction center is discussed.     

Direct observation of delta-crystallin accumulation by laser light-scattering spectroscopy in the chicken embryo lens.

By using the technique of laser light-scattering spectroscopy, direct observation has been made on the intracellular accumulation of a crystallin protein within the cells of chicken embryo lens during the process of development. Appearance of delta-crystallin has been detected as early as day 4, and its concentration reaches a plateau at day 19. The measurements constitute a noninvasive determination of accumulation of protein molecules that specifically characterize the process of cell differentiation.     

Direct observation of the torsional dynamics of DNA and RNA by picosecond spectroscopy.

Picosecond time-dependent fluorescence depolarization techniques have been used to monitor the reorientation of ethidium bromide intercalated in DNA and RNA. The fluorescence polarization anisotropy reveals a nonexponential, exp(-at 1/2), torsional relaxation of the DNA double helix and provides an accurate value for its torsional rigidity, C = 1.3 +/- 0.2 X 10(-19) erg cm. Furthermore, from accurate measurements of the limiting anisotropy at zero time, we conclude that there is an additional fast (< 10 psec) internal motion that depends on the viscosity of the medium. Denatured DNA is considerably more flexible than the intact double helix, thus demonstrating the influence of secondary structure on internal motions.     

Direct vibrational structure of protein metal-binding sites from near-infrared Yb3+ vibronic side band spectroscopy.

Near-infrared Yb3+ vibronic side band (VSB) spectroscopy is used to obtain structural information of metal binding sites in metalloproteins. This technique provides a selective "IR-like" vibrational spectrum of those ligands chelated to the Yb3+ ion. VSB spectra of various model complexes of Yb3+ representing different ligand types were studied to provide references for the VSB spectra of Yb(3+)-reconstituted metalloproteins. Ca2+ in the calcium-binding protein parvalbumin and Fe3+ in the iron-transporting protein transferrin were replaced with Yb3+. The fluorescence of Yb3+ reconstituted into these two proteins exhibits weak VSBs whose energy shifts, with respect to the main 2F5/2-->2F7/2 Yb3+ electronic transition, represent the vibrational frequencies of the Yb3+ ligands. The chemical nature of the ligands of the Yb3+ in these proteins, as deduced by the observed VSB frequencies, is entirely in agreement with their known crystal structures. For transferrin, replacement of the 12CO3(2-) metal counterion with 13CO3(2-) yielded the expected isotopic shift for the VSBs corresponding to the carbonate vibrational modes. This technique demonstrates enormous potential in elucidating the localized structure of metal binding sites in proteins.     

Primary acceptor in bacterial photosynthesis: obligatory role of ubiquinone in photoactive reaction centers of Rhodopseudomonas spheroides.

Reaction centers were found to bind two ubiquinones, both of which could be removed by o-phenanthroline and the detergent lauryldimethylamine oxide. One ubiquinone was more easily removed than the other. The low-temperature light-induced optical and electron paramagnetic resonance (EPR) changes were eliminated and restored upon removal and readdition of ubiquinone and were quantitatively correlated with the amount of tightly bound ubiquinone. We, therefore, conclude that this ubiquinone plays an obligatory role in the primary photochemistry. The easily removed ubiquinone is thought to be the secondary electron acceptor. The low-temperature charge recombination kinetics, as well as the optical and EPR spectra, were the same for untreated reaction centers and for those reconstituted with ubiquinone. This indicates that extraction and reconstitution were accomplished without altering the conformation of the active site. Reaction centers reconstituted with other quinones also showed restored photochemical activity, although they exhibited changes in their low-temperature recombination kinetics and light-induced (g = 1.8) EPR signal is interpreted in terms of a magnetically coupled ubiquinone--Fe2+ acceptor complex. A possible role of iron is to facilitate electron transfer between the primary and secondary ubiquinones.     

Femtosecond infrared spectroscopy of reaction centers from Rhodobacter sphaeroides between 1000 and 1800 cm-1.

Time-resolved pump-and-probe experiments of reaction centers of the purple bacterium Rhodobacter sphaeroides (R26) in the mid-IR region between 1000 and 1800 cm-1 are recorded with a time resolution of 300-400 fs. The difference spectra of the states P*, P+HA-, and P+QA- with respect to the ground state P predominantly reflect changes of the special pair. They show positive and negative bands due to changes of distinct vibrational modes superimposed on a broad background of enhanced absorption. A number of certain bands can be assigned to the special pair P, to the bacteriopheophytin HA, and to the quinone QA. The temporal evolution of the IR absorbance changes is well described by the time constants known from femtosecond spectroscopy of the electronic states. Differences occur only at very early times, which are indicative of fast vibrational relaxation with a time constant of a few hundred femtoseconds.     

Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes

Photosynthetic bacteria emerged on Earth more than 3 Gyr ago. To date, despite a long evolutionary history, species containing (bacterio)chlorophyll-based reaction centers have been reported in only 6 out of more than 30 formally described bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, and Acidobacteria. Here we describe a bacteriochlorophyll a-producing isolate AP64 that belongs to the poorly characterized phylum Gemmatimonadetes. This red-pigmented semiaerobic strain was isolated from a freshwater lake in the western Gobi Desert. It contains fully functional type 2 (pheophytin-quinone) photosynthetic reaction centers but does not assimilate inorganic carbon, suggesting that it performs a photoheterotrophic lifestyle. Full genome sequencing revealed the presence of a 42.3-kb–long photosynthesis gene cluster (PGC) in its genome. The organization and phylogeny of its photosynthesis genes suggests an ancient acquisition of PGC via horizontal transfer from purple phototrophic bacteria. The data presented here document that Gemmatimonadetes is the seventh bacterial phylum containing (bacterio)chlorophyll-based phototrophic species. To our knowledge, these data provide the first evidence that (bacterio)chlorophyll-based phototrophy can be transferred between distant bacterial phyla, providing new insights into the evolution of bacterial photosynthesis.Photosynthesis is one of the most ancient and fundamental biological processes (1, 2). Phototrophic organisms transform solar radiation into metabolic energy, which fuels most of the Earth’s ecosystems (3). It is generally assumed that the earliest phototrophs were anaerobic (i.e., living in the absence of free oxygen) anoxygenic (i.e., not producing oxygen) prokaryotes (2). After the rise of oxygenic Cyanobacteria ∼2.7 Gyr ago, the Earth’s atmosphere started to become gradually oxygenated, reaching the present oxygen concentration roughly 0.6 Gyr ago (4, 5). Thus, early anaerobic phototrophs were forced either to adapt to the new oxic conditions or to retreat to anoxic habitats, leading to present phylogenetically and physiologically diverse phototrophic lineages.To date, species using (bacterio)chlorophyll-based photosynthetic reaction centers (chlorophototrophs) have been reported in six bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, and Acidobacteria (6). Each of these lineages contains a unique apparatus for solar energy conversion differing in light-harvesting complex architecture, pigment composition, and function of reaction centers (7). In general, photosynthetic reaction centers can be divided into two main groups. FeS-based (type 1) reaction centers are used by green sulfur bacteria (classified into Chlorobi), heliobacteria (phototrophic Firmicutes), and phototrophic Acidobacteria. Pheophytin-quinone (type 2) reaction centers are present in green nonsulfur bacteria (Chloroflexi) and purple bacteria (phototrophic Proteobacteria). Oxygenic Cyanobacteria contain both type 1 and type 2 reaction centers.Although Cyanobacteria, green sulfur bacteria, and purple bacteria were discovered more than 100 y ago (8), green nonsulfur bacteria and heliobacteria were not described until the second half of the 20th century (9, 10). The most recently identified organism representing a novel phylum containing chlorophototrophs is Candidatus Chloracidobacterium thermophilum, described in 2007 (11). These six phyla account for only a small portion of described phyla within the domain Bacteria (12, 13). Given that (bacterio)chlorophyll-based phototrophy represents an ancient process, we hypothesized that there remain chlorophototrophic lineages awaiting discovery, and, based on this notion, conducted a large isolate-screening project in various freshwater lakes with the aim of discovering novel phototrophic lineages.     

Energies and kinetics of radical pairs involving bacteriochlorophyll and bacteriopheophytin in bacterial reaction centers

Absorbance changes reflecting the formation of a transient radical-pair state, P^F, were measured in reaction centers from Rhodopseudomonas sphaeroides under conditions that blocked electron transfer to a later carrier (a quinone, Q). The temperature dependence of the absorbance changes suggests that P^F is an equilibrium mixture of two states, which appear to be mainly ¹[P^[unk]B^[unk]] and ¹[P^[unk]H^[unk]]. P is a bacteriochlorophyll dimer, B is a bacteriochlorophyll absorbing at 800 nm, and H is a bacteriopheophytin. In the presence of Q^[unk], the energy of ¹[P^[unk]B^[unk]] is about 0.025 eV above that of ¹[P^[unk]H^[unk]], ¹[P^[unk]H^[unk]] can decay to a triplet state, P^R, which also is an equilibrium mixture of two states, separated by about 0.03 eV. The lower of these appears to be mainly a locally excited triplet state of P, ³P; the upper state contains a major contribution from a triplet charge-transfer state, ³[P^[unk]B^[unk]]. The temperature dependence of delayed fluorescence from P^R indicates that ³P lies 0.40 eV below the excited singlet state, P^*, which is about 0.05 eV above ¹[P^[unk]H^[unk]]. The ^1,3[P^[unk]B^[unk]] charge-transfer states thus appear to interact with the locally excited states of P and B to give singlet and triplet states that are separated in energy by about 0.35 eV. This is 10⁶ times larger than the splitting between ¹[P^[unk]H^[unk]] and ³[P^[unk]H^[unk]] and implies strong orbital overlap between P^[unk] and B^[unk]. This is consistent with recent picosecond studies which suggest that electron transfer from P^* to B occurs within 1 ps and is followed in 4 to 10 ps by electron transfer from B^[unk] to H.     

Shared thematic elements in photochemical reaction centers.

The structural, functional, and evolutionary relationships between photosystem II and the purple nonsulfur bacterial reaction center have been recognized for several years. These can be classified as "quinone type" (type II) photosystems because the terminal electron acceptor is a mobile quinone molecule. The analogous relationship between photosystem I and the green sulfur bacterial (and helicobacterial) reaction centers has only recently become clear. These can be classified as "iron-sulfur type" (type I) photosystems because the terminal electron acceptor consists of one or more bound iron-sulfur clusters. At a fundamental level, the quinone type and iron-sulfur type reaction centers share a common photochemical motif in the early process of charge separation, leading to the speculation that all photochemical reaction centers have a common evolutionary origin. This review summarizes the current state of knowledge in comparative reaction center biochemistry between prokaryotic bacteria, cyanobacteria, and green plants.     

Quantum coherence spectroscopy reveals complex dynamics in bacterial light-harvesting complex 2 (LH2)

Light-harvesting antenna complexes transfer energy from sunlight to photosynthetic reaction centers where charge separation drives cellular metabolism. The process through which pigments transfer excitation energy involves a complex choreography of coherent and incoherent processes mediated by the surrounding protein and solvent environment. The recent discovery of coherent dynamics in photosynthetic light-harvesting antennae has motivated many theoretical models exploring effects of interference in energy transfer phenomena. In this work, we provide experimental evidence of long-lived quantum coherence between the spectrally separated B800 and B850 rings of the light-harvesting complex 2 (LH2) of purple bacteria. Spectrally resolved maps of the detuning, dephasing, and the amplitude of electronic coupling between excitons reveal that different relaxation pathways act in concert for optimal transfer efficiency. Furthermore, maps of the phase of the signal suggest that quantum mechanical interference between different energy transfer pathways may be important even at ambient temperature. Such interference at a product state has already been shown to enhance the quantum efficiency of transfer in theoretical models of closed loop systems such as LH2.