X-ray structure analysis of a membrane protein complex. Electron density map at 3 A resolution and a model of the chromophores of the photosynthetic reaction center from Rhodopseudomonas viridis

Functional expression and characterisation of membrane transport proteins

Membrane transporters set the framework organising the complexity of plant metabolism in cells, tissues and organisms. Their substrate specificity and controlled activity in different cells is a crucial part for plant metabolism to run pathways in concert. Transport proteins catalyse the uptake and exchange of ions, substrates, intermediates, products and cofactors across membranes. Given the large number of metabolites, a wide spectrum of transporters is required. The vast majority of in silico annotated membrane transporters in plant genomes, however, has not yet been functionally characterised. Hence, to understand the metabolic network as a whole, it is important to understand how transporters connect and control the metabolic pathways of plant cells. Heterologous expression and in vitro activity studies of recombinant transport proteins have highly improved their functional analysis in the last two decades. This review provides a comprehensive overview of the recent advances in membrane protein expression and functional characterisation using various host systems and transport assays.

Excited states of four hemes in a c-type cytochrome subunit of the photosynthetic reaction center of Rhodopseudomonas viridis: SAC-CI calculations

The excited states of four hemes, c-552, c-554, c-556, and c-559, in a c-type cytochrome subunit of the photosynthetic reaction center (PSRC) of Rhodopseudomonas (Rps.) viridis were studied using the symmetry-adapted cluster (SAC)-configuration interaction (CI) method. c-552 has two imidazole ligands, while the other three hemes have imidazole and methionine ligands. The electronic states of these four hemes are affected significantly by both the ligands and protein and water environments. The ligand effect classifies the four hemes into two groups, while the environmental effect is unique in each heme. The HOMO–LUMO energy separation of c-552 is much smaller than those of the other hemes, and therefore, the low-lying excited states of c-552 are more stable than those of the other hemes. The low-lying excited states and their oscillator strengths of c-559 are significantly modified by the environment when compared with c-556 and c-554. Some observed UV peaks of the PSRC of Rps. viridis were found to have been assigned reasonably to the excited states of these four hemes in a previous report. The calculated linear dichroism angles also supported our assignment.

Mechanism of charge transport by redox metal complexes confined in polymer matrices

The mechanism of charge transport by metal complexes confined in polymer matrices is reviewed. There are two possibilities, one where the charge propagates in the matrix by diffusion of redox center molecules, and the other where the charge propagates by hopping between redox center molecules. The mechanism can be decided by investigating the dependence of the charge propagation rate on the redox center concentration, since in the diffusion mechanism the rate is first-order with respect to the concentration, while in the hopping mechanism it is second-order. In the hopping mechanism the charge-hopping distance can be analyzed by assuming a random distribution of the redox center in the matrix. The mechanism of charge transport by typical redox centers such as metal porphyrins, metal phthalocyanines, [Formula: see text] and methylviologen confined in a polymer membrane is presented and the charge-hopping distance is determined.

Spectroscopic properties of p/p and o/o type iron(III)-metal-free porphyrin dimers and their catalysis as Cytochrome P450 model

Two series of p/p and o/o type iron(III)-metal-free porphyrin dimers were synthesized and characterized. The dimers consist of a ferric porphyrin and a free-base porphyrin, covalently linked with an alkoxy chain - O ( CH 2)n O -(n = 2–10) at the para and ortho position of two phenyl rings. The ferric paramagnetic effect and ring current effect on these dimers were discussed by 1 H NMR study; vibration modes sensitive to the conformations of the dimers were investigated from IR spectra; the electron density and spin state of ferric ion were examined using XPS and EPR spectroscopy. The catalytic activities of p/p and o/o type dimers on the hydroxylation of cyclohexane were studied under mild conditions. As a chemical mimic model of Cyto. P450, these porphyrins exhibit higher catalytic activities than the corresponding monomer FeTPPCl . With increase of the carbon numbers of alkoxy chain, the catalytic activity order of p/p dimers is C 2 < C 3 < C 4 < C 5 < C 6 > C 8 > C 10, the corresponding order of o/o dimers is C 2 > C 4 > C 6 > C 8 > C 10. Catalytic results of dimers are shown to strongly depend on their special conformation equilibrium, which affect the steric hindrance and electron transfer between two porphyrin rings.

Synthesis and Characterization of meso-Tetraphenylporphyrin-Corrole Unsymmetrical Dyads

Flat and gable meso-tetraphenylporphyrin-corrole heterodimers have been synthesized following a stepwise approach. The macrocyclic precursor for both isomers is a functionalized meso-tetraphenylporphyrin (TPP) bearing a formyl group at one of the peripheral phenyl groups. The preparation of these starting materials has been improved with respect to the previously reported method. Acidic condensation with pyrrole 8 allows the preparation of a TPP-dipyrromethane intermediate. Subsequent decarboxylation followed by reaction with formylpyrrole 2 affords the corresponding TPP–a,c-biladiene species. Final cyclization of this intermediate affords the desired heterodimer. Attempts to use the functionalized corrole 5 as starting material were unsuccessful, as this corrole failed to condense with pyrrole and benzaldehyde. This synthetic approach provides new examples of tetrapyrrolic heterodimers, which can represent useful biomimetic models to study photochemical processes.

Excited State Dynamics of Novel Diporphyrins with Dissimilar Cores

The singlet and triplet excited state properties of two diporphyrins, H 2- H and Zn - H , are described. Steady state fluorescence studies indicate that the emission of the H 2- H diporphyrin is dependent on the excitation wavelength and is dominated by the emission of the individual constituent monomers at their respective excitation. Time-resolved studies show two lifetimes ascribable to the normal and thiaporphyrin subunits. However, the emission of the Zn - H diporphyrin is dominated by the thiaporphyrin subunit irrespective of the wavelength of excitation, suggesting an energy transfer from the Zn porphyrin subunit to the thiaporphyrin subunit. Lifetime measurements in toluene show two lifetimes due to open and folded conformations, while in DMF an additional component due to axial ligation is observed. The efficiency of energy transfer is moderately higher in DMF (72%) than in toluene (68%). Triplet ESR studies on the H 2- H dimer reveal a localized triplet with ZFS parameters and ESP pattern the same as for the individual monomers. On the other hand, triplet ESR of the Zn - H diporphyrin reveals triplet characteristics of the thiaporphyrin subunit, indicating an energy transfer in the triplet state.

Spectroscopic properties of porphyrin dimers incorporating phenylenevinylene linkers

A series of free-base, zinc and mixed free-base-zinc porphyrin dimers were investigated using electrochemistry, electronic absorption, resonance Raman and emission studies. The spectroelectrochemistry of these compounds was also examined. The electronic absorption and resonance Raman data suggest that the two porphyrins in the dimer are behaving as independent chromophores with limited communication. However, emission studies show that energy transfer occurs between the two units. The linking unit is seen to have limited influence on the properties of chromophores.

Excitonic Interactions in Covalently Linked Porphyrin Dimers with Rotational Freedom

Experimental and calculated absorption spectra are compared for four different porphyrin dimers covalently linked by alkyl- or phenyl bridges. The spectra of the corresponding monomers were used as a reference to determine the experimental exciton,ic shift(s) of the absorption spectrum in the Soret region. The excitonic interaction was calculated using the point dipole approximation and taking into account the restricted conformational freedom of the monomeric units in the dimers due to steric constraints. The constraints were independently verified by magnetic dipole-dipole broadening of the EPR spectra of several ( CuTPP )2-substituted dimers. The observed and calculated absorption spectra agree at least semiquantitatively.

Primary electron donor(s) in isolated reaction center of photosystem II from Chlamydomonas reinhardtii

Isolated reaction centers (RCs) from wild-type Chlamydomonas (C.) reinhardtii of Photosystem II (PSII), at different levels of intactness, were studied to provide more insight into the nature of the charge-separation (CS) pathway(s). We argue that previously studied D1/D2/Cytb559 complexes (referred to as RC680), with ChlD1 serving as the primary electron donor, contain destabilized D1 and D2 polypeptides and, as a result, do not provide a representative model system for the intact RC within the PSII core. The shapes of nonresonant transient hole-burned (HB) spectra obtained for more intact RCs (referred to as RC684) are very similar to P(+)QA(-) - PQA absorbance difference and triplet minus singlet spectra measured in PSII core complexes from Synechocystis PCC 6803 [Schlodder et al. Philos. Trans. R. Soc. London, Ser. B2008, 363, 1197]. We show that in the RC684 complexes, both PD1 and ChlD1 may serve as primary electron donors, leading to two different charge separation pathways. Resonant HB spectra cannot distinguish the CS times corresponding to different paths, but it is likely that the zero-phonon holes (ZPHs) observed in the 680-685 nm region (corresponding to CS times of ∼1.4-4.4 ps) reveal the ChlD1 pathway; conversely, the observation of charge-transfer (CT) state(s) in RC684 (in the 686-695 nm range) and the absence of ZPHs at λB > 685 nm likely stem from the PD1 pathway, for which CS could be faster than 1 ps. This is consistent with the finding of Krausz et al. [Photochem. Photobiol. Sci.2005, 4, 744] that CS in intact PSII core complexes can be initiated at low temperatures with fairly long-wavelength excitation. The lack of a clear shift of HB spectra as a function of excitation wavelength within the red-tail of the absorption (i.e., 686-695 nm) and the absence of ZPHs suggest that the lowest-energy CT state is largely homogeneously broadened. On the other hand, in usually studied destabilized RCs, that is, RC680, for which CT states have never been experimentally observed, ChlD1 is the most likely electron donor.

Highlights from recently determined structures of membrane proteins: a focus on channels and transporters

After decades of absent or lackluster growth, recent years have at long last witnessed an exponential growth in the number of novel membrane protein structures determined. Every single achievement has had a tremendous impact on the scientific community, providing an unprecedented wealth of information that typically only an atomic resolution structure can contribute to our molecular understanding of how a protein functions. Presented here is a review of some of the most exciting novel structures of channels and transporters determined by X-ray crystallography in the last two years, and a discussion of their analogies, differences and mechanistic implications.

New insights into the structure of the reaction centre from Blastochloris viridis: evolution in the laboratory

Newly determined crystal structures of the photosynthetic RC (reaction centre) from two substrains of the non-sulfur purple bacterium Blastochloris viridis strain DSM 133, together with analysis of their gene sequences, has revealed intraspecies evolutionary changes over a period of 14 years. Over 100 point mutations were identified between these two substrains in the four genes encoding the protein subunits of the RC, of which approximately one-fifth resulted in a total of 16 amino acid changes. The most interesting difference was in the M subunit where the change from a leucine residue to glycine in the carotenoid-binding pocket allowed NS5 (1,2-dihydroneurosporene) to adopt a more sterically favoured conformation, similar to the carotenoid conformation found in other related RCs. The results of the present study, together with a high rate of mutations in laboratory bacterial cultures described recently, suggest that bacteria evolve faster than has been generally recognized. The possibility that amino acid changes occur within protein sequences, without exhibiting any immediately observable phenotype, should be taken into account in studies that involve long-term continuous growth of pure bacterial cultures. The Blc. viridis RC is often studied with sophisticated biophysical techniques and changes such as those described here may well affect their outcome. In other words, there is a danger that laboratory-to-laboratory variation could well be due to different groups not realising that they are actually working with slightly different proteins. A way around this problem is suggested.

Cofactor-specific photochemical function resolved by ultrafast spectroscopy in photosynthetic reaction center crystals

High-resolution mapping of cofactor-specific photochemistry in photosynthetic reaction centers (RCs) from Rhodobacter sphaeroides was achieved by polarization selective ultrafast spectroscopy in single crystals at cryogenic temperature. By exploiting the fixed orientation of cofactors within crystals, we isolated a single transition within the multicofactor manifold, and elucidated the site-specific photochemical functions of the cofactors associated with the symmetry-related active A and inactive B branches. Transient spectra associated with the initial excited states were found to involve a set of cofactors that differ depending upon whether the monomeric bacteriochlorophylls, BChl(A), BChl(B), or the special pair bacteriochlorophyll dimer, P, was chosen for excitation. Proceeding from these initial excited states, characteristic photochemical functions were resolved. Specifically, our measurements provide direct evidence for an alternative charge separation pathway initiated by excitation of BChl(A) that does not involve P*. Conversely, the initial excited state produced by excitation of BChl(B) was found to decay by energy transfer to P. A clear sequential kinetic resolution of BChl(A) and the A-side bacteriopheophytin, BPh(A), in the electron transfer proceeding from P* was achieved. These experiments demonstrate the opportunity to resolve photochemical function of individual cofactors within the multicofactor RC complexes using single crystal spectroscopy.

Cell membranes: the lipid perspective

Although cell membranes are packed with proteins mingling with lipids, remarkably little is known about how proteins interact with lipids to carry out their function. Novel analytical tools are revealing the astounding diversity of lipids in membranes. The issue is now to understand the cellular functions of this complexity. In this Perspective, we focus on the interface of integral transmembrane proteins and membrane lipids in eukaryotic cells. Clarifying how proteins and lipids interact with each other will be important for unraveling membrane protein structure and function. Progress toward this goal will be promoted by increasing overlap between different fields that have so far operated without much crosstalk.

Syntheses and excitation transfer studies of near-orthogonal free-base porphyrin-ruthenium phthalocyanine dyads and pentad

A new series of molecular dyads and pentad featuring free-base porphyrin and ruthenium phthalocyanine have been synthesized and characterized. The synthetic strategy involved reacting free-base porphyrin functionalized with one or four entities of phenylimidazole at the meso position of the porphyrin ring with ruthenium carbonyl phthalocyanine followed by chromatographic separation and purification of the products. Excitation transfer in these donor-acceptor polyads (dyad and pentad) is investigated in nonpolar toluene and polar benzonitrile solvents using both steady-state and time-resolved emission techniques. Electrochemical and computational studies suggested that the photoinduced electron transfer is a thermodynamically unfavorable process in nonpolar media but may take place in a polar environment. Selective excitation of the donor, free-base porphyrin entity, resulted in efficient excitation transfer to the acceptor, ruthenium phthalocyanine, and the position of imidazole linkage on the free-base porphyrin could be used to tune the rates of excitation transfer. The singlet excited Ru phthalocyanine thus formed instantly relaxed to the triplet state via intersystem crossing prior to returning to the ground state. Kinetics of energy transfer (k(ENT)) was monitored by performing transient absorption and emission measurements using pump-probe and up-conversion techniques in toluene, respectively, and modeled using a Förster-type energy transfer mechanism. Such studies revealed the experimental k(ENT) values on the order of 10(10)-10(11) s(-1), which readily agreed with the theoretically estimated values. Interestingly, in polar benzonitrile solvent, additional charge transfer interactions in the case of dyads but not in the case of pentad, presumably due to the geometry/orientation consideration, were observed.

Purification of the photosynthetic reaction center from Heliobacterium modesticaldum

We have developed a purification protocol for photoactive reaction centers (HbRC) from Heliobacterium modesticaldum. HbRCs were purified from solubilized membranes in two sequential chromatographic steps, resulting in the isolation of a fraction containing a single polypeptide, which was identified as PshA by LC-MS/MS of tryptic peptides. All polypeptides reported earlier as unknown proteins (in Heinnickel et al., Biochemistry 45:6756-6764, 2006; Romberger et al., Photosynth Res 104:293-303, 2010) are now identified by mass spectrometry to be the membrane-bound cytochrome c (553) and four different ABC-type transporters. The purified PshA homodimer binds the following pigments: 20 bacteriochlorophyll (BChl) g, two BChl g', two 8(1)-OH-Chl a (F), and one 4,4'-diaponeurosporene. It lacks the PshB polypeptide binding the F(A) and F(B) [4Fe-4S] clusters. It is active in charge separation and exhibits a trapping time of 23 ps, as judged by time-resolved fluorescence studies. The charge recombination rate of the P(800) (+)F(X)(-) state is 10-15 ms, as seen before. The purified HbRC core was able to reduce cyanobacterial flavodoxin in the light, exhibiting a K (M) of 10 μM and a k (cat) of 9.5 s(-1) under near-saturating light. There are ~1.6 menaquinones per HbRC in the purified complex. Illumination of frozen HbRC in the presence of dithionite can cause creation of a radical at g = 2.0046, but this is not a semiquinone. Furthermore, we show that high-purity HbRCs are very stable in anoxic conditions and even remain active in the presence of oxygen under low light.

Porphyrin supramolecules by complementary coordination for units constructing photosynthetic systems

Among unique structural arrangements provided by nature, special pair and macroring antenna complexes in bacterial photosynthetic systems have been mimicked by simple organization of choromophores. The special pair was mimicked by imidazolyl-substituted porphyrinatozinc which gave a complementary coordination dimer of slipped cofacial orientation with an extremely large stability constant of 1010 M-1 in CHCl 3. When two imidazolylporphyrinatozinc units were linked directly at the meso positions, linear and continuous growth of the complementary coordination lead to porphyrin arrays of a few hundreds nanometer scale, corresponding to molecular weights of a few 105. At the same time, the porphyrin array could be dissociated into the monomeric unit by competitive coordination of solvents. This provided a way of terminating or initiating the oligomeric porphyrin array with appropriate chain terminals/initiators. Two imidazolylporphyrinatozinc complexes were then linked by a m-phenylene unit with an angle of 120°. The linear and macrocyclic oligomer mixtures initially obtained were converged smoothly by reorganization equilibrium into a mixture of hexameric and pentameric macrocycles under high-dilution conditions. The ring mimicked the structure and function of the light harvesting complexes of bacterial photosynthetic systems. The covalent linking of coordination organized porphyrins was also developed to maintain the structure even in highly coordinating solvents such as pyridine. The linear array formation and the facile introduction of specific terminal/initiator groups by complementary coordination were then applied to introduce antenna function onto solar cell. Through thiolate attachment on a gold surface, imidazolylporphyrinatozinc initiated the growth of meso-meso linked porphyrin arrays by successive complementary coordination. This methodology improved the efficiency of absorption of incident photon and increased significantly the total photocurrent generation efficiency.

Calculation and prediction of rate and equilibrium constants for aggregation of porphyrin by molecular dynamics, Docking and QSPR methods

The aggregation of 85 porphyrin derivatives and a report on a kinetic and thermodynamic study of such aggregation behavior on varying the derivatives of porphyrin was carried out using molecular dynamics simulation and Docking. Distance diagrams of simulated compounds were obtained and decrease of curves is a clear evidence of the aggregation. Aggregation rates were studied by origin software. In order to calculate interaction energies of derivatives, compounds were docked and the equilibrium constant of porphyrin-porphyrin interaction were obtained. Quantitative Structure-Property Relationship (QSPR) studies were performed for the sets of 85 Porphyrin derivatives. Multiple Linear Regression method (MLR) and Principal Component Analysis (PCA) were used and resulted in useful models with good prediction ability. This models were able to predict the kinetic and equilibrium constant for all sets of our compounds. The correlation coefficients for prediction of rate and logarithm of equilibrium constants were 0.67 and 0.97 by MLR method respectively and 0.90 for prediction of equilibrium constant by PCA analyses. In order to have a better prediction, compounds were divided into two groups, oxygenated and non-oxygenated group and correlation coefficient for prediction of rate constants of them were obtained 0.89 and 0.94 by MLR model respectively. Results of structure-property relationship showed that, larger, more hydrophobe and more planner derivatives have higher aggregation rate.

SHKUROPATOV ANATOLI, SHUVALOV VLADIMIRA. WAVE PACKET MOTIONS COUPLED TO ELECTRON TRANSFER IN REACTION CENTERS OF CHLOROFLEXUS AURANTIACUS

Transient absorption difference spectroscopy with ~20 femtosecond (fs) resolution was applied to study the time and spectral evolution of low-temperature (90 K) absorbance changes in isolated reaction centers (RCs) of Chloroflexus (C.) aurantiacus. In RCs, the composition of the B-branch chromophores is different with respect to that of purple bacterial RCs by occupying the BB binding site of accessory bacteriochlorophyll by bacteriopheophytin molecule (ΦB). It was found that the nuclear wave packet motion induced on the potential energy surface of the excited state of the primary electron donor P* by ~20 fs excitation leads to a coherent formation of the states [Formula: see text] and [Formula: see text] (BA is a bacteriochlorophyll monomer in the A-branch of cofactors). The processes were studied by measuring coherent oscillations in kinetics of the absorbance changes at 900 nm and 940 nm (P* stimulated emission), at 750 nm and 785 nm (ΦB absorption bands), and at 1,020–1028 nm ([Formula: see text] absorption band). In RCs, the immediate bleaching of the P band at 880 nm and the appearance of the stimulated wave packet emission at 900 nm were accompanied (with a small delay of 10–20 fs) by electron transfer from P* to the B-branch with bleaching of the ΦB absorption band at 785 nm due to [Formula: see text] formation. These data are consistent with recent measurements for the mutant HM182L Rb. sphaeroides RCs (Yakovlev et al., Biochim Biophys Acta1757:369–379, 2006). Only at a delay of 120 fs was the electron transfer from P* to the A-branch observed with a development of the [Formula: see text] absorption band at 1028 nm. This development was in phase with the appearance of the P* stimulated emission at 940 nm. The data on the A-branch electron transfer in C. aurantiacus RCs are consistent with those observed in native RCs of Rb. sphaeroides. The mechanism of charge separation in RCs with the modified B-branch pigment composition is discussed in terms of coupling between the nuclear wave packet motion and electron transfer from P* to ΦB and BA primary acceptors in the B-branch and A-branch, respectively.

Photooxidation of cobalt(II) meso-tetraphenylporphyrin by p-benzoquinone and its mechanism studied by optical absorption and resonance Raman spectroscopies

Laser excitation of Co II TPP within the Soret absorption band in the presence of p-benzoquinone (p-BQ) results in oxidation of the complex. Oxidation occurs both at the metal center and the porphyrin ring depending upon the experimental conditions. Under anaerobic conditions, oxidation takes place at the metal center to produce the cobaltic species Co III( TPP )+, while in the presence of molecular oxygen oxidation also occurs at the porphyrin ring giving Co III( TPP )2+• cation radical as oxidation product. From the inhibiting effect of peroxy radical trapping agent on the photooxidation of Co II TPP under aerobic conditions, the two-electron oxidation is suggested to involve solvent radicals and we discuss the mechanistic details of the process in this work.

Excited states of analogue models of M-bacteriochlorophylls (M = Mg, Zn) in the photosynthetic reaction center: a time-dependent density functional theory study

Using time-dependent density functional theory (TDDFT), the excited states of the analogue model Mg -bacteriochlorophyll b - imidazole ( BChl -Im) dimer (P) for a special pair in the photosynthetic reaction center (RC) of Rhodopseudomonas (Rps.) viridis were examined. The calculated low-lying excited states and optimal geometries are in good agreement with experimental data. The order of the lowest unoccupied molecular orbital (LUMO) energies of P, the monomeric "accessory" BChl -Im (B), and bacteriopheophytin b ( H ) indicates the possibility of the light-induced electron transfer from P to H via B. The Im ligand of B destabilizes Goutermann's four-orbitals of BChl by 0.3-0.4 eV. With no energetic difference in the LUMOs between H and BChl , the Im ligands of P and B play an important role in providing a greater energetic gradient to the LUMOs along with the pathway for the excited-electron transfer in RC, resulting in the reduced reverse electron transfer from H to P (via B). Thus it is expected that the asymmetric Mg -Im interactions will directly affect the pathway of the excited-electron transfer. Using the deformed heterodimer (P') formed by the BChl halves with and without Im as the primary donor model, its cation radical P'+ was calculated as to whether the experimental asymmetric spin-density distribution can reproduce. The excited states of the analogue model Zn - BChl -Im dimer for a special pair in RC of the recently discovered Acidiphilium rubrum were also examined for a comparison with P.

Spectral properties of cationic water-soluble metallo-porphyrins immobilized in a perfluorosulfonated ion-exchange membrane

The behavior of palladium(II), platinum(II) and rhodium(III) complexes with two cationic water-soluble porphyrins: meso-tetrakis(4-N-methylpyridyl)porphyrin and meso-tetrakis(4-N,N,N-trimethylaminophenyl)porphyrin in Nafion® membrane and in Nafion® solution have been studied by UV-visible absorption and emission spectroscopy. All metalloporphyrins are localized in the interfacial region of Nafion®. The six-coordinate Rh(III) complexes are monomeric inside Nafion®, but immobilized four-coordinate Pd(II) and Pt(II) complexes form face-to-face dimers with a characteristic blue shifted Soret band. All immobilized complexes exhibit a strong red phosphorescence at room temperature in the absence of oxygen. Phosphorescence decays for all metalloporphyrins were found to be a single exponential but phosphorescence lifetimes noticeably increased in the Nafion® membrane as compared to lifetimes in aqueous solution.

Primary charge separation within P870* in wild type and heterodimer mutants in femtosecond time domain

Primary charge separation dynamics in the reaction center (RC) of purple bacterium Rhodobacter sphaeroides and its P870 heterodimer mutants have been studied using femtosecond time-resolved spectroscopy with 20 and 40fs excitation at 870nm at 293K. Absorbance increase in the 1060-1130nm region that is presumably attributed to P(A)(δ+) cation radical molecule as a part of mixed state with a charge transfer character P*(P(A)(δ+)P(B)(δ-)) was found. This state appears at 120-180fs time delay in the wild type RC and even faster in H(L173)L and H(M202)L heterodimer mutants and precedes electron transfer (ET) to B(A) bacteriochlorophyll with absorption band at 1020nm in WT. The formation of the P(A)(δ+)B(A)(δ-) state is a result of the electron transfer from P*(P(A)(δ+)P(B)(δ-)) to the primary electron acceptor B(A) (still mixed with P*) with the apparent time delay of ~1.1ps. Next step of ET is accompanied by the 3-ps appearance of bacteriopheophytin a(-) (H(A)(-)) band at 960nm. The study of the wave packet formation upon 20-fs illumination has shown that the vibration energy of the wave packet promotes reversible overcoming of an energy barrier between two potential energy surfaces P* and P*(P(A)(δ+)B(A)(δ-)) at ~500fs. For longer excitation pulses (40fs) this promotion is absent and tunneling through an energy barrier takes about 3ps. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.

Quantum chemical description of absorption properties and excited-state processes in photosynthetic systems

The theoretical description of the initial steps in photosynthesis has gained increasing importance over the past few years. This is caused by more and more structural data becoming available for light-harvesting complexes and reaction centers which form the basis for atomistic calculations and by the progress made in the development of first-principles methods for excited electronic states of large molecules. In this Review, we discuss the advantages and pitfalls of theoretical methods applicable to photosynthetic pigments. Besides methodological aspects of excited-state electronic-structure methods, studies on chlorophyll-type and carotenoid-like molecules are discussed. We also address the concepts of exciton coupling and excitation-energy transfer (EET) and compare the different theoretical methods for the calculation of EET coupling constants. Applications to photosynthetic light-harvesting complexes and reaction centers based on such models are also analyzed.

Diversity and modularity of G protein-coupled receptor structures

G protein-coupled receptors (GPCRs) comprise the most 'prolific' family of cell membrane proteins, which share a general mechanism of signal transduction, but greatly vary in ligand recognition and function. Crystal structures are now available for rhodopsin, adrenergic, and adenosine receptors in both inactive and activated forms, as well as for chemokine, dopamine, and histamine receptors in inactive conformations. Here we review common structural features, outline the scope of structural diversity of GPCRs at different levels of homology, and briefly discuss the impact of the structures on drug discovery. Given the current set of GPCR crystal structures, a distinct modularity is now being observed between the extracellular (ligand-binding) and intracellular (signaling) regions. The rapidly expanding repertoire of GPCR structures provides a solid framework for experimental and molecular modeling studies, and helps to chart a roadmap for comprehensive structural coverage of the whole superfamily and an understanding of GPCR biological and therapeutic mechanisms.

Metalloporphyrin mixed-valence π-cation radicals: [Fe(oxoOEC(•/2))(Cl)]2SbCl6, structure, magnetic properties, and near-IR spectra

The preparation and characterization of a mixed-valence π-cation radical derivative of an iron(III) oxochlorinato complex is reported. The new complex has been synthesized by the one-electron oxidation of a pair of [Fe(oxoOEC)(Cl)] molecules to form the dimeric cation [Fe(oxoOEC)(Cl)]₂⁺. The cation has been characterized by X-ray analysis, Mössbauer spectroscopy, UV-vis and near-IR spectroscopy, and magnetic susceptibility measurements from 6-300 K. The crystal structure shows that the two rings have a smaller overlap area than those of the formally related nickel and copper octaethylporphinate derivatives, reflecting the larger steric congestion at the periphery in part of the oxochlorin rings. The Mössbauer data is consistent with two equivalent iron(III) centers. The unpaired electron is delocalized over the two oxochlorin rings and mediates a strong antiferromagnetic interaction between the high-spin iron(III) centers.

X-ray crystallography at the heart of life science

X-ray crystallography is the fundamental research tool that shaped our notion on biological structure & function at the molecular level. It generates the information vital to understand life processes by providing the information required for creating accurate three-dimensional models (namely mapping the position of each and every atom that makes up the studied object). The use of this method begun in the middle of last century following Max von Laue discovery of the phenomenon of diffraction of X-rays by crystals, and the successful application of this discovery for the determination of the electronic distribution within simple inorganic molecules by Sir William Henry Bragg and his son, William Lawrence Bragg. The idea of extension of this method to biological molecules met initially with considerable skepticism. For over two decades many respected scientists doubted whether it could be done. Yet, despite its bottlenecks (some of which are described below), the superiority of X-ray crystallography over all other approaches for shedding light on functional aspects at the molecular level became evident once the first structure was determined. The power of this method inspired continuous efforts and spectacular innovations, which vastly accelerated its incredible expansion. Consequently, over the last six decades biological crystallography has produced a constantly growing number of structures, some of which were considered formidable. This remarkable advance yielded numerous new insights into intricate functional aspects. Owing to space limitation this article focuses on selected studies performed recently and highlights some recent exciting developments.

Small angle X-ray scattering as a complementary tool for high-throughput structural studies

Structural crystallography and nuclear magnetic resonance (NMR) spectroscopy are the predominant techniques for understanding the biological world on a molecular level. Crystallography is constrained by the ability to form a crystal that diffracts well and NMR is constrained to smaller proteins. Although powerful techniques, they leave many soluble, purified structurally uncharacterized protein samples. Small angle X-ray scattering (SAXS) is a solution technique that provides data on the size and multiple conformations of a sample, and can be used to reconstruct a low-resolution molecular envelope of a macromolecule. In this study, SAXS has been used in a high-throughput manner on a subset of 28 proteins, where structural information is available from crystallographic and/or NMR techniques. These crystallographic and NMR structures were used to validate the accuracy of molecular envelopes reconstructed from SAXS data on a statistical level, to compare and highlight complementary structural information that SAXS provides, and to leverage biological information derived by crystallographers and spectroscopists from their structures. All the ab initio molecular envelopes calculated from the SAXS data agree well with the available structural information. SAXS is a powerful albeit low-resolution technique that can provide additional structural information in a high-throughput and complementary manner to improve the functional interpretation of high-resolution structures.

The Q cycle of cytochrome bc complexes: a structure perspective

Aspects of the crystal structures of the hetero-oligomeric cytochrome bc(1) and b(6)f ("bc") complexes relevant to their electron/proton transfer function and the associated redox reactions of the lipophilic quinones are discussed. Differences between the b(6)f and bc(1) complexes are emphasized. The cytochrome bc(1) and b(6)f dimeric complexes diverge in structure from a core of subunits that coordinate redox groups consisting of two bis-histidine coordinated hemes, a heme b(n) and b(p) on the electrochemically negative (n) and positive (p) sides of the complex, the high potential [2Fe-2S] cluster and c-type heme at the p-side aqueous interface and aqueous phase, respectively, and quinone/quinol binding sites on the n- and p-sides of the complex. The bc(1) and b(6)f complexes diverge in subunit composition and structure away from this core. b(6)f Also contains additional prosthetic groups including a c-type heme c(n) on the n-side, and a chlorophyll a and β-carotene. Common structure aspects; functions of the symmetric dimer. (I) Quinone exchange with the bilayer. An inter-monomer protein-free cavity of approximately 30Å along the membrane normal×25Å (central inter-monomer distance)×15Å (depth in the center), is common to both bc(1) and b(6)f complexes, providing a niche in which the lipophilic quinone/quinol (Q/QH(2)) can be exchanged with the membrane bilayer. (II) Electron transfer. The dimeric structure and the proximity of the two hemes b(p) on the electrochemically positive side of the complex in the two monomer units allow the possibility of two alternate routes of electron transfer across the complex from heme b(p) to b(n): intra-monomer and inter-monomer involving electron cross-over between the two hemes b(p). A structure-based summary of inter-heme distances in seven bc complexes, representing mitochondrial, chromatophore, cyanobacterial, and algal sources, indicates that, based on the distance parameter, the intra-monomer pathway would be favored kinetically. (III) Separation of quinone binding sites. A consequence of the dimer structure and the position of the Q/QH(2) binding sites is that the p-side QH(2) oxidation and n-side Q reduction sites are each well separated. Therefore, in the event of an overlap in residence time by QH(2) or Q molecules at the two oxidation or reduction sites, their spatial separation would result in minimal steric interference between extended Q or QH(2) isoprenoid chains. (IV) Trans-membrane QH(2)/Q transfer. (i) n/p-side QH(2)/Q transfer may be hindered by lipid acyl chains; (ii) the shorter less hindered inter-monomer pathway across the complex would not pass through the center of the cavity, as inferred from the n-side antimycin site on one monomer and the p-side stigmatellin site on the other residing on the same surface of the complex. (V) Narrow p-side portal for QH(2)/Q passage. The [2Fe-2S] cluster that serves as oxidant, and whose histidine ligand serves as a H(+) acceptor in the oxidation of QH(2), is connected to the inter-monomer cavity by a narrow extended portal, which is also occupied in the b(6)f complex by the 20 carbon phytyl chain of the bound chlorophyll.

Construction and structural analysis of tethered lipid bilayer containing photosynthetic antenna proteins for functional analysis

The construction and structural analysis of a tethered planar lipid bilayer containing bacterial photosynthetic membrane proteins, light-harvesting complex 2 (LH2), and light-harvesting core complex (LH1-RC) is described and establishes this system as an experimental platform for their functional analysis. The planar lipid bilayer containing LH2 and/or LH1-RC complexes was successfully formed on an avidin-immobilized coverglass via an avidin-biotin linkage. Atomic force microscopy (AFM) showed that a smooth continuous membrane was formed there. Lateral diffusion of these membrane proteins, observed by a fluorescence recovery after photobleaching (FRAP), is discussed in terms of the membrane architecture. Energy transfer from LH2 to LH1-RC within the tethered membrane was observed by steady-state fluorescence spectroscopy, indicating that the tethered membrane can mimic the natural situation.

Light-induced quinone reduction in photosystem II

The photosystem II core complex is the water:plastoquinone oxidoreductase of oxygenic photosynthesis situated in the thylakoid membrane of cyanobacteria, algae and plants. It catalyzes the light-induced transfer of electrons from water to plastoquinone accompanied by the net transport of protons from the cytoplasm (stroma) to the lumen, the production of molecular oxygen and the release of plastoquinol into the membrane phase. In this review, we outline our present knowledge about the "acceptor side" of the photosystem II core complex covering the reaction center with focus on the primary (Q(A)) and secondary (Q(B)) quinones situated around the non-heme iron with bound (bi)carbonate and a comparison with the reaction center of purple bacteria. Related topics addressed are quinone diffusion channels for plastoquinone/plastoquinol exchange, the newly discovered third quinone Q(C), the relevance of lipids, the interactions of quinones with the still enigmatic cytochrome b559 and the role of Q(A) in photoinhibition and photoprotection mechanisms. This article is part of a Special Issue entitled: Photosystem II.

Solution NMR spectroscopy of supra-molecular systems, why bother? A methyl-TROSY view

With the development of appropriate labeling schemes and the associated experiments that exploit them it has become possible to record high quality solution NMR spectra of supra-molecular complexes with molecular masses extending to 1MDa. One such approach involves selective (13)CH(3) methyl labeling in highly deuterated proteins using experiments that make use of a methyl-TROSY effect that significantly improves both resolution and sensitivity in spectra. The utility of this methodology has been demonstrated on a growing number of interesting particles. It seems appropriate at this juncture, therefore, to 'step back' and evaluate the role that solution NMR spectroscopy can play in what has traditionally been the domain of X-ray crystallography and more recently cryo-electron microscopy. It is argued here that solution NMR can make a critical contribution to our understanding of how dynamics regulate function in these high molecular weight systems. Several examples from work in my laboratory on the proteasome are presented as an illustration.