The photosynthetic bacterial reaction center in native and artificial envirnoments: effects on light-induced electron transfer

In this thesis we focussed on the characterization of the reaction center (RC) protein purified from the photosynthetic bacterium Rhodobacter sphaeroides. In particular, we discussed the effects of native and artificial environment on the light-induced electron transfer processes. The native environment consist of the inner antenna LH1 complex that copurifies with the RC forming the so called core complex, and the lipid phase tightly associated with it. In parallel, we analyzed the role of saccharidic glassy matrices on the interplay between electron transfer processes and internal protein dynamics. As a different artificial matrix, we incorporated the RC protein in a layer-by-layer structure with a twofold aim: to check the behaviour of the protein in such an unusual environment and to test the response of the system to herbicides. By examining the RC in its native environment, we found that the light-induced charge separated state P+QB - is markedly stabilized (by about 40 meV) in the core complex as compared to the RC-only system over a physiological pH range. We also verified that, as compared to the average composition of the membrane, the core complex copurifies with a tightly bound lipid complement of about 90 phospholipid molecules per RC, which is strongly enriched in cardiolipin. In parallel, a large ubiquinone pool was found in association with the core complex, giving rise to a quinone concentration about ten times larger than the average one in the membrane. Moreover, this quinone pool is fully functional, i.e. it is promptly available at the QB site during multiple turnover excitation of the RC. The latter two observations suggest important heterogeneities and anisotropies in the native membranes which can in principle account for the stabilization of the charge separated state in the core complex. The thermodynamic and kinetic parameters obtained in the RC-LH1 complex are very close to those measured in intact membranes, indicating that the electron transfer properties of the RC in vivo are essentially determined by its local environment. The studies performed by incorporating the RC into saccharidic matrices evidenced the relevance of solvent-protein interactions and dynamical coupling in determining the kinetics of electron transfer processes. The usual approach when studying the interplay between internal motions and protein function consists in freezing the degrees of freedom of the protein at cryogenic temperature. We proved that the “trehalose approach” offers distinct advantages with respect to this traditional methodology. We showed, in fact, that the RC conformational dynamics, coupled to specific electron transfer processes, can be modulated by varying the hydration level of the trehalose matrix at room temperature, thus allowing to disentangle solvent from temperature effects. The comparison between different saccharidic matrices has revealed that the structural and dynamical protein-matrix coupling depends strongly upon the sugar. The analyses performed in RCs embedded in polyelectrolyte multilayers (PEM) structures have shown that the electron transfer from QA - to QB, a conformationally gated process extremely sensitive to the RC environment, can be strongly modulated by the hydration level of the matrix, confirming analogous results obtained for this electron transfer reaction in sugar matrices. We found that PEM-RCs are a very stable system, particularly suitable to study the thermodynamics and kinetics of herbicide binding to the QB site. These features make PEM-RC structures quite promising in the development of herbicide biosensors. The studies discussed in the present thesis have shown that, although the effects on electron transfer induced by the native and artificial environments tested are markedly different, they can be described on the basis of a common kinetic model which takes into account the static conformational heterogeneity of the RC and the interconversion between conformational substates. Interestingly, the same distribution of rate constants (i.e. a Gamma distribution function) can describe charge recombination processes in solutions of purified RC, in RC-LH1 complexes, in wet and dry RC-PEM structures and in glassy saccharidic matrices over a wide range of hydration levels. In conclusion, the results obtained for RCs in different physico-chemical environments emphasize the relevance of the structure/dynamics solvent/protein coupling in determining the energetics and the kinetics of electron transfer processes in a membrane protein complex.

Relationship between respiration and Electron Transfer System (ETS) in zooplankton

[EN]Respiration of zooplanktonic organisms is an significant fraction of the global carbon cycle. However, it estimation in order to obtain the data required in oceanography is still a problem. In this work, we studied respiration rates in laboratory and field experiments. Laboratory experiments using Daphnia spp. showed a significant decrease of respiration rates during starvation. In addition, we measured the gut fluorescence and enzymatic activity (electron transfer system, ETS). The former did not show the expected decrease probably due to the volume of the incubators. The relationship between respiration and ETS presented the classical variability ranging between 0.5 and 1 as observed in previous works. Copepod respiration rates were measured during RAPROCAN 1504 cruise around the Canary Islands.

The coupling between electron transfer and Protein/Solvent Dynamics in Photosynthetic Reaction Centers: Spectroscopic Studies in Amorphous Matrices

We investigated at the molecular level protein/solvent interactions and their relevance in protein function through the use of amorphous matrices at room temperature. As a model protein, we used the bacterial photosynthetic reaction center (RC) of Rhodobacter sphaeroides, a pigment protein complex which catalyzes the light-induced charge separation initiating the conversion of solar into chemical energy. The thermal fluctuations of the RC and its dielectric conformational relaxation following photoexcitation have been probed by analyzing the recombination kinetics of the primary charge-separated (P+QA-) state, using time resolved optical and EPR spectroscopies. We have shown that the RC dynamics coupled to this electron transfer process can be progressively inhibited at room temperature by decreasing the water content of RC films or of RC-trehalose glassy matrices. Extensive dehydration of the amorphous matrices inhibits RC relaxation and interconversion among conformational substates to an extent comparable to that attained at cryogenic temperatures in water-glycerol samples. An isopiestic method has been developed to finely tune the hydration level of the system. We have combined FTIR spectral analysis of the combination and association bands of residual water with differential light-minus-dark FTIR and high-field EPR spectroscopy to gain information on thermodynamics of water sorption, and on structure/dynamics of the residual water molecules, of protein residues and of RC cofactors. The following main conclusions were reached: (i) the RC dynamics is slaved to that of the hydration shell; (ii) in dehydrated trehalose glasses inhibition of protein dynamics is most likely mediated by residual water molecules simultaneously bound to protein residues and sugar molecules at the protein-matrix interface; (iii) the local environment of cofactors is not involved in the conformational dynamics which stabilizes the P+QA-; (iv) this conformational relaxation appears to be rather delocalized over several aminoacidic residues as well as water molecules weakly hydrogen-bonded to the RC.

Direct electron transfer to cytochrome c oxidase investigated by electrochemistry and time-resolved surface-enhanced infrared absorption spectroscopy

Cytochrom c Oxidase (CcO), der Komplex IV der Atmungskette, ist eine der Häm-Kupfer enthaltenden Oxidasen und hat eine wichtige Funktion im Zellmetabolismus. Das Enzym enthält vier prosthetische Gruppen und befindet sich in der inneren Membran von Mitochondrien und in der Zellmembran einiger aerober Bakterien. Die CcO katalysiert den Elektronentransfer (ET) von Cytochrom c zu O2, wobei die eigentliche Reaktion am binuklearen Zentrum (CuB-Häm a3) erfolgt. Bei der Reduktion von O2 zu zwei H2O werden vier Protonen verbraucht. Zudem werden vier Protonen über die Membran transportiert, wodurch eine elektrochemische Potentialdifferenz dieser Ionen zwischen Matrix und Intermembranphase entsteht. Trotz ihrer Wichtigkeit sind Membranproteine wie die CcO noch wenig untersucht, weshalb auch der Mechanismus der Atmungskette noch nicht vollständig aufgeklärt ist. Das Ziel dieser Arbeit ist, einen Beitrag zum Verständnis der Funktion der CcO zu leisten. Hierzu wurde die CcO aus Rhodobacter sphaeroides über einen His-Anker, der am C-Terminus der Untereinheit II angebracht wurde, an eine funktionalisierte Metallelektrode in definierter Orientierung gebunden. Der erste Elektronenakzeptor, das CuA, liegt dabei am nächsten zur Metalloberfläche. Dann wurde eine Doppelschicht aus Lipiden insitu zwischen die gebundenen Proteine eingefügt, was zur sog. proteingebundenen Lipid-Doppelschicht Membran (ptBLM) führt. Dabei musste die optimale Oberflächenkonzentration der gebundenen Proteine herausgefunden werden. Elektrochemische Impedanzspektroskopie(EIS), Oberflächenplasmonenresonanzspektroskopie (SPR) und zyklische Voltammetrie (CV) wurden angewandt um die Aktivität der CcO als Funktion der Packungsdichte zu charakterisieren. Der Hauptteil der Arbeit betrifft die Untersuchung des direkten ET zur CcO unter anaeroben Bedingungen. Die Kombination aus zeitaufgelöster oberflächenverstärkter Infrarot-Absorptionsspektroskopie (tr-SEIRAS) und Elektrochemie hat sich dafür als besonders geeignet erwiesen. In einer ersten Studie wurde der ET mit Hilfe von fast scan CV untersucht, wobei CVs von nicht-aktivierter sowie aktivierter CcO mit verschiedenen Vorschubgeschwindigkeiten gemessen wurden. Die aktivierte Form wurde nach dem katalytischen Umsatz des Proteins in Anwesenheit von O2 erhalten. Ein vier-ET-modell wurde entwickelt um die CVs zu analysieren. Die Methode erlaubt zwischen dem Mechanismus des sequentiellen und des unabhängigen ET zu den vier Zentren CuA, Häm a, Häm a3 und CuB zu unterscheiden. Zudem lassen sich die Standardredoxpotentiale und die kinetischen Koeffizienten des ET bestimmen. In einer zweiten Studie wurde tr-SEIRAS im step scan Modus angewandt. Dafür wurden Rechteckpulse an die CcO angelegt und SEIRAS im ART-Modus verwendet um Spektren bei definierten Zeitscheiben aufzunehmen. Aus diesen Spektren wurden einzelne Banden isoliert, die Veränderungen von Vibrationsmoden der Aminosäuren und Peptidgruppen in Abhängigkeit des Redoxzustands der Zentren zeigen. Aufgrund von Zuordnungen aus der Literatur, die durch potentiometrische Titration der CcO ermittelt wurden, konnten die Banden versuchsweise den Redoxzentren zugeordnet werden. Die Bandenflächen gegen die Zeit aufgetragen geben dann die Redox-Kinetik der Zentren wieder und wurden wiederum mit dem vier-ET-Modell ausgewertet. Die Ergebnisse beider Studien erlauben die Schlussfolgerung, dass der ET zur CcO in einer ptBLM mit größter Wahrscheinlichkeit dem sequentiellen Mechanismus folgt, was dem natürlichen ET von Cytochrom c zur CcO entspricht.

Novel porphyrin amino acids as building blocks for artificial photosynthetic reaction centers : photoinduced energy and electron transfer

This thesis reports on the synthesis and characterisation of trans-(M)AB2C meso-substituted porphyrin amino acid esters (PAr) (M = 2H or Zn) with tunable electron donating and electron withdrawing Ar substituents at B positions (Ar = 4-C6H4OnBu, 4-C6H4OMe, 2,4,6-C6H2Me3, 4-C6H4Me, C6H5, 4-C6H4F, 4-C6H4CF3, C6F5). These porphyrins were used as key building blocks for photosynthetic LHC (LHC = light-harvesting antenna complex) and RC (RC = reaction center) model compounds.rnBased on free-base or zinc(II) porphyrin amino acid esters and porphyrin acids several amide linked free-base bis(porphyrins) PAr1-PAr2 (Ar1 = 2,4,6-C6H2Me3, C6F5 and Ar2 = 2,4,6-C6H2Me3, 4-C6H4F, 4-C6H4CF3, C6F5), mono metallated bis(porphyrin) PAr1-(Zn)PAr2 (Ar1 = 2,4,6-C6H2Me3 and Ar2 =4-C6H4F) and its doubly zincated complexes (Zn)PAr1-(Zn)PAr2 were prepared. In the fluorescence spectra of free-base bis(porphyrins) the porphyrin with the strongest electron donating power of Ar substituents at B positions is the light emitting unity. The emission of mono metallated bis(porphyrin) occurs only from the free-base porphyrin building block. This phenomenon is caused by an efficient energy transfer likely via the Dexter through-bond mechanism.rnLinking of anthraquinone (Q) as electron acceptor (A) to the N-terminus of porphyrin amino acid esters ((M)PAr) and aminoferrocene (Fc) as electron donor (D) to the C-terminus of the porphyrin resulting in Q-(M)PAr-Fc triads (M = 2H or Zn, Ar = 4-C6H4OnBu, 4-C6H4OMe, 2,4,6-C6H2Me3, 4-C6H4Me, C6H5, 4-C6H4F, 4-C6H4CF3, C6F5) with tunable electron density at the porphyrin chromophore. In these triads initial oxidative PET (Q←(M)PAr) and reductive PET ((M)PAr→Fc) (PET = photoinduced electron transfer) are possible. Both processes leads to an emission quenching of (M)PAr. The efficiency of the PET pathways occurring in the Marcus normal region is controlled by the specific porphyrin electron density.rnAmide-linked conjugates PAr-Fc (Ar = 2,4,6-C6H2Me3, C6F5) and Fmoc-Fc-PAr1 (N-Fmoc-Fc = N-Fmoc protected 1,1’-ferrocene amino acid; Ar1 = C6H5, 4-C6H4F, 4-C6H4CF3, C6F5) as well as hinges PAr2-Fc-PAr1 (Ar1 = C6H5, 4-C6H4F and Ar2 = 2,4,6-C6H2Me3) were studied with respect to the reductive PET. The PET driving force (−GET) in dyads increases with the increasing electron withdrawing character of Ar substituents. Additionally, intramolecular energy transfer between porphyrins PAr1 and PAr2 is feasible in the hinges via the Förster mechanism.rn

Annulation of Tetrathiafulvalene to the Bay Region of Perylenediimide: Fast Electron-Transfer Processes in Polar and Nonpolar Solvents

A tetrathiafulvalene donor has been annulated to the bay region of perylenediimide through a 1H-benzo-[d]pyrrolo[1,2-a]imidazol-1-one spacer affording an extended pi-conjugated molecular dyad (TTF-PDI). To gain insight into its ground- and excited-state electronic properties, the reference compound Ph-PDI has been prepared via a direct Schiff-base condensation of N,N'-bis(1-octylnonyl) benzoperylene-1',2':3,4:9,10-hexacarboxylic-1',2'-anhydride-3,4:9,10-bis (imide) with benzene-1,2-diamine. Both the experimental and the computational (DFT) results indicate that TTF-PDI exhibits significant intramolecular electronic interactions giving rise to an efficient photoinduced charge-separation process. Free-energy calculations verify that the process from TTF to the singlet-excited state of PDI is exothermic in both polar and nonpolar solvents. Fast adiabatic electron-transfer processes of a compactly fused, pi-conjugated TTF-PDI dyad in benzonitrile, 2-methyltetrahydrofuran, anisole and toluene were observed by femtosecond transient absorption spectral measurements. The lifetimes of radical-ion pairs slightly increase with decreasing the solvent polarities, suggesting that the charge-recombination occurs in the Marcus inverted region. By utilizing the nanosecond transient absorption technique, the intermolecular electron-transfer process in a mixture of has been observed via the triplet excited PDI for the first time.

Enhancement of excess electron transfer efficiency in DNA containing a phenothiazine donor and multiple stable phenanthrenyl base pairs

EET grown ohm: Excess electron transfer (EET) was observed within a DNA duplex containing π-stacked phenothiazine as an electron donor, phenanthrenes as electron carriers and 5-bromouracil as an electron trap. Increasing the number of phenanthrenyl base pairs increased EET efficiency.

Agrobacterium ParA/MinD-like VirC1 spatially coordinates early conjugative DNA transfer reactions.

Agrobacterium tumefaciens translocates T-DNA through a polar VirB/D4 type IV secretion (T4S) system. VirC1, a factor required for efficient T-DNA transfer, bears a deviant Walker A and other sequence motifs characteristic of ParA and MinD ATPases. Here, we show that VirC1 promotes conjugative T-DNA transfer by stimulating generation of multiple copies per cell of the T-DNA substrate (T-complex) through pairwise interactions with the processing factors VirD2 relaxase, VirC2, and VirD1. VirC1 also associates with the polar membrane and recruits T-complexes to cell poles, the site of VirB/D4 T4S machine assembly. VirC1 Walker A mutations abrogate T-complex generation and polar recruitment, whereas the native protein recruits T-complexes to cell poles independently of other polar processing factors (VirC2, VirD1) or T4S components (VirD4 substrate receptor, VirB channel subunits). We propose that A. tumefaciens has appropriated a progenitor ParA/MinD-like ATPase to promote conjugative DNA transfer by: (i) nucleating relaxosome assembly at oriT-like T-DNA border sequences and (ii) spatially positioning the transfer intermediate at the cell pole to coordinate substrate-T4S channel docking.

Real-time observation of the charge-transfer-to-solvent dynamics

Intermolecular electron-transfer reactions have a crucial role in biology, solution chemistry and electrochemistry. The first step of such reactions is the expulsion of the electron to the solvent, whose mechanism is determined by the structure and dynamical response of the latter. Here we visualize the electron transfer to water using ultrafast fluorescence spectroscopy with polychromatic detection from the ultraviolet to the visible region, upon photo-excitation of the so-called charge transfer to solvent states of aqueous iodide. The initial emission is short lived (~60 fs) and it relaxes to a broad distribution of lower-energy charge transfer to solvent states upon rearrangement of the solvent cage. This distribution reflects the inhomogeneous character of the solvent cage around iodide. Electron ejection occurs from the relaxed charge transfer to solvent states with lifetimes of 100–400 fs that increase with decreasing emission energy.

NADH-quinone oxidoreductase: PSST subunit couples electron transfer from iron–sulfur cluster N2 to quinone

The proton-translocating NADH-quinone oxidoreductase (EC 1.6.99.3) is the largest and least understood enzyme complex of the respiratory chain. The mammalian mitochondrial enzyme (also called complex I) contains more than 40 subunits, whereas its structurally simpler bacterial counterpart (NDH-1) in Paracoccus denitrificans and Thermus thermophilus HB-8 consists of 14 subunits. A major unsolved question is the location and mechanism of the terminal electron transfer step from iron–sulfur cluster N2 to quinone. Potent inhibitors acting at this key region are candidate photoaffinity probes to dissect NADH-quinone oxidoreductases. Complex I and NDH-1 are very sensitive to inhibition by a variety of structurally diverse toxicants, including rotenone, piericidin A, bullatacin, and pyridaben. We designed (trifluoromethyl)diazirinyl[3H]pyridaben ([3H]TDP) as our photoaffinity ligand because it combines outstanding inhibitor potency, a suitable photoreactive group, and tritium at high specific activity. Photoaffinity labeling of mitochondrial electron transport particles was specific and saturable. Isolation, protein sequencing, and immunoprecipitation identified the high-affinity specifically labeled 23-kDa subunit as PSST of complex I. Immunoprecipitation of labeled membranes of P. denitrificans and T. thermophilus established photoaffinity labeling of the equivalent bacterial NQO6. Competitive binding and enzyme inhibition studies showed that photoaffinity labeling of the specific high-affinity binding site of PSST is exceptionally sensitive to each of the high-potency inhibitors mentioned above. These findings establish that the homologous PSST of mitochondria and NQO6 of bacteria have a conserved inhibitor-binding site and that this subunit plays a key role in electron transfer by functionally coupling iron–sulfur cluster N2 to quinone.