Low-temperature spectroscopy of isolated FMO-protein and a membrane-free reaction center complex from the green sulfur bacteriumChlorobium tepidum

A Time-Dependent Quantum Approach to Allostery and a Comparison With Light-Harvesting in Photosynthetic Phenomenon

The allosteric effect is one of the most important processes in regulating the function of proteins, and the elucidation of this phenomenon plays a significant role in understanding emergent behaviors in biological regulation. In this process, a perturbation, generated by a ligand in a part of the macromolecule (the allosteric site), moves along this system and reaches a specific (active) site, dozens of Ångströms away, with a great efficiency. The dynamics of this perturbation in the macromolecule can model precisely the allosteric process. In this article, we will be studying the general characteristics of allostery, using a time-dependent quantum approach to obtain rules that apply to this kind of process. Considering the perturbation as a wave that moves within the molecular system, we will characterize the allosteric process with three of the properties of this wave in the active site: (1) t_a, the characteristic time for reaching that site, (2) A_a, the amplitude of the wave in this site, and (3) B_a, its corresponding spectral broadening. These three parameters, together with the process mechanism and the perturbation efficiency in the process, can describe the phenomenon. One of the main purposes of this paper is to link the parameters t_a, A_a, and B_a and the perturbation efficiency to the characteristics of the system. There is another fundamental process for life that has some characteristics similar to allostery: the light-harvesting (LH) process in photosynthesis. Here, as in allostery, two distant macromolecular sites are involved—two sites dozens of Ångströms away. In both processes, it is particularly important that the perturbation is distributed efficiently without dissipating in the infinite degrees of freedom within the macromolecule. The importance of considering quantum effects in the LH process is well documented in literature, and the quantum coherences are experimentally proven by time-dependent spectroscopic techniques. Given the existing similarities between these two processes in macromolecules, in this work, we suggest using Quantum Mechanics (QM) to study allostery.

Alternative Excitonic Structure in the Baseplate (BChl a-CsmA Complex) of the Chlorosome from Chlorobaculum tepidum

In the photosynthetic green sulfur bacterium Chlorobaculum tepidum, the baseplate mediates excitation energy transfer from the light-harvesting chlorosome to the Fenna-Matthews-Olson (FMO) complex and subsequently toward the reaction center (RC). Literature data suggest that the baseplate is a 2D lattice of BChl a-CsmA dimers. However, recently, it has been proposed, using 2D electronic spectroscopy (2DES) at 77 K, that at least four excitonically coupled BChl a are in close contact within the baseplate structure [ Dostál , J. ; et al., J. Phys. Chem. Lett. 2014 , 5 , 1743 ]. This finding is tested via hole burning (HB) spectroscopy (5 K). Our results indicate that the four excitonic states identified by 2DES likely correspond to contamination of the baseplate with the FMO antenna and possibly the RC. In contrast, HB reveals a different excitonic structure of the baseplate chromophores, where excitation is transferred to a localized trap state near 818 nm via exciton hopping, which leads to emission near 826 nm.

A novel and mild isolation procedure of chlorosomes from the green sulfur bacterium Chlorobaculum tepidum

In this article, we developed a new and mild procedure for the isolation of chlorosomes from a green sulfur bacterium Chlorobaculum tepidum. In this procedure, Fenna-Matthews-Olson (FMO) protein was released by long cold treatment (6°C) of cells under the presence of a chaotrope (2 M NaSCN) and 0.6 M sucrose. Chlorosomes were released by an osmotic shock of the cold-treated cells after the formation of spheroplasts without mechanical disruption. Chlorosomes were finally purified by a sucrose step-wise density gradient centrifugation. We obtained two samples with different density (20 and 23% sucrose band, respectively) and compared them by SDS-PAGE, absorption spectroscopy at 80 K, fluorescence and CD spectroscopy at room temperature. Cells whose absorption maximum was longer than 750 nm yielded higher amount of the 20% sucrose fraction than those having an absorption maximum shorter than 750 nm.

Characterization of the FMO protein from the aerobic chlorophototroph, Candidatus Chloracidobacterium thermophilum

Candidatus Chloracidobacterium (Cab.) thermophilum is a recently discovered aerobic chlorophototroph belonging to the phylum Acidobacteria. From analyses of genomic sequence data, this organism was inferred to have type-1 homodimeric reaction centers, chlorosomes, and the bacteriochlorophyll (BChl) a-binding Fenna-Matthews-Olson protein (FMO). Here, we report the purification and characterization of Cab. thermophilum FMO. Absorption, fluorescence emission, and CD spectra of the FMO protein were measured at room temperature and at 77 K. The spectroscopic features of this FMO protein were different from those of the FMO protein of green sulfur bacteria (GSB) and suggested that exciton coupling of the BChls in the FMO protein is weaker than in FMO of GSB especially at room temperature. HPLC analysis of the pigments extracted from the FMO protein only revealed the presence of BChl a esterified with phytol. Despite the distinctive spectroscopic properties, the residues known to bind BChl a molecules in the FMO of GSB are well conserved in the primary structure of the Cab. thermophilum FMO protein. This suggests that the FMO of Cab. thermophilum probably also binds seven or possibly eight BChl a(P) molecules. The results imply that, without changing pigment composition or structure dramatically, the FMO protein has acquired properties that allow it to perform light harvesting efficiently under aerobic conditions.

Photoinduced transient absorbance spectra of P840/P840(+) and the FMO protein in reaction centers of Chlorobium vibrioforme

The kinetics of photoinduced absorbance changes in the 400-ns to 100-ms time range were studied between 770 and 1025 nm in reaction center core (RCC) complexes isolated from the green sulfur bacterium Chlorobium vibrioforme. A global, multiple stretched-exponential analysis shows the presence of two distinct but strongly overlapping spectra. The spectrum of the 70-micros component consists of a broad bleaching with two minima at 810 and 825 nm and a broad positive band at wavelengths greater than 865 nm and is assigned to the decay of (3)Bchl a of the Fenna-Matthews-Olson (FMO) protein. The contribution of the 70-micros component correlates with the amount of FMO protein in the isolated RCC complex. The spectrum of the 1.6-micros component has a sharp bleaching at 835 nm, a maximum at 805 nm, a broad positive band at wavelengths higher than 865 nm, and a broad negative band at wavelengths higher than 960 nm. When the RCC is incubated with inorganic iron and sulfur, the 1.6-micros component is replaced by a component with a lifetime of approximately 40 micros, consistent with the reconstruction of the F(X) cluster. We propose that the 1.6-micros component results from charge recombination between P840(+) and an intermediate electron acceptor operating between A(0) and F(X). Our studies in Chlorobium RCCs show that approaches that employ a single wavelength in the measurement of absorption changes have inherent limitations and that a global kinetic analysis at multiple wavelengths in the near-infrared is required to reliably separate absorption changes due to P840/P840(+) from the decay of (3)Bchl a in the FMO protein.

The triplet state of the FMO complex of the green sulfur bacterium Prosthecochloris aestuarii studied with single-crystal EPR

Triplet-electron paramagnetic resonance (EPR) spectra were obtained of single crystals of the FMO complex of the green sulfur bacterium Prostecochloris aestuarii. The experiments support the results presented in a previous paper (Louwe et al., J. Phys. Chem. 101 (1997) 11280), which showed that the experimental optical spectra of this pigment-protein complex are best reproduced by assuming that one bacteriochlorophyll (BChl 3) is energetically isolated and that this BChl is the triplet-carrying BChl of the FMO complex at cryogenic temperatures for low excitation density. When comparing the experimental and simulated data sets of the triplet-EPR spectra in single crystals, the best fit is obtained for two triplet states, one localized at BChl 3 and the other at BChl 1. The existence of two different triplet states is traced to the relatively high excitation power necessary to observe the small triplet-EPR signal of the FMO single crystals.

Isolation and properties of photochemically active reaction center complexes from the green sulfur bacterium Prosthecochloris aestuarii

A new and rapid procedure was developed for the isolation of the reaction center core (RCC)-complex from the green sulfur bacterium Prosthecochloris aestuarii. Reaction center preparations containing the Fenna Matthews Olson (FMO) protein were also obtained. The procedure involved incubation of broken cells with the detergents Triton X-100 and SB12, sucrose gradient centrifugation and hydroxyapatite chromatography. Three different pigment protein complexes were obtained: one containing (about) three FMO trimers per RCC, one with one FMO per RCC and one consisting of RCC only. The last one contained polypeptides with apparent molecular masses of 64 kDa (pscA) and 35 kDa (pscB, the FA/FB, FeS subunit), but no cytochrome. Bacteriochlorophyll a and the chlorophyll a isomer functioning as primary electron acceptor were present at a ratio of 4.8:1. The complexes were also characterized spectroscopically and in terms of photochemical activity, at room temperature as well as at cryogenic temperatures. Illumination caused oxidation of the primary donor P840, with the highest activity in the RCC complex (DeltaA840/A810 = 0.06). At room temperature in the RCC complex essentially all of the P840+ produced in a flash was re-reduced slowly in the dark (several seconds). At low temperatures (150-10 K) a triplet was formed in a fraction of the reaction centers, presumably by a reversal of the charge separation, whereas in others P840+ formed in the light was re-reduced in 40-50 ms.

Electron transfer and electronic energy relaxation under high hydrostatic pressure

The following question has been addressed in the present work. How external high (up to 8 kbar) hydrostatic pressure acts on photoinduced intramolecular electron transfer and on exciton relaxation processes? Unlike phenomena, as they are, have been studied in different systems: electron transfer in an artificial Zn-porphyrin-pyromellitimide (ZnP-PM) supramolecular electron donor-acceptor complex dissolved in toluene measured at room temperature; exciton relaxation in a natural photosynthetic antenna protein called FMO protein measured at low temperatures, between 4 and 100 K. Spectrally selective picosecond time-resolved emission technique has been used to detect pressure-induced changes in the systems. The following conclusions have been drawn from the electron transfer study: (i) External pressure may serve as a potential and sensitive tool not only to study, but also to control and tune elementary chemical reactions in solvents; (ii) Depending on the system parameters, pressure can both accelerate and inhibit electron transfer reactions; (iii) If competing pathways of the reaction are available, pressure can probably change the branching ratio between the pathways; (iv) The classical nonadiabatic electron transfer theory describes well the phenomena in the ZnP-PM complex, assuming that the driving force or/and reorganisation energy depend linearly on pressure; (v) A decrease in the ZnP-PM donor-acceptor distance under pressure exerts a minor effect on the electron transfer rate. The effect of pressure on the FMO protein exciton relaxation dynamics at low temperatures has been found marginal. This may probably be explained by a unique structure of the protein [D.E. Trondrud, M.F. Schmid, B.W. Matthews, J. Mol. Biol. 188 (1986) p. 443; Y.-F. Li, W. Zhou, E. Blankenship, J.P. Allen, J. Mol. Biol., submitted]. A barrel made of low compressibility beta-sheets may, like a diving bell, effectively screen internal bacteriochlorophyll a molecules from external influence of high pressure. The origin of the observed slow pico = and subnanosecond dynamics of the excitons at the exciton band bottom remains open. The phenomenon may be due to weak coupling of phonons to the exciton states or/and to low density of the relevant low-frequency ( approximately 50 cm(-1)) phonons. Exciton solvation in the surrounding protein and water-glycerol matrix may also contribute to this effect. Drastic changes of spectral, kinetic and dynamic properties have been observed due to protein denaturation, if the protein was compressed at room temperature and then cooled down, as compared to the samples, first cooled and then pressurised.

Energy transfer from carotenoid and FMO-protein in subcellular preparations from green sulfur bacteria. Spectroscopic characterization of an FMO-reaction center core complex at low temperature

The Fenna-Matthews-Olson (FMO)-protein and the FMO-reaction center (RC) core complex from the green sulfur bacterium Chlorobium tepidum were examined at 6 K by absorption and fluorescence spectroscopy. The absorption spectrum of the RC core complex was obtained by a subtraction method and found to have fiye peaks in the QY region, at 797, 808, 818, 834 and 837 nm. The efficiency of energy transfer from carotenoid to bacteriochlorophyll a in the RC core complex was 23% at 6 K, and from the FMO-protein to the core it was 35%. Energy transfer from the FMO-protein to the core complex was also measured in isolated membranes of Prosthecochloris aestuarii from the action spectra of charge separation. Again, a low efficiency of energy transfer was obtained, both at 6 K and at room temperature.

Stable photobleaching of P840 in Chlorobium reaction center preparations: presence of the 42-kDa bacteriochlorophyll a protein and a 17-kDa polypeptide

Simple procedures for the anaerobic preparation of photoactive and stable P840 reaction centers from Chlorobium tepidum and Chlorobium limicola in good yield are presented and quantitated. The subunit composition was tested by cosedimentation in sucrose density gradients. For C. limicola, it minimally comprises four subunits: the P840 reaction center protein PscA, the BChla antenna protein FMO, the FeS protein PscB with centers A and B, and a positively charged 17-kDa protein denoted PscD. The preparation from Chlorobium tepidum additionally contained PscC, a cytochrome c-551. The BChla absorption peak of the purified complexes was at 810 nm, with a shoulder at 835 nm. The ratio of the shoulder to the peak was 0.25, which corresponds to 1 reaction center per 70 BChla molecules if a uniform extinction coefficient of BChla is assumed. However, bleaching at 610 nm in continuous light corresponded up to 1 photoactive reaction center per 50 BChla molecules. Therefore, either the extinction coefficient of BChla in the reaction center is overestimated or the one for photobleaching is underestimated. In any case, the major portion of the reaction center was photoactive in the preparations. A P840 reaction center subcomplex, lacking PscD and deficient in FMO and PscB, but retaining the cytochrome c subunit, was obtained as a side product. It was photoinactive and had an absorption peak at 814 nm and a 835/814 absorbance ratio of 0.42. FMO and PscB show the tendency to form a complementary subcomplex. FMO and PscD are apparently required to stabilize the photoactive reaction center, while the cytochrome c subunit is not.

Genetic transfer by conjugation in the thermophilic green sulfur bacterium Chlorobium tepidum

The broad-host-range IncQ group plasmids pDSK519 and pGSS33 were transferred by conjugation from Escherichia coli into the thermophilic green sulfur bacterium Chlorobium tepidum. C. tepidum exconjugants expressed the kanamycin and ampicillin-chloramphenicol resistances encoded by pDSK519 and pGSS33, respectively. Ampicillin resistance was a particularly good marker for selection in C. tepidum. Both pDSK519 and pGSS33 were stably maintained in C. tepidum at temperatures below 42 degrees C and could be transferred between C. tepidum and E. coli without modifications. Conjugation frequencies ranged from 10(-1) to 10(-4) exconjugants per donor cell, and frequencies of 10(-2) to 10(-3) were consistently obtained when ampicillin resistance was used as a selectable marker. Methods for growth of C. tepidum on agar, isolation of plating strains and antibiotic-resistant mutants of wild-type C. tepidum cells, and optimum conditions for conjugation were also investigated.