Model of aggregation of pigments in the chlorosomal antenna of the green bacteria Chloroflexus aurantiacus

Independent experimental and theoretical evaluation was performed for the adequacy of our previously proposed general molecular model of structural organization of light-harvesting pigments in chlorosomal bacteriochlorophyll (BChl) c/d/e-containing superantenna of different green bacteria. Simultaneous measurement of hole burning in the optical spectra of chlorosomal BChl c and temperature dependence of steady-state fluorescence spectra of BChl c was accomplished in intact cells of photosynthetic green bacterium Chloroflexus aurantiacus; this allows unambiguous determination of the structure of exciton levels of BChl c oligomers in this natural antenna, which is a fundamental criterion for adequacy of any molecular model for in vivo aggregation of antenna pigments. Experimental data were shown to confirm our model of organization of oligometric pigments in chlorosomal BChl c antenna of green bacterium Chloroflexus aurantiacus. This model, which is based on experimental data and our theory of spectroscopy of oligomeric pigments, implies that the unit building block of BChl c antenna is a cylindrical assembly containing six excitonically coupled linear pigment chains whose exciton structure with intense upper levels provides for the optimal spectral properties of the light-harvesting antenna.     

Vibrations-determined properties of green fluorescent protein

The physicochemical characteristics of the green fluorescent protein (GFP), including the thermodynamic properties (entropy, enthalpy, Gibbs' free energy, heat capacity), normal mode vibrations, and atomic fluctuations, were investigated. The Gaussian 03 computational chemistry program was employed for normal mode analysis using the AMBER force field. The thermodynamic parameters and atomic fluctuations were then calculated from the vibrational eigenvalues (frequencies) and eigenvectors. The regions of highest rigidity were shown to be the beta-sheet barrel with the central alpha-helix, which bears the chromophore. The most flexible parts of the GFP molecule were the outlying loops that cover the top and bottom of the beta-barrel. This way, the balance between rigidity and flexibility is maintained, which is the optimal relationship for protein stability in terms of Gibbs' free energy. This dual-schemed structure satisfies the requirements for GFP function. In this sense, the structure of GFP resembles a nanoscale drum: a stiff cylinder with flexible vibrating end(s).     

Control of the blue fluorescent protein with advanced evolutionary pulse shaping

We demonstrate optical coherent control of the two-photon fluorescence of the blue fluorescent protein (BFP), which is of interest in investigations of protein-protein interactions. In addition to biological relevance, BFP represents an interesting target for coherent control from a chemical perspective due to its many components of highly nonexponential fluorescence decay and low quantum yield resulting from excited state isomerization. Using a genetic algorithm with a multiplicative (rather than ratiometric) fitness parameter, we are able to control the ratio of BFP fluorescence to second-harmonic generation without a considerable drop in the maximized signal. The importance of linear chirp and power-scaling on the discrimination process is investigated in detail.     

Excitation energy transfer in chlorosomes of green bacteria: theoretical and experimental studies.

A theory of excitation energy transfer within the chlorosomal antennae of green bacteria has been developed for an exciton model of aggregation of bacteriochlorophyll (BChl) c (d or e). This model of six exciton-coupled BChl chains with low packing density, approximating that in vivo, and interchain distances of approximately 2 nm was generated to yield the key spectral features found in natural antennae, i.e., the exciton level structure revealed by spectral hole burning experiments and polarization of all the levels parallel to the long axis of the chlorosome. With picosecond fluorescence spectroscopy it was demonstrated that the theory explains the antenna-size-dependent kinetics of fluorescence decay in chlorosomal antenna, measured for intact cells of different cultures of the green bacterium C. aurantiacus, with different chlorosomal antenna size determined by electron microscopic examination of the ultrathin sections of the cells. The data suggest a possible mechanism of excitation energy transfer within the chlorosome that implies the formation of a cylindrical exciton, delocalized over a tubular aggregate of BChl c chains, and Forster-type transfer of such a cylindrical exciton between the nearest tubular BChl c aggregates as well as to BChl a of the baseplate.     

The Model of Pigment Aggregation in the Chlorosomal Antenna of the Green Bacterium Chloroflexus aurantiacus

Independent experimental and theoretical evaluation was performed for the adequacy of our previously proposed general molecular model of the structural organization of light-harvesting pigments in chlorosomal bacteriochlorophyll (BChl) /d/e-containing superantennae of different green bacteria. Measurement of the temperature dependence of steady-state fluorescence spectra of BChl c was accomplished in intact cells of a photosynthetic green bacterium Chloroflexus aurantiacus; this allows in vivodetermination of the structure of exciton levels of BChl c oligomers in this natural antenna. Experimental data confirm our model of organization of oligomeric pigments in chlorosomal BChl c antenna of green bacterium Chloroflexus aurantiacus. This model implies that the unit building block of the antenna is a cylindrical assembly containing six excitonically coupled linear pigment chains, whose exciton structure with intense upper levels provides for the optimal spectral properties of the light-harvesting antenna.     

Dynamics of Typha latifolia L. populations in treatment wetlands in Estonia

The aim of this paper is to evaluate and compare broadleaved cattail (Typha latifolia L.) biomass production and the nitrogen (N) and phosphorus (P) content in phytomass in three treatment wetland systems and to propose suitable areas for treatment wetlands in Estonia for raw material production. The biomass samples (roots/rhizomes, shoots with leaves and spadixes) and litter were collected from 1 m × 1 m plots—15 plots in the Tänassilma semi-natural wetland, 15 plots in the Põltsamaa free water surface (FWS) constructed wetland (CW), and 10 plots in the Häädemeeste FWS CW. The average aboveground biomass of T. latifolia varied from 0.37 to 1.76 kg DW m^?2 in autumn and from 0.33 to 1.38 kg DW m^?2 in winter. The greatest average nitrogen (22,950 mg N kg^?1) concentration was found in spadixes in 2002, and the phosphorus (6500 mg P kg^?1) concentration was measured in roots–rhizomes in 2003. Average standing stock of nitrogen and phosphorus was higher in aboveground than belowground phytomass. In FWS CWs with high hydraulic and nutrient loadings, however, the harvesting of aboveground biomass is not an effective means for the removal of nutrients. Cattail biomass is a valuable insulation material, whereas the fibre from spadixes mixed with clay gives elasticity to clay plasters. According to our estimates, about 5412 km² could be used for Typha cultivation in Estonia.     

Energy selection is not correlated in the Qx and Qy bands of a Mg-porphyrin embedded in a protein

The Qx-Qy splitting observed in the fluorescence excitation spectra of Mg-mesoporphyrin-IX substituted horseradish peroxidase (MgMP-HRP) and of its complex with naphthohydroxamic acid (NHA) was studied by spectral hole burning techniques. The width of a hole directly burnt in the Qy band and that of a satellite hole indirectly produced in Qy as a result of hole burning in Qx was compared. We also studied the dependence of the satellite hole in the Qy band on the burning frequency used in the Qx band. Both the directly and indirectly burnt holes were very broad in the (higher energy) Qy band. The width of the satellite hole in the Qy band was equal to the entire width of the inhomogeneously broadened band, independently from the position of hole burning in Qx. This is indicative of a clear lack of correlation between the electronic transition energies of the Qx and Qy bands. A photoproduct was produced by laser irradiation of the MgMP-HRP/NHA complex and was identified as a species with lowered Q-splitting. Conversion of the photoproduct could be achieved by thermal activation measured in temperature-cycling experiments, with a characteristic temperature of 25 K. We attribute the phototransformation to a conformational change of MgMP.     

Efficiency and dimensioning of riparian buffer zones in agricultural catchments

A strong linear correlation was found between the log-transformed load and retention of nitrogen and phosphorus in riparian buffer zones (r=0.99 and 0.997, respectively). Analyses of N and P budgets in four riparian forests of varying age (two grey alder stands in Estonia and two riparian deciduous forests in USA) show a significant efficiency. Despite the different input load (72.9–110.4 kg N ha⁻¹ year⁻¹ and 2.5–3.0 kg P ha⁻¹ year⁻¹), the outputs into streams from the alder stands systems were comparably low (9.0–13.2 and 0.38–0.62 kg ha⁻¹ year⁻¹). The older forests from the USA showed less efficiency. Plant uptake of both N and P in younger stands was significantly higher than in older forests. Methods to determine the buffer zones' and buffer strips' width and their efficiency are presented. The testing of efficiency assessment in a watershed in Estonia demonstrated an expected efficiency of buffers.     

Strongly exciton-coupled BChle chromophore system in the chlorosomal antenna of intact cells of the green bacteriumChlorobium phaeovibrioides: A spectral hole burning study

Spectral hole burning studies of intact cells of the green bacteriumChlorobium phaeovibrioides have proven that the Q_y-absorption system of antenna bacteriochlorophylle (BChle) should be interpreted in terms of the delocalized exciton level structure of an aggregate. For the first time the 0-0 band of the lowest exciton state of BChle aggregates has been directly detected as the lowest energy inhomogeneously broadened band (FWHM 100 cm^–1; position of maximum, at 739 nm) of the near-infrared BChle band in the 1.8 K excitation spectrum (FWHM=750 cm^–1; position of maximum, at 715 nm). The comparative analysis of the hole spectra, measured for the three species of BChlc- ande-containing green bacteria, has shown that the 0-0 transition bands of the lowest exciton state of BChlc ande aggregates display fundamentally similar spectral features: (1) the magnitude of inhomogeneous broadening of these bands is about 100 cm^–1; (2) at the wavelength of the maximum of each band, the amplitude of the preburnt excitation spectrum makes up 20% of the maximum amplitude of the spectrum; (3) the spectral position of each band coincides with the spectral position of the longest wavelength band of the circular dichroism spectrum; (4) the width of these bands is 2.3-times less than that of monomeric BChl in vitro.     

Physicochemical properties of blue fluorescent protein determined via molecular dynamics simulation

Blue fluorescent protein (BFP) is a mutant of green fluorescent protein (GFP), where the chromophore has been modified to shift the emitted fluorescence into the blue spectral region. In this study, MD calculations were performed with the GROMACS simulation package and AMBER force field to investigate the dependence of BFPs physicochemical properties on temperature and applied pressure. The MD approach enabled us to calculate the compressibility of protein itself, separately from the nontrivial contribution of the hydration shell, which is difficult to achieve experimentally. The computed compressibility of BFP (3.94 x10(-5) MPa(-1)) is in agreement with experimental values of globular proteins. The center-of-mass diffusion coefficient of BFP and its dependence on temperature and pressure, which plays an important role in its application as a probe for intracellular liquid viscosity measurement, was calculated and found to be in good agreement with photobleaching recovery experimental data. We have shown that decreased temperature as well as applied pressure increases the water viscosity, but the concomitant decrease of the BFP diffusion coefficient behaves differently from Stokes-Einstein formula. It is shown that the number of hydrogen bonds around the protein grows with pressure, which explains the aforementioned deviation. Pressure also reduces root mean square (RMS) fluctuations, especially those of the most flexible residues situated in the loops. The analysis of the RMS fluctuations of the backbone Calpha atoms also reveals that the most rigid part of BFP is the center of the beta-barrel, in accord with temperature B factors obtained from the Protein Data Bank.