A time dependent density functional theory study of alpha-84 phycocyanobilin chromophore in C-phycocyanin

The optical characteristics of absorption and circular dichroism (CD) spectroscopy of an alpha-subunit of C-phycocyanin (C-PC) were investigated by using time dependent density functional theory (TDDFT) combined with the polarizable continuum model (PCM). When the protonation of alpha-84 phycocyanobilin (PCB) and its interaction with the protein moiety in C-PC have been taken into account, satisfactory assignment of the absorption and CD spectra of alpha-84 PCB can be achieved. The TDDFT-PCM calculations conclude that in the visible absorption region the main peak arises from the pi electron excitation of the pyrrole rings and the shoulder peak comes from the charge transfer from Asp87 (a nearby amino acid residue) to PCBH(+).     

Excitation energy-transfer processes between two trimers in C-phycocyanin hexamer from the cyanobacterium Anabaena variabilis. Investigation by group theory and time-resolved fluorescence spectroscopy

We have employed group theory and picosecond time-resolved fluorescence isotropy and anisotropy spectroscopy methods to explore the excitation transfers within an isolated C-phycocyanin (C-PC) hexamer (αβ)₆^PCL²⁷_RC, situated at the end of the rod proximal to the core of the pycobilisome (PBS) in the cyanobacterium Anabaena variabilis. The group-theory results imply that excitation energy transfer between two trimers occurs between the lowest exciton level of each trimer. The excitation energy-transfer process might occur at a rate of 10–20 ps, and it may be described by an exciton hopping-like Förster transfer mechanism. Dynamic components of 45–50 ps are assigned to the excitation transfer from β₁₅₅-PCB chromophores to the exciton states of dimers, which consist of two neighbouring monomers of the same trimer in an isolated C-PC hexamer.     

Understanding the electronic energy transfer pathways in the trimeric and hexameric aggregation state of cyanobacteria phycocyanin within the framework of Förster theory

In the present study, the electronic energy transfer pathways in trimeric and hexameric aggregation state of cyanobacteria C‐phycocyanin (C‐PC) were investigated in term of the Förster theory. The corresponding excited states and transition dipole moments of phycocyanobilins (PCBs) located into C‐PC were examined by model chemistry in gas phase at time‐dependent density functional theory (TDDFT), configuration interaction‐singles (CIS), and Zerner's intermediate neglect of differential overlap (ZINDO) levels, respectively. Then, the long‐range pigment‐protein interactions were approximately taken into account by using polarizable continuum model (PCM) at TDDFT level to estimate the influence of protein environment on the preceding calculated physical quantities. The influence of the short‐range interaction caused by aspartate residue nearby PCBs was examined as well. Only when the protonation of PCBs and its long‐ and short‐range interactions were properly taken into account, the calculated energy transfer rates (1/K) in the framework of Förster model at TDDFT/B3LYP/6‐31+G* level were in good agreement with the experimental results of C‐PC monomer and trimer. Furthermore, the present calculated results suggested that the energy transfer pathway in C‐PC monomer is predominant from β‐155 to β‐84 (1/K = 13.4 ps), however, from α‐84 of one monomer to β‐84 (1/K = 0.3–0.4 ps) in a neighbor monomer in C‐PC trimer. In C‐PC hexamer, an additional energy flow was predicted to be from β‐155 (or α‐84) in top trimer to adjacent β‐155 (or α‐84) (1/K = 0.5–2.7 ps) in bottom trimer. © 2013 Wiley Periodicals, Inc.     

COMPUTER SIMULATION OF EXCITON JUMPING STATISTICS AND ENERGY FLOW IN C-PHYCOCYANIN OF ALGAE Agmenellum quadruplicatum IN THE PRESENCE OF TRAPS

Abstract—Energy migration has been studied in C-phycocyanin (C-PC) rods with traps located in the terminal trimer disc, using the Monte Carlo method and the system of differential equations. It has been found that jump time statistics can be described by the function F = C(t/0>)exp(-t/ < t_o>), where C is the constant, t and < t₀ > are, respectively, the exciton jump time and its averaged value for chromophores of the corresponding spectral types (α 84 , β84 or β155). The values < t₀ > were calculated for the cases of C-PC monomers, trimers and higher associates.
The C-PC model, which consists of three hexamers with traps located in the β84 chromophores of the peripheral trimer, was examined. It was found that the total efficiency of excitation capturing, ø_tr, exceeds 90%, provided "local" quantum yield of energy trapping ø₀ > 10%. The ø₀ value influences both the excitation lifetime (τ) and the mean number of excitation jumps (N_iump) before its conversion. For the ø₀ = 100% and 10%, the corresponding lifetimes and numbers of jumps were calculated to be τ= 75 and 155 ps and N_jump= 105 and 222 jumps, respectively.
The dynamics of excitation redistribution along the C-PC rods and the fluorescence kinetics for various ø₀ values were calculated for C-PC chromophores excited by a +, and the correlation between these processes and ø ₀ , was disclosed. The transient processes of excitation redistribution were shown to proceed within a time period t < 30 ps.     

Energy transfer kinetics of phycoerythrocyanins (PECs) from the cyanobacteriumAnabaena variabilis (I)

The exritation energy transfer processes in monomeric phycoerythrocyanins (PEC) have been studied in detail using steady-state and time-resolved fluorescence spectra techniques as well as the deconvolution tech-nique of spectra. The results indicate that the energy transfer processes should take place between α₈₄,-PVB and β₈₄- or β₁₅₅-PCB chromophores. the time constants of energy transfer are 34.7 and 130 ps individually; the component with lifetime of 1.57 ns originates from the fluorescence lifetime of the terminal emitter of β₈₄- and /or β₁₅₅ -PCB chro-mophores; and the component with lifetime of 515 ps might be assigned to the energy transfer between two PCB chro-mophores of β subunit. Project supported by the National Natural Science Foundation of China.     

Computer simulation on the energy transfer processes in allophycocyanins

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Energy transfer from C-phycocyanin to phthalocyanine metal complex in reverse micelles

A new mimic system of photosynthetic apparatus was constructed from C-phycocyanin and phthalocyanine zinc. C-PC was solubilized in the reverse micelles of non ionic surfactant Tween-80, cosurfactant pentanol, and solvent cyclohexane, in which the overall concentration of surfactant was 20% (w/v) and the mass ratio of Tween-80 to pentanol was 4:1. When the molar ratio of water to Tween-80 (R_w)≥9.0, the characteristic properties of C-PC were maintained. When it was excited, the energy transfer from C-PC to phthalocyanine zinc took place. The energy transfer efficiency was only related with the concentration of phthalocyanine, but not that of C-PC. Furthermore, the energy transfer was roughly in keeping with Perrin formulation, which indicated that the energy transfer took place approximately through dipole-dipole interaction in rigid system. The radii of the quenching sphere were calculated from the experimental results. For example, when the concentration of phthalocyanine zinc was 2.10 × 10~(-4) mol/     

Determination of Fluorescence Polarization and Absorption Anisotropy in Molecular Complexes Having Threefold Rotational Symmetry

Abstract— The current work concerns investigation of the polarization properties of complex molecular ensembles exhibiting threefold (C₃) rotational symmetry, particularly with regard to the interplay between their structure and dynamics of internal energy transfer. We assume that the molecules or chromophores in such complexes possess strongly overlapped spectra both for absorption and fluorescence. Such trimeric structures are widely found in biological preparations, as for example the trimer of C-phycocyanin (C-PC). Higher order aggregates, e.g. hex-amers and three-hexamer rods, are also investigated and compared with the trimer case. The theory addresses both steady-state and 8-pulse excitation and establishes some links between them. Monochromophoric, bichro-mophoric and trichromophoric molecular complexes are individually examined. For steady-state excitation, analytical formulas are reported for the degree of fluorescence polarization and absorption anisotropy. It is shown that the polarization is dependent on the chromophore inclination relative to the symmetry axis, the relative efficiencies of absorption and fluorescence by chromophores of different spectral types, and the rates of energy equilibration. To assess the validity of the theory, it has been applied to C-PC aggregates. Here it was found that different C-PC aggregates provide practically identical polarization response. For S-pulse excitation we give analytical formulas for determination of the fluorescence depolarization, and also the depolarization associated with absorption recovery, both for a monochromophoric trimer and some particular cases of bichromophoric trimer. More complicated systems are analyzed by computer modeling. Thus it transpires that the initial polarization anisotropy r(t = 0) takes the value 0.4 for all considered aggregates; the long-time limit r(t →∞) has about the same value as is associated with steady-state excitation. We also show that with steady-state excitation the degree of fluorescence polarization is practically equal for various C₃ aggregates of C-PC, and that the major factor determining the polarization is the chromophore orientation relative to the symmetry axis.     

多变鱼腥藻藻胆蛋白共价复合物的合成及其分子内能量传递

利用双功能基偶联剂3-(2-吡啶联巯基)丙酸N-羟基琥珀酰亚胺酯(SPDP)合成了两个藻胆蛋白复合物,藻红蓝蛋白-变藻蓝蛋白复合物PEC-APC和藻红蓝蛋白-藻蓝蛋白复合物PEC-PC.利用吸收光谱和荧光光谱证明了藻胆蛋白构型与构象在反应后得到保持。通过荧光光谱观察到能量传递现象。计算出复合物PEC-APC的分子内能量传递效率约为90%.复合物PEC-PC中藻红蓝蛋白PEC的荧光寿命比PEC本身的寿命大大缩短,证明存在分子内能量传递。二硫苏糖醇(DTT)还原二硫桥键后能量传递被阻断。这进一步证明复合物合成成功及分子内能量传递。     

A study of the phase transition behaviours of cholesterol and saturated egg lecithin, and their interaction by differential scanning calorimetry.

The thermal behaviours of hydrogenated egg lecithin (PC) and cholesterol (C) in anhydrous form and in aqueous dispersions were studied by differential scanning calorimetry. The role of C in phase transitions of C-PC mixtures prepared by physical mixing or coprecipitating from chloroform has been examined. C underwent a phase transition at 34 degrees C and a second one at 76-78 degrees C which depended on the thermal history of the samples. C lowered the gel to liquid crystalline phase transition temperature (Tt) of the aqueous dispersions prepared from C-PC coprecipitates, broadened the endothermic peak at the Tt, and at 1:1 molar ratio the C-PC system did not undergo the phase transition. The C-PC interaction was observed below the Tt. In aqueous dispersions prepared from C-PC physical mixtures, C did not influence the phase transition and acted like an inert diluent. Pellets prepared from C-PC mixtures formed myelin bodies as a result of their erosion in 0.185 M borate buffer (pH 7.4) at below Tt, but the thermal behaviours of these myelin bodies were different for pellets prepared differently. Addition of bovine serum albumin (BSA) (10%, w/w) to the physical mixtures or coprecipitates of C-PC, or to PC alone did not show any effect on the thermal behaviours of their aqueous dispersions at the Tt.     

Clarifying and illustrating the electronic energy transfer pathways in trimeric and hexameric aggregation state of cyanobacteria allophycocyanin within the framework of Förster theory

Within the framework of the Förster theory, the electronic excitation energy transfer pathways in the cyanobacteria allophycocyanin (APC) trimer and hexamer were studied. The associated physical quantities (i.e., excitation energy, oscillator strength, and transition dipole moments) of the phycocyanobilins (PCBs) located in APC were calculated at time‐dependent density functional theory (TDDFT) level of theory. To estimate the influence of protein environment on the preceding calculated physical quantities, the long‐range interactions were approximately considered with the polarizable continuum model at the TDDFT level of theory, and the short‐range interaction caused by surrounding aspartate residue of PCBs were taken into account as well. The shortest energy transfer time calculated in the framework of the Förster model at TDDFT/B3LYP/6–31+G* level of theory are about 0.10 ps in the APC trimer and about 170 ps in the APC monomer, which are in qualitative agreement with the experimental finding that a very fast lifetime of 0.43–0.44 ps in APC trimers, whereas its monomers lacked any corresponding lifetime. These results suggest that the lifetime of 0.43–0.44 ps in the APC trimers determined by Sharkov et al. was most likely attributed to the energy transfer of α¹‐84 ? β³‐84 (0.23 ps), β¹‐84 ? α²‐84 (0.11 ps) or β²‐84 ? α³‐84 (0.10 ps). So far, no experimental or theoretical energy transfer rates between two APC trimmers were reported, our calculations predict that the predominate energy transfer pathway between APC trimers is likely to occur from α³‐84 in one trimer to α⁵‐84 in an adjacent trimer with a rate of 32.51 ps. © 2014 Wiley Periodicals, Inc.     

Energy transfer processes in phycobilisome model complex at 77 K

Ultra time-resoived huorescence spectra were used to study the energy transter processes and mechanism of complex PEC/PC/APC at 77 K, which was reconstructed with phycobiliproteins (PEC, PC and APC) of Anabaena variabilis, and has intact light-harvesting system and single terminal emitter. The energy transfer relationships between different chromophores especially between rod and core were also discussed based on fluorescence decay kinetic under different detected wavelengths. As a result, we got the possible energy transfer pathways and transfer time constants to be 29 ps between two PEC trimers, 12 ps between PEC and C-PC, 51 ps between rod and core.     

Primary and secondary relaxations in bis-5-hydroxypentylphthalate

Broadband dielectric spectroscopy was used to study the relaxation dynamics in bis-5-hydroxypentylphthalate (BHPP) under both isobaric and isothermal conditions. The relaxation dynamics exhibit complex behavior, arising from hydrogen bonding in the BHPP. At ambient pressure above the glass transition temperature T(g), the dielectric spectrum shows a broad structural relaxation peak with a prominent excess wing toward higher frequencies. As temperature is decreased below T(g), the excess wing transforms into two distinct peaks, both having Arrhenius behavior with activation energies equal to 58.8 and 32.6 kJmol for slower (beta) and faster (gamma) processes, respectively. Furthermore, the relaxation times for the beta process increase with increasing pressure, whereas the faster gamma relaxation is practically insensitive to pressure changes. Analysis of the properties of these secondary relaxations suggests that the beta peak can be identified as an intermolecular Johari-Goldstein (JG) process. However, its separation in frequency from the alpha relaxation, and both its activation energy and activation volume, differ substantially from values calculated from the breadth of the structural relaxation peak. Thus, the dynamics of BHPP appear to be an exception to the usual correlation between the respective properties of the structural and the JG secondary relaxations.     

Excitation energy transfer mechanism in C-phycocyanin hexamer

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FÖRSTER TRANSFER CALCULATIONS BASED ON CRYSTAL STRUCTURE DATA FROM Agmenellum quadruplicatum C-PHYCOCYANIN

Excitation energy transfer in C-phycocyanin is modeled using the Forster inductive resonance mechanism. Detailed calculations are carried out using coordinates and orientations of the chromophores derived from X-ray crystallographic studies of C-phycocyanin from two different species (Schirmer et al, J. Mol. Biol. 184 , 257–277 (1985) and ibid. , 188 , 651-677 (1986)). Spectral overlap integrals are estimated from absorption and fluorescence spectra of C-phycocyanin of Mastigocladus laminosus and its separated subunits. Calculations are carried out for the β-subunit, αβ-monomer, (αβ)₃-trimer and (αβ)₀-hexamer species with the following chromophore assignments: β155 = 's'(sensitizer), β84 ='f (fluorescer) and α84 ='m'(intermediate):]:. The calculations show that excitation transfer relaxation occurs to 3=98% within 200 ps in nearly every case; however, the rates increase as much as 10-fold for the higher aggregates. Comparison with experimental data on fluorescence decay and depolarization kinetics from the literature shows qualitative agreement with these calculations. We conclude that Forster transfer is sufficient to account for all of the observed fluorescence properties of C-phycocyanin in aggregation states up to the hexamer and in the absence of linker polypeptides.     

FLUORESCENCE AND CIRCULAR DICHROISM STUDIES ON THE PHYCOERYTHROCYANINS FROM THE CYANOBACTERIUM

Two phycoerythrocyanin (PEC) fractions have been obtained from the phycobilisomes of the cyanobac-terium Westiellopsis prolifica ARM 365. They have been characterized by absorption, fluorescence and circular dichroism spectroscopy. One of them is spectroscopically similar to a PEC trimer known from other organisms. Whereas efficient energy transfer from its violin (α-84) to the cyanin (β-84, 155) chromophores is efficient in the trimer (αβ it is impeded after dissociation to the monomer (α,β). A second fraction of PEC which we earlier termed PEC(X) (Maruthi Sai et al., Photochem. Photobiol. 55 ,119–124, 1992), exhibited the spectral properties similar to that of the α-subunit of PEC from Mastigocladus laminosus. With this highly photoactive fraction, the circular dichroism spectra of the violobilin chromophore in both photoreversible states were obtained.     

Classical differential cross sections and rotational energy transfer distributions for realistic ion—molecule potentials in the CPST limit

Classical differential cross sections, rotational energy transfer distributions at specified scattering angles and the first moments of the rotational energy transfer distributions are calculated for two ion—molecule systems: K⁺ ?CSCl and Li⁺ ?CO. The deflection angles and change in angular momentum are calculated using classical perturbation scattering theory (CPST). Monte Carlo techniques are then used to calculate the orientation averaged total differential cross sections and the rotational energy transfer distributions. Results are compared with experiment and agreement is found to be satisfactory. These two systems represent two extremes in anisotropy. For Li⁺ ?CO a strong classical rainbow peak is still seen in the differential cross section, while in the K⁺ ?CSCl system the rainbow is complete quenched. In the rotational energy transfer distributions of both systems, rotational rainbow peaks are clearly observed. The calculations also predict a leveling off of the first moment of the rotational energy transfer distribution at high angles, corresponding to the transition to repulsive scattering. On the basis of these results some comments are made on the nature of classical rainbow scattering for anisotropic systems.     

An improved method for the capillary gas chromatographic derivatization of polyhydroxylated steroids having tert-hydroxyl groups.

An improved method for a suitable derivatization of polyhydroxylated steroids having one or two tert-hydroxyl groups at the 5beta-, 14alpha-, 17alpha-, 24-, and/or 25-positions by capillary gas chromatography (CGC) is described. By using trimethylsilyl triflate as a silylating reagent and 2,6-lutidine as a catalyst, each of 5beta-cholane and 5alpha-cholestane series of steroids was successfully transformed into trimethylsilyl (TMS) ether derivatives to give a single CGC peak under mild conditions. More bulky triethylsilyl (TES) etherification of 14alpha- and 17alpha-hydroxy compounds provided multiple CGC peaks arising from completely- and/or incompletely-derivatized TES ethers accompanied by their thermal elimination products.     

INTRAMOLECULAR ENERGY TRANSFER IN NATIVE tRNA AT ROOM TEMPERATURE

Abstract— The odd nucleoside 4-thiouridine, which is present in position 8 of 70% of E. coli tRNAs, possesses unusual spectroscopic properties which make it suitable for intramolecular energy transfer studies. Both its luminescence excitation spectrum and the action spectrum (230–380 nm) for the 8–13 link formation have been established in native E. coli tRNA at room temperature. The spectra are identical and present a new unexpected peak around 260 nm. At this wavelength, they are amplified by a factor of nine as compared with the absorption and excitation spectra of the free nucleoside in aqueous solution.
The origin of this new peak is discussed and it is concluded that energy transfer does occur from the common nucleosides to the 4-thiouridine residue. Using the values of the nucleosides to 4-thiouridine distances inferred from the sets of atomic coordinates obtained on yeast tRNA^phe crystals, a satisfactory account of our finding can be obtained assuming singlet-singlet energy transfer. The efficiency of the mechanism is probably favoured by a good overlap between the emission spectra of the common nucleosides and the absorption spectrum of 4-thiouridine.