Computer simulation on the energy transfer processes in allophycocyanins

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THE STRUCTURE OF PHYCOBILISOMES IN MUTANTS OF Synechococcus sp. STRAIN PCC 7942 DEVOID OF SPECIFIC LINKER POLYPEPTIDES

Abstract— The effect of elimination of the 30, 33 and 9 kDa phycobilisome rod-linker polypeptides on rod length was examined by electron microscopy of phycobilisomes isolated from wild-type Synechococcus sp. strain PCC 7942 and from genetically engineered mutants with lesions in the genes encoding the rod-linker polypeptides. The maximum rod length in the absence of the 33 kDa linker polypeptide was two phycocyanin hexamers, whereas rods with up to five hexamers were found in the mutant strain lacking the 30 kDa linker polypeptide. Elimination of the 9 kDa linker polypeptide did not have a significant effect on rod length. Finally, mutants lacking either the 30 or 33 kDa rod-associated linker polypeptides had an increased number of rods that terminated with a phycocyanin trimer. These observations are discussed with respect to the role of the linker polypeptides in the biosynthesis of the rod substructure.     

UVB-induced photodamage to phycobilisomes of Synechococcus sp. PCC 7942

The effect of UVB irradiation on the phycobilisomes (PBSs) of Synechococcus sp. PCC 7942 cells was studied. The sucrose density-gradient-isolated PBSs from in vivo UVB-treated (280–320 nm) cells showed a strong decrease in β-phycocyanin (βPC) and -phycocyanin (PC) polypeptides. In addition to a decrease in the linker polypeptides LCM 75 (linker connecting the core to the thylakoid membranes), LR 33 (linker in the rod structure), LRC 31.5 (linker connecting the rod to the core) and LRC 29. In vitro UVB treatment of gradient-isolated intact PBSs for 1 h had no effect on any of the constituent polypeptides, and only after 2 h was a degradation of LCM 75 and LR 33 and a decrease in βPC evident. Further investigation of phycobiliproteins (4 h of UVB irradiation) using polyclonal antibody directed against purified whole PBSs revealed that, in vivo, there was a gradual decline in the levels of LCM 75, LR 33, LRC 31.5, LRC 29, βPC and PC.     

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.     

Studies of the Energy Transfer among Allophycocyanin from Phycobilisomes of Polysiphonia urceolata by Time-Resolved Fluorescence Isotropic and Anisotropic Spectroscopy

Abstract— The excitation energy transfer processes in the allophycocyanin (APC) monomer and trimer from phycobilisomes of Polysiphonia urceolata were studied using picosecond time-resolved fluorescence isotropic and anisotropic spectroscopy. Based on our experimental results, conclusions could be drawn as follows: (1) After the processes of exciton localization are finished, the localized excitation energy on any chromophore can be transferred to the other chromophores due to the weak couplings between them, and the processes among three p₈₄-phycocyaninbilin (PCB) chromophores in the center of the ring shape of the APC trimer are more important than those of between a₈₄- and p₈₄-PCB chromophores in the same monomer. (2) The decay time constants of 95 ± 5 ps and 40 ± 5 ps components, observed by us in this work, were assigned to the excitation energy transfer or redistribution between α₈₄- and β₈₄-PCB chromophores in the same monomer of the APC trimer and among three β₈₄-PCB chromophores in the center of the ring shape of the APC trimer, respectively. Specifically, the assignment of the decay constants for the 40 ± 5 ps component was different from those of previous results. (3) Based on the model of Debreczeny, and using the fluorescence residual anisotropy r(∞) with a probing wavelength of 650 nm, the angles between the C₃ symmetry axis and transition dipoles of α₈₄- and -PCB chromophores were found to be φ_a84= 67° and φ_β84= 148°, respectively, which are in agreement with the prediction of the X-ray crystal structure of APC. (4) The results show that anisotropy decays, observed with the APC trimer, did exhibit a strongly probing wavelength dependence that did not show up in the monomer.     

Molecular mechanisms for interaction of glycine betaine with supra-molecular phycobiliprotein complexes

Glycine betaine (GB) is a biologically important small molecule protecting cells, proteins and enzymes in vivo and in vitro under environmental stresses. Recently, it was found that GB could also relax the structure and inactivate the function of phycobiliproteins and phycobilisome (PBS), a kind of supra-molecular complexes, in cyanobacterial cells. The molecular mechanisms for the opposite phenomena are quite ambiguous. Taking PBS and a trimeric or monomeric C-phycocyanin (C-PC) as models, the molecular mechanism for the interaction of GB with supra-molecular complexes or nuclear proteins was investigated. The energetic decoupling of PBS components induced by GB suggests that the PBS core-membrane linking polypeptide was the most sensitive site while the rod-core linker was the next. Biochemistry analysis proves that PBS structure was loosened but not dissociated into the components. On the basis of the results and structure knowledge, it was proposed that GB screened the electrostatic attraction of the opposite charges on a linker and a protein leading to a much looser structure. It was observed that GB induced a spectral blue shift for trimeric C-PC but a red shift for a monomeric C-PC (a nuclear protein), which were ascribed to GB’s screening of the electrostatic attraction of a linker to a protein and strengthening of the hydrophobic interaction between C-PC monomers. The trimers and monomers’ forming of the same products under high concentration of GB was ascribed to a compromise of the opposite interaction forces.     

甜菜碱与藻胆蛋白超分子复合体相互作用的分子机制

甘氨酸甜菜碱是具有重要生物学意义的生物小分子,它可以保护细胞、蛋白和酶的结构功能完整性,也会导致蛋白超分子结构松散、功能钝化,这两种相反作用的分子机制尚不清楚．本文以超分子藻胆蛋白和藻胆体为模型,证明甜菜碱导致超分子藻胆体结构松散、各组份能量失耦合,最敏感的作用位点是核．膜连接多肽,其次是杆一核连接多肽．C－藻蓝蛋白三聚体与单体对甜菜碱的相应完全不同,前者结构松散而后者相对聚集．甜菜碱屏蔽静电吸引力导致结构松散但强化基元蛋白之间的疏水作用力是两种相反现象的本质,甜菜碱最终导致C－藻蓝蛋白三聚体和单体相同的光谱特征是两种机制的“折中”．     

Spectroscopic investigation on the energy transfer process in photosynthetic apparatus of cyanobacteria

In this work, we employ cyanobacteria, Spirulina platensis, and separate their photosynthetic apparatus, phycobilisome (PBS), thylakoid membrane and phycobilisome-thylakoid membrane complex. The steady state absorption spectra, fluorescence spectra and corresponding deconvoluted spectra and picosecond time-resolved spectra are used to investigate the energy transfer process in phycobilisome-thylakoid membrane complex. The results on steady state spectra show chlorophylls of the photosystem II are able to transfer excitation energy to phycobilisome with Chla molecules selectively excited. The decomposition of the steady state spectra further suggest the uphill energy transfer originate from chlorophylls of photosystem II to cores of phycobilisome, while rods and cores of phycobilisome cannot receive energy from the chlorophylls of photosystem I. The time constant for the back energy transfer process is 18 ps.     

ORIGIN OF THE RED SHIFTED ABSORPTION IN PHYCOCYANIN 632 FROM Mastigocladus laminosus

A phycocyanin (PC) with γ_max= 632 nm (PC632) was isolated from extracts of the cyanobacterium Mastigocladus laminosus. The complex contained three polypeptides migrating in SDS-PAGE around 22 kDa. The N-termini of the three polypeptides are identical. They are homologous to rod-core linker polypeptides from this and another cyanobacterium and are identical to one of them. Reconstitution of PC (γ_max=614–620 nm) with the 22 kDa polypeptide produced again the red-shifted PC632. Phycobilisomes isolated at pH 6 or 7 contain, if any, only traces of 22 kDa polypeptides. Origin and functions of the polypeptides are discussed, they are most likely proteolytic fragments of allophycocyanin-PC rod-core linkers that contain the PC-binding domain.     

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.     

藻胆体核心复合物结构与功能的研究(Ⅱ)──4种变藻蓝蛋白复合物发色团相互作用机制

从螺旋藻藻胆体中分离出4种不同结构和光谱形式的变藻蓝蛋白复合物APⅠ、APⅡ、APⅢ和APB, 利用吸收光谱、荧光光谱比较了三聚体和单体的光谱特性, 通过对吸收光谱的光谱解曾以及各组分的归属, 研究了变藻蓝蛋白复合物内各色团间相互作用的性质和在能量传递中的功能.结果表明, 复合物内色团间的作用关系可以用Forster偶极-隅极作用机制来解释, 由于连接蛋白和同源亚基的存在影响其结构的对称性, 进而影响各色团间相互作用的形式和性质.     

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.     

Allophycocyanin complexes from the phycobilisome of a thermophilic blue-green alga Myxosarcina concinna Printz

The core polypeptide components of the intact phycobilisomes (PBSs) prepared by the sucrose gradients in 0.9 M phosphate buffer from a thermophilic cyanobacterium Myxosarcina concinna Printz were investigated. Three allophycocyanins, designated AP1, AP2, and AP3, of the PBS cores were successfully prepared by using the gradient polyacrylamide gel electrophoresis (PAGE) performed in neutral, instead of alkaline, buffer system. The spectral properties of AP2 and AP3 demonstrated that they both had fluorescence emission maxima at 684/685 nm at 77 K, which was identical to those of the intact PBSs, and showed the absorption of allophycocyanin B (AP-B) subunit. Sodium dodecyl sulfate-PAGE revealed that the three biliprotein complexes were all composed of heterogeneous subunits and two more linker polypeptides (Ls), AP1 alpha(22.3)alpha(19.5)beta(17.4)beta(15.7)L(13.8)L(11.3)L(9.5), AP2 alpha(22.3)alpha(19.5)beta(17.4)beta(15.7)beta(15.1)L(11.3)L(9.5), and AP3 alpha(22.3)alpha(19.5)beta(17.4)beta(15.7)beta(15.1)L(11.3)L(9.5)L(8.3). Compared with the characteristics of AP1, beta(15.1), which belonged to the beta subunit group, was the AP-B subunit of AP2 and AP3. Because AP2 was only obtained together with the PBS by the aid of 2% (v/v) Triton X-100, but not AP3, it was closely related to anchoring the PBS core on thylakoid membranes though the polypeptide analysis showed that AP2 had no core-membrane linker (LCM). Aggregates of the three AP biliproteins were proposed based on the present results, and their functions in the PBS core construction and the energy transfer to PS II and PS I were discussed.     

RESONANCE-ENHANCED CARS SPECTROSCOPY OF BILIPROTEINS. INFLUENCE OF AGGREGATION and LINKER PROTEINS ON CHROMOPHORE STRUCTURE IN ALLOPHYCOCYANIN (Mastigocladus laminosus)

Abstract— Resonance-enhanced coherent anti-Stokes Raman spectra (CARS) are reported for monomers and for trimers with and without linker proteins of allophycocyanin isolated from Mastigocladus laminosus. The CARS spectrum of the monomer is independent of the presence of linker proteins and is very similar to that of phycocyanin monomers indicating that the equivalent chromophores exhibit like structures in both biliproteins. Large differences are, however, observed between the spectra of phycocyanin trimers and those of allophycocyanin trimers with or without linker proteins (L_c^8,9). The observed differences between monomer and trimer spectra are consistent with a change of the α-chromophore-protein arrangement upon aggregation without linker. If linker proteins are present in the trimer, then additional geometry changes of the β-chromophores are induced; these could relate to a transition from the 15Z- anti to 15Z- syn conformation.     

A semiempirical approach to the intra-phycocyanin and inter-phycocyanin fluorescence resonance energy-transfer pathways in phycobilisomes

A semiempirical methodology to model the intra-phycocyanin and inter-phycocyanin fluorescence resonance energy-transfer (FRET) pathways in the rods of the phycobilisomes (PBSs) from Fremyella diplosiphon is presented. Using the F?rster formulation of FRET and combining experimental data and PM3 calculation of the dipole moments of the aromatic portions of the chromophores, transfer constants between pairs of chromophores in the phycocyanin (PC) structure were obtained. Protein docking of two PC hexamers was used to predict the optimal distance and axial rotation angle for the staked PCs in the PBSs' rods. Using the distance obtained by the docking process, transfer constants between pairs of chromophores belonging to different PC hexamers were calculated as a function of the angle of rotation. We show that six preferential FRET pathways within the PC hexameric ring and 15 pathways between hexamers exist, with transfer constants consistent with experimental results. Protein docking predicted the quaternary structure for PCs in rods with inter-phycocyanin distance of 55.6 A and rotation angle of 20.5 degrees . The inter-phycocyanin FRET constant between chromophores at positions beta(155) is maximized at the rotation angle predicted by docking revealing the crucial role of this specific inter-phycocyanin channel in defining the complete set of FRET pathways in the system.     

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.     

Self-assembly of oligothiophene chromophores by m-calix[3]amide scaffold

m-Calix[3]amides carrying the bithiophene chromophore (BTC3A) and terthiophene chromophore (TTC3A) were synthesized by the cyclic trimerization of m-aminobenzoic acid esters for the purpose of the control and understanding of the self-assembly of oligothiophene chromophores. Polymers and model compounds were also prepared for comparison. From the (1)H NMR experiments, cyclic trimer BTC3A showed the syn/anti equilibrium in solution, and the syn/anti conformer ratio (76/24 in CDCl(3)) was influenced by the solvent character. Namely, the population of the syn conformer was lowest (70%) in THF-d(8) and was highest (86%) in CDCl(3)/CD(3)OD (1/1 in volume). On the other hand, the population of the syn conformer of cyclic trimer TTC3A was high (84%) even in CDCl(3). In a CHCl(3) solution of cyclic trimer BTC3A, the absorption maximum (342 nm) blue-shifted and the emission maximum (448 nm) red-shifted compared with those of polymer BTPA and model compound BTM. The solvent character also had an impact on the optical properties of cyclic trimer BTC3A. The red-shifted emission maximum (481 nm) of cyclic trimer BTC3A in CH(3)OH indicated the interaction between three bithiophene chromophores. The emission maxima of cyclic trimer TTC3A (486 nm) demonstrated a small red-shift from model compound TTM (477 nm), and no solvent dependency was observed, unlike cyclic trimer BTC3A.     

Localized emitting state and energy transfer properties of quadrupolar chromophores and (multi)branched derivatives

In order to better understand the nature of intramolecular charge and energy transfer in multibranched molecules, we have synthesized and studied the photophysical properties of a monomer quadrupolar chromophore with donor-acceptor-donor (D-A-D) electronic push-pull structure, together with its V-shaped dimer and star-shaped trimers. The comparison of steady-state absorption spectra and fluorescence excitation anisotropy spectra of these chromophores show evidence of weak interaction (such as charge and energy transfer) among the branches. Moreover, similar fluorescence and solvation behavior of monomer and branched chromophores (dimer and trimer) implies that the interaction among the branches is not strong enough to make a significant distinction between these molecules, due to the weak interaction and intrinsic structural disorder in branched molecules. Furthermore, the interaction between the branches can be enhanced by inserting π bridge spacers (-C═C- or -C≡C-) between the core donor and the acceptor. This improvement leads to a remarkable enhancement of two-photon cross-sections, indicating that the interbranch interaction results in the amplification of transition dipole moments between ground states and excited states. The interpretations of the observed photophysical properties are further supported by theoretical investigation, which reveal that the changes of the transition dipole moments of the branched quadrupolar chromophores play a critical role in observed the two-photon absorption (2PA) cross-section for an intramolecular charge transfer (ICT) state interaction in the multibranched quadrupolar chromophores.     

两种螺旋藻核复合物结构特性的研究

从螺旋藻藻胆体中分离出两种复合物:核复合物(APC)和杆-核复合物(APCR),通过吸收光谱及其二阶导数光谱、荧光光谱研究了二者的结构和光谱特性,讨论了在这两种沉降系数分别为36S和16S的超分子复合物内几种连接多肽:L^29.5,L_C^8.9和LCM对复合物结构和功能的影响。     

Molecular aniline clusters. II. The low-lying electronic excited states

The lowest electronically excited states of the aniline dimer and trimer related to the lowest π(?)←π transition of the monomer are investigated by applying time-dependent coupled cluster theory, primarily at the level of the (spin-component-scaled) CC2 model. Minimum energy structures in the vicinity of the Franck-Condon points were determined on the individual potential energy surfaces. For the dimer we find an excimer and a head-to-tail configuration (with the monomers substantially displaced relative to the ground state minimum) for the lowest (dark) and second lowest (bright) states, respectively. The excitation is delocalized on both chromophores for both of these states. For the trimer three distinct minima with quite different hydrogen-bonding arrangements are found for the three lowest states. In strong contrast to the dimer the excitation here is clearly localized on the individual aniline chromophores for each of these three states. One of the three geometries is rather similar to the ground state minimum, while the two others are rather different and thus have presumably quite small Franck-Condon factors. It can be expected that only the electronic origin of the first conformer can eventually be detected in the absorption spectrum of the trimer, provided that it is separated by high-enough barriers from other, energetically lower configurations.