The guanidine hydrochloride-induced denaturation of CP43 and CP47 studied by terahertz time-domain spectroscopy

Terahertz time-domain spectroscopy (THz-TDS) is a new technique in studying the conformational state of a molecule in recent years. In this work, we reported the first use of THz-TDS to examine the denaturation of two photosynthesis membrane proteins: CP43 and CP47. THz-TDS was proven to be useful in discriminating the different conformational states of given proteins with similar structure and in monitoring the denaturation process of proteins. Upon treatment with guanidine hydrochloride (GuHCl), a 1.8 THz peak appeared for CP47 and free chlorophyll a (Chl a). This peak was deemed to originate from the interaction between Chl a and GuHCl molecules. The Chl a molecules in CP47 interacted with GuHCl more easily than those in CP43.     

The guanidine hydrochloride-induced denaturation of CP43 and CP47 studied by terahertz time-domain spectroscopy

Terahertz time-domain spectroscopy (THz-TDS) is a new technique in studying the conformational state of a molecule in recent years. In this work, we reported the first use of THz-TDS to examine the dena- turation of two photosynthesis membrane proteins: CP43 and CP47. THz-TDS was proven to be useful in discriminating the different conformational states of given proteins with similar structure and in monitoring the denaturation process of proteins. Upon treatment with guanidine hydrochloride (GuHCl), a 1.8 THz peak appeared for CP47 and free chlorophyll a (Chl a). This peak was deemed to originate from the interaction between Chl a and GuHCl molecules. The Chl a molecules in CP47 interacted with GuHCl more easily than those in CP43.     

Structural characteristics of extra-membrane domains and guanidine hydrochloride-induced denaturation of photosystem 2 core antenna complexes CP43 and CP47

The structural characteristics of the extra-membrane domains and guanidine hydrochloride-induced denaturation of photosystem 2 (PS2) core antenna complexes CP43 and CP47 were investigated using fluorescence emission and circular dichroism (CD) spectra. The extra-membrane domains of CP43 and CP47 possessed a certain degree of secondary and tertiary structure and not a complete random coil conformation. The tertiary structure and the chlorophyll (Chl) a microenvironment of CP47 were more sensitive to guanidine hydrochloride (GuHCl) than that of CP43. Changes in energy transfer from β-carotene to Chl a corresponded well to changes in the tertiary structure while their correlation with changes in the secondary structure was rather poor. Unlike most of water-soluble proteins, both CP43 and CP47 are partly resistant to denaturation induced by guanidine hydrochloride (GuHCl); the denaturation of CP43 or CP47 is not a two-state process. Those features most probably reflect their character as intrinsic membrane proteins.     

Thermal denaturation of CP43 studied by Fourier transform-infrared spectroscopy and terahertz time-domain spectroscopy

Thermal denaturation of CP43 was studied by Fourier transform-infrared (FT-IR) spectroscopy, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and terahertz time-domain spectroscopy (THz-TDS). Under heat treatment, the secondary structure of CP43 changed, and the main thermal transition occurred at 59 degrees C. During the process, CP43 aggregated at first, and then with increasing temperature degraded. The low-frequency collective vibrational modes of CP43 changed with increasing temperature and decreasing mass. THz-TDS is a new technique used to study the conformational state of a molecule, and it is the first use of this technique to study the photosynthesis membrane proteins in this paper. The results presented here demonstrate that THz-TDS has both advantages and disadvantages in monitoring the thermal denaturation of membrane proteins, which is important in applying THz-TDS technique to study of biomolecules.     

The structure and function of CP47 and CP43 in Photosystem II

This Minireview presents a summary of recent investigations examining the structure and functions of the Photosystem II chlorophyll-proteins CP47 and CP43, updating our previous review which appeared in 1990 (TM Bricker, Photosynth Res 24: 1–13). Since this time, numerous studies have clarified the roles of these chlorophyll-proteins within the photosystem. Biochemical, molecular and structural studies (electron and X-ray diffraction) have demonstrated the close association of these components with the photochemical reaction center of the photosystem and with the extrinsic oxygen evolution enhancer proteins. This revised version was published online in June 2006 with corrections to the Cover Date.     

光系统п核心天线复合物CP43和CP47结构与功能研究进展

ＣＰ４３和ＣＰ４７是构成光合生物内周天线的两个重要的色素蛋白复合物,在生物体内主要起着传递激发能的作用。最近,大量研究证明,它们在放氧等过程中也起着重要作用。因此,近年来人们借助各种先进的研究技术对它们的结构进行了探讨,以揭示它们行使不同生理功能的分子机理。分子生物学技术可以使人们在整体水平上研究蛋白复合物的结构与功能,因此是一个非常有用的研究手段。本文即对近年来人们通过分子生物手段,以蓝藻为转化     

Detection of living cervical cancer cells by transient terahertz spectroscopy

The photonic energy of terahertz wave is in the same order of magnitude as the rotational and vibrational energy levels of organic and biological macromolecules, so it has unique advantages in detecting cells and biological macromolecules. However, in the life environment, the dynamic time scale of cell-environment interaction and structural conformation change of biological macromolecules are within picosecond to millisecond, and water has strong absorption to terahertz wave, which has become the bottleneck problem for the detection of cells and biological macromolecules by terahertz technology. In this article, we developed a set of terahertz single measurement system based on the tilt wave front of grating pulse technique. The system was employed for the terahertz detection of trace living cervical cancer cells. We achieved transient detection of the terahertz pulse time-domain waveform of the living HeLa cells. The characteristic absorption peaks were identified by Lambert-Beer law, respectively, at 0.49, 0.71, 1.04, 1.07, 1.26 and 1.37 THz. The absorbance is proportional to the cell concentration.     

Probing the collective vibrational dynamics of a protein in liquid water by terahertz absorption spectroscopy

Biological polymers are expected to exhibit functionally relevant, global, and subglobal collective modes in the terahertz (THz) frequency range (i.e., picosecond timescale). In an effort to monitor these collective motions, we have experimentally determined the absorption spectrum of solvated bovine serum albumin (BSA) from 0.3 to 3.72 THz (10-124 cm(-1)). We successfully extract the terahertz molar absorption of the solvated BSA from the much stronger attenuation of water and observe in the solvated protein a dense, overlapping spectrum of vibrational modes that increases monotonically with increasing frequency. We see no evidence of distinct, strong, spectral features, suggesting that no specific collective vibrations dominate the protein's spectrum of motions, consistent with the predictions of molecular dynamics simulations and normal mode analyses of a range of small proteins. The shape of the observed spectrum resembles the ideal quadratic spectral density expected for a disordered ionic solid, indicating that the terahertz normal mode density of the solvated BSA may be modeled, to first order, as that of a three-dimensional elastic nanoparticle with an aperiodic charge distribution. Nevertheless, there are important detailed departures from that of a disordered inorganic solid or the normal mode densities predicted for several smaller proteins. These departures are presumably the spectral features arising from the unique molecular details of the solvated BSA. The techniques used here and measurements have the potential to experimentally confront theoretical calculations on a frequency scale that is important for macromolecular motions in a biologically relevant water environment.     

Rapid and label‐free detection and assessment of bacteria by terahertz time‐domain spectroscopy

Here we demonstrated the potential and applicability of terahertz (THz) spectroscopy to detect four commonly found bacteria in the infectious diseases. Besides the different spectral characteristics between bacterial species, THz absorption differences for living bacteria, dead bacteria and bacterial powder of the same species were also investigated. Our results revealed that small differences in water contents between bacterial cells account for distinct discrepancies of the absorption coefficients, which can be used for bacterial species identification. Furthermore, living and dead bacteria showed different absorption coefficients as a result of their different hydration levels, suggesting that THz spectroscopy can be used to rapidly assess the living state of bacteria under test. Our results clearly demonstrated the ability of THz spectroscopy for time‐saving and label‐free detection of bacteria with minimal sample preparation, potentially to be utilized for point‐of‐care tests in the near future.

Schematic representation of bacterial detection by THz spectroscopy. Different bacteria have distinctive absorption coefficients as a result of their different water contents.     

The 38 kDa chlorophyll a/b protein of the prokaryote Prochlorothrix hollandica is encoded by a divergent pcb gene

The chlorophyll (Chl) a/b proteins of the photosynthetic prokaryotes appear to have evolved by gene duplication and divergence of the core Chl a antenna family, which also includes CP43 and CP47 and the iron-stress induced Chl a-binding IsiA proteins. We show here that Prochlorothrix hollandica has a cluster of three pcb (prochlorophyte chlorophyll b) genes which are co-transcribed. The major antenna polypeptides of 32 and 38 kDa are encoded by pcbA and pcbC respectively. The pcbC gene is significantly divergent from the other two and may have originated by a gene duplication independent of the one that led to isiA and the other prochlorophyte pcb genes. The distant relatedness of the three prochlorophyte genera implies that not only the ability to make Chl b and use it for light-harvesting arose independently in the three lineages, but also that the pcb genes may have arisen as the result of independent gene duplications in each lineage.     

Observation of terahertz vibrations in Pyrococcus furiosus rubredoxin via impulsive coherent vibrational spectroscopy and nuclear resonance vibrational spectroscopy--interpretation by molecular mechanics

We have used impulsive coherent vibrational spectroscopy (ICVS) to study the Fe(S-Cys)(4) site in oxidized rubredoxin (Rd) from Pyrococcus furiosus (Pf). In this experiment, a 15 fs visible laser pulse is used to coherently pump the sample to an excited electronic state, and a second <10 fs pulse is used to probe the change in transmission as a function of the time delay. PfRd was observed to relax to the ground state by a single exponential decay with time constants of approximately 255-275 fs. Superimposed on this relaxation are oscillations caused by coherent excitation of vibrational modes in both excited and ground electronic states. Fourier transformation reveals the frequencies of these modes. The strongest ICV mode with 570 nm excitation is the symmetric Fe-S stretching mode near 310 cm(-1), compared to 313 cm(-1) in the low temperature resonance Raman. If the rubredoxin is pumped at 520 nm, a set of strong bands occurs between 20 and 110 cm(-1). Finally, there is a mode at approximately 500 cm(-1) which is similar to features near 508 cm(-1) in blue Cu proteins that have been attributed to excited state vibrations. Normal mode analysis using 488 protein atoms and 558 waters gave calculated spectra that are in good agreement with previous nuclear resonance vibrational spectra (NRVS) results. The lowest frequency normal modes are identified as collective motions of the entire protein or large segments of polypeptide. Motion in these modes may affect the polar environment of the redox site and thus tune the electron transfer functions in rubredoxins.     

Debranched cassava starch crystallinity determination by Raman spectroscopy: Correlation of features in Raman spectra with X-ray diffraction and C CP/MAS NMR spectroscopy

Because starch crystallinity influences the physical, mechanical, and technological aspects of numerous starch-based products during production and storage, rapid techniques for its assessment are vital. Samples of different levels of crystallinity were obtained by debranching gelatinized cassava starch, followed by subjection to various hydrothermal treatments. The recrystallized products were further subjected to partial hydrolysis with a mixture of α-amylase and glucoamylase prior to freeze-drying. Crystallinities were determined using X-ray diffraction (XRD) and ¹³C CP/MAS NMR spectroscopy, and correlated with FT-Raman spectra features. XRD crystallinities ranged between 0 and 58%, and agreed with crystalline-phase fractions (R² = 0.99) derived from the respective ¹³C CP/MAS NMR spectra. A strong linear correlation was found between crystallinities and integrated areas of the skeletal mode Raman band at 480 cm⁻¹ (R² = 0.99). With appropriate calibration, FT-Raman spectroscopy is a promising tool for rapid determination of starch crystallinity.     

The role of CP 47 in the evolution of oxygen and the binding of the extrinsic 33-kDa protein to the core complex of Photosystem II as determined by limited proteolysis

In order to identify the domain within Photosystem II complexes that functions in the evolution of oxygen, we performed limited proteolysis with lysylendopeptidase of the core complex of Photosystem II which had been depleted of the extrinsic 33-kDa protein (Mn-stabilizing protein). The cleavage sites were estimated from the amino-terminal sequences of the degradation fragments, their apparent molecular masses and amino-acid compositions. Under certain conditions, the D2 protein was cleaved at Lys13; and a chlorophyll a-binding protein, CP 47, was cleaved at Lys227 and Lys389. Another chlorophyll a-binding protein, CP 43, was degraded more rapidly than CP 47. The oxygen-evolving activity and the capacity for rebinding of the 33-kDa protein to the core complex of Photosystem II decreased in parallel, with kinetics very similar to those of the cleavage of CP 47 at Lys389. These observations strongly suggest that the hydrophilic domain around Lys389 of CP 47, which are located on the lumenal side, is important in the binding of the 33-kDa protein and in maintaining the oxygen-evolving activity of the Photosystem II complex.Abbreviations CP 47 and CP 43- intrinsic chlorophyll a-binding proteins with apparent molecular masses of 47 and 43 kDa, respectively - PBQ- phenyl-p-benzoquinone - TLCK- N--p-tosyl-L-lysine chloromethyl ketone     

The effect of calcium and vitamin D supplementation on osteoporotic rabbit bones studied by vibrational spectroscopy

Fourier transform infrared spectroscopy is utilized to examine the effects of increased calcium, vitamin D, and combined calcium-vitamin D supplementation on osteoporotic rabbit bones with induced inflammation. The study includes different bone sites (femur, tibia, humerus, vertebral rib) in an effort to explore possible differences among the sites. We evaluate the following parameters: mineral-to-matrix ratio, carbonate content, and non-apatitic species (labile acid phosphate and labile carbonate) contribution to bone mineral. Results show that a relatively high dose of calcium or calcium with vitamin D supplementation increases the bone mineralization index significantly. On the other hand, vitamin D alone is not as effective in promoting mineralization even with high intake. Mature B-type apatite was detected for the group with calcium supplementation similar to that of aged bone. High vitamin D intake led to increased labile species concentration revealing bone formation. This is directly associated with the suppression of pro-inflammatory cytokines linked to induced inflammation. The latter is known to adversely alter bone metabolism, contributing to the aetiopathogenesis of osteoporosis. Thus, a high intake of vitamin D under inflammation-induced osteoporosis does not promote mineralization but suppresses bone resorption and restores metabolic balance.     

The globule diameter and some electron and conformational properties of the flavoprotein fragment of mitochondrial NADH dehydrogenase studied by fluorescence spectroscopy

The globule dimensions and some electron and conformational properties of the flavoprotein (peripheral) fragment of the mitochondrial NADH dehydrogenase were determined by the time-resolved, phase-modulating, and polarization fluorescence spectroscopies, as well as correlated confocal microscopy. The rotational and the diffusion (translocation) diameters of the protein fragment were shown to be no less than 44 and ∼72 ?, respectively. The diameter of protomitochondrial particles from the bovine heart, which were used for the isolation of the fraction of peripheral fragments, was no less than 2300 ?. The fluorescence from tryptophan and flavin fluorophores in the fragment is strongly quenched by iron of the iron-sulfur clusters, which suggests that a strong electron-vibrational interaction of iron with Trp residues and flavin takes place. An overlapping of the electron clouds of iron-sulfur clusters, Trp residues, and flavin is likely to facilitate the electron transfer through the protein. The heat inactivation of the enzyme was accompanied by neither its substantial conformational changes, nor a considerable release of iron ions from the clusters located near the Trp residues.     

Elucidation of structure-function relationships in photosynthetic light-harvesting antenna complexes by non-linear polarization spectroscopy in the frequency domain (NLPF)

Photosynthetically active pigments are usually organized into pigment-protein complexes. These include light-harvesting antenna complexes (LHCs) and reaction centers. Site energies of the bound pigments are determined by interactions with their environment, i.e., by pigment-protein as well as pigment-pigment interactions. Thus, resolution of spectral substructures of the pigment-protein complexes may provide valuable insight into structure-function relationships. By means of conventional (linear) and time-resolved spectroscopic techniques, however, it is often difficult to resolve the spectral substructures of complex pigment-protein assemblies. Nonlinear polarization spectroscopy in the frequency domain (NLPF) is shown to be a valuable technique in this regard. Based on initial experimental work with purple bacterial antenna complexes as well as model systems NLPF has been extended to analyse the substructure(s) of very complex spectra, including analyses of interactions between chlorophylls and "optically dark" states of carotenoids in LHCs. The paper reviews previous work and outlines perspectives regarding the application of NLPF spectroscopy to disentangle structure-function relationships in pigment-protein complexes.     

The induction of CP43′ by iron-stress in Synechococcus sp. PCC 7942 is associated with carotenoid accumulation and enhanced fatty acid unsaturation

Comparative lipid analysis demonstrated reduced amount of PG (50%) and lower ratio of MGDG/DGDG in iron-stressed Synechococcus sp. PCC 7942 cells compared to cells grown under iron sufficient conditions. In parallel, the monoenoic (C:1) fatty acids in MGDG, DGDG and PG increased from 46.8%, 43.7% and 45.6%, respectively in control cells to 51.6%, 48.8% and 48.7%, respectively in iron-stressed cells. This suggests increased membrane dynamics, which may facilitate the diffusion of PQ and keep the PQ pool in relatively more oxidized state in iron-stressed compared to control cells. This was confirmed by chlorophyll fluorescence and thermoluminescence measurements. Analysis of carotenoid composition demonstrated that the induction of isiA (CP43′) protein in response to iron stress is accompanied by significant increase of the relative abundance of all carotenoids. The quantity of carotenoids calculated on a Chl basis increased differentially with nostoxanthin, cryptoxanthin, zeaxanthin and β-carotene showing 2.6-, 3.1-, 1.9- and 1.9-fold increases, respectively, while the relative amount of caloxanthin was increased only by 30%. HPLC analyses of the pigment composition of Chl-protein complexes separated by non-denaturating SDS-PAGE demonstrated even higher relative carotenoids content, especially of cryptoxanthin, in trimer and monomer PSI Chl-protein complexes co-migrating with CP43′ from iron-stressed cells than in PSI complexes from control cells where CP43′ is not present. This implies a carotenoid-binding role for the CP43′ protein which supports our previous suggestion for effective energy quenching and photoprotective role of CP43′ protein in cyanobacteria under iron stress.     

The D1-173 amino acid is a structural determinant of the critical interaction between D1-Tyr161 (TyrZ) and D1-His190 in Photosystem II

The main cofactors of Photosystem II (PSII) are borne by the D1 and D2 subunits. In the thermophilic cyanobacterium Thermosynechococcus elongatus, three psbA genes encoding D1 are found in the genome. Among the 344 residues constituting the mature form of D1, there are 21 substitutions between PsbA1 and PsbA3, 31 between PsbA1 and PsbA2, and 27 between PsbA2 and PsbA3. In a previous study (Sugiura et al., J. Biol. Chem. 287 (2012), 13336-13347) we found that the oxidation kinetics and spectroscopic properties of Tyr_Z were altered in PsbA2-PSII when compared to PsbA(1/3)-PSII. The comparison of the different amino acid sequences identified the residues Cys144 and Pro173 found in PsbA1 and PsbA3, as being substituted in PsbA2 by Pro144 and Met173, and thus possible candidates accounting for the changes in the geometry and/or the environment of the Tyr_Z/His190 phenol/imidizol motif. Indeed, these amino acids are located upstream of the α-helix bearing Tyr_Z and between the two α-helices bearing Tyr_Z and its hydrogen-bonded partner, D1/His190. Here, site-directed mutants of PSII, PsbA3/Pro173Met and PsbA2/Met173Pro, were analyzed using X- and W-band EPR and UV-visible time-resolved absorption spectroscopy. The Pro173Met substitution in PsbA2-PSII versus PsbA3-PSII is shown to be the main structural determinant of the previously described functional differences between PsbA2-PSII and PsbA3-PSII. In PsbA2-PSII and PsbA3/Pro173Met-PSII, we found that the oxidation of Tyr_Z by P₆₈₀^+● was specifically slowed during the transition between S-states associated with proton release. We thus propose that the increase of the electrostatic charge of the Mn₄CaO₅ cluster in the S₂ and S₃ states could weaken the strength of the H-bond interaction between Tyr_Z^● and D1/His190 in PsbA2 versus PsbA3 and/or induce structural modification(s) of the water molecules network around Tyr_Z.