Molecular replacement studies on crystal structure of allophycocyanin from red algae Porphyra yezoensis

Using the crystal structure of allophycocyanin from cyanobacterium Spirulina platensis (APC-SP) as a search model,the crystal structure of allophycocyanin from red algae Porphyra yezoensis (APC-PY) has been studied by molecular replacement methods.The APC-PY crystals (Form 3) belong to the space group of R32,cell dimensions a=b= 10.53 nm,c=18.94 nm,α= β= 90°,γ=120°;there is one αβ monomer in each crystallographic asymmetric unit in the cell.The translation function search gave a unique peak with a correlation coefficient (Cc) of 67.0% and an R-factor of 36.1% for reflection data from 1.0 to 0.4 nm.Using the results by molecular replacement,the initial model of APC-PY was built,and the coincidence of the chromophore in APC-PY initial model with its 2Fo-Fc OMIT map further confirms the results by molecular replacement.     

Molecular replacement study on form-B monoclinic crystal of insulin

The form-B monodinic insulin crystal was obtained from the sodium citrate buffer with 1% zinc chloride, keeping phenolic content between 0.76% and 1.25%. Its space group is P21, cell constants are: a = 4.924nm, b=6.094nm, c=4.818nm, β=95.8°. There are 6 insulin molecules which form a hexamer. The initial phase was obtained by using rotation function program of X-PLOR program package and molecular packing program of our laboratory. The molecular model was chosen from 4 zinc bovine insulin hexamer. After the preliminary refinement by using the rnacromolecular rigid body refinement technique, the molecular model was further refined and adjusted by using the energy-minimizing stereochemically restrained least-squared refinement on the difference Fourier maps. The finial R-factor is 214% at 0.3nm resolution, the r.m.s. deviations from standard bond length and bond angle are 0.0022nm and 4.7°, respectively.     

Molecular replacement studies on crystal structure of DesBl-B2 Despentapeptide (B26-B30) insulin

Using the crystal structure of Despentapeptide (B26-B30) insulin (DPI) as the search model, the crystal structure of DesBl-B2 Despentapeptide (B26-B30) insulin (DesBl-2 DPI) has been studied by the molecular replacement method. There is one DesBl-2 DPI molecule in each crystallographic asymmetric unit. The cross rotation function search and the translation function search show apparent peaks and thus determine the orientation and position of DesBl-2 DPI molecule in the cell respectively. The subsequent three-dimensional structural rebuilding and refine-ment of DesBl-2 DPI molecule confirm the results by molecular replacement method.     

Crystal structure of allophycocyanin from red algae Porphyra yezoensis at 2.2-A resolution.

The crystal structure of allophycocyanin from red algae Porphyra yezoensis (APC-PY) at 2.2-A resolution has been determined by the molecular replacement method. The crystal belongs to space group R32 with cell parameters a = b = 105.3 A, c = 189.4 A, alpha = beta = 90 degrees, gamma = 120 degrees. After several cycles of refinement using program X-PLOR and model building based on the electron density map, the crystallographic R-factor converged to 19.3% (R-free factor is 26.9%) in the range of 10.0 to 2.2 A. The r.m.s. deviations of bond length and angles are 0.015 A and 2.9 degrees, respectively. In the crystal, two APC-PY trimers associate face to face into a hexamer. The assembly of two trimers within the hexamer is similar to that of C-phycocyanin (C-PC) and R-phycoerythrin (R-PE) hexamers, but the assembly tightness of the two trimers to the hexamer is not so high as that in C-PC and R-PE hexamers. The chromophore-protein interactions and possible pathway of energy transfer were discussed. Phycocyanobilin 1alpha84 of APC-PY forms 5 hydrogen bonds with 3 residues in subunit 2beta of another monomer. In R-PE and C-PC, chromophore 1alpha84 only forms 1 hydrogen bond with 2beta77 residue in subunit 2beta. This result may support and explain great spectrum difference exists between APC trimer and monomer.     

海洋红藻和蓝藻中的别藻蓝蛋白结构特征的比较

红毛菜、坛紫菜和条斑紫菜三种海洋红藻中的别藻蓝蛋白的特征吸收光谱(λ_(max)650 nm),荧光发射光谱(F_(max)662nm)、等电点(pI 4.42)、聚集态(分子量:134 kD)及其亚基分子量(α17kD,β18.5kD)均相同;结合它们各自吸收光谱的二阶导数光谱、圆二色谱和氨基酸残基组成等,与蓝藻--螺旋藻中的别藻蓝蛋白进行了比较。研究结果表明:四种来源不同的别藻蓝蛋白结构具有同一性,都是由α和β两个亚基组成的(αβ)_3结构。     

Crystal structure determination of basic phospholipase A_2 from venom of Agkistrodon halys pallas by molecular replacement method

Basic phospholipase A2 (BPLA2) from the venom of Agkistrodon halys pallas has a strong ability to hemolyze erythrocytes. The asymmetrical unit of P212121 crystal of BPLA2 contains two molecules. Self-rotation function was used to study the orientation relationship of these two molecules. Cross-rotation and translation functions were then used to determine the orientations and positions of the two molecules in the unit cell. The model building and preliminary structure refinement were carried out. The result shows that the two molecules in the asymmetrical unit of orthorhombic crystal are related by a non-crystallographic 2-fold symmetry axis.     

Characterization and transcript analysis of the major phycobiliprotein subunit genes from Aglaothamnion neglectum (Rhodophyta)

The genes encoding the and subunits of allophycocyanin, phycocyanin and phycoerythrin from the red alga Aglaothamnion neglectum were isolated and characterized. While the operons containing the different phycobiliprotein genes are dispersed on the plastid genome, the genes encoding the and subunits for each phycobiliprotein are contiguous. The subunit gene is 5 for both the phycocyanin and phycoerythrin operons, while the subunit gene is 5 for the allophycocyanin operon. The amino acid sequences of A. neglectum phycobiliproteins, as deduced from the nucleotide sequences of the genes, are 65–85% identical to analogous proteins from other red algae and cyanobacteria. The conserved nature of the plastid-encoded red algal and cyanobacterial phycobiliprotein genes supports the proposed origin of red algal plastids from cyanobacterial endosymbionts.Many environmental factors effect phycobilisome biosynthesis. The effect of both nutrient availability and light quantity on the level of A. neglectum phycobiliprotein subunits and the mRNA species encoding those subunits is described.     

中国淡水红藻一新记录属--巴尔比亚藻属

报道中国产的淡水红藻一个新记录属--巴尔比亚藻属(Balbiania Sirodot).     

Two simple procedures for isolation of allophycocyanin II from Anacystis nidulans

Allophycocyanin II purification using initial extraction of phycobiliproteins by acetone treatment is introduced. An additional fast method using Al2O3 is described. Both extraction procedures are followed up by conventional hydroxylapatite chromatography.     

Genes encoding phycobilisome linker polypeptides on the plastid genome of Aglaothamnion neglectum (Rhodophyta)

The genes encoding the phycobilisome anchor protein (apcE) and rod-core linker (cpcG) are on the plastid genome of the red alga Aglaothamnion neglectum. The apcE gene product is 5 to and in the same operon as the and subunit genes of allophycocyanin. This arrangement is identical to the arrangement observed in many cyanobacteria. The cpcG gene product is 5 to the operon encoding the and subunits of phycoerythrin, but is transcribed from the opposite DNA strand. This gene arrangement is different from that observed in cyanobacteria.The amino acid sequences of the A. neglectum anchor protein and rod-core linker polypeptide, as deduced from the nucleotide sequences of the genes, are approximately 50% identical to analogous polypeptides from cyanobacteria and another eukaryotic alga Cyanophora paradoxa. The conserved nature of these proteins suggests that the structure of the core and the rod-core interface are very similar in phycobilisomes of cyanobacteria and eukaryotic red algae.     

Simple brominated phenols in red algae

By using TLC and GLC-MS techniques, 23 species of red algae, representing nine orders, were analyzed for the presence of simple bromophenols. Ten bromophenols were detected, five of which might be artefacts. Furthermore, lanosol was identified in sea water from the Polysiphonia Brodiaei—zone. Bromophenols were detected in species from the families Ceramiaceae, Delesseriaceae, Bonnemaisoniaceae, Rhodophyllaceae, Corallinaceae and Rhodomelaceae.     

Bacterial communities of some brown and red algae from Peter the Great Bay, the Sea of Japan

The structure of microbial communities of brown algae, red algae, and of the red alga Gracilaria verrucosa, healthy and affected with thallus rot, were comparatively investigated; 61 strains of heterotrophic bacteria were isolated and characterized. Most of them were identified to the genus level, some Vibrio spp., to the species level according to their phenotypic properties and the fatty acid composition of cellular lipids. The composition of the microflora of two species of brown algae was different. In Chordaria flagelliphormis, Pseudomonas spp. prevailed, and in Desmarestia viridis, Bacillus spp. The composition of the microflora of two red algae, G. verrucosa and Camphylaephora hyphaeoides, differed mainly in the ratio of prevailing groups of bacteria. The most abundant were bacteria of the CFB cluster and pseudoalteromonads. In addition, the following bacteria were found on the surface of the algae: Sulfitobacter spp., Halomonas spp., Acinetobacter sp., Planococcus sp., Arthrobacter sp., and Agromyces sp. From tissues of the affected G. verrucosa, only vibrios were isolated, both agarolytic and nonagarolytic. The existence of specific bacterial communities characteristic of different species of algae is suggested and the relation of Vibrio sp. to the pathological process in the tissues of G. verrucosa is supposed.     

The structure of a centrosymmetric protein crystal

Crystals of racemic rubredoxin, prepared by independent chemical synthesis of the two enantiomers, have been grown and characterized. The unit cell contains two molecules, one of each enantiomer. Examination of the intensity distribution in the diffraction pattern revealed that the crystals are centrosymmetric. This was confirmed by solution of thestructure to 2 Å resolution via molecular replacement methods. The electron density maps are of very high quality due to the fact that the phaseof each reflection must be exactly 0° or exactly 180°. These results demonstrate the feasibility of using synthetic racemic proteins to yield centrosymmetric protein crystals with electron density maps that have very low phase error and model bias. © 1993 Wiley-Liss, Inc.     

A simple method for efficient separation and purification of c-phycocyanin and allophycocyanin from Spirulina platensis

c-Phycocyanin and allophycocyanin were separated and purified from Spirulina platensis by precipitation with ammonium sulphate, ion exchange chromatography and gel filtration chromatography. Pure c-phycocyanin and allophycocyanin were finally obtained with an A₆₂₀/A₂₈₀value of 5.06 and an A₆₅₅/A₂₈₀ value of 5.34, respectively.     

Partial structure and properties of the ferredoxin from Rhodymenia palmata

A ferredoxin of MW 11 000 was isolated from the marine alga Rhodymenia palmata (Palmaria palmata). In its oxidised form the ferredoxin had absorption maxima at 276, sh 281, 328, 423 and 465 nm, and contained a single [2Fe-2S] cluster. The midpoint potential of the ferredoxin was ?400 mV and it effectively mediated electron transport in NADP⁺-photoreduction by higher plant chloroplasts, and pyruvate decarboxylation by the phosphoroclastic system of an anacrobic bacterium. The amino acid composition was Lys₃, His₁, Arg₁, Asx₁₂, Thr₉, Ser₈, Glx₁₃, Pro₄, Gly₈, Ala₇, Cys₅, Val₈, Ile₄, Leu₉, Tyr₄, Phe₂; tryptophan and methionine were absent from the molecule. The N-terminal amino acid region consisting of ca half the total amino acid sequence was determined using an automatic sequencer.     

A selenite-induced decrease in the lipid content of a red alga

Two unicellular marine algae (Dunaliella primolecta and Porphyridium cruentum) have been found to contain a selenium-inducible, non-enzymatic glutathione peroxidase activity when cultured in the presence of selenite. To test the possibility that selenium functions in vivo as an antioxidant in these algae, a detailed examination of the lipid content of algae cultured in the presence or absence of selenite was conducted. If selenium augments the antioxidant defenses of algal cells, an increase in the content of oxidation-sensitive lipids would be expected. The fatty acid, chlorophyll, phospholipid and glycolipid content of the green alga D. primolecta was not affected by growth in selenite. At low light intensity there was a moderate decrease in the chlorophyll and polyunsaturated fatty acid content of the red alga P. cruentum when cultured in selenite. At higher light intensity the content of all fatty acids, phospholipid, glycolipid, chlorophyll, carotenoid and phycoerythrin decreased in P. cruentum grown in selenite. Since growth in selenite did not increase the quantity of oxidation-sensitive lipids in either alga, there is no evidence for an in vivo functioning of selenium as an antioxidant. Instead, the observed decrease in lipids of the red alga P. cruentum can best be explained as a selenite-induced oxidative effect.     

Antiviral carbohydrates from marine red algae

The solubility of the O₂ in the Dead Sea brine was determined over the temperature range 5 °C–50 °C using a modified Winkler titration, volumetric analysis, and a polarographic sensor. The solubility at room temperature and 1 atmosphere pressure was ca. 1 mg l^–1, and the temperature coefficient 0.006 mg 1^–1° C^–1 . The data are nearly consistent with sea water solubility extrapolated to Dead Sea brine salinity.     

Crystal structure determination of basic phospholipase A2 from venom of Agkistrodon halys pallas by molecular replacement method

Basic phospholipase A₂ (BPLA₂) from the venom of Agkistrodon halys pallas has a strong ability to hemolyze erythrocytes. The asymmetrical unit of P2₁2₁2₁ crystal of BPLA₂ contains two molecules. Self-rotation function was used to study the orientation relationship of these two molecules. Cross-rotation and translation functions were then used to determine the orientations and positions of the two molecules in the unit cell. The model building and preliminary structure refinement were carried out. The result shows that the two molecules in the asymmetrical unit of orthorhombic crystal are related by a non-crystallographic 2-fold symmetry axis.