The effect of norflurazon on protein composition and chlorophyll organization in pigment–protein complex of Photosystem II

The pyridazinone-type herbicide norflurazon SAN 9789 inhibiting the biosynthesis of long-chain carotenoids results in significant decrease in PS II core complexes and content of light-harvesting complex (LHC) polypeptides in the 29.5–21 kDa region. The Chl a forms at 668, 676, and 690 nm that belong to LHC and antenna part of PS I disappear completely after treatment. The intensity of the Chl b form at 648 nm is sharply decreased in treated seedlings grown under 30 or 100 lx light intensity. The bands of carotenoid absorption at 421, 448 (Chl a), 452, 480, 492, 496 (β-carotene), and 508 nm also disappear. The band shift from 740 to 720 nm and decrease in its intensity relative to the 687 nm emission peak in the low-temperature fluorescence spectrum (77 K) suggests a disturbance of energy transfer from LHC to the Chla form at 710–712 nm.     

Supramolecular organization of lysophosphatidylcholine-packaged gramicidin A′

Heat derived gramicidin A′/l-α-lysophosphatidylcholine complexes were separated on a sucrose gradient to form two fractions: Fraction A which had an approximately constant Gramicidin A′ to phospholipid ratio of 8 to 10 lipid molecules per Gramicidin A′ molecule and Fraction B which had a larger but variable ratio. Fluorescence and circular dichroism studies confirmed Fraction A to be a lipid-incorporated channel state. Electron microscopic studies, using uranyl acetate negative staining, showed fraction A to be a membranous state with the formation of bilayer vesicles, that is, the interaction of peptide and phospholipid micelles causes the lipid to reorganize into a bilayer structure. Freeze-fracture replicas of the channel incorporated state demonstrated the presence of a supramolecular organization of particles exhibiting a tendency to form rows with a 50–60 Å periodicity along the row and with 70–80 Å distance between rows. An idealized working model for the incorporated state is presented.     

The fluorescence yield of the trimeric fucoxanthin–chlorophyll–protein FCPa in the diatom Cyclotella meneghiniana is dependent on the amount of bound diatoxanthin

The fluorescence yield of isolated fucoxanthin chlorophyll proteins, serving as light harvesting proteins in diatoms, was compared to the amount of diatoxanthin bound. Diatoxanthin was earlier shown to be involved in the xanthophyll cycle in diatoms as a functional analogue of zeaxanthin in higher plants. By growing cells under different light conditions, the amount of diatoxanthin in both the trimeric FCPa as well as the oligomeric FCPb of the diatom Cyclotella meneghiniana was increased. In the trimeric FCPa, the fluorescence yield decreased with increasing diatoxanthin content, whereas in the oligomeric FCPb fluorescence was generally lower, albeit constant. No pH dependence of fluorescence yield could be demonstrated except for artificially aggregated FCPa. Thus, diatoxanthin is able to quench fluorescence in FCPa, but the yield is also influenced by pH when the protein becomes aggregated.     

Spatial organization of Dps and DNA–Dps complexes

DNA co-crystallization with Dps family proteins is a fundamental mechanism, which preserves DNA in bacteria from harsh conditions. Though many aspects of this phenomenon are well characterized, the spatial organization of DNA in DNA–Dps co-crystals is not completely understood, and existing models need further clarification. To advance in this problem we have utilized atomic force microscopy (AFM) as the main structural tool, and small-angle X-scattering (SAXS) to characterize Dps as a key component of the DNA-protein complex. SAXS analysis in the presence of EDTA indicates a significantly larger radius of gyration for Dps than would be expected for the core of the dodecamer, consistent with the N-terminal regions extending out into solution and being accessible for interaction with DNA. In AFM experiments, both Dps protein molecules and DNA–Dps complexes adsorbed on mica or highly oriented pyrolytic graphite (HOPG) surfaces form densely packed hexagonal structures with a characteristic size of about 9 nm. To shed light on the peculiarities of DNA interaction with Dps molecules, we have characterized individual DNA–Dps complexes. Contour length evaluation has confirmed the non-specific character of Dps binding with DNA and revealed that DNA does not wrap Dps molecules in DNA–Dps complexes. Angle analysis has demonstrated that in DNA–Dps complexes a Dps molecule contacts with a DNA segment of ~6 nm in length. Consideration of DNA condensation upon complex formation with small Dps quasi-crystals indicates that DNA may be arranged along the rows of ordered protein molecules on a Dps sheet.     

Role of mitochondria–cytoskeleton interactions in respiration regulation and mitochondrial organization in striated muscles

The aim of this work was to study the regulation of respiration and energy fluxes in permeabilized oxidative and glycolytic skeletal muscle fibers, focusing also on the role of cytoskeletal protein tubulin βII isotype in mitochondrial metabolism and organization. By analyzing accessibility of mitochondrial ADP, using respirometry and pyruvate kinase–phosphoenolpyruvate trapping system for ADP, we show that the apparent affinity of respiration for ADP can be directly linked to the permeability of the mitochondrial outer membrane (MOM). Previous studies have shown that MOM permeability in cardiomyocytes can be regulated by VDAC interaction with cytoskeletal protein, βII tubulin. We found that in oxidative soleus skeletal muscle the high apparent K_m for ADP is associated with low MOM permeability and high expression of non-polymerized βII tubulin. Very low expression of non-polymerized form of βII tubulin in glycolytic muscles is associated with high MOM permeability for adenine nucleotides (low apparent K_m for ADP).     

Excitation relaxation dynamics and energy transfer in fucoxanthin–chlorophyll a/c-protein complexes,probed by time-resolved fluorescence

In algae, light-harvesting complexes contain specific chlorophylls (Chls) and keto-carotenoids; Chl a, Chl c, and fucoxanthin (Fx) in diatoms and brown algae; Chl a, Chl c, and peridinin in photosynthetic dinoflagellates; and Chl a, Chl b, and siphonaxanthin in green algae. The Fx–Chl a/c-protein (FCP) complex from the diatom Chaetoceros gracilis contains Chl c₁, Chl c₂, and the keto-carotenoid, Fx, as antenna pigments, in addition to Chl a. In the present study, we investigated energy transfer in the FCP complex associated with photosystem II (FCPII) of C. gracilis. For these investigations, we analyzed time-resolved fluorescence spectra, fluorescence rise and decay curves, and time-resolved fluorescence anisotropy data. Chl a exhibited different energy forms with fluorescence peaks ranging from 677 nm to 688 nm. Fx transferred excitation energy to lower-energy Chl a with a time constant of 300 fs. Chl c transferred excitation energy to Chl a with time constants of 500–600 fs (intra-complex transfer), 600–700 fs (intra-complex transfer), and 4–6 ps (inter-complex transfer). The latter process made a greater contribution to total Chl c-to-Chl a transfer in intact cells of C. gracilis than in the isolated FCPII complexes. The lower-energy Chl a received excitation energy from Fx and transferred the energy to higher-energy Chl a. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: Keys to Produce Clean Energy.     

Synthesis of chlorophyll–amino acid conjugates as models for modification of proteins with chromo/fluorophores

A chlorophyll-a derivative bonded directly with epoxide at the peripheral position of the chlorin π-system was reacted with N-urethane and C-ester protected amino acids bearing an alcoholic or phenolic hydroxy group as well as a carboxy group at the residue to give chlorophyll–amino acid conjugates. The carboxy residues of N,C-protected aspartic and glutamic acids were esterified with the epoxide in high yields. The synthetic conjugates in dichloromethane had absorption bands throughout the visible region including intense red-side Qy and blue-side Soret bands. By their excitation at the visible bands, strong and efficient fluorescence emission was observed up to the near-infrared region. The chromo/fluorophores are promising for preparation of functional peptides and modification of proteins.     

Cis–trans isomerization of omega dihedrals in proteins

Peptide bonds in protein structures are mainly found in trans conformation with a torsion angle ω close to 180°. Only a very low proportion is observed in cis conformation with ω angle around 0°. Cis–trans isomerization leads to local conformation changes which play an important role in many biological processes. In this paper, we reviewed the recent discoveries and research achievements in this field. First, we presented some interesting cases of biological processes in which cis–trans isomerization is directly implicated. It is involved in protein folding and various aspect of protein function like dimerization interfaces, autoinhibition control, channel gating, membrane binding. Then we reviewed conservation studies of cis peptide bonds which emphasized evolution constraints in term of sequence and local conformation. Finally we made an overview of the numerous molecular dynamics studies and prediction methodologies already developed to take into account this structural feature in the research area of protein modeling. Many cis peptide bonds have not been recognized as such due to the limited resolution of the data and to the refinement protocol used. Cis–trans proline isomerization reactions represents a vast and promising research area that still needs to be further explored for a better understanding of isomerization mechanism and improvement of cis peptide bond predictions.     

Comparative biochemistry of chondroitin sulphate–proteins of cartilage and notochord

Fragments that consisted mainly of two polysaccharide chains joined by a short polypeptide bridge (doublets) were prepared from chondroitin sulphate-proteins of lamprey, sturgeon, elasmobranch and ox connective tissues after hydrolysis with trypsin and chymotrypsin. Consideration of molecular parameters, compositions and behaviour on gel electrophoresis and density-gradient fractionation leads to a proposed parent structure for chondroitin sulphate-proteins. A single polypeptide chain of about 2000 amino acid residues contains alternating short and long repeating sequences. A short sequence consists of less than 10 amino acid residues with one N-terminal and one C-terminal serine residue, each of which carries a polysaccharide chain linked glycosidically to its hydroxyl group. This structure constitutes the doublet subunit. Some variation is introduced when the doublet subunit carries only a single polysaccharide chain. The long sequence contains about 35 amino acid residues and is subject to cleavage by trypsin and chymotrypsin. The main polypeptide is probably homologous in the vertebrate sub-phylum with strong conservation of structure suggested for the short sequence. However, polymorphism of polypeptide structures cannot be excluded.     

Templates of food–habitat resources for the organization of soil animals in temperate and tropical forests

The functioning and structure of terrestrial ecosystems are shaped and maintained by plant–decomposer interactions. The food and habitat of animal populations are biogenic and are mainly of plant origin (plant litter) in terrestrial ecosystems. Primary resources of the food-habitat template for the organization of soil animals are provided by the primary production of plants, and are then modified through decomposition processes by microbial populations. In the microbial decomposition system, the efficiency of carbon utilization by microbial decomposers characterizes the decomposition processes between tropical and temperate forest ecosystems. Tropical forests show poor development of soil reservoir systems because of the high efficiency of lignin decomposition by microbial populations. The decomposition processes of leaf litter are described briefly for the understanding of organization of soil animal communities in tropical and temperate forests. A comparison of decomposition processes shows qualitative differences in decomposition between temperate and tropical forests. The composition of functional groups of soil animals is well explained by the decomposition processes in both forests.     

Characterization of the peridinin–chlorophyll a-protein complex in the dinoflagellate Symbiodinium

The water-soluble peridinin–chlorophyll a-proteins (PCPs) are one of the major light harvesting complexes in photosynthetic dinoflagellates. PCP contains the carotenoid peridinin as its primary pigment. In this study, we identified and characterized the PCP protein and the PCP gene organization in Symbiodinium sp. CS-156. The protein molecular mass is 32.7 kDa, revealing that the PCP is of the monomeric form. The intronless PCP genes are organized in tandem arrays. The PCP gene cassette is composed of 1095-bp coding regions and spacers in between. Despite the heterogeneity of PCP gene tandem repeats, we identified a single form of PCP, the sequence of which exactly matches the deduced sequence of PCP gene clone 7 (JQ395030) by LC–MS/MS analysis of tryptic digested PCP, revealing the mature PCP apoprotein is 312 amino acids in length. Pigment analysis showed a peridinin-to-Chl a ratio of 4. The peridinin-to-Chl a Q_y energy transfer efficiency is 95% in this complex.     

Seasonality of chlorophyll and nutrients in Lake Erken – effects of weather conditions

The effect of submerged macrophytes on interactions among epilimnetic phosphorus, phytoplankton, and heterotrophic bacterioplankton has been acknowledged, but remains poorly understood. Here, we test the hypotheses that the mean summer phytoplankton biomass (chlorophyll a): phosphorus ratios decrease with increased macrophyte cover in a series of nine lakes. Further, we test that both planktonic respiration and bacterioplankton production increase with respect to phytoplankton biomass along the same gradient of increasing macrophyte cover. Increased macrophyte cover was associated with a lower fraction of particulate phosphorus in epilimnia, with total particulate phosphorus declining from over 80% of total phosphorus in a macrophyte free lake to less than 50% in a macrophyte rich lake. Phytoplankton biomass (chlorophyll a) too was lower in macrophyte dominated lakes, despite relatively high levels of total dissolved phosphorus. Planktonic respiration and bacterioplankton production were higher in macrophyte rich lakes than would be expected from phytoplankton biomass alone, pointing to a subsidy of bacterioplankton metabolism by macrophyte beds at the whole lake scale. The results suggest that the classical view of pelagic interactions, which proposes phosphorus determines phytoplankton abundance, which in turn determines bacterial abundance through the production of organic carbon, becomes less relevant as macrophyte cover increases.     

Effects of enhanced UV-B radiation in the field on the concentration of phenolics and chlorophyll fluorescence in two boreal and arctic–alpine lichens

Lichens constitute a prominent part of the vegetation at high latitudes and altitudes, but the effects of UV-B radiation on these symbiotic organisms are not well known. In a northern boreal site (Abisko, northern Sweden), the usnic acid-producing lichens Flavocetraria nivalis and Nephroma arcticum were exposed to enhanced UV-B radiation, corresponding to 25% ozone depletion, for two and one growing seasons, respectively. They were compared with lichens grown under ambient UV-B and harvested fresh from the field. The treated thalli of F. nivalis had been transplanted from a site 24 km from the treatment site. From this source locality, untreated thalli were also harvested. Enhanced UV-B did not affect concentrations of usnic acid and the two depsides phenarctin and nephroarctin. A gradual decline of usnic acid, probably coupled to unusually long periods of dry, sunny weather, was observed both under enhanced and ambient UV-B and in untreated thalli. Photosystem II efficiency in both species was slightly reduced by enhanced UV-B. However, differences between seasons were larger than differences between treatments, which indicate that UV-B effects are minor in comparison to other climatic variables. Concentrations of UV-B-absorbing phenolics in lichens do not show a simple relationship to UV-B dose and therefore cannot be used as bioindicators of UV-B levels.     

Lipid modifications of proteins – slipping in and out of membranes

Protein lipid modification, once thought to act as a stable membrane anchor for soluble proteins, is now attracting more widespread attention for its emerging role in diverse signaling pathways and regulatory mechanisms. Most multicellular organisms have recruited specific types of lipids and a suite of unique enzymes to catalyze the modification of a select number of proteins, many of which are evolutionarily conserved in plants, animals and fungi. Each of the three known types of lipid modification – palmitoylation, myristylation and prenylation – allows cells to target proteins to the plasma membrane, as well as to other subcellular compartments. Among the lipid modifications, protein prenylation might also function as a relay between cytoplasmic isoprene biosynthesis and regulatory pathways that control cell cycle and growth. Molecular and genetic studies of an Arabidopsis mutant that lacks farnesyl transferase suggest that the enzyme has a role in abscisic acid signaling during seed germination and in the stomata. It is becoming clear that lipid modifications are not just fat for the protein, but part of a highly conserved intricate network that plays a role in coordinating complex cellular functions.     

Measurement of eight scalar and dipolar couplings for methine–methylene pairs in proteins and nucleic acids

A new 3D, spin-state-selective coherence transfer NMR experiment is described that yields accurate measurements for eight scalar or dipolar couplings within a spin system composed of a methylene adjacent to a methine group. Implementations of the experiment have been optimized for proteins and for nucleic acids. The experiments are demonstrated for C–C moieties of the third IgG-binding domain from Streptococcal Protein G (GB3) and for C –C groups in a 24-nt RNA oligomer. Chemical shifts of C, C and H (respectively C , C and H ) are dispersed in the three orthogonal dimensions, and the absence of heteronuclear decoupling leads to distinct and well-resolved E.COSY multiplet patterns. In an isotropic sample, the E.COSY displacements correspond to ¹J_CH, ²J_CH2+²J_CH3, ²J_CH, ¹J_CH2+¹J_CH3, ¹J_CH2–²J_H2H3, ¹J_CH3–²J_H2H3, ³J_HH2 and ³J_HH3 for proteins, and ¹J , ²J J , ²J , ¹J +¹J , ¹J J , ¹J J , ³J and ³J in nucleic acids. The experiment, based on relaxation-optimized spectroscopy, yields best results when applied to residues where the methine–methylene group corresponds to a reasonably isolated spin system, as applies for C, F, Y, W, D, N and H residues in proteins, or the C –C groups in nucleic acids. Splittings can be measured under either isotropic or weakly aligned conditions, yielding valuable structural information both through the ³J couplings and the one-, two- and three-bond dipolar interactions. Dipolar couplings for 10 out of 13 sidechains in GB3 are found to be in excellent agreement with its X-ray structure, whereas one residue adopts a different backbone geometry, and two residues are subject to extensive ₁ rotamer averaging. The abundance of dipolar couplings can also yield stereospecific assignments of the non-equivalent methylene protons. For the RNA oligomer, dipolar data yielded stereospecific assignments for six out of the eight C H₂ groups in the loop region of the oligomer, in all cases confirmed by ¹J ^{1} $$" align="middle" border="0"> J , and H resonating downfield of H .Supplementary material to this paper is available in electronic form at http://dx.doi.org/10.1007/s10858-005-0175-z.     

Relative binding affinities of chlorophylls in peridinin–chlorophyll–protein reconstituted with heterochlorophyllous mixtures

Peridinin–chlorophyll–protein (PCP), containing differently absorbing chlorophyll derivatives, are good models with which to study energy transfer among monomeric chlorophylls (Chls) by both bulk and single-molecule spectroscopy. They can be obtained by reconstituting the N-terminal domain of the protein (N-PCP) with peridinin and chlorophyll mixtures. Upon dimerization of these “half-mers”, homo- and heterochlorophyllous complexes are generated, that correspond structurally to monomeric protomers of native PCP from Amphidinium carterae. Heterochlorophyllous complexes contain two different Chls in the two halves of the complete structure. Here, we report reconstitution of N-PCP with binary mixtures of Chl a, Chl b, and [3-acetyl]-Chl a. The ratios of the pigments were varied in the reconstitution mixture, and relative binding constants were determined from quantification of these pigments in the reconstituted PCPs. We find higher affinities for both Chl b and [3-acetyl]-Chl a than for the native pigment, Chl a.