Study of the Radiosensitive Structure of T2 Bacteriophage Using Low Energy Electron Beams

Hydrated T2 bacteriophage were irradiated with 0.75 to 90 kev electron beams. A thin foil isolated the sample chamber from the electron gun source. Survival (plaque formation) was observed. Apparent cross-sections and D₃₇ doses were determined. The maximum cross-section of about 5 × 10^-3 μ² is roughly equal to the cross-sectional area presented by the phage core. As beam energy was increased the average D₃₇ dose first attained a minimum value of about 23 kr for 1 kev electrons (which penetrate the relatively inert protein coat) after which the average D₃₇ dose rose with beam energy to a maximum value of about 50 kr for fully penetrating beams. These dependencies suggest that the radiosensitive structure exists as a peripheral shell rather than a uniformly sensitive core. A tentative model for the phage structure, based on this and other evidence, is presented.     

Structure of a bacteriochlorophyll a-protein from the green photosynthetic bacterium Prosthecochloris aestuarii.

The three-dimensional structure of a water-soluble bacteriochlorophyll a-containing protein from the green photosynthetic bacterium Prosthecochloris aestuarii has been determined by X-ray crystallography from a 2.8 Å resolution electron density map based on four isomorphous derivatives. Details of the crystallographic procedures used to obtain the map are presented.The bacteriochlorophyll a-protein is shown to consist of three identical subunits, tightly packed around a 3-fold symmetry axis. Each subunit consists of a core of seven bacteriochlorophyll a molecules enclosed within a “bag” of protein. The polypeptide chain forms an extensive 15-strand β-sheet, which is almost planar in its central region, and twisted at its extremities, and wraps around the chlorophyll core to form an efficient amphipathic layer between the chlorophylls and the aqueous environment. There are extensive contacts between the phytyl chains of the seven bacteriochlorophylls within each subunit. These hydrocarbon chains constitute an inner hydrophobic core of the molecule which may be important in forming the complex. There are also extensive contacts between the protein and both the bacteriochlorophyll head groups and tails, but relatively few contacts between the respective head groups. The seven magnesiums all appear to be five co-ordinated. In five cases the presumed ligand is a histidine side-chain, in one case a polypeptide carbonyl oxygen, and in the other case a water molecule.At low temperature, both the absorption and circular dichroism spectra of the bacteriochlorophyll a-protein show splitting which can be interpreted in general terms as due to exciton interactions between the seven chromophores, but calculations of the expected splitting based on the bacteriochlorophyll co-ordinates determined crystallographically are in poor agreement with the observed spectra. Furthermore, the observed red shift of the Q_y absorption band of bacteriochlorophyll a, from about 770 nm in organic solvents to 809 nm in the bacteriochlorophyll a-protein, is not explained by the exciton calculations. It seems likely that the red shift is due to perturbations of the spectra of the individual bacteriochlorophylls by the protein environment, but, pending the determination of the amino acid sequence, it is not possible at this time to define in detail all the proteinchlorophyll interactions. It is suggested that the bacteriochlorophyll a-protein serves as a good model for the organization of chlorophyll in vivo, and that the types of interaction seen here between chlorophyll and protein are likely to be found in other chlorophyll proteins.     

Immunolocalization of the 110,000 molecular weight cytoskeletal protein of intestinal microvilli

The core structures of microvilli from absorptive cells of the intestinal epithelium are primarily composed of calmodulin (M_r 16,000), actin (M_r 43,000), villin (M_r 95,000) and a protein of M_r 110,000. We have isolated this protein and raised antibodies against it. The antibodies interact specifically with villin and M_r 110,000 polypeptides present in isolated microvilli or brush borders. However, after absorption on an immobilized villin preparation, these antibodies still immunoprecipitate the M_r 110,000 protein but not villin. Thus, these two proteins appear to share some antigenic determinants but also contain other determinants specific for each protein. Immunolocalization studies have been performed using specific antibodies against the M_r 110,000 protein. Immunofluorescent studies on thin frozen sections of intestinal cells show that this protein is located in the brush border and at the basolateral faces of these polarized cells. Immunoferritin studies on rat brush borders demembranated with the detergent Triton X-100 show the association of the M_r 110,000 protein with core filaments of microvilli, as well as with some filaments localized in the terminal web network.Using sealed, right-side-out vesicles prepared from pig intestinal mucosa in the presence of Ca²⁺ and Mg²⁺, a polypeptide of M_r 140,000 was found to be a major component of the Triton X-100 insoluble pellet. This protein is a minor component of an equivalent pellet obtained from isolated microvilli prepared in the presence of EDTA. The significance of this M_r 140,000 polypeptide associated with the core residue of intestinal microvilli is discussed.     

Characterizing the effects of the protein environment on the reduction potentials of metalloproteins

The reduction potentials of electron transfer proteins are critically determined by the degree of burial of the redox site within the protein and the degree of permanent polarization of the polypeptide around the redox site. Although continuum electrostatics calculations of protein structures can predict the net effect of these factors, quantifying each individual contribution is a difficult task. Here, the burial of the redox site is characterized by a dielectric radius R _p (a Born-type radius for the protein), the polarization of the polypeptide is characterized by an electret potential ? _p (the average electrostatic potential at the metal atoms), and an electret-dielectric spheres (EDS) model of the entire protein is then defined in terms of R _p and ? _p. The EDS model shows that for a protein with a redox site of charge Q, the dielectric response free energy is a function of Q ², while the electret energy is a function of Q. In addition, R _p and ? _p are shown to be characteristics of the fold of a protein and are predictive of the most likely redox couple for redox sites that undergo different redox couples.     

Nonlinear Dependences of Optical Properties of Spherical Core–Shell Silver–Gold and Gold–Silver Nanoparticles on Their Parameters

Modeling of nonlinear optical properties of spherical core–shell gold–silver and silver–gold nanoparticles (NPs) placed in water was carried out on the base of extended Mie theory. Efficiency cross sections of absorption σ _abs, scattering σ _sca, and extinction σ _ext of radiation with wavelengths λ?=?400 and 532 nm for core–shell NPs with constant core radii r ₀₀?=?5, 10, 20, and 40 nm and in the range of relative radii r ₁/r ₀₀?=?1–8 were calculated (r ₁ is the radius of shell). Dependences of optical properties of gold–silver and silver–gold NPs on increasing of core radius r ₀ in the range 0???r ₁ under condition r ₁?=?const and increasing of r ₀ under r ₁???r ₀?=?const were investigated. Results show the nonlinear behavior of optical properties of core–shell gold–silver and silver–gold NPs on radiation wavelengths (optical indexes of metals), different core and shell radii, and their correlation, on relative NP radii r ₁/r ₀₀. An increase and decrease of absorption, scattering, and extinction efficiency cross sections of core–shell NPs with changing of wavelengths, core and shell radii, and relative NP radii r ₁/r ₀₀ are established. These dependences can be used for experimental investigation of the interesting first stages of shell formation on core and optical determination of core–shell NP parameters.     

Cloning and sequencing of the gene for the DNA-binding 17 K protein of Escherichia coli

The skp gene encoding the 17 K protein, a basic DNA-binding nucleoid-associated protein of Escherichia coli, was cloned as part of a 2.3-kb genomic fragment. The gene was sequenced and a polypeptide of 161 amino acids (aa) was deduced from the nucleotide sequence. The primary translation product was processed by cutting off the N-terminal 20 aa residues, yielding a mature polypeptide of 141 aa. The M_r of the mature polypeptide was 15674. An E. coli transformant containing the skp gene on the plasmid pGAH317 was shown to overproduce the gene product some 20-fold.     

Primary Structure of Cytochrome b(5) from Cauliflower (Brassica oleracea L.) Deduced from Peptide and cDNA Sequences

Cytochrome b₅ is a microsomal protein that functions as an intermediate electron donor in fatty acid desaturation and other oxidation/reduction reactions. cDNA clones were isolated from cauliflower (Brassica oleracea L.) by using oligonucleotides based on the partial amino acid sequence of the protein. The deduced amino acid sequence of the polypeptide exhibited approximately 30% sequence identity with the homologous protein from vertebrates.     

A mouse submandibular sialomucin containing both N- and O-glycosylic linkages

A sialomucin from mouse submandibular glands was treated with mild base-Me₂SO. This treatment cleaves O-glycosylically linked oligosaccharides, but preserves the integrity of the protein core. After treatment with mild base-Me₂SO, 49.2% (by weight) of the oligosaccharides were removed from the polypeptide; they were composed of residues of 2-acetamido-2-deoxy-d-glucose, 2-acetamido-2-deoxy-d-galactose, sialic acid, and d-galactose. These oligosaccharides were linked O-glycosylically via 2-acetamido-2-deoxy-d-galactose. Chromatography of the base-Me₂-SO-treated mucin on Sephacryl S-300 indicated that the protein core, with its base-resistant oligosaccharides, is a single, high-molecular-weight species. The mild-base-resistant linkages remaining on the protein core (50.8% of the total carbohydrates by weight) also contained d-mannose. The presence of these mild-base-resistant linkages, and the formation of 2-acetamido-2-deoxy-d-glucitol following treatment with m NaOH-m NaBH₄, confirmed the presence of N-glycosylic linkages.     

Molecular weight and symmetry of the pyruvate dehydrogenase multienzyme complex of Escherichia coli.

The molecular weight and polypeptide chain stoichiometry of the native pyruvate dehydrogenase multienzyme complex from Escherichia coli were determined by independent techniques. The translational diffusion coefficient (D^o_20,w) of the complex was measured by laser light intensity fluctuation spectroscopy and found to be 0.90 (±0.02) × 10^?11m²/s. When this was combined in the Svedberg equation with the measured sedimentation coefficient (s^o_20,w = 60.2 (±0.4) S) and partial specific volume ($\text{v}\text{?}\text{= 0.735 (±0.01)}\text{ml/g}$), the molecular weight of the intact native complex was calculated to be 6.1 (±0.3) × 10⁶. The polypeptide chain stoichiometry (pyruvate decarboxylase: lipoate acetyltransferase: lipoamide dehydrogenase) of the same sample of pyruvate dehydrogenase complex was measured by the radioamidination technique of Bates et al. (1975) and found to be 1.56:1.0:0.78.From this stoichiometry and the published polypeptide chain molecular weights estimated by sodium dodecyl sulphate/polyacrylamide gel electrophoresis, a minimum chemical molecular weight of 283,000 was calculated. This structure must therefore be repeated approximately 22 times to make up the native complex, a number which is in good agreement with the expected repeat of 24 times if the lipoate acetyltransferase core component has octahedral symmetry. It is consistent with what appears in the electron microscope to be trimer-clustering of the lipoate acetyltransferase chains at the corners of a cube. It rules out any structure based on 16 lipoate acetyltransferase chains comprising the enzyme core.The preparation of pyruvate dehydrogenase complex was polydisperse: in addition to the major component, two minor components with sedimentation coefficients (s^o_20,w) of 90.3 (±0.9) S and 19.8 (±0.3) S were observed. Together they comprised about 17% of the total protein in the enzyme sample. Both were in slowly reversible equilibrium with the major 60.2 S component but appeared to be enzymically active in the whole complex reaction. The faster-sedimenting species is probably a dimer of the complex, whereas the slower-sedimenting species has the properties of an incomplete aggregate of the component enzymes of the complex based on a trimer of the lipoate acetyltransferase chain.     

Influence of thylakoid membrane lipids on the structure and function of the plant photosystem II core complex

Main conclusion

MGDG leads to a dimerization of isolated, monomeric PSII core complexes. SQDG and PG induce a detachment of CP43 from the PSII core, thereby disturbing the intrinsic PSII electron transport. The influence of the four thylakoid membrane lipids monogalactosyldiacylglycerol (MGDG), digalactosyldiacylglycerol (DGDG), sulfoquinovosyldiacylglycerol (SQDG) and phosphatidylglycerol (PG) on the structure and function of isolated monomeric photosystem (PS) II core complexes was investigated. Incubation with the negatively charged lipids SQDG and PG led to a loss of the long-wavelength 77 K fluorescence emission at 693 nm that is associated with the inner antenna proteins. The neutral galactolipids DGDG and MGDG had no or only minor effects on the fluorescence emission spectra of the PSII core complexes, respectively. Pigment analysis, absorption and 77 K fluorescence excitation spectroscopy showed that incubation with SQDG and PG led to an exposure of chlorophyll molecules to the surrounding medium followed by conversion to pheophytin under acidic conditions. Size-exclusion chromatography and polypeptide analysis corroborated the findings of the spectroscopic measurements and pigment analysis. They showed that the negatively charged lipid SQDG led to a dissociation of the inner antenna protein CP43 and the 27- and 25-kDa apoproteins of the light-harvesting complex II, that were also associated with a part of the PSII core complexes used in the present study. Incubation of PSII core complexes with MGDG, on the other hand, induced an almost complete dimerization of the monomeric PSII. Measurements of the fast PSII fluorescence induction demonstrated that MGDG and DGDG only had a minor influence on the reduction kinetics of plastoquinone Q_A and the artificial PSII electron acceptor 2,5-dimethyl-p-benzoquinone (DMBQ). SQDG and, to a lesser extent, PG perturbed the intrinsic PSII electron transport significantly.     

Selective inhibition of the spinach thylakoid LHC II protein kinase

Treatment of spinach thylakoids with the adenosine affinity inhibitor 5′-p-fluorosulfonylbenzoyl adenosine (FSBA) resulted in at least 95% inhibition of phosphorylation of the light-harvesting protein complex of Photosystem II (LHC II), while the M_r 10 000 polypeptide showed a 35% decrease in phosphorylation. This residual kinase activity after FSBA treatment appears to have the same properties as the control, since phosphorylation of the M_r 10 000 polypeptide subsequent to FSBA treatment could be achieved with either light or reducing conditions in the dark. [¹⁴C]FSBA labelled several polypeptides, but only the M_r 50 000 band was protected against the label by prior addition of ADP or adenosine, making it a possible candidate for the LHC II kinase. FSBA had no effect on electron transport, and [¹⁴C]FSBA did not label LHC II or the M_r 10 000 polypeptide, indicating that the FSBA was not interfering with activation of the kinase or modifying the substrates, but rather acting at the level of the LHC II protein kinase. Inhibition of LHC II phosphorylation by FSBA resulted in the elimination of the slow ATP-induced decrease in variable fluorescence, a parameter believed to be associated with phosphorylation of the LHC II. The half-times and time-course for inhibition of LHC II phosphorylation and inhibition of the ATP-induced decrease of fluorescence yield were identical, consistent with the concept that LHC II phosphorylation plays a major role in this fluorescence change.     

Oligomeric structure of a simian virus 40 T antigen in free form and bound to DNA

The structure of the D2 protein, a polypeptide structurally and functionally related to the simian virus 40 large T antigen, was examined by electron microscopy. The observed size of the protein indicates that it most commonly exists as a tetrameric assembly of its 107,000 M_r monomer. In addition to the tetramers, both monomers and dodecamers are seen. Binding of D2 protein to a fragment of simian virus 40 DNA was found to occur preferentially at the origin of replication. The major binding species of the protein is the tetramer.     

Plasmon Spectroscopy for Subnanometric Copper Particles: Dielectric Function and Core–Shell Sizing

In the last years, there has been a growing interest in the study of transition metal nanoparticles (Nps) due to their potential applications in several fields of science and technology. In particular, their optical properties are governed by the characteristics of the dielectric function of the metal, its size and environment. This work analyses the separated contribution of free and bound electrons on the optical properties of copper Nps. Usually, the contribution of free electrons to the dielectric function is corrected for particle size through the modification of the damping constant, which is changed as usual introducing a term inversely proportional to the particle’s radius to account for the extra collisions with the boundary when the size approaches the electronic mean free path limit (about 10 nm). For bound electron contribution, the interband transitions from the d-band to the conduction band are considered together with the fact that the electronic density of states in the conduction band must be made size-dependent to account for the larger spacing between electronic energy levels as the particle decreases in size below 2 nm. Taking into account these specific modifications of free and bound electron contributions to the dielectric function, it was possible to fit the bulk complex dielectric function, and consequently, determine optical parameters and band energy values such as the coefficient for bound electron contribution Q _bulk?=?2?×?10²⁴, gap energy E _g?=?1.95 eV, Fermi energy E _F?=?2.15 eV, and damping constant for bound electrons γ _b?=?1.15?×?10¹⁴ Hz. With both size-dependent contributions to the dielectric function, extinction spectra of copper Nps in the subnanometer radius range can be calculated using Mie’s theory and its behaviour with size can be analysed. These studies are applied to fit experimental extinction spectra of very small spherical core–shell Cu–Cu₂O Nps generated by ultrafast laser ablation of a solid target in water. Theoretical calculations for subnanometric core radius are in excellent agreement with experimental results obtained from core–shell colloidal Nps. From the fitting, it is possible determining core radius and shell thickness of the Nps, showing that optical extinction spectroscopy is a good complementary technique to standard high-resolution electron microscopy for sizing spherical nanometric-subnanometric Nps.     

Subunit composition of the globulin fraction of rapeseed (Brassica napus L.)

Multidimensional gel electrophoretic procedures have been employed to studythe polypeptide composition of the 12 S globulin (cruciferin) from rapeseed (Brassica napus L. cv. Tandem). Cruciferin was shown to consist of three main groups of proteins with M_r in the range of 60-52 (A group), 37-35 and 31-29 (respectively B₁ and B₂ groups) and 24-22 (C group). When reduced the A protein group gave rise to two classes of polypeptide constituents. The larger had M_r and isoelectric points (6.4–7.1) corresponding to those of B protein groups whereas the smaller were essentially composed of M_r 22 and a specific 25 kilodaltons (kD) polypeptide with basic isoelectric points. The initial B and C protein groups were unaltered by reducing conditions. These results support the notion that native cruciferin is composed of subunits with large and small polypeptides linked by disulphide bonds and of similar or closely-related polypeptides which are not covalently bonded.     

Role of inter-domain cavity in the attachment of the orange carotenoid protein to the phycobilisome core and to the fluorescence recovery protein

Using molecular modeling and known spatial structure of proteins, we have derived a universal 3D model of the orange carotenoid protein (OCP) and phycobilisome (PBS) interaction in the process of non-photochemical PBS quenching. The characteristic tip of the phycobilin domain of the core-membrane linker polypeptide (L_CM) forms the attachment site on the PBS core surface for interaction with the central inter-domain cavity of the OCP molecule. This spatial arrangement has to be the most advantageous one because the L_CM, as the major terminal PBS-fluorescence emitter, accumulates energy from the most other phycobiliproteins within the PBS before quenching by OCP. In agreement with the constructed model, in cyanobacteria, the small fluorescence recovery protein is wedged in the OCP’s central cavity, weakening the PBS and OCP interaction. The presence of another one protein, the red carotenoid protein, in some cyanobacterial species, which also can interact with the PBS, also corresponds to this model.     

The Water Oxidation Complex of Chlamydomonas: Accumulation and Maturation of the Largest Subunit in Photosystem II Mutants

Photosystem II particles of Chlamydomonas reinhardtii contain three extrinsic polypeptides of 29, 20, and 16 kilodaltons, whose functions are incompletely defined. We prepared a monospecific polyclonal antibody against the 29 kilodalton protein and determined that it also specifically recognizes a protein of approximately 33 kilodaltons in thylakoid membrane fractions of several vascular plants, eukaryotic algae, and a cyanobacterium. The cross-reacting 33 kilodalton protein of pea was removed from inverted thylakoid vesicles by CaCl₂ washes demonstrating the structural relationship between the Chlamydomonas polypeptide and the largest subunit of the water oxidation complex of vascular plants. Functional identity of the Chlamydomonas polypeptide was confirmed by antibody inhibition of O₂ evolution in inverted pea vesicles. In contrast to wild-type cells, only low levels of the 29 kilodalton polypeptide are recovered with purified thylakoid membranes of the mutants examined. However, we show that the mature form of the 29 kilodalton polypeptide accumulates to wild-type levels in whole cell extracts of photosystem II deficient mutants and a water oxidation mutant of Chlamydomonas. Impaired membrane assembly has no effect on the maturation or stability of this component of the multi-subunit water oxidation complex.     

Studies on beef heart ubiquinol-cytochrome c reductase. Quantification and distribution of the core proteins as determined by radioimmunoassay

Core proteins I (M_r 50 000) and II (M_r 47 000) were isolated from beef heart ubiquinol-cytochrome c reductase, and radioimmunoassays were developed for both. Immunoreplica experiments show that antisera against each protein react with a single peptide in both isolated Complex III and in mitochondria. Thus, core proteins are not aggregated forms of smaller peptides as suggested for the yeast protein (Jeffrey, A., Power, S. and Palmer, G., Biochem. Biophys. Res. Commun. (1979) 86, 271–277). Core proteins were quantitated in Complex III and in mitochondria using radioimmunoassay. Approx. 2 mol core protein II per mol core protein I were found. A molar ratio of 1 : 2 : 2 : 1 is suggested for core protein I : core protein II : cytochrome b : cytochrome c₁. Radioimmunoassay shows that the antibodies react as extensively with Complex III-bound core protein as with the isolated core proteins. In spite of this, the antibodies do not inhibit electron transport in submitochondrial particles or isolated Complex III, and they have no oligomycin- or uncoupler-like effects on submitochondrial particles oxidizing NADH. The combined results from radioimmunoassay and immunoreplica experiments strongly suggest, however, that core proteins are specifically associated with Complex III in the mitochondria, implying a specific role there.     

The Study of Surface Plasmon in Au/Ag Core/Shell Compound Nanoparticles

Au/Ag core/shell nanoparticles are fabricated by laser-ablating Ag plates in Au colloid solution. The absorption band is found to blue shift with increasing ablation time. Mie theory calculations show that the shift is caused by the increase of the Ag shell thickness. The average Ag shell thickness can be determined from the measured absorption peak. Using the plasmon hybridization approach, we show that the absorption band around 510 nm originates from an anti-bonding mode ω _?+ caused by the interaction between a bonding Ag shell mode ω _?? and Au sphere mode ω _S-Au. The blue shift of the ω _?+ mode with the increase of Ag shell thickness is also well predicted by the hybridization theory.     

Physical measurements on the lipid-containing bacteriophage φ6

Bacteriophage φ6 has been studied by small-angle X-ray scattering, intensity-fluctuation spectroscopy, analytical ultracentrifugation, and spectroscopy. The sedimentation coefficient (s₂₀⁰, w) is 375 S, the diffusion coefficient (D₂₀⁰, w) is 2.66 · 10^?8 cm²/s. Using the Svedberg equation and an estimate of the partial specific volume, the M_r is 1.49 ± 0.32 · 10⁸.A simple model which describes φ6, is a central sphere consisting of RNA and protein of radius 330 Å and an outer shell of low electron density 40 Å thick. The RNA may form five concentric shells in the region $\text{r = 140?290}\text{A}\text{?}$