Octams

Fig. 2. Silica ring stmctures, where 0= Si Q — O (a) 12-membered Si02 hexamer, and (b) 16-membered Si02 octamer.

Cyclopentadiene oligomers up to octamers can be effectively analy2ed and quantified by supercritical fluid chromatography using a chemically bonded methyl siUcone capillary column. 

Klemm, J.D., et al. Crystal structure of the Oct-1 POU domain bound to an octamer site DNA recognition with tethered DNA-binding modules. Cell 77 21-32, 1994. 

Figure 18.3 Protein crystals contain large channels and holes filled with solvent molecules, as shown in this diagram of the molecular packing in crystals of the enzyme glycolate oxidase. The subunits (colored disks) form octamers of molecular weight around 300 kDa, with a hole in the middle of each of about 15 A diameter. Between the molecules there are channels (white) of around 70 A diameter through the crystal. (Courtesy of Ylva Lindqvist, who determined the structure of this enzyme to 2.0 A resolution in the laboratory of Carl Branden, Uppsala.)...

Histone core octamer (here shown in cross section)... 

FIGURE 11.23 A diagram of the histone octamer. Nucleosomes consist of two turns of DNA supercoiled about a histone core octamer. 

If chromatin is swelled suddenly in water and prepared for viewing in the electron microscope, the nucleosomes are evident as beads on a string, dsDNA being the string (Figure 12.28). The structure of the histone octamer core has been determined by X-ray crystallography without DNA by E. N. Moudrianakis s laboratory (Figure 12.29) and wrapped with DNA by T. J. 

Richmond and collaborators (Figure 12.30). The octamer (Figure 12.29) has surface landmarks that guide the course of the DNA around the octamer 146 bp of B-DNA in a flat, left-handed superhelical conformation make 1.65 turns around the histone core (Figure 12.30), which itself is a protein superhelix consisting of a spiral array of the four histone dimers. Histone 1, a three-domain protein, serves to seal the ends of the DNA turns to the nucleosome core and to organize the additional 40 to 60 bp of DNA that link consecutive nucleo-... 

FIGURE 12.31 A model for chromosome structure, human chromosome 4. The 2-um DNA helix is wound twice around histone octamers to form 10-um uucleosomes, each of which contains 160 bp (80 per turn). These uucleosomes are then wound in solenoid fashion with six uucleosomes per turn to form a 30-nm filament. In this model, the 30-nm filament forms long DNA loops, each containing about 60,000 bp, which are attached at their base to the nuclear matrix. Eighteen of these loops are then wound radially around the circumference of a single turn to form a miniband unit of a chromosome. Approximately 10 of these minibands occur in each chromatid of human chromosome 4 at mitosis. 

Arents, G., et al., 1991. The nncleo.some core hi.stone octamer at 3.1 A re.s-olntion A tripartite protein a.s.sembly and a left-hand. snperhelix. Proceedings of the National Academy of Sciences U.S.A. 88 10148—10152. 

The original blue (K.A. Hofmann, 1908) was obtained from the reaction of Pt(MeCN)2Cl2 with silver salts over some hours. Under these conditions, the nitrite is hydrolysed to acetamide. Very recently, the structure of the complex [(H3N)2Pt(MeCONH)2Pt(NH3)2]4(NO3)10 has been determined (Figure 3.37). The average oxidation state of the platinums in the octamer is 2.25. 

The SUR-Kir6.2 complex is a non-covalently bonded octamer (4 x SUR/4 x Kir6.2), with the poreforming Kir6.2 channels located at the centre (Fig. 2). 

Chromatin is composed of nucleosomes, where each comprise 147 base pairs of DNA wrapped around an octamer oftwo copies of each histone H2A, H2B, H3, and H4. Nucleosomes are folded into higher-order structures that are stabilized by linker histones. Chromatin structure can be altered by enzymes that posttranslationally modify histones (e.g., through phosphorylation, acetylation, methylation, or ubiquitination) or by ATP-driven chromatin-remodeling complexes that alter nucleosome position and/or composition. 

Histones are small, basic proteins required to condense DNA into chromatin. They have been first described and named in 1884 by Albrecht Kossel. There are five main histones HI, H2A, H2B, H3 andH4. An octamer of core histones H2A, H2B, H3 andH4 is located inside a nucleosome, the central building block of chromatin, with about 150 base pairs of DNA wrapped around. The basic nature of histones, mediated by the high content of lysine and arginine residues, allows a direct interaction with the acidic phosphate back bone of DNA. The fifth histone HI is located outside at the junction between nucleosomes and is referred to as the linker histone. Besides the main histones, so-called histone variants are known, which replace core histones in certain locations like centromers. 

The nucleosome represents the first level of DNA condensation and is the basic building block of all chromatin structures. It was discovered in 1973 and consists of a central histone octamer with about 150 base pairs of DNA wrapped around. 

The core unit of the chromatin, the nucleosome, consists of histones arranged as an octamer consisting of a (H3/ H4)2-tetramer complexed with two histone H2A/H2B dimers. Accessibility to DNA-binding proteins (for replication, repair, or transcription) is achieved by posttranslational modifications of the amino-termini of the histones, the histone tails phosphorylation, acetylation, methylation, ubiquitination, and sumoyla-tion. Especially acetylation of histone tails has been linked to transcriptional activation, leading to weakened interaction of the core complexes with DNA and subsequently to decondensation of chromatin. In contrast, deacetylation leads to transcriptional repression. As mentioned above, transcriptional coactivators either possess HAT activity or recruit HATs. HDACs in turn act as corepressors. 

Figures 15 and 16 demonstrate folding in the l,l,l,3,3,3-hexafluoro-2-propanol/ethylene glycol (HFP/EG) mixture (1 2) and in 1,3-propandiol in comparison to Fig. 13, which describes helix formation in water. The structure formation is much more pronounced. This is indicated by the more negative signals of the CD spectrum at 198 nm. The negative values of 0 for the octamer increase from -1.8 x 10-4 deg cm2 dmol-1 in...

Myosin may be extracted via high-ionic-strength buffers and purified. Synthetic thick filaments of myosin spontaneously assemble upon lowering the ionic strength of its solution, exhibiting the morphological characteristics of native thick filaments. This process initiates with myosin monomers assembled into parallel dimers. The dimers assemble into antiparallel tetramers, the tetramers into octamers, and the octamers into minifilaments... 

When the histone octamer is mixed with purified, double-stranded DNA, the same x-ray diffraction pattern is formed as that observed in freshly isolated chromatin. Electron microscopic studies confirm the existence of reconstituted nucleosomes. Furthermore, the reconsti-mtion of nucleosomes from DNA and histones H2A, H2B, H3, and H4 is independent of the organismal or cellular origin of the various components. The histone HI and the nonhistone proteins are not necessary for the reconstitution of the nucleosome core. 

In the nucleosome, the DNA is supercoiled in a left-handed helix over the surface of the disk-shaped histone octamer (Figure 36-2). The majority of core histone proteins interact with the DNA on the inside of the supercoil without protruding, though the amino terminal tails of all the histones probably protrude outside of this structure and are available for regulatory covalent modifications (see Table 36-1). 

Figure 36-2. Model for the structure of the nucleosome, in which DNA is wrapped around the surface of a flat protein cylinder consisting of two each of histones H2A, H2B, H3, and H4 that form the histone octamer. The 146 base pairs of DNA, consisting of 1.75 superhelical turns, are in contact with the histone octamer. This protects the DNA from digestion by a nuclease. The position of histone HI, when it is present, is indicated by the dashed outline at the bottom of the figure.

Much of the DNA is associated with histone proteins to form a structure called the nucleosome. Nucleo-somes are composed of an octamer of histones and 150 bp of DNA. 

Intrigued by the finding that Eca PLs exhibit notable differences in their kinetics, HPAEC analyses were carried out to examine the products from the depolymerization of PGA and 31% esterified pectin. After 18 h of incubation with PGA, PL1 and PL2 had produced mainly di- and trimers. Similariy, main products of PL3 action were trimers, followed by dimers. Moreover, it was the only enzyme found to produce monomers from unesterified substrates with a degree of polymerization >3. Using 31% esterified pectin as a substrate, similar end products were released by the PLs as from PGA. In addition to the products described, traces of tetra- up to octamers were detectable. While PL1 and PL2 released di- and trimers at almost... 

Poly-(methacrylic acid) was prepared in 1880 by Fittig and Engel-horn. Mjoen separated the polymer by precipitation and attempted to determine its molecular weight by cryoscopic and ebullioscopic methods. He decided that his product, which he regarded as a colloid, was an octamer but reached no conclusions as to its constitution other than that it was an octabasic acid of the formula C24H4o(COOH)8. 

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