Double-stranded "cores

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. 

The four histone groups that are composed of ho-mogeneous proteins, H2A, H2B, H3, and H4, make up the nucleosome core. Each core consists of two copies of the four histones. The double-stranded DNA is wrapped twice around each core in a left-handed superhelix. A superhelix is the name given to the additional helix made by the double-stranded, helical DNA as it is wrapped around the nucleosome core. A familiar superhelix in everyday life is a twisted spiral telephone cord. The nucleosome core of histones do not recognize specific DNA structures rather, they can bind to any stretch of DNA as long as it is not too close to a neighboring nucleosome. The order of contact of histones to the DNA is as follows ... 

Fig. 6. (a) A schematic model of the helical, double-stranded, unstaggered, H4 fiber (Sperling and Amos, 1977). The asymmetric unit is an axial dimer and there are six such dimers per strand per repeat. The repeat distance is 330 A. The two different types of axial bonds—within and between dimers—are denoted by a thick and thin line, respectively. The tetrameric grouping is indicated, (b) A model of (a) upon which is superimposed a schematic representation of a nucleosome core particle... 

Sperling and Wachtel, 1979) containing a tetramer of histones and 1.75 turns of smoothly bent DNA (Finch et al., 1977). The superposition illustrates how an H3-H4 double-stranded fiber could form the core of the H3-H4 subnucleosomal particle as well as serving as the arginine-rich kernel of the histone core of closely packed nucleo-... 

In arrays of closely packed nucleosomes composed of all four core histones, strands of H2A-H2B dimers could be incorporated in the grooves between the two H3-H4 strands, producing a four-stranded polymer. Alternatively, they could bind to the H3-H4 double-stranded fiber to give an octamer of the histones per nucleosome. This latter model is supported by the photochemical cross-linking of histones to DNA which have shown that within the nucleosome core the four core histones are not equivalently positioned with respect to... 

The genetic information of eukaryotic cells is propagated in the form of chromosomal DNA. Besides the nucleic acid component, chromosomes contain architectural proteins as stoichiometric components, which are involved in the protective compaction of the fragile DNA double strands. Together, the DNA and proteins form a nucleoprotein structure called chromatin. The fundamental repeating unit of chromatin is the nucleosome core particle. It consists of about 147 base pairs of DNA wrapped around a histone octamer of a (H3/H4)2 tetramer and two (H2A-H2B) heterodimers. One molecule of the linker histone HI (or H5) binds the linker DNA region between two nucleosome core particles (Bates and Thomas 1981). 

Ueda K, Kinoshita Y, Xu ZJ, Ide N, Ono M, Akahori Y, Tanaka I, Inoue M (2000) Unusual core histones specifically expressed in male gametic cells of Lilium longiflorum. Chromosoma 108 491—500 Unal E, Arbel-Eden A, Sattler U, Shroff R, Lichten M, Haber JE, Koshland D (2004) DNA damage response pathway uses histone modification to assemble a double-strand break-specific cohesin domain. Mol Cell 16 991-1002... 

The nucleosome is the fundamental repeating structural unit of chromatin. It is composed of two molecules of the core histones H2A, H2B, H3, H4, approximately two superhelical turns of double-stranded DNA, and linker histone HI (H5). In addition to biochemical studies, the existence of the nucleosome was established in electron micrographs (Fig. la) [1,2], and the name nucleosome, coined to incorporate the concept of the spherical nu-bodies [3]. Micrococcal nuclease limit digestion of chromatin established the nucleosome core particle (NCP) as the portion of the nucleosome containing only the core histones surrounded by 1.75 superhelical turns of double-stranded DNA [4,5]. 

BTV belongs to the family Reoviridae, viruses with double-stranded RNA segmented genomes. They contain two capsid layers the internal capsid, or core, contains transcription complexes which transcribe the viral RNA. The BTV core is approximately 700 A in diameter and is composed of two principal structural proteins 780 copies of VP7 (38 kDa) arranged as trimers on a T = 13 quasiequivalent lattice form the bristly core surface and 120 copies of VP3 (100 kDa) the subcore shell. 

Fig. 14.8. DNA binding domain of the tnmor suppressor protein p53 in complex with DNA. Crystal structure of the core domain of p53 (amino acids 102-292) in complex with a double-stranded DNA that contains a specific binding site for p53 (Cho et al., 1994). The amino acid positions are highhghted at which frequent oncogenic mutations are observed (see Fig. 14.9). MOLSKRIPT representation according to Krauhs, (1991).

The most easily identifiable characteristics are those related to the shape of the complexes, with their double-stranded helical cores. In this respect, the electrochemical and photochemical properties of Cu2(K-84)2+ are not much different from those of the open-chain helical precursor or its O-methylated version. The strong electronic coupling between the two copper centers is clearly a consequence of the 1,3-phenylene bridges between the two complex subunits and the topological properties of the ligand have virtually no influence. 

During the prophase of the first meiotic division (meiosis I) two homologous pairs of partially "condensed" chromosomes must find each other and pair with appropriate orientation. A protein in the telomeres of the chromosomes seems to be involved.269 277 The key structure in meiotic crossing-over is the ribbonlike synaptonemal complex formed by the pairs of homologous chroma fids.271/278 2791 This complex, in which a proteinaceous core or axial element separates the greatly extended chromatid pairs (Fig. 26-13), is fully formed in the pachytene stage of meiosis. Formation of the synaptonemal complex is preceded by development of a few double-stranded breaks in... 

At the far left, we can see the nucleic acid and protein structures shown in frame 1. In addition, we show a much larger protein, the immunoglobulin G antibody molecule. Four separate polypeptide chains join to make up an antibody molecule two heavy chains (blue) of about 400 amino acids and two light chains (purple) of about 200 amino acids. The antibody is about 16 nm in width. Finally, at the far right, we show the core particle from a small plant virus, the reovirus. Only the icosahedral protein coat of the virus can be seen. The reovirus particle is about 60 nm across. The nucleic acids of the virus are sequestered inside the virus core. The reovirus family is unusual in that its nucleic acids are all double-stranded RNA molecules. 

Raman difference spectroscopy has also been used to understand the molecular mechanism of viral core assemblies yielding information on viral subunits from precursor and mature states. Benevides et al. employed Raman difference spectroscopy to investigate conformational changes of the protein building blocks of the icosahedral core of a double-stranded RNA (p6 virus during viral procapsid and capsid assembly [18],... 

Figure 10.26 Appearance of the two types of nucleosomes. The cores are histone octamers, around which is wound the double-stranded DNA. The cylindrical object in the right frame represents HI histones. (Reproduced by permission from Saenger W. Principles of Nucleic Acid Structure. New York Springer-Verlag, 1984, p. 442.)...

Human immunodeficiency virus (HIV) is a member of the retrovirus family, classified under the lentivirus genus. Retroviruses are enveloped RNA viruses, which contain a core of capsid proteins, viral RNA, and enzymes. All infectious retroviral virions contain an enzyme, reverse transcriptase, which catalyzes the formation of a complementary DNA strand from an RNA template. A double-stranded DNA copy of the viral RNA genome (proviral DNA) may then be integrated into and replicated with the host cell genome. 

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