Nucleosome core particles

Page 1171 (Figure 28 7) is adapted from crystallograpliic coordinates deposited with The Protein Data Bank PDB ID lAOl Luger A Mader W Richmond R K Sargent D F Richmond T J Crystal Structure of the Nucleosome Core Particle at 2 8 A Resolution Nature 1997 V 389 251... 

Fig. 3.18 Nucleosome core particle (NCP)-polyamide co-crystal structures (PDB codes 1M18 and 1M19). (Top) Partial structure, viewed down the superhelical axis. Base pairs 58-145 (shown in white) and associated proteins (H3, blue H4, green H2A, yellow H2B, red) are shown for each complex. Superhelix locations (SHLs) are labeled as each major...

C.L. White, C. Melander, J.M. Gotteseeld, P. B. Dervan, and K. Luger Crystal stmctures of nucleosome core particles in complex with minor groove DNA-binding ligands. J. Mol. Biol. 2003, 326, 371-380. 

Luger L et al Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 1997 398 251. 

Smooth COSMO solvation model. We have recently extended our smooth COSMO solvation model with analytical gradients [71] to work with semiempirical QM and QM/MM methods within the CHARMM and MNDO programs [72, 73], The method is a considerably more stable implementation of the conventional COSMO method for geometry optimizations, transition state searches and potential energy surfaces [72], The method was applied to study dissociative phosphoryl transfer reactions [40], and native and thio-substituted transphosphorylation reactions [73] and compared with density-functional and hybrid QM/MM calculation results. The smooth COSMO method can be formulated as a linear-scaling Green s function approach [72] and was applied to ascertain the contribution of phosphate-phosphate repulsions in linear and bent-form DNA models based on the crystallographic structure of a full turn of DNA in a nucleosome core particle [74],... 

Fig. 10 Charge transport is observed in a variety of nucleic acid assemblies over a wide distance regime (3.4-200 A). Shown are examples of nucleic acid structures through which charge transport has been examined a B-form DNA b DNA-RNA hybrids c cross-over junctions and d nucleosome core particles. In all assemblies, the charge transport chemistry is extremely sensitive to the structure of the -stacked nucleic acid bases...

SADP or sulfo-SADP also have been used to study the phenylalanine-methionine-arginine-phenylalanine-amide-activated sodium channel (Coscoy et al., 1998), various apolipoprotein E isoforms (Mann et al., 1995), the high-affinity phenylalkylamine Ca2+ antagonist binding protein from guinea pig (Moebius et al., 1994), the interaction of non-histone proteins with nucleosome core particles (Reeves and Nissen, 1993), and the interactions among cytochromes P-450 in the endoplasmic reticulum (Alston et al., 1991). See Chapter 28 for methods of using photoreactive heterobifunctional crosslinkers to study protein interactions. 

Reeves, R., and Nissen, M.S. (1993) Interaction of high mobility group-I (Y) nonhistone proteins with nucleosome core particles./. Biol. Chem. 268, 21137-21146. 

Time-dependent fluorescence measurements have been made on tyrosine in calf thymus nucleosome core particles by Ashikawa et al. S7) Based on the salt dependence of the decay data, the tyrosines were divided into two classes. At 20 to 400 mM salt, about half of the tyrosine residues appear to be partially quenched, possibly by resonance energy transfer to DNA bases. The other half are thought to be statically quenched, possibly by hydrogen bonds this quenching is partially eliminated at about 2 M salt. In view of the number of tyrosines per nucleosome core particle (estimated at 30), it is impossible to make a more detailed analysis of the decay data. 

I. Ashikawa, Y. Nishimura, M. Tsuboi, K. Watanabe, and K. Iso, Lifetime of tyrosine fluorescence in nucleosome core particles, J. Biochem. (Tokyo) 91, 2047-2055 (1982). 

Though derived for DNA, and nucleosome core particles, these twisting correlation functions are potentially useful for the analysis of other filamentous biopolymers. Such analyses of optical anisotropy data for actin filaments... 

The nucleosome is composed of 200 base pairs of DNA and an octamer of the histones H2A, H2B, H3, and H4 as well as histone HI (Komberg, 1974, 1977). Nucleosomes can be obtained by mild digestion of chromatin with micrococcal nuclease (Noll, 1974a Axel, 1975), followed by fractionation on a sucrose gradient. Further digestion of the nucleosomes results in the formation of nucleosome core particles composed of 145 base pairs of DNA and an octamer of the histones H2A, H2B, H3, and H4 (Rill and Van Holde, 1973 Sollner-Webb and Felsenfeld, 1975 Axel, 1975 Bakayev et al., 1975 Whitlock and Simpson, 1976 Noll and Komberg, 1977). The DNA piece thus excised is called linker DNA which serves as a link... 

The histone octamer of nucleosome core particles was cross-linked by dimethylsuberimidate and isolated from the DNA by precipitation in 3 M NaCl (0.05 M sodium phosphate buffer, pH 7.0). The cross-linked octamer, dissolved at low ionic strength, was reconstituted by mixing with DNA at 1.0 M NaCl (pH 8.0 Tris buffer) and dialyzed against 0.6 M NaCl in the same buffer. The reconstituted particle had properties similar to those of the cross-linked core particle. It sedi-... 

Simon et al. (1978). The complex with an H3 H4 octamer more closely resembled the nucleosome core particle with respect to compaction, suggesting that H3 and H4 could replace H2A and H2B in the compaction of the DNA into nucleosome core particles. 

Fig. 5. Schematic model of the nucleosome, with histone HI shown as stabilizing the fold of the DNA molecule around the core histones [based on results of Sperling and Sperling (1978)]. The nucleosome dimensions are derived from X-ray (Finch et al., 1977) and neutron (Baldwin et al., 1975 Pardon et al., 1977 Suauet al., 1977) scattering experiments. The histone core dimensions are derived from electron microscopic and X-ray studies (Sperling and Amos, 1977 Wachtel and Sperling, 1979 Sperling and Wachtel, 1979). The regions of the DNA molecule indicated by dashed lines indicate those base pairs which are not present in nucleosome core particles.

A low-energy in vitro form of nucleosome packing was observed in nucleosome core particle crystals (Finch et al., 1977). Two variants of these crystals occurred, (a) Wavy columns of nucleosomes stacked one on top of each other with an axial repeat of 340 A were obtained upon crystallization of nucleosomes containing proteolytically cleaved histones (Finch et al., 1977). (b) Straight columns of closely packed nucleosomes, 110 A in diameter, were obtained upon crystallization of nucleosomes with intact histones (Finch and Klug, 1978). In both these structures histone-histone contacts between nucleosomes are implied. Similar face-to-face packing of nucleosomes in arcs and helical patterns was observed in the EM by Dubochet and Noll (1978). 

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... 

Mahy NL, Perry PE, Gilchrist S, Baldock RA, Bickmore WA (2002) Spatial organization of active and inactive genes and noncoding DNA within chromosome territories. J Cell Biol 157 579-589 Mangenot S, Leforestier A, Vachette P, Durand D, Livolant F (2002) Salt-induced conformation and interaction changes of nucleosome core particles. Biophys J 82 345-356 Marsden MP, Laeimnh UK (1979) Metaphase chromosome structure evidence for a radial loop model. Cell 17 849-858... 

Simon RH, Eelsenfeld G (1979) A new procedure for purifying histone pairs H2A + H2B and H3 + H4 from chromatin using hydroxylapatite. Nucleic Acids Res 6 689-696 Simpson RT (1978) Structure of the chromatosome, a chromatin particle containing 160 base pairs of DNA and all the histones. Biochemistry 17 5524-5531 Simpson RT, Stafford DW (1983) Structural features of a phased nucleosome core particle. Proc Natl Acad Sci U S A 80 51-55... 

Luger K, Mader, AW., Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389 251-260 Ma Y, Jacobs SB, Jackson-Grusby L, Mastrangelo MA, Torres-Betancourt JA, Jaenisch R, Rasmussen TP (2005) DNA CpG hypomethylation induces heterochromatin reorganization involving the histone variant macroH2A. J Cell Sci 118 1607-1616... 

Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403 41-45 Suto RK, Clarkson MJ, Tremethick DJ, Luger K (2000) Crystal structure of a nucleosome core particle containing the variant histone H2A.Z. Nature Struct. Biol. 7 1121-1124 Swaminathan J, Baxter EM, Corces VG (2005) The role of histone H2Av variant replacement and histone H4 acetylation in the establishment of Drosophila heterochromatin. Genes Dev 19 65-76... 

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). 

Nucleosomes core particles containing H2A only have 118 base pairs of DNA incorporated compared to the canonical nucleosomes protecting about 147 base pairs from micrococcal nuclease (Bao et al. 2004). These nucleosomes are more flexible in structure and might facilitate passage of RNA polymerase II. However, the function of this histone variant in mammalian cells is not fully understood. As... 

The genome of the eukaryotic cell is packaged in a topologically complex, fibrous superstructure known as chromatin. The nucleosome core particle is the fundamental building block of chromatin and contains 146 bp of DNA wrapped in roughly two super helical turns around an octamer of four core histones (H3, H2B, H2A and H4) resulting in a beads on a string structure. This 10 nm structure further folds and... 

Chopped core particle means nucleosome core particle with the N-terminal tails of core histones removed by tryptic digestion. 

---