Nucleosome model

It is not widely appreciated that the major aspects of core histone interactions were well understood even before the development of the nucleosome model. Evidence for strong H2A H2B dimer interactions and an FI3 H4 tetramer was available in the early seventies (see Ref. [1], Chapter 2). By 1978, the rigorous sedimentation equilibrium studies from Moudrianakis laboratory had elucidated the thermodynamics of octamer formation [7]. What was missing, of course, was any structural information concerning these interactions. This was overcome by arduous X-ray diffraction studies, culminating in the elegantly detailed structures we have today [15,17,18], see also Flarp et al., this volume, p. 13. We now know how the core... 

FIGURE 28 7 Molecu lar models of a nucleosome and Its components The nu cleosome has a protein core around which is wound a su percoil of duplex DNA... 

Fig. 5. Solenoid model of the 30-nm filament of chromatin, where the disks represent nucleosomes and the dark line unbound DNA.

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.

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. 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 second model to explain the 200- to 300-A fiber is the superbead. In this model the thick fiber is discontinuous and is made up of 200-A beads containing 8 nucleosomes per globule (Renz et al., 1977). 

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... 

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... 

There is good agreement between the overall dimensions of the histone octamer found by Klug et al. and data obtained from other types of histone fibers discussed here. Similarity of cross-linking data of histone octamer fibers, octamer free in solution, and octamer in nucleosomes makes the extrapolation from the octamer model in the fibers to the octameric core of nucleosome valid (Klug et al., 1980). This further substantiates the idea that histones are part of an assembly system, and therefore the histone core of the nucleosome can be regarded as a truncated histone fiber (see Section IV). 

Figure 1. Hierarchical model of chromosome structure, (a) In interphase cells, DNA is packed in a nucleus as forming nucleosome and chromatin, (b) DNA forms nucleosome structure together with core histone octamer, which is then folded up into 30nm fiber with a help of linker histone HI. This 30 nm fiber is further folded into 80 nm fiber and 300 nm loop structures in a nucleus. In mitosis, chromosome is highly condensed. Proteins which are involved in each folding step are indicated above and non-protein factors are indicated below, (c) The amino acid sequences of histone tails (H2A, H2B, H3 and H4) are shown to indicate acetylation, methylation and phosphorylation sites. (See Colour Plate 1.)...

Although the existence of the 30nm fiber is widely accepted, several models have been proposed for its structure (Felsenfeld and McGhee, 1986). Thoma and colleagues proposed a solenoid model, in which the nucleosomes are ordered in a spiral manner (Thoma et al, 1979). Woodcock and colleagues postulated a helical ribbon model, in which the nucleosomes are arranged in a zig-zag manner and the sheet of the zig-zag nucleosomes winds up helically to form a ribbon-like stmcture (Woodcock ef a/., 1984). 

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... 

Figure 1. Schematic representation of remodelling mechanisms. (Adapted form Langst and Becker, 2004.) The schemes show nucleosomes from the top. (a) The twist diffusion model - Twisting of DNA moves it over the histone surface in one base pair increments. This changes the position of the DNA with respect to the histone, as shown by the open and closed circles, (b) The Loop recapture model - Extranucleosomal DNA is pulled into the nucleosomes to replace a DNA segment which consequently loops out. This loop is then propragated over the histone surface like ripples of a wave. The star,, indicates how this leads to a change in the position of DNA relative to the nucleosome. (See Colour Plate 4.)...

There have been two basic approaches. First one involves isolation of the chromatin and nucleosome from the healthy and diseased cell line. The second approach is the reconstitution of the model target such as nucleosome followed by the association with the drug(s). The second approach has been extensively employed to identify the binding site in the protein-nucleic acid complex. A pre-knowledge about the components and their arrangements in the reconstituted system sometime makes it the preferred approach. Different biophysical, biochemical and genetic techniques have been employed to understand the mode of association and the effect of the drugs upon chromatin/nucleosome structure and function. 

Two approaches are usually taken to study the effect of the association of DNA binding anticancer drugs upon the structure of chromatin and nucleosome. The first one is reconstitution of the model nucleosome in the presence of the drugs. This has been reported earlier in the case of mithramycin (Fox and Cons, 1993 Carpenter et al., 1993). In our laboratory, so far we have taken the second approach of comparing the association of the anticancer drugs with isolated chromatin at various levels. 

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