Superhelical axis

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...

The idealized structure of the coiled coil has been parameterized by Crick (Figs. 2a and 3). The distance required for the superhelix to complete a full turn is called the pitch (P), and the angle of a helix relative to the superhelical axis is called the pitch angle (n) [also called... 

Figure 15.1 Schematic representation of a modelled antiparallel coiled coil homodimer in both a side view (top) and a view along the superhelical axis (bottom). Hydrophobic side-chains (Leu) are represented in yellow, complementary salt bridges in red (Clu), and blue (Lys or Arg). See color plate 15.1.

A new property appears in the conversion of a linear DNA molecule into a closed circular molecule. The axis of the double helix can itself be twisted into a superhelix (Figure 5.18B). A circular DNA molecule without any superhelical turns is known as a relaxed molecule. Supercoiling is biologically important for two reasons. First, a supercoiled DNA molecule has a more compact shape than does its relaxed counterpart. Second, supercoiling may hinder or favor the capacity of the double helix to unwind and thereby affects the interactions between DNA and other molecules. These topological features of DNA will be considered further in Section 27.3. 

Many naturally occurring DNA molecules have superhelical densities of about -0.06. To get an idea of what this means, consider a hypothetical DNA molecule of 10,000 bp, which is in the "classical" B form, with 10.0 bp/tum. Then LO is 10,000 bp/(10.0 bp/tum), or 1000 turns. Each DNA strand crosses the other 1000 times in the relaxed circle. If the topoisomerase gyrase twisted the molecule to a superhelical density of -0.06, then AL = -0.06 LO, or AL = -60. This change could be accommodated, for example, by the helix axis writhing about itself 60 times in a left-hand sense, which would correspond to AW = -60, AT = 0 the molecule would have 60 left-hand superhelical turns. 

Fig. 8.10 Superhelical configuration of LAj peptide at the end of the simulation. Lime dashed line is axis connects centers on the beginning and ends of peptide. The peptide tilts around this axis...

When the lipoprotein molecules are arranged in a superhelix (Fig. 13B), a number of ionic interactions are formed between adjacent molecules stabilizing the entire assembly. As can be seen in Fig. 12, the hydrophilic bands Pa and Pb which run parallel to the hydrophobic band H are complementary to each other in terms of ionic properties when an acidic residue is located on one side, a basic residue is located on the other side. In the superhelical arrangement, as many as seven stable ionic interactions are formed between the Pa band of one a-helix, and the Pb band of the adjacent a-helix. In Fig. 12, the residues denoted by (x) indicate those residues on the Pb band of an adjacent helix (helix 2) interacting with the residues of the Pa band of helix 1. It should be noted that the superimposed residues of the Pb band of helix 2 are not plotted at the same level as those of helix 1. This is because corresponding points of adjacent helices are displaced by 5.8 A, due to the inclination of 25° between the axis of the superhelix and the axis of the a-helix, assuming that the average diameter and... 

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