Solenoidal structure

The primary Junction of the nucleosomes is to condense DNA. Further condensation of nucleosome DNA requires nonhistone nuclear proteins. These proteins make up a scaffoldlike structure around an additional helix consisting of coiled nucleosomes. This produces a structure that resembles a solenoid, with six nucleosome subunits per turn. The solenoid structure can form large loops that give additional structure to the incipient chromosome. 

VI. Relationship Between /5-Solenoid Structures and Their Functions. 85... 

B. Functional Implications of Highly Regular /5-Solenoid Structures. 86... 

Nonredundant Set of Known Right-Handed /i-Solenoid Structures... 

V. Relationship Between /3-Solenoid Structures and Their Amino Acid Sequences... 

Another computational approach for detecting /1-solenoid sequences is implemented in a program called BETAWRAP (Bradley et al., 2001). This approach aims to identify /1-solenoid sequences by using hydrophobic-residue sequence patterns of strand-turn-strand regions that were learned from non-/l-solenoid structures. This method also takes into consideration the repetitive character of these patterns in /1-solenoids. Unlike the sequence profile approaches, BETAWRAP can make ab initio predictions of /1-solenoid domains. However, it is less sensitive than the profile search and, sometimes, cannot distinguish /1-solenoids from other solenoids (A. V. K, unpublished observation) such as, for example, LRR proteins (Kobe and Deisenhofer, 1994 Kobe and Kajava, 2001). The latest modification of BETAWRAP algorithm, which is called BETAWRAPPRO (McDonnell et al., 2006), employs additional data provided by sequence profiles and this improves the results of /1-solenoid predictions. 

E. Examples and Perspectives of Sequence-Based Prediction of (3-Solenoid Structures... 

These protruding structures may form catalytic sites or binding sites for small molecules. Remarkably, some polysaccharide modification enzymes of pathogenic bacteria are similar to enzymes of their host cells. For example, during cell development, pectin, a principal component in the primary cell wall of plants, is modified by its own pectin methylesterases that have /1-solenoid structures (Johansson et al, 2002) and in this respect, resemble pectin lyases secreted by bacteria to break down these structures (Lietzke et al., 1996). 

Minsky et recently suggested that the emergence of eukaryotes led to a highly crowded environment that may have promoted DNA self-assembly, leading to extremely condensed and thermodynamically stable DNA aggregates such as nucleosomes and solenoid structures of chromatin. 

Fig. 4. Schematic diagram of proposed solenoid structure of chromatin to yield a 30 nm fiber. The structure consists of six nucleosomes per turn of the helix and hence would be three nucleosomes wide. In the diagram, only three nucleosomes of each turn are visible the other three nucleosomes per turn are hidden from view.

Our results on the formation of stable helical and solenoidal structures on cylinders and spheres in the strong adsorption limit are applicable in a wide range of physical systems. They include, e.g., the separation of carbon nanombes by helical sequence-specific wrapping of single-stranded DNA molecules, which has been studied experimentally [199-203], theoretically [200, 204—208], and by computer simulations [209-211], as well as in helical patterning of charged interfaces [80-82, 212]. 

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