Super-helix

Collagen, the principal fibrous protein in mammalian tissue, has a tertiary structure made up of twisted a-helices. Three polypeptide chains, each of which is a left-handed helix, are twisted into a right-handed super helix to form an extremely strong tertiary structure. It has remarkable tensile strength, which makes it important in the structure of bones, tendons, teeth, and cartilage. 

Bertoft, E. (2004). On the nature of categories of chains in amylopectin and their connection to the super helix model. Carbohydr. Polym., 57, 211-224. 

Figure 40. Helical arrangement of hydrogen bonded chains of 142 and 4,4 -biphe-nol. Five of these strands form a super-helix.

The terms major and minor helix are used here as defined by Crick (1953) in his original presentation of the coiled-coil (or super-helix) concept. The minor helix defines the turns of the residues of an individual chain around its own axis. The major helix defines the turns of the minor helix around an axis outside of itself e.g., the common axis running up the center of the group of three chains in the collagen case. 

A disoriented a-pattern, however, could arise from the collapse of a super helix when restraints imposed by disulfide bonds are removed (as in peracetic acid or caustic soda solutions). Disoriented patterns, either a or could equally well arise from partial solution of proteins within the fibers and deposition within the cells upon washing out the solubilizing agent and drying (Happey et al., 1953 Harrap, 1963). 

Fig. 4.5 Glycine residues make up the interior of a tropocollagen triple helix. The same three-stranded collagen super-helix is depicted as in Fig. 4.4, but looking down the center of a ball-and-stick representation. Glycine residues ( 11) are shown in red. Because of its small size, glycine is required where the three chains contact The balls in this illustration do not represent the van der Waals radii of the individual atoms (Figure 4-12d in Lehninger Principles of Biochemistry. D.L. Nelson and M.M. Cox, 4th Ed. 2005. W.H. Freeman Co., New York)...

The crystal structure of the duplex [r(guauaca)dC]2, which would be expected to form a self-complementary duplex with an AC mismatch, has been solved and instead shown to form only six Watson-Crick base pairs with two 3 -overhang-ing bases. There are two independent duplexes, each of which is bent, and which stack end to end to form a right-handed super-helix. The overhanging nucleotides are looped out of the structure, with the penultimate adenosine residues forming A-GC base triples. 

Fig. 2.8. Scaffold formation/disruption assays based on supramolecular self-assemblies. In this scheme, a cyanine is helicogenic. Molecular self-assembly of cyanine upon linear chiral polymer such as CMA, CMC, or HA results in a conformation transition of the polymer to adopt a super-helix structure. Scaffold disrupting glycosidases (hyaluronidase, amylase, cellulase) trigger fluorescence attenuation by disruption of the helical scaffold...

Fig. 25 Polymer structures of (a) PS4o-i -PIAAio, right-handed polypeptide backbone and (b) PS4o-b-PIAHi5, left handed polypeptide backbone, (c) Left-handed super-helix from PS4o-i>-PIAAio- (d) Representation of the helix in (c). (e) Right-handed super-helical aggregate formed by PS4o-b-PIAHi5. From [140]. Reprinted with permission from AAAS...

The mechanism by which topoisomerase mediates knotting of supercoiled DNA was investigated by Wasserman and Cozzarelli. Data were interpreted in terms of a model for knot formation in which random strand passage mediated by the topoisomerase links bent or branched portions of a super-helix that has a specific interwound geometry. The very high frequency of knotting was explained by superhelix interwinding and DNA contacts stabilized by enzyme molecules. 

The twisted double helix (superhelical form Figure 10.44b) involves the introduction of torsional stress into a circular DNA molecule and an increase of energy. If the twisting of the DNA superhelix is in the same direction as that of the double helix then the supercoiling is -i-ve. If the super helix is twisted in the opposite manner, the super coiling is -ve (Figure 11.38). Most DNA molecules are observed to be negatively supercoiled which makes it easier for the double helix to be unwound and... 

The authors discussed two models either the polymer serves as a seeding centre for the formation of helical dye associates, or the dye molecules are added to the polymer helix in highly ordered orientation and thus form what is termed a dye super-helix . 

Mason et al [30] later measured the CD spectra in steady and streaming solution and showed that the acridine orange complex has the form of a left-handed super-helix bound to the core of the right-handed a-helix of the poly-a-L-glutamic acid (see Figure 6). 

Other dye molecules are bound to the sugar phosphate residues of the DNA and form a super-helix around its core. No Cotton effect is seen if acridine orange is added to DNA which has been denaturated by heat or acid. 

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