Super helical structures

Structure in solution Bombyx mori (Iizuka and Yang, 1966 Yao et al, 2004), MA, MI, FLAG, and CYL (Dicko et al., 2004b), Acinous and Pyriform (Fig. 8), Antheraea pemyi (Tsukada et al, 1994). The helix-like structure is loosely defined as a structure with a CD spectrum similar to myoglobin. /(-Spiral structure is defined as a super helical structure formed of straight sections and /(-turns. 

Fig. 26d, the width and screw pitch of the assemblies are similar to those observed in SEM images. The orientation of the height contour indicates that these superhelices have a right-handed sense. Many possible interacticMis, including hydrophobic, dipolar rt-jr interactions, and ordered packing tendency of a-helical polypeptide segments, are believed to be responsible for the formation of super-helical structures. 

In relation to the specific effects described above, electrochemically synthesized polythiophenes also exhibit interesting morphologies [17, 30, 31, 33]. The STM images again indicate that the (super)helical structures are involved. The cooperation between the host polymers and dopant ions seems responsible for those structures as well. In this context, Hotta [37] pointed out that rapid deposition of the polymer chains that follows umnediately after the electrochemical generation of those polymers may well lead to rather unusual crystal structures. 

Using a regioregular poly thiophene, Bouman and Meijer [50] observed a mirror image circular dichroic spectra for the samples that underwent different thermal treatments. They referred this observation to stereomutation associated with main-chain chirality. This might be related to the existence of the (super)helical structure [31] mentioned in the previous section. 

Argos, P., Rossmann, M.G., Johnsson, J.E. A four-helical super-secondary structure. Biochem. Biophys. Res. Comm. 75 83-86, 1977. 

Anderson, W.F., et al. Proposed a-helical super-secondary structure associated with protein-DNA recognition. 

The association of secondary structures to give super-secondary structures, which frequently constitute compactly folded domains in globular proteins, is completed by the a-a motifs in which two a-helices are packed in an anti-parallel fashion, with a short connecting loop (Figure 4.8c). Examples of these three structural domains, often referred to as folds, are illustrated in Figures 4.9—4.11. The schematic representation of the main chains of proteins, introduced by Jane Richardson, is used with the polypeptide backbone... 

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... 

Normally, this DNA would have a linking number equal to 25, so it is underwound. The DNA double helical structures in the previous figure have the same value of Lk however, the DNA can be super-coiled, with the two underwindings taken up by the negative supercoils. This is equivalent to two turns -worth of single-stranded DNA and no supercoils. This interconversion of helical and superhelical turns is important in gene transcription and regulation. 

An interesting recent study of a phospholipid-nucleoside conjugate [30] shows the possibility of spontaneous formation in water of super-helical strands. These structures are of interest with regard to the origin of life, as they can function as templates for polymerisation of nucleic acids. We observe that the helicoid is a zero cur ature surface with the different relevant and seemingly necessary properties also possessed by cubosomes catalytic effects, etc. These helical assemblies are therefore alternatives to cubosomes as candidates of prebiotic assemblies, crucial to the first level of evolution. In any case, two-dimensional hyperbolic forms certainly offer many features essential to the most primitive forms of life. 

The X-ray structure of horse spleen ferritin reveals that each of the subunits is based on a 4-a-helical bundle type of super-secondary structure (46). This is also likely to be the type of structure of the bacfer subunits, given the overall similarity of the two types of ferritins (63). This view is supported by the secondary structure prediction analysis for E. coli bacfer reported by Andrews et al. (5). 

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...

Coiled coil, motifs of super-secondary structure found in proteins. Approximately 2-3% of aU proteins form coiled coils, where two to seven amphipathic a-helices are wrapped around each other, like the strands of a rope. The interaction surface of these amphipathic helices is of hydrophobic nature, and leucine is often found in the position of the hydrophobic amino acids (leucine zipper). This hydrophobic interaction provides, in an aqueous environment, the driving force for the di- or oligomerization. Coiled coils of two or three helical domains are the most commonly found types. In the former case, the two helices are wound up against each other in a left-handed twist with a seven-residue periodicity. Packing of unpolar side chains (u) into a hydrophobic core mainly contributes to the stability of this super-secondary fold. The dimeric coiled coU is, for example, responsible for DNA recognition by some transcription factors. 

Macroconformations consisting of two or three helices intertwined with each other are also sometimes called super helices or super secondary structures. An example is deoxyribonucleic acid, which forms a double helix from two complementary chains, each in the form of a helix (see Section 29). With synthetic polymers, both it-poly(methyl methacrylate) and poly(/ -hydroxybenzoic acid) appear to form double helices. Triple helices are, for example, formed by the protein, collagen (see Section 30). 

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 right-handed helices, which seem to be the preferred secondary structure, have 3.6 amino acids per tnm and are stabilised by hydrogen bonding between the NH and the CO groups further along the chain. Helices of this kind are associated in different ways to form tertiary structures of super helices in other fibrous proteins such as collagen, elastin, wool and so forth (Figure 10.16). 

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