Super-secondary structures

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. 

Sauer, R.T., et al. Homology among DNA-binding proteins suggests use of a conserved super-secondary structure. Nature 298 447-451, 1982. 

Figure 4.8 Super-secondary structures found in proteins (a) P-a-P motifs (b) anti-parallel P-sheets connected by hairpin loops (c) a-a motifs. (From Voet and Voet, 2004. Reproduced with permission from John Wiley Sons., Inc.)...

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... 

There has been considerable effort on the prediction of secondary and tertiary structures of protein from the amino acid sequence using computeraided minimal potential energy calculations8). The question as to how a primary amino acid sequence begins to produce secondary and super-secondary structures and fold into its equilibrium tertiary structure and functional domains is a very active field of structural biochemistry. A related problem is the mechanism by which a protein unfolds or denatures 20) which is of fundamental interest in the protein adsorption process. 

Nagano, K. Logical analysis of the mechanism of protein folding IV. Super secondary structures. J. Molec. Biol. 109, 235-250 (1977). 

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). 

The tertiary structure of proteins, also called the super-secondary structure, denotes the way in which the secondary structures are assembled in the biologically active molecule, (Figure 7.27b). These are described in terms of motifs3, that consist of a small number of secondary structure elements linked by turns, such as (oc-helix - turn -a-helix). Motifs are further arranged into larger arrangements called folds, which can be, for example, a collection of / -sheets arranged in a... 

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. 

Taylor, W. and Thorton, J. Recognition of super-secondary structure in proteins. J. Mol. Biol. 173 487-514, 1984. 

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). 

Super-secondary Structure.—As can be seen from Table 1 the majority of globular protein structures can be described in terms of varying amounts of close packed a-helical or yS-sheet secondary structure. Similarities in the packing pattern of these... 

The basic thesis has served as the stimulus for a large number of studies directed towards the prediction of protein three-dimensional structures from their amino-acid sequences alone. Implicit in most of the predictive methods investigated are two concepts (i) that there is in the protein the clearly-observed hierarchical structural arrangement (primary structure - secondary structure - secondary aggregates or super-secondary structure - domains - total structure) which has already been discussed in the previous section and (ii) that the folding process of a random chain to give the stable native structure is kinetically-controlled and that it proceeds via a characteristic and predictable pathway. This pathway is visualized as requiring nucleation at various sites around which the subsequent... 

FIGURE 18.5 (a) a-Helix (1) or (2) (b) P-sheet (c) PaP (a super secondary structure) (d) a twin (e) a helix-loop-helix binding (/) a catalytic triad. 

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