Helical structures 310 helix

A polymer of I-a,y-diaminobutanoic acid almost quantitatively substituted with azobenzene units in the side chains [Scheme 5, VIII(n= 2)] was not completely soluble in HFP when the sample was kept in the dark. The initial, slightly turbid solution became clear on irradiation at 360 nm and the consequent photoconversion of the azo moieties from their trans to the cis configuration (for photosolubility effects see Section 13.2.3). The cis polymer was found to adopt an essentially random coil conformation. Exposure to 460 nm light and the consequent back-isomerization of the azo units to about 70/30 trans-cis isomeric composition gave rise to a reversible photoinduced change from random coil to a-helical structure (helix content, about 60%).1411... 

The polypeptide chain of the 92 N-terminal residues is folded into five a helices connected by loop regions (Figure 8.6). Again the helices are not packed against each other in the usual way for a-helical structures. Instead, a helices 2 and 3, residues 33-52, form a helix-turn-helix motif with a very similar structure to that found in Cro. 

They started from the sequence of a domain, Bl, from an IgG-binding protein called Protein G. This domain of 56 amino acid residues folds into a four-stranded p sheet and one a helix (Figure 17.16). Their aim was to convert this structure into an all a-helical structure similar to that of Rop (see Chapter 3). Each subunit of Rop is 63 amino acids long and folds into two a helices connected by a short loop. The last seven residues are unstructured and were not considered in the design procedure. Two subunits of Rop form a four-helix bundle (Figure 17.16). 

The properties of optimized helical structures, which were derived from torus C54D and Cs7a, >yps (A), (proposed by Dunlap) and torus C ,o> Dpe (B), (proposed by us) by molecular dynamics were compared. (see Figs. 9 (a) and 10). (Although the torus Cs7f, is thermodynamically stable, helix 57 was found to be thermodynamically unstable 14]. Hereafter, we use helix C to denote a helix consisting of one torus (C ) in one pitch. 

From elongated tori, such as type (C), type (D), and type (E), helical structures are derived. For example, from the type (C) elongated torus of mentioned in 3.2.2, helix C756 (/t = 6, /t2 = 3, L = 1) and... 

Fig. 12. Elongated helical structures (a) helix C75, and (b) helix C2if,ci.

There are several other far less common types of helices found in proteins. The most common of these is the Sjq helix, which contains 3.0 residues per turn (with 10 atoms in the ring formed by making the hydrogen bond three residues up the chain). It normally extends over shorter stretches of sequence than the a-helix. Other helical structures include the 27 ribbon and the 77-helix, which has 4.4 residues and 16 atoms per turn and is thus called the 4.4ig helix. 

The DNA isolated from different cells and viruses characteristically consists of two polynucleotide strands wound together to form a long, slender, helical molecule, the DNA double helix. The strands run in opposite directions that is, they are antiparallel and are held together in the double helical structure through interchain hydrogen bonds (Eigure 11.19). These H bonds pair the bases of nucleotides in one chain to complementary bases in the other, a phenomenon called base pairing. 

DNA is made up ot two intertwined strands. A sugar-phosphate chain makes up the backbone of each, and the two strands are joined by way of hydrogen bonds betwen parrs of nucleotide bases, adenine, thymine, guanine and cytosine. Adenine may only pair with thymine and guanine with cytosine. The molecule adopts a helical structure (actually, a double helical stnrcture or double helix ). 

The ability of DNA to replicate lies in its double-helical structure. There is a precise correspondence between the bases in the two strands. Adenine in one strand always forms two hydrogen bonds to thymine in the other, and guanine always forms three hydrogen bonds to cytosine so, across the helix, the base pairs are always AT and GC (Fig. 19.29). Any other combination would not be held together as well. During replication of the DNA, the hydrogen bonds, which are... 

Early biochemical studies supported the hypothesis that the HRl and the HR2 peptides would interact to form a helical structure (Chen et al. 1995 Lu et al. 1995). This hypothesis was strengthened when X-ray structures were resolved for co-crystals of HRl and HR2 peptides (Chan et al. 1997 Tan et al. 1997 Weissenhom et al. 1997). The results showed that in the six-helix bundle, three HRl domains were packed tightly together in the center of the bundle, with the HR2 domains bound in an antiparallel manner in grooves formed along the HRl core. 

As such, the magainins provide a useful initial target for peptoid-based peptido-mimetic efforts. Since the helical structure and sequence patterning of these peptides seem primarily responsible for their antibacterial activity and specificity, it is conceivable that an appropriately designed, non-peptide helix should be capable of these same activities. As previously described (Section 1.6.2), peptoids have been shown to form remarkably stable hehces, with physical characterishcs similar to those of peptide polyprohne type-I hehces (e.g. cis-amide bonds, three residues per helical turn, and 6A pitch). A faciaUy amphipathic peptoid helix design, based on the magainin structural motif, would therefore incorporate cationic residues, hydrophobic aromatic residues, and hydrophobic aliphathic residues with threefold sequence periodicity. 

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