Helical conformation characteristics

FIGURE 7.22 Suspensions of amylose in water adopt a helical conformation. Iodine (b) can insert into the middle of the amylose helix to give a bine color that is characteristic and diagnostic for starch. 

The secondary structure of a protein is the shape adopted by the polypeptide chain—in particular, how it coils or forms sheets. The order of the amino acids in the chain controls the secondary structure, because their intermolecular forces hold the chains together. The most common secondary structure in animal proteins is the a helix, a helical conformation of a polypeptide chain held in place by hydrogen bonds between residues (Fig. 19.19). One alternative secondary structure is the P sheet, which is characteristic of the protein that we know as silk. In silk, protein... 

A peptoid pentamer of five poro-substituted (S)-N-(l-phenylethyl)glycine monomers, which exhibits the characteristic a-helix-like CD spectrum described above, was further analyzed by 2D-NMR [42]. Although this pentamer has a dynamic structure and adopts a family of conformations in methanol solution, 50-60% of the population exists as a right-handed helical conformer, containing all cis-amide bonds (in agreement with modeling studies [3]), with about three residues per turn and a pitch of 6 A. Minor families of conformational isomers arise from cis/trans-amide bond isomerization. Since many peptoid sequences with chiral aromatic side chains share similar CD characteristics with this helical pentamer, the type of CD spectrum described above can be considered to be indicative of the formation of this class of peptoid helix in general. 

These y9 -peptides are not expected to adopt a 3i4-helical conformation in an aqueous environment because of the destabihzing effect of cationic charges. The circular dichroism spectrum of a non-labeled analog of 165 does not display the characteristic signature of the 3i4-helix in aqueous solution however it is highly hehcoidal in MeOH. 

As mentioned above, which of the sequential NOEs d j, d j, and dj j is observed depends on the conformation of the backbone for the residues involved. Repetition of a particular type of connectivity for a sequence of amino acids often occurs in regions of regular secondary structure (19). For example a stretch of d jj-type NOEs is a signature of extended conformation, whereas a sequence of dj j -type NOEs is characteristic of helical conformation. Turns, on the other hand, are characterized by short, distinct patterns of dj j and d j connectivities. 

When the collagen rod can be extracted in the native form it is soluble in acidic solutions, at room temperature. If the solutions are heated, the collagen is denaturated the chains lose their helical conformation. The characteristic temperature of this helix —> coil transition is around 36 C. The solution then contains principally single chains, but also some double and triple chains which were initially covalently bound and some sub-units of the single chains. This product is gelatin. 

The presence of helical conformations in nascent vinyl polymers has often been advanced as an explanation for some of the characteristics of stereoregular... 

Type C repeats are very common in proteins. They are quantal in length, but the repeats themselves do not contain residues that are conserved absolutely in any position. However, several positions within the repeats are strongly conserved in character. A classic example of a Type C repeat is that given by the heptad substructure in a-fibrous proteins. This has the form (a—b-c—d—e—f—g)n with the a and d positions generally occupied by apolar residues, and the e and g positions by charged or hydrophilic residues. The heptad is characteristic of an Q-helical conformation (Cohen and Parry, 1986, 1990 Lupas, 1996), but comparison of any two sequences with a heptad substructure generally reveals only about 15—20% identity. The motif also implies that several Q-helices will aggregate to form a multistranded left-handed coiled-coil rope to shield the apolar stripes on the surface of the Q-helices from the aqueous environment. 

Segment 1A is defined in large part by its underlying heptad repeat, which has the form (a-b-c-d-e-f-g) n, where positions a and d are largely occupied by apolar residues. Such a motif is characteristic of an a-helical conformation that aggregates with others to form a multistranded coiled-coil rope. In the case of IF molecules, there are two strands only, which are aligned parallel to one another and in axial register (see, for example,... 

In terms of physiological conditions, DNA exists almost totally in the double-helical conformation. Certain oligonucleotides also exhibit the ability to form triple-helixes with the DNA double strands. The stability of DNA secondary structures strongly depends on the environmental conditions, such as ionic strength, pH, temperature and solvents. Temperature is the most widely used environmental variable for the quantitative characterization of the helix-coil transitions. A commonly accepted characteristic of the thermal stability of DNA secondary structures is melting temperature, Tm. The binding of cationic species, such as multivalent... 

Chiral amplification phenomena of sergeants and soldiers and majority rule effects, which are characteristic features for dynamic helical polymers [4,58], are, therefore, observed for the noncovalent helix induction in the poly(phenylacetylene)s. For example, when 28 was mixed with 50% ee of 2-amino-1-propanol in DMSO, the complex showed an intense ICD like that of 100% ee. In the presence of a small amount of (R)-39, 28 showed a very weak ICD due to the lack of a single-handed helical conformation. However, the coaddition of the excess bulky, achiral 1-naphthylmethylamine 40 with... 

A zinc(n) meso-meso linked porphyrin oligomer 57 exists in a nonhelical conformation in solution, but may adopt a dynamic helical conformation upon complexation with an achiral urea 58 through complementary hydrogen bonding interactions [115]. In the presence of the chiral diamine (S)-59, the 57-58 complex forms a predominantly one-handed helical conformation, thus showing a characteristic ICD in the absorption region of the porphyrin chromophore. This system may be used to sense the chirality of chiral diamines. 

C-CP-MAS NMR produces a broad resonance with a chemical shift of 31.2 ppm,129 a characteristic of mid-chain methylene carbons of fatty acids in the V-amylose complex. The results showed that up to 43% of amylose in non-waxy rice starch, 33% in oat starch, and 22% in normal maize and wheat starch granules are complexed with lipids at a single helical conformation, and the remaining amylose is free of lipids and is in a random coil conformation.212 Up to 60% of apparent amylose in waxy barley starch is complexed with lipids.212... 

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