Rotated helical conformation

X-ray diffraction studies indicate the existence of a novel double-stranded DNA helical conformation in which AZ (the rise per base pair) = 0.32 nm and P (the pitch) = 3.36 nm. What are the other parameters of this novel helix (a) the number of base pairs per turn, (b) Abase pair), and (c) c (the true repeat) ... 

PPII helix is illustrated in Figure 8a. It consists of a left-handed extended helical conformation in which the angles of the constituent residues are restricted to values around —78°, +146° corresponding to a region of the Ramachandran surface adjacent to the /3-region (Fig. 8b). This imparts a perfect threefold rotational symmetry to the structure... 

By contrast, in the CD spectrum of the p derivative (39), no bands were observed even at —80°C, as shown in Figure 4.19b. This is because the Cotton band of the p derivative is canceled by an oppositely signed CD band originating in an equivalent proportion of opposite screw sense helical segments (which may be referred to as masked helicity or masked circular dichro-ism ). The difference between the helical conformations of m and p derivatives may be due to the degree of steric hindrance of (S>2-methylbutoxyphenyl rings, since the p derivative may have enough space to freely rotate the... 

Both spectra were almost mirror images of one another as expected from their opposite rotations. The relative intensities of the peaks were nearly proportional to the ratio of the specific rotations. The peaks at 208 and 232 nm may be assigned to the absorptions of the phenyl and ester groups, respectively. The spectral pattern is very similar to that of the copolymer 9 of TrMA with a small amount of (S)-a-methylbenzyl methacrylate illustrated in Figure 5. This also indicates that the large positive rotations of the copolymers 7-9 in Table are attributed to the helical conformation of isotactic TrMA units preferential in one screw sense. 

The average conformation of an a-helix-forming polypeptide was formulated first by Zimm and Bragg (4) and then by several authors (5-9). A comprehensive survey of these theories can be found in a book by Poland and Scheraga 10) or in our companion review article (//). In this section, we outline the formulation of Nagai (5). For convenience of presentation, a peptide residue (-CO-HC R-NH-) is called helix unit when distorted to the a-helical conformation, while it is called random-coil unit when allowed to rotate about the bonds C C and C -N. These units are designated h and c. Thus a particular conformation of an a-helix-forming polypeptide chain is represented by a sequence of h and c. 

In the presence of chiral lithium alkoxides as initiators, chloral forms completely isotactic, crystalline polymers that are insoluble in all solvents (Scheme 71) (166). The polychloral film displays rotation values as high as 3000-5000°. The stereoregular helicity comes about at the stage of the trimer (167). A pure enantiomer of a tert-butoxy-initiated, acetate end-capped pentamer of chloral, which has 4r-helical conformation in both chloroform solution at 35 °C and in the crystalline state, can be obtained by HPLC resolution on a chiral stationary phase (168). 

The helical conformation is defined by the dihedral angles < > and i j, corresponding to rotations about the backbone N-Ca and C°—C bonds, respectively. The < > and i(> angles for an L-residue in a right-handed a-helix are typically -57 and -47°, respectively. 4 The less-stable left-handed a-helix is rarely encountered 5 and will not be included in the methods described here. 

After Ala, residues with long side chains exhibit higher tendencies to form helices due to possible position-dependent, side-chain interactions that are helix stabilizing, such as salt bridges and hydrogen bonding. However, aromatic or ((-branched side chains act as helix breakers in monomeric peptides due to constraints on side-chain rotational entropy when in an a-helical conformation/11,14 201... 

Nuclease behaves like a typical globular protein in aqueous solution when examined by classic hydrodynamic methods (40) or by measurements of rotational relaxation times for the dimethylaminonaphth-alene sulfonyl derivative (48)- Its intrinsic viscosity, approximately 0.025 dl/g is also consistent with such a conformation. Measurements of its optical rotatory properties, either by estimation of the Moffitt parameter b , or the mean residue rotation at 233 nin, indicate that approximately 15-18% of the polypeptide backbone is in the -helical conformation (47, 48). A similar value is calculated from circular dichroism measurements (48). These estimations agree very closely with the amount of helix actually observed in the electron density map of nuclease, which is discussed in Chapter 7 by Cotton and Hazen, this volume, and Arnone et al. (49). One can state with some assurance, therefore, that the structure of the average molecule of nuclease in neutral, aqueous solution is at least grossly similar to that in the crystalline state. As will be discussed below, this similarity extends to the unique sensitivity to tryptic digestion of a region of the sequence in the presence of ligands (47, 48), which can easily be seen in the solid state as a rather anomalous protrusion from the body of the molecule (19, 49). 

Isocyanide Polymers Bulky isocyanides give polymers having a 4 1 helical conformation (115) [154]. An optically active polyisocyanide was first obtained by chromatographic resolution of poly(f-butyl isocyanide) (poly-116) using optically active poly((S)-sec-butyl isocyanide) as a stationary phase and the polymer showing positive rotation was found to possess an M-helical conformation on the basis of CD spectral analysis [155,156]. Polymerization of bulky isocyanides with chiral catalysts also leads to optically active polymers. 

Olefin Polymers Isotactic polymers of propylene and 1-butene obtained by optically active metallocene catalyst (145) have been reported to show large specific rotation in suspension ([a]D-123°, -250° for polypropylene [a]D+130° for polybutene), which was lost when the polymers were completely dissolved or heated [176,177]. The optical activity was ascribed to a helical conformation of the polymer chain with preferential screw sense. 

---