Helical forms

Hydrogen bonding stabilizes some protein molecules in helical forms, and disulfide cross-links stabilize some protein molecules in globular forms. We shall consider helical structures in Sec. 1.11 and shall learn more about ellipsoidal globular proteins in the chapters concerned with the solution properties of polymers, especially Chap. 9. Both secondary and tertiary levels of structure are also influenced by the distribution of polar and nonpolar amino acid molecules relative to the aqueous environment of the protein molecules. Nonpolar amino acids are designated in Table 1.3. 

The first structure, flavodoxin (Figure 4.14a), has one such position, between strands 1 and 3. The connection from strand 1 goes to the right and that from strand 3 to the left. In the schematic diagram in Figure 4.14a we can see that the corresponding a helices are on opposite sides of the p sheet. The loops from these two p strands, 1 and 3, to their respective a helices form the major part of the binding cleft for the coenzyme FMN (flavin mononucleotide). 

Figure 7.2 Three helical forms of DNA, each containing 22 nucleotide pairs, shown in both side and top views. The sugar-phosphate backbone is dark the paired nucleotide bases are light, (a) B-DNA, which is the most common form in cells, (b) A-DNA, which is obtained under dehydrated nonphysiological conditions. Notice the hole along the helical axis in this form, (c) Z-DNA, which can be formed by certain DNA sequences under special circumstances. (Courtesy of Richard Feldmann.)...

The L and the M subunits are firmly anchored in the membrane, each by five hydrophobic transmembrane a helices (yellow and red, respectively, in Figure 12.14). The structures of the L and M subunits are quite similar as expected from their sequence similarity they differ only in some of the loop regions. These loops, which connect the membrane-spanning helices, form rather flat hydrophilic regions on either side of the membrane to provide interaction areas with the H subunit (green in Figure 12.14) on the cytoplasmic side and with the cytochrome (blue in Figure 12.14) on the periplasmic side. The H subunit, in addition, has one transmembrane a helix at the car-boxy terminus of its polypeptide chain. The carboxy end of this chain is therefore on the same side of the membrane as the cytochrome. In total, eleven transmembrane a helices attach the L, M, and H subunits to the membrane. 

In the crystalline region isotactic polystyrene molecules take a helical form with three monomer residues per turn and an identity period of 6.65 A. One hundred percent crystalline polymer has a density of 1.12 compared with 1.05 for amorphous polymer and is also translucent. The melting point of the polymer is as high as 230°C. Below the glass transition temperature of 97°C the polymer is rather brittle. 

It may be prepared in two stereo-regular forms, cis- and trans-. The cii-polymer, which crystallises in zig-zag form, has a of 235°C, whilst the fran -polymer, which crystallises in helical form, melts at the much lower temperature of 145°C. Tensile strengths of both forms are reportedly similar to that of Penton whilst the tensile modulus of 2300 MPa is about twice as high. Unfortunately the material is rather brittle with an impact strength only about half that of polystyrene although this may be improved by orientation. 

The toroidal and helical forms that we consider here are created as such examples these forms have quite interesting geometrical properties that may lead to interesting electrical and magnetic properties, as well as nonlinear optical properties. Although the method of the simulations through which we evaluate the reality of the structure we have imagined is omitted, the construction of toroidal forms and their properties, especially their thermodynamic stability, are discussed in detail. Recent experimental results on toroidal and helically coiled forms are compared with theoretical predictions. 

FIGURE 10.35 The amino acid sequences of several amphipathic peptide antibiotics, a-Helices formed from these peptides cluster polar residues on one face of the helix, with nonpolar residues at other positions. 

Wire rope is most often furnished preformed, but can be furnished non-preformed, upon special request by the purchaser. A preformed rope has the strands shaped to the helical form they assume in the finished rope before the strands have been fabricated into tbe rope. The strands of such preformed rope shall not spring from their normal position when the seizing bands are removed. Cable tool is one of the few applications for which nonpreformed is still used. 

Spiraled wellbore A wellbore that has attained a changing configuration such as a spiral or helical form. 

The phenyl ether oxygen atoms allow the two borazaphenanthrene rings to pivot with respect to each other, therefore this dimeric boronic acid anhydride can potentially exist in two isomeric forms, either face-to-face or helical (Fig. 18). In the face-to-face form the boron atoms of the bis(borazaphe-nanthrene) moieties have syn-orientation, while they have approximate anti-orientation in the helical form. Compound 68 has been characterized by X-ray crystallography in the helical form [109]. The dimensions of the cavity can be described by the transannular C C contacts between the carbon atoms in 2-position of the phenyl ether units, which have values of 5.12 and 6.21 A. 

Fig. 18. The dimeric boronic acid anhydride 68 can potentially exist in a face-to-face or a helical form. X-ray crystallography proves the helical conformation...

Sanborn, T., Wu, C., Zuckermann, R., and Barron, A. Extreme stability of helices formed by water-soluble poly-7M-sub-stituted glycines (polypeptoids) with alpha-chiral side chains. Biopolymers 2002, 63, 12-20. 

Abstract Protoberberine alkaloids and related compounds represent an important class of molecules and have attracted recent attention for their various pharmacological activities. This chapter deals with the physicochemical properties of several isoquinoline alkaloids (berberine, palmatine and coralyne) and many of their derivatives under various environmental conditions. The interaction of these compounds with polymorphic DNA structures (B-form, Z-form, H -form, protonated form, triple helical form and quadruplex form) and polymorphic RNA structures (A-form, protonated form, triple helical form and quadruplex form) reported by several research groups, employing various analytical techniques such as spectrophotometry, spectrofluorimetry, circular dichro-ism, NMR spectroscopy, viscometry as well as molecular modelling and thermodynamic analysis to elucidate their mode and mechanism of action for structure-activity relationships, are also presented. 

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