Helix hydrogen bonds

Fic. 10.—Parallel packing arrangement of 6-fold, A-amylose (8) molecules, (a) A stereo side view of less than 2 turns of a pair of double helices 10.62 A (=al2) apart. The two strands in each helix are distinguished by open and filled bonds, and the helix axis is also drawn, for convenience. Note that atom 0-6 mediates both intra- and inter-double helix hydrogen bonds. 

Fig. 30. — Packing arrangement of 4-fold antiparallel double helices of potassium hyaluronate (32). (a) Stereo view of a unit cell approximately normal to the line of separation of the two helices. The two chains in each duplex, drawn in open and filled bonds for distinction, are linked by not only direct hydrogen bonds, but also water bridges. Inter double-helix hydrogen bonds are mediated between hydroxymethyl and iV-acetyl groups. Potassium ions (crossed circles) at special positions have only a passive role in the association of hyaluronate chains.

Figure 6. Molecular drawings of the best arrangement of two anti-parallel double-helices, a) Projection perpendicular to the chain axis, b) Projection along the chain axis. Inter double-helix hydrogen bonds are shown as dotted lines.

Monte Carlo and molecular dynamics calculations predict that, in aqueous solutions, the a-helix is substantially more stable than the 310-helix for (Ala), 79 and even for a decamer of Aib. 80 Thus, it seems very unlikely that Ala-rich peptides in water have any significant level of molecules that are wholly or largely in the 310-helix. However, isolated 310-helix hydrogen bonds or perhaps short stretches of 310-helix near the termini are possible. High-resolution NMR of the peptides Ac-(A4K)A-NH2 and Ac-AMAAKAWAAKAAAARA-NH2 81 have led to estimates of about 50% 3i0-helix population at the termini and 25% in the interior. The CD spectrum for a mixed a-310-helix has not been determined. 

Figure 10.12 Schematic representation of alpha helix. Hydrogen bonds (dotted) connect carbonyl oxygens (red) to amino nitrogens (blue) four amino-acid units down the chain.

Figure 4. Elements of secondary structure. (A) The hydrogen-bonding pattern of an a-helix. Hydrogen bonds (denoted by dashed lines) form between residues four positions away from each other in the helix. Unmarked atoms are hydrogens. (B) Two-dimensional projections of the hydrogen-bonding patterns of parallel and antiparallel pleated sheets. Parallel and antiparallel pleated-sheets have different three-dimensional structures.

Figure 7.24 The a-helix (a) the succession of carbon and nitrogen atoms along the backbone of an a-helix, hydrogen bonds form between O atoms on carbon and H atoms on nitrogen linked by dashed lines, R represents a general organic side-group and for clarity not all hydrogen atoms are shown (b) schematic depiction of the coiled a-helix, with four hydrogen bonds indicated by double headed arrows (c) cartoon depiction of an a-helix as a coiled ribbon...

Figure 6. AB projection of the unit cell of the dry form of (1 3)- -D-glucan showing the inter triple helix hydrogen bonds. The intrachain hydrogen bonds of...

An example of a protein which has a well studied secondary structure is keratin, found in hair. Each protein molecule in keratin is arranged in the shape of a spiral, called a helix. Hydrogen bonding holds the helix together, by linking to different sections of the same chain. The arrangement of the spiral in keratin is called an alpha helix. This means that it is a helix with a right-handed turn, as in Fig. 18.4. 

FIGURE 1 5.22 Complementary hydrogen bonding in the DNA double helix. Hydrogen bonds in the thymine-adenine (T—A) and cytosine-guanine (C—G) pairs stabilize the double helix. 

In a DNA double helix, hydrogen bonding occurs between... 

Fig. 10.23 Three examples of zipper type junction zones double helix, hydrogen-bonded ladder (with small loops), and eggbox junction. (Reprinted with permission from Ref. [67].)...

In the a helix, hydrogen bonds form between the oxygen... 

Figure 1. The four base pairs used to construct the double helix hydrogen bonds (IIIII).

Fig. 3.3. Secondary structure of proteins. A. Polypeptide chains in the j8-form associated to give a pleated sheet structure. B. Right handed a-helix structure of the polypeptide chain side chains of amino acid residues labelled R. Bold broken line traces the turns of the helix. Hydrogen bonds involved in associating 8-chains and in stabilising the a-helix as less bold broken lines (between oxygen and hydrogen atoms). (From Paul Doty, Scientific American Reprint, No. 7, Sept. 1957.)...

---