a-helix with all hydrogen bonds shown
a-helix top view
Figure 9.13. The a helix: (a) the nitrogen atom in each peptide bond forms a hydrogen bond with the oxygen of the peptide bond four ahead. (b) An a helix, with one hydrogen bond drawn. (c) An a helix, with all the hydrogen bonds drawn. (d) An end-on view of an a helix.
with the disulfide bonds indicated. Lysozyme was the first enzyme to have its three-dimensional structure fully determined (in 1965). Figure 9.12ft shows that structure, with all of the atoms that form the molecule displayed. We see little except an irregular surface. However, if the amino acid side chains are stripped away and the path of the peptide-bonded backbone drawn (Fig. 9.12c), we see that some regions of the protein backbone are ordered in a repeating pattern. Two types of protein backbone organization are common to many proteins. These are named the a helix and the 3 sheet. Figure 9.12d redraws the peptide backbone of lysozyme to emphasize these patterns, with the lengths of peptide participating in p sheets represented as arrows. Collectively these repeating patterns are known as secondary structures. There are other regions of the protein that do not have any such ordered pattern.
In an a helix the polypeptide chain twists around in a spiral, each turn of the helix taking 3.6 amino acid residues. This allows the nitrogen atom in each peptide bond to form a hydrogen bond with the oxygen four residues ahead of it in the polypeptide chain (Fig. 9.13). All the peptide bonds in the helix are able to form such hydrogen bonds, producing a rod in which the amino acid side chains point outward. Because it introduces a kink into the polypeptide chain, proline cannot participate in an a helix.
In a p sheet lengths of polypeptide run alongside each other, and hydrogen bonds form between the peptide bonds of the strands. This generates a sheet that has the side chains protruding above and below it (Fig. 9.14). Along a single strand the side chains alternate up then down, up then down. Because the actual geometry prevents them from being completely flat, they are sometimes called p pleated sheets. A polypeptide chain can form two types of p sheet: Either all of the strands in the p sheet are running in the same direction (Fig. 9.14a) forming a parallel 3 sheet or they can alternate in direction (Fig. 9.14b) making an antiparallel 3 sheet. The polypeptide chains in p sheets are fully extended unlike the chain in an a helix.
In structural proteins like the keratin in hair or the fibroin in silk, the whole polypeptide chain is ordered into one of these secondary structures. Such fibrous proteins have relatively simple repeating shapes and do not have binding sites for other molecules. Most proteins have regions without secondary structures, the precise folding and packing of the amino acids being unique to the protein, side by side with regions of secondary structure. We have seen that secondary structures such as the a helix and p sheet are formed because of hydrogen bonds involving the peptide bonds of the backbone. The three-dimensional structure is held together by various interactions most of which are individually weak but collectively produce stable molecules. These interactions involve the amino acid side chains that interact with one another, with the backbone, with water molecules, and (if there is one) with a prosthetic group or cofactor (page 205). These interactions are hydrogen bonds, electrostatic interactions, van der Waals forces, hydrophobic interactions, and (in some proteins) disulfide bonds.
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