Figure 3–7 The regular conformation of the polypeptide backbone in the α helix and the β sheet. The α helix is shown in (A) and (B). The N–H of every peptide bond is hydrogen-bonded to the C=O of a neighboring peptide bond located four peptide bonds away in the same chain. Note that all of the N–H groups point up in this diagram and that all of the C=O groups point down (toward the C-terminus); this gives a polarity to the helix, with the C-terminus having a partial negative and the N-terminus a partial positive charge (Movie 3.2). The β sheet is shown in (C) and (D). In this example, adjacent peptide chains run in opposite (antiparallel) directions. Hydrogen-bonding between peptide bonds in different strands holds the individual polypeptide chains (strands) together in a β sheet, and the amino acid side chains in each strand alternately project above and below the plane of the sheet (Movie 3.3). (A) and (C) show all the atoms in the polypeptide backbone, but the amino acid side chains are truncated and denoted by R. In contrast, (B) and (D) show only the carbon and nitrogen backbone atoms.
The cores of many proteins contain extensive regions of β sheet. As shown in Figure 3–8, these β sheets can form either from neighboring segments of the polypeptide backbone that run in the same orientation (parallel chains) or from a polypeptide backbone that folds back and forth upon itself, with each section of the chain running in the direction opposite to that of its immediate neighbors (antiparallel chains). Both types of β sheet produce a very rigid structure, held together by hydrogen bonds that connect the peptide bonds in neighboring chains (see Figure 3–7C).
An α helix is generated when a single polypeptide chain twists around on itself to form a rigid cylinder. A hydrogen bond forms between every fourth peptide bond, linking the C=O of one peptide bond to the N–H of another (see Figure 3–7A). This gives rise to a regular helix with a complete turn every 3.6 amino acids. The SH2 protein domain illustrated in Figure 3–6 contains two α helices, as well as a three-stranded antiparallel β sheet.
Regions of α helix are abundant in proteins located in cell membranes, such as transport proteins and receptors. As we discuss in Chapter 10, those portions of a transmembrane protein that cross the lipid bilayer usually cross as α helices composed largely of amino acids with nonpolar side chains. The polypeptide backbone, which is hydrophilic, is hydrogen-bonded to itself in the α helix and shielded from the hydrophobic lipid environment of the membrane by its protruding nonpolar side chains (see also Figure 3–75A).
In other proteins, α helices wrap around each other to form a particularly stable structure, known as a coiled-coil. This structure can form when the two (or in some cases, three or four) α helices have most of their nonpolar (hydrophobic) side chains on one side, so that they can twist around each other with these side chains facing inward (Figure 3–9). Long rodlike coiled-coils provide the structural framework for many elongated proteins. Examples are α-keratin, which forms the intracellular fibers that reinforce the outer layer of the skin and its appendages, and the myosin molecules responsible for muscle contraction.
Even a small protein molecule is built from thousands of atoms linked together by precisely oriented covalent and noncovalent bonds. Biologists are aided in visualizing these extremely complicated structures by various graphic and computer-based three-dimensional displays. The student resource site that accompanies this book contains computer-generated images of selected proteins, displayed and rotated on the screen in a variety of formats.