Secondary Structures Are the Core Elements of Protein Architecture

The second level in the hierarchy of protein structure consists of the various spatial arrangements resulting from the folding of localized parts of a polypeptide chain; these arrangements are referred to as secondary structures. A single polypeptide may exhibit multiple types of secondary structure depending on its sequence. In the absence of stabilizing noncovalent interactions, a polypeptide assumes a random-coil structure. However, when stabilizing hydrogen bonds form between certain residues, parts of the backbone fold into one or more well-defined periodic structures: the alpha (a) helix, the beta (p) sheet, or a short U-shaped turn. In an average protein, 60 percent of the polypeptide chain exist as a helices and p sheets; the remainder of the molecule is in random coils and turns. Thus, a helices and p sheets are the major internal supportive elements in proteins. In this section, we explore forces that favor the formation of secondary structures. In later sections, we examine how these structures can pack into larger arrays.

The a Helix In a polypeptide segment folded into an a helix, the carbonyl oxygen atom of each peptide bond is hydrogen-bonded to the amide hydrogen atom of the amino acid four residues toward the C-terminus. This periodic arrangement of bonds confers a directionality on the helix because all the hydrogen-bond donors have the same orientation (Figure 3-3).

▲ FIGURE 3-3 The a helix, a common secondary structure in proteins. The polypeptide backbone (red) is folded into a spiral that is held in place by hydrogen bonds between backbone oxygen and hydrogen atoms. The outer surface of the helix is covered by the side-chain R groups (green).

► FIGURE 3-4 The p sheet, another common secondary structure in proteins. (a) Top view of a simple two-stranded p sheet with antiparallel p strands. The stabilizing hydrogen bonds between the p strands are indicated by green dashed lines. The short turn between the p strands also is stabilized by a hydrogen bond. (b) Side view of a p sheet. The projection of the R groups (green) above and below the plane of the sheet is obvious in this view. The fixed angle of the peptide bond produces a pleated contour.

The stable arrangement of amino acids in the a helix holds the backbone in a rodlike cylinder from which the side chains point outward. The hydrophobic or hydrophilic quality of the helix is determined entirely by the side chains because the polar groups of the peptide backbone are already engaged in hydrogen bonding in the helix.

The p Sheet Another type of secondary structure, the p sheet, consists of laterally packed p strands. Each p strand is a short (5- to 8-residue), nearly fully extended polypeptide segment. Hydrogen bonding between backbone atoms in adjacent p strands, within either the same polypeptide chain or between different polypeptide chains, forms a p sheet (Figure 3-4a). The planarity of the peptide bond forces a p sheet to be pleated; hence this structure is also called a p pleated sheet, or simply a pleated sheet. Like a helices, p strands have a directionality defined by the orientation of the peptide bond. Therefore, in a pleated sheet, adjacent p strands can be oriented in the same (parallel) or opposite (antiparallel) directions with respect to each other. In both arrangements, the side chains project from both faces of the sheet (Figure 3-4b). In some proteins, p sheets form the floor of a binding pocket; the hydrophobic core of other proteins contains multiple p sheets.

Turns Composed of three or four residues, turns are located on the surface of a protein, forming sharp bends that redirect the polypeptide backbone back toward the interior. These short, U-shaped secondary structures are stabilized by a hydrogen bond between their end residues (see Figure 3-4a). Glycine and proline are commonly present in turns. The lack of a large side chain in glycine and the presence of a built-in bend in proline allow the polypeptide backbone to fold into a tight U shape. Turns allow large proteins to fold into highly compact structures. A polypeptide backbone also may contain longer bends, or loops. In contrast with turns, which ex hibit just a few well-defined structures, loops can be formed in many different ways.

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