The β-sheet is another form of secondary structure in which all of the peptide bond components are involved in hydrogen bonding (Fig. 2.7A). Because the surfaces of β-sheets appear “pleated,” they are often called βpleated sheets. [Note: Pleating results from successive α-carbons being slightly above or below the plane of the sheet.] Illustrations of protein structure often show β-strands as broad arrows (Fig. 2.7B).
1.
Formation: A β-sheet is formed by two or more peptide chains (βstrands) aligned laterally and stabilized by hydrogen bonds between the carboxyl and amino groups of amino acids that either are far apart in a single polypeptide (intrachain bonds) or are in different polypeptide chains (interchain bonds). The adjacent β-strands are arranged either antiparallel to each other (with the N-termini alternating as shown in Fig. 2.7B) or parallel to each other (with the N-termini together as shown in Fig. 2.7C). On each β-strand, the R groups of adjacent amino acids extend in opposite directions, above and below the plane of the β-sheet. [Note: β-sheets are not flat and have a right-handed curl (twist) when viewed along the polypeptide backbone.] 2.
Comparing α-helices and β-sheets: In β-sheets, the β-strands are almost fully extended and the hydrogen bonds between the strands are perpendicular to the polypeptide backbone (see Fig. 2.7A). In contrast, in α-helices, the polypeptide is coiled and the hydrogen bonds are parallel to the backbone (see Fig. 2.6).
The orientation of the R groups of the amino acid residues in both the αhelix and the β-sheet can result in formation of polar and nonpolar sides in these secondary structures, thereby making them amphipathic.
C. β-Bends (reverse turns, β-turns) β-Bends reverse the direction of a polypeptide chain, helping it form a compact, globular shape. They are usually found on the surface of protein molecules and often include charged residues. [Note: β-Bends were given this name because they often connect successive strands of antiparallel βsheets.] β-Bends are generally composed of four amino acids, one of which may be proline, the amino acid that causes a kink in the polypeptide chain. Glycine, the amino acid with the smallest R group, is also frequently found in β-bends. β-Bends are stabilized by the formation of hydrogen bonds between the first and last residues in the bend.
D. Nonrepetitive secondary structure
Approximately one half of an average globular protein is organized into repetitive structures, such as the α-helix and β-sheet. The remainder of the polypeptide chain is described as having a loop or coil conformation. These nonrepetitive secondary structures are not random but rather simply have a less regular structure than those described above. [Note: The term “random coil” refers to the disordered structure obtained when proteins are denatured (see p. 20).]
E. Supersecondary structures (motifs)
Globular proteins are constructed by combining secondary structural elements (that is, α-helices, β-sheets, and coils), producing specific geometric patterns, or motifs. These form primarily the core (interior) region of the molecule. They are connected by loop regions (for example, β-bends) at the surface of the protein. Supersecondary structures are usually produced by the close packing of side chains from adjacent secondary structural elements. For example, α-helices and β-sheets that are adjacent in the amino acid sequence are also usually (but not always) adjacent in the final, folded protein. Some of the more common motifs are illustrated in Figure 2.8.
Motifs may be associated with particular functions. Proteins that bind to DNA contain a limited number of motifs. The helix–loop–helix motif is an example found in a number of proteins that function as transcription factors (see p. 438).
IV. TERTIARY STRUCTURE