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Berg JM, Tymoczko JL, Stryer L. Biochemistry. 5th edition. New York: W H Freeman; 2002.

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Biochemistry. 5th edition.

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Section 3.3Secondary Structure: Polypeptide Chains Can Fold Into Regular Structures Such as the Alpha Helix, the Beta Sheet, and Turns and Loops

Can a polypeptide chain fold into a regularly repeating structure? In 1951, Linus Pauling and Robert Corey proposed two periodic structures called the α helix (alpha helix) and the β pleated sheet (beta pleated sheet). Subsequently, other structures such as the β turn and omega (Ω) loop were identified. Although not periodic, these common turn or loop structures are well defined and contribute with α helices and β sheets to form the final protein structure.

Structural Insights

Image mouse.jpg appearing throughout the book, are molecular modeling-based tutorials that enable you to review structure and learn what the latest research tells us about the workings of the molecule. To access, go to the Web site: www.whfreeman.com/biochem5, and select the chapter, Structural Insights, and the title.

Structural Insights, Elements of Protein Structure

Image mouse.jpg provides interactive representations of some of the important elements of protein architecture described in this chapter, including a summary of secondary structure motifs.

3.3.1. The Alpha Helix Is a Coiled Structure Stabilized by Intrachain Hydrogen Bonds

In evaluating potential structures, Pauling and Corey considered which conformations of peptides were sterically allowed and which most fully exploited the hydrogen-bonding capacity of the backbone NH and CO groups. The first of their proposed structures, the α helix, is a rodlike structure (Figure 3.29). A tightly coiled backbone forms the inner part of the rod and the side chains extend outward in a helical array. The α helix is stabilized by hydrogen bonds between the NH and CO groups of the main chain. In particular, the CO group of each amino acid forms a hydrogen bond with the NH group of the amino acid that is situated four residues ahead in the sequence (Figure 3.30). Thus, except for amino acids near the ends of an α helix, all the main-chain CO and NH groups are hydrogen bonded. Each residue is related to the next one by a rise of 1.5 Å along the helix axis and a rotation of 100 degrees, which gives 3.6 amino acid residues per turn of helix. Thus, amino acids spaced three and four apart in the sequence are spatially quite close to one another in an α helix. In contrast, amino acids two apart in the sequence are situated on opposite sides of the helix and so are unlikely to make contact. The pitch of the α helix, which is equal to the product of the translation (1.5 Å) and the number of residues per turn (3.6), is 5.4 Å. The screw sense of a helix can be right-handed (clockwise) or left-handed (counterclockwise). The Ramachandran diagram reveals that both the right-handed and the left-handed helices are among allowed conformations (Figure 3.31). However, right-handed helices are energetically more favorable because there is less steric clash between the side chains and the backbone. Essentially all α helices found in proteins are right-handed. In schematic diagrams of proteins, α helices are depicted as twisted ribbons or rods (Figure 3.32).

Screw sense—

Describes the direction in which a helical structure rotates with respect to its axis. If, viewed down the axis of a helix, the chain turns in a clockwise direction, it has a right-handed screw sense. If the turning is counterclockwise, the screw sense is left-handed.

Figure 3.29. Structure of the α Helix.

Figure 3.29

Structure of the α Helix. (A) A ribbon depiction with the α-carbon atoms and side chains (green) shown. (B) A side view of a ball-and-stick version depicts the hydrogen bonds (dashed lines) between NH and CO groups. (C) An end view shows (more...)

Figure 3.30. Hydrogen-Bonding Scheme For an α helix.

Figure 3.30

Hydrogen-Bonding Scheme For an α helix. In the α helix, the CO group of residue n forms a hydrogen bond with the NH group of residue n+ 4.

Figure 3.31. Ramachandran Diagram for Helices.

Figure 3.31

Ramachandran Diagram for Helices. Both right- and left-handed helices lie in regions of allowed conformations in the Ramachandran diagram. However, essentially all α helices in proteins are right-handed.

Figure 3.32. Schematic Views OF α Helices.

Figure 3.32

Schematic Views OF α Helices. (A) A ball-and-stick model. (B) A ribbon depiction. (C) A cylindrical depiction.

Pauling and Corey predicted the structure of the α helix 6 years before it was actually seen in the x-ray reconstruction of the structure of myoglobin. The elucidation of the structure of the α helix is a landmark in biochemistry because it demonstrated that the conformation of a polypeptide chain can be predicted if the properties of its components are rigorously and precisely known.

The α-helical content of proteins ranges widely, from nearly none to almost 100%. For example, about 75% of the residues in ferritin, a protein that helps store iron, are in α helices (Figure 3.33). Single α helices are usually less than 45 Å long. However, two or more α helices can entwine to form a very stable structure, which can have a length of 1000 Å (100 nm, or 0.1 μm) or more (Figure 3.34). Such α-helical coiled coils are found in myosin and tropomyosin in muscle, in fibrin in blood clots, and in keratin in hair. The helical cables in these proteins serve a mechanical role in forming stiff bundles of fibers, as in porcupine quills. The cytoskeleton (internal scaffolding) of cells is rich in so-called intermediate filaments, which also are two-stranded α-helical coiled coils. Many proteins that span biological membranes also contain α helices.

Figure 3.33. A Largely α Helical Protein.

Figure 3.33

A Largely α Helical Protein. Image mouse.jpg Ferritin, an iron-storage protein, is built from a bundle of α helices.

Figure 3.34. An α -Helical Coiled Coil.

Figure 3.34

An α -Helical Coiled Coil. Image mouse.jpg The two helices wind around one another to form a superhelix. Such structures are found in many proteins including keratin in hair, quills, claws, and horns.

3.3.2. Beta Sheets Are Stabilized by Hydrogen Bonding Between Polypeptide Strands

Pauling and Corey discovered another periodic structural motif, which they named the β pleated sheet (β because it was the second structure that they elucidated, the α helix having been the first). The β pleated sheet (or, more simply, the β sheet) differs markedly from the rodlike α helix. A polypeptide chain, called a β strand, in a β sheet is almost fully extended rather than being tightly coiled as in the α helix. A range of extended structures are sterically allowed (Figure 3.35).

Figure 3.35. Ramachandran Diagram For β Strands.

Figure 3.35

Ramachandran Diagram For β Strands. The red area shows the sterically allowed conformations of extended, β-strand-like structures.

The distance between adjacent amino acids along a β strand is approximately 3.5 Å, in contrast with a distance of 1.5 Å along an α helix. The side chains of adjacent amino acids point in opposite directions (Figure 3.36). A β sheet is formed by linking two or more β strands by hydrogen bonds. Adjacent chains in a β sheet can run in opposite directions (antiparallel β sheet) or in the same direction (parallel β sheet). In the antiparallel arrangement, the NH group and the CO group of each amino acid are respectively hydrogen bonded to the CO group and the NH group of a partner on the adjacent chain (Figure 3.37). In the parallel arrangement, the hydrogen-bonding scheme is slightly more complicated. For each amino acid, the NH group is hydrogen bonded to the CO group of one amino acid on the adjacent strand, whereas the CO group is hydrogen bonded to the NH group on the amino acid two residues farther along the chain (Figure 3.38). Many strands, typically 4 or 5 but as many as 10 or more, can come together in β sheets. Such β sheets can be purely antiparallel, purely parallel, or mixed (Figure 3.39).

Figure 3.36. Structure of a β Strand.

Figure 3.36

Structure of a β Strand. The side chains (green) are alternately above and below the plane of the strand.

Figure 3.37. An Antiparallel β Sheet.

Figure 3.37

An Antiparallel β Sheet. Adjacent β strands run in opposite directions. Hydrogen bonds between NH and CO groups connect each amino acid to a single amino acid on an adjacent strand, stabilizing the structure.

Figure 3.38. A Parallel β Sheet.

Figure 3.38

A Parallel β Sheet. Adjacent β strands run in the same direction. Hydrogen bonds connect each amino acid on one strand with two different amino acids on the adjacent strand.

Figure 3.39. Structure of a Mixed β Sheet.

Figure 3.39

Structure of a Mixed β Sheet.

In schematic diagrams, β strands are usually depicted by broad arrows pointing in the direction of the carboxyl-terminal end to indicate the type of β sheet formed—parallel or antiparallel. More structurally diverse than α helices, β sheets can be relatively flat but most adopt a somewhat twisted shape (Figure 3.40). The β sheet is an important structural element in many proteins. For example, fatty acid-binding proteins, important for lipid metabolism, are built almost entirely from β sheets (Figure 3.41).

Figure 3.40. A Twisted β Sheet.

Figure 3.40

A Twisted β Sheet. (A) A ball-and-stick model. (B) A schematic model. (C) The schematic view rotated by 90 degrees to illustrate the twist more clearly.

Figure 3.41. A Protein Rich in β Sheets.

Figure 3.41

A Protein Rich in β Sheets. Image mouse.jpg The structure of a fatty acid-binding protein.

3.3.3. Polypeptide Chains Can Change Direction by Making Reverse Turns and Loops

Most proteins have compact, globular shapes, requiring reversals in the direction of their polypeptide chains. Many of these reversals are accomplished by a common structural element called the reverse turn (also known as the β turn or hairpin bend), illustrated in Figure 3.42. In many reverse turns, the CO group of residue i of a polypeptide is hydrogen bonded to the NH group of residue i + 3. This interaction stabilizes abrupt changes in direction of the polypeptide chain. In other cases, more elaborate structures are responsible for chain reversals. These structures are called loops or sometimes Ω loops (omega loops) to suggest their overall shape. Unlike α helices and β strands, loops do not have regular, periodic structures. Nonetheless, loop structures are often rigid and well defined (Figure 3.43). Turns and loops invariably lie on the surfaces of proteins and thus often participate in interactions between proteins and other molecules. The distribution of α helices, β strands, and turns along a protein chain is often referred to as its secondary structure.

Figure 3.42. Structure of a Reverse Turn.

Figure 3.42

Structure of a Reverse Turn. The CO group of residue i of the polypeptide chain is hydrogen bonded to the NH group of residue i + 3 to stabilize the turn.

Figure 3.43. Loops on a Protein Surface.

Figure 3.43

Loops on a Protein Surface. Image mouse.jpg A part of an antibody molecule has surface loops (shown in red) that mediate interactions with other molecules.

By agreement with the publisher, this book is accessible by the search feature, but cannot be browsed.

Copyright © 2002, W. H. Freeman and Company.
Bookshelf ID: NBK22580

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