The nature of the bonds in the peptide backbone plays an important role here. Within each amino acid residue are two bonds with reasonably free rotation:

• The bond between the α ­-carbon and the amino nitrogen of that residue and
• The bond between the ­ α -carbon and the carboxyl carbon of that residue.

The combination of the planar peptide group and the two freely rotating bonds has important implications for the three-dimensional conformations of peptides and proteins.

A peptide-chain backbone can be visualized as a series of playing cards, each card representing a planar peptide group. The cards are linked at opposite corners by swivels, representing the bonds about which there is considerable freedom of rotation (Figure).

The side chains also play a vital role in determining the three-dimensional shape of a protein, but only the backbone is considered in the secondary structure.

The angle  Φ (phi) and Ψ (psi), frequently called Ramachandran angles (after their originator, G. N. Ramachandran), are used to designate rotations around the C-N and C-C bonds, respectively. The conformation of a protein backbone can be described by specifying the values of Φ (phi) and Ψ (psi), for each residue (-180° to 180°).

Two kinds of secondary structures that occur frequently in proteins are the repeating α-helix and β-pleated sheet (or ‑ β-sheet) hydrogen-bonded structures.

The α and β angles repeat themselves in contiguous amino acids in regular secondary structures. The ­ α -helix and ‑ β -pleated sheet are not the only possible secondary structures, but they are by far the most important and deserve a closer look.

α -helix - one of the most frequently encountered folding patterns in the protein backbone.

β -pleated sheet - one of the most important types of secondary structure, in which the protein backbone is almost fully extended with hydrogen bonding between adjacent strands.

The α -Helix

The ­-helix is stabilized by hydrogen bonds parallel to the helix axis within the backbone of a single polypeptide chain.

Counting from the N-terminal end, the C-O group of each amino acid residue is hydrogen bonded to the N-H group of the amino acid four residues away from it in the covalently bonded sequence.

Why is the α ­-helix so prevalent?

The helical conformation allows a linear arrangement of the atoms involved in the hydrogen bonds, which gives the bonds maximum strength and thus makes the helical conformation very stable.

There are 3.6 residues for each turn of the helix, and the pitch of the helix (the linear distance between corresponding points on successive turns) is 5.4 Å.

The angstrom unit, 1 Å = 10^-8 cm = 10-¹⁰ m, is convenient for interatomic distances in molecules, but it is not a Système International (SI) unit.

Nanometers (1 nm = 10^-9 m) and picometers (1 pm = 10^-12 m) are the SI units used for interatomic distances. In SI units, the pitch of the ­ α -helix is 0.54 nm or 540 pm.

See figure shows the structures of two proteins with a high degree of ­ α -helical content. Proteins have varying amounts of α ­-helical structures, varying from a few percent to nearly 100%. Several factors can disrupt the α ­-helix.

The amino acid proline creates a bend in the backbone because of its cyclic structure.

It cannot fit into the ­-helix because

• rotation around the bond between the nitrogen and the ­-carbon is severely restricted, and
• proline’s ­-amino group cannot participate in intrachain hydrogen bonding.

Other localized factors involving the side chains include strong electrostatic repulsion due to the proximity of several charged groups of the same sign, such as groups of positively charged lysine and arginine residues or groups of negatively charged glutamate and aspartate residues.

Another possibility is crowding (steric repulsion) caused by the proximity of several bulky side chains. In the α-helical conformation, all the side chains lie outside the helix; there is not enough room for them in the interior.

Three-dimensional structure of two proteins with substantial amounts of a-helix in their structures

The ­ α -carbon is just outside the helix, and crowding can occur if it is bonded to two atoms other than hydrogen, as is the case with valine, isoleucine, and threonine.

The β -Pleated Sheet

The arrangement of atoms in the  β -pleated sheet conformation differs markedly from that in the ­-helix. The peptide backbone in the  β -sheet is almost completely extended.

Hydrogen bonds can be formed between different parts of a single chain that is doubled back on itself (intrachain bonds) or between different chains (interchain bonds).

If the peptide chains run in the same direction (i.e., if they are all aligned in terms of their N-terminal and C-terminal ends), a parallel pleated sheet is formed. When alternating chains run in opposite directions, an antiparallel pleated sheet is formed (Figure).

The hydrogen bonding between peptide chains in the ‑-pleated sheet gives rise to a repeated zigzag structure; hence, the name “pleated sheet” (Figure 4.5).

Note that the hydrogen bonds are perpendicular to the direction of the protein chain, not parallel to it as in the ­ α -helix.

Irregularities in Regular Structures

Other helical structures are found in proteins. These are often found in shorter stretches than with the ­-helix, and they sometimes break up the regular nature of the ­-helix.

The most common is the 310 helix, which has three residues per turn and 10 atoms in the ring formed by making the hydrogen bond. Other common helices are designated 27 and 4.416, following the same nomenclature as the 310 helix.

A b-bulge is a common nonrepetitive irregularity found in antiparallel ‑-sheets. It occurs between two normal ‑-structure hydrogen bonds and involves two residues on one strand and one on the other. Figure 4.6 shows typical –bulges

B-bulge - a common nonrepetitive irregularity in ‑B-sheets

Protein folding requires that the peptide backbones and the secondary structures be able to change directions. Often a reverse turn marks a transition between one secondary structure and another.

Reverse turns - parts of proteins where the polypeptide chain folds back on itself

For steric (spatial) reasons, glycine is frequently encountered in reverse turns, at which the polypeptide chain changes direction; the single hydrogen of the side chain prevents crowding (Figures A and B).

Because the cyclic structure of proline has the correct geometry for a reverse turn, this amino acid is also frequently encountered in such turns (Figure 4.7C).

Supersecondary Structures and Domains

The a ­-helix, ‑b-pleated sheet, and other secondary structures are combined in many ways as the polypeptide chain folds back on itself in a protein. The combination of ­- and ‑-strands produces various kinds of supersecondary structures in proteins.

The most common feature of this sort is the ‑­‑ unit, in which two parallel strands of ‑-sheet are connected by a stretch of ­-helix (Figure A). An ­­ unit (helix-turn-helix) consists of two antiparallel ­-helices (Figure B).

In such an arrangement, energetically favorable contacts exist between the side chains in the two stretches of helix. In a ‑-meander, an antiparallel sheet is formed by a series of tight reverse turns connecting stretches of the polypeptide chain (Figure C).

Another kind of antiparallel sheet is formed when the polypeptide chain doubles back on itself in a pattern known as the Greek key, named for a decorative design found on pottery from the classical period (Figure E).

A motif is a repetitive supersecondary structure. Protein sequences that allow for a ‑-meander or Greek key can often be found arranged into a ‑-barrel in the tertiary structure of the protein (Figure).

Motif - a repetitive supersecondary structure

Motifs are important and tell us much about the folding of proteins. However, these motifs do not allow us to predict anything about the biological function of the protein because they are found in proteins and enzymes with very dissimilar functions.

Many proteins that have the same type of function have similar protein sequences; consequently, domains with similar conformations are associated with the particular function. Many types of domains have been identified, including three different types of domains by which proteins bind to DNA.

In addition, short polypeptide sequences within a protein direct the posttranslational modification and subcellular localization. For example, several sequences play a role in the formation of glycoproteins (ones that contain sugars in addition to the polypeptide chain).

Other specific sequences indicate that a protein is to be bound to a membrane or secreted from the cell. Still other specific sequences mark a protein for phosphorylation by a specific enzyme.

The Collagen Triple Helix

Collagen, a component of bone and connective tissue, is the most abundant protein in vertebrates. It is organized in water-insoluble fibers of great strength. A collagen fiber consists of three polypeptide chains wrapped around each other in a ropelike twist or triple helix.

Each of the three chains has, within limits, a repeating sequence of three amino acid residues, X-Pro-Gly or X- Hyp-Gly, where Hyp stands for hydroxyproline, and any amino acid can occupy the first position, designated by X.

Proline and hydroxyproline can constitute up to 30% of the residues in collagen. Hydroxyproline (Figure) is formed from the proline by a specific hydroxylating enzyme after the amino acids are linked together.

Hydroxylysine (Figure) also occurs in collagen. In the amino acid sequence of collagen, every third position must be occupied by glycine. The triple helix is arranged so that every third residue on each chain is inside the helix.

Only glycine is small enough to fit into the space available (Figure). The three individual collagen chains are themselves helices that differ from the ­-helix. They are twisted around each other in a superhelical arrangement to form a stiff rod.

This triple helical molecule is called tropocollagen; it is 300 nm (3000 Å) long and 1.5 nm (15 Å) in diameter. The three strands are held together by hydrogen bonds involving the hydroxyproline and hydroxylysine residues.

The molecular weight of the triple-stranded array is about 300,000; each strand contains about 800 amino acid residues. Collagen is both intramolecularly and intermolecularly linked by covalent bonds formed by reactions of lysine and histidine residues. The amount of cross-linking in tissue increases with age.

That is why meat from older animals is tougher than meat from younger animals. Collagen in which the proline is not hydroxylated to hydroxyproline to the usual extent is less stable than normal collagen. Symptoms of scurvy, such as bleeding gums and skin discoloration, are the results of fragile collagen.

The enzyme that hydroxylates proline and thus maintains the normal state of collagen requires ascorbic acid (vitamin C) to remain active. Scurvy is ultimately caused by a dietary deficiency of vitamin C.

Two Types of Protein Conformations:

Fibrous and Globular

It is difficult to draw a clear separation between secondary and tertiary structures. The nature of the side chains in a protein (part of the tertiary structure) can influence the folding of the backbone (the secondary structure).

Comparing collagen with silk and wool fibers can be illuminating. Silk fibers consist largely of the protein fibroin, which, like collagen, has a fibrous structure, but which, unlike collagen, consists largely of ‑-sheets.

Fibers of wool consist largely of the protein keratin, which is largely ­-helical. The amino acids of which collagen, fibroin, and keratin are composed determine which conformation they will adopt, but all are fibrous proteins (Figure A).

A comparison of the shapes of fibrous and globular proteins

Their helical and pleated-sheet sections can be arranged so as to bring the ends of the sequence close to each other in three dimensions. Globular proteins, unlike fibrous proteins, are water-soluble and have compact structures; their tertiary and quaternary structures can be quite complex

Fibrous proteins - proteins whose overall shape is that of a long, narrow rod

Globular proteins - proteins whose overall shape is more or less spherical