Molecular Biology: Protein Structure and Functions - Stepanov V.M. 2005

Secondary Structure
ß-Structure

The set of angles corresponding to this Structure maps to a broad, deep depression on the Ramachandran plot. Unlike the α-Helix, the β-structure is stabilized by interactions between adjacent segments of the peptide chain, i.e., somewhat more distant contacts. These segments can run in the same direction—parallel β-structure (φ = -119°, ψ ⁼ +113°)—or in opposite directions—antiparallel β-structure (φ = -139°, ψ = +135°).

Let us examine The system of Hydrogen Bonds between two segments of the peptide chain that form a parallel β-structure. In this case (Fig. 5.7), the NH group of a certain residue in segment A forms a Hydrogen bond with the carbonyl group of the i-th residue of peptide chain B, while the carbonyl group of the same amino acid residue in chain A interacts with the NH group of the (i+2)-th residue in the parallel chain B. Crucially, the (i+1)-th residue of chain B is effectively skipped, and its NH and carbonyl groups do not participate in the interaction with chain A. Likewise, far from all C=O and NH groups of chain A participate in interactions with chain B.

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Fig. 5.7. Parallel β-structure.

A model of a parallel β-pleated sheet in flavodoxin is shown. Hydrogen bonds (dashed lines) form 19-membered rings. Arrows indicate the direction of the peptide chains

Thus, two segments of a parallel β-structure are linked by hydrogen bonds, leading to The formation of large 12-membered rings. To reiterate, in each of the chains, only half of the groups capable of forming hydrogen bonds actually participate in the interaction with the neighboring chain. Consequently, each of these peptide chain regions can form an identical system of hydrogen bonds with yet another segment, which in turn can do so with others, and so on. Unlike the α-helix, which is saturated with Hydrogen bonds and therefore unable to interact with other protein regions at the Secondary structure level, each segment of the peptide chain in a β-structure remains open to forming a more extended network of hydrogen bonds.

In an antiparallel β-structure (Fig. 5.8), Hydrogen bonds are formed between oppositely oriented peptide groups of adjacent segments, resulting in alternating 8- and 14-membered rings. Here too, not all, but every second amino acid residue participates in the interaction with the neighboring peptide chain. Half of the peptide groups remain free, making it possible to attach yet another peptide chain segment to each of the two antiparallel segments, and so forth. Thus, the antiparallel β-structure is likewise unsaturated with hydrogen bonds and capable of forming highly extended structures that incorporate multiple peptide chain segments.

Fig. 5.8. Antiparallel β-structure.

Shown is an antiparallel β-pleated sheet in superoxide dismutase. Hydrogen bonds (dashed lines) form alternating 8- and 14-membered rings

The number of amino acid residues in a peptide chain segment forming a β-structure typically ranges from 3 to 8. An extended β-structure—the so-called β-sheet or β-pleated sheet (Fig. 5.9)—most commonly consists of 2 to 6 chains, although their number sometimes reaches ten.

The side chains of adjacent amino acid residues in the peptide chain end up on opposite sides of the β-structure surface. The surface itself has a pleated conformation, with the pleats formed by the α-carbon atoms of residues located in neighboring chains. The side groups projecting from the α-carbon atoms form distinct ridges. This allows for the creation of fairly extensive surfaces saturated with similar types of side chains (e.g., hydrophobic ones). By interacting with each other or with the hydrophobic ridges of α-helices, the hydrophobic surfaces of the β-pleated sheet can contribute to the formation of intramolecular hydrophobic cores that stabilize the Three-Dimensional Cell/13.html">Protein Structure.

It should be noted that The surface of a β-pleated sheet is rarely flat; more often, it is twisted to the left when viewed perpendicularly to the direction of the segments. The angle between adjacent chain segments is about 25°. The repeated occurrence of this motif causes the sheet to twist into a staircase-like structure. As a result, the angle between the outermost peptide chain segments in a β-sheet ranges from 0° in concanavalin A, to 70–80° in deoxyribonuclease I, to 100° in the nucleotide-binding domain of dehydrogenases, and even reaches 220° in Carbonic anhydrase (Fig. 5.10).

Fig. 5.9. β-Pleated sheet.

A — antiparallel β-pleated sheet, top view; dashed lines indicate hydrogen bonds, β-atoms of side chains are blackened. B — side view; the pleating and the arrangement of side groups on both sides of the sheet are clearly visible

Also described are "barrels" formed by the rolling up of an extended β-sheet, where the terminal segments of the peptide chain close in on each other, establishing the hydrogen-bonding network characteristic of β-structures. Obviously, in such cases, the β-structure ceases to be a purely local feature, sometimes spanning the entire protein globule (thus transcending the definition of secondary structure given at the beginning of the chapter). Given this, extended β-pleated sheets, which play a crucial role in forming the Tertiary Structure of Proteins, are referred to by the term supersecondary structure.

Fig. 5.10. Extended β-pleated sheet (in human carbonic anhydrase). Ten β-structure segments (predominantly antiparallel) are twisted relative to one another, forming a supersecondary structure that resembles a spiral staircase. The angle between the first and last segments is close to 220°. The acetylated amino terminus (AcNH) and carboxy terminus (COOH) of the polypeptide chain are indicated

Fig. 5.11. Schematic diagram of secondary structures in the NAD-binding domain of glyceraldehyde-3-phosphate dehydrogenase.

Thin lines indicate hydrogen bonds in α-helices (e.g., from the NH group of residue 19 to the C=O of residue 15, etc.), regions of parallel (from the NH and C=O of residue 3 to the C=O of residue 27 and NH of residue 29, respectively) and antiparallel β-structure (segments 56–61 and 62–67). There are also sequence stretches, such as 134–141, that do not form hydrogen-bonding systems

Fig. 5.11 shows a diagram of the NAD-binding domain of glyceraldehyde-3-phosphate dehydrogenase, illustrating The Diversity of secondary structures within this molecule.