Mechanism of Formation
The spatial configuration of a protein depends on the free rotation around the bonds of the α-carbon atom (with nitrogen and with the carbonyl carbon). However, secondary structure arises due to the formation of hydrogen bonds directly between the elements of the peptide backbone: carbonyl oxygen ($-C=O$) and the hydrogen of the amide group ($-NH-$). Amino acid side chains are not involved in this process.
α-Helix
In an α-helix, hydrogen bonds form between the carbonyl oxygen atom of one amino acid and the amide hydrogen of the fourth amino acid down the chain.
Amino acid side chains are projected outward to the periphery of the helix. Formation of this structure can be disrupted by:
- Positively or negatively charged or excessively bulky side chains (due to electrostatic repulsion and steric hindrance).
- Proline. In its structure, the nitrogen is incorporated into a rigid ring and lacks a hydrogen atom, so it cannot form a hydrogen bond. The fixed bond with the α-carbon causes the peptide chain to bend at the site of proline, disrupting the regularity of the helix.
β-Structure (Pleated Sheet)
A β-structure forms through the interaction of linear segments of the same or different polypeptide chains. Visually, it resembles a folded sheet and is depicted in diagrams by broad arrows.
There are two types of β-structures depending on the direction of the chains:
- Parallel: The N- and C-termini of the interacting segments point in the same direction. They are usually connected by longer loops.
- Antiparallel: The chains run in opposite directions (N- and C-termini are reversed). They are often connected by short β-turns.
Irregular Regions and Classification
A polypeptide chain is not always entirely composed of regular elements. It contains loops, turns, and bends that alter the direction of the chain and help compact the molecule (e.g., connecting parallel β-strands).
Proteins can be categorized based on their predominant secondary structure type. For example, the third category includes proteins consisting exclusively of β-structures (immunoglobulins, superoxide dismutase). The fourth category unites proteins with a very low content of regular structures (small cysteine-rich proteins and metalloproteins). There are also proteins with mixed folding that combine both α-helices and β-sheets.