SECONDARY STRUCTURE OF PROTEINS: CHARACTERISTICS - BIOLOGY - 2024

The secondary structure of proteins is the name by which the locally folded conformation of some parts of the polypeptide chain is defined. This structure consists of several patterns that are repeated on a regular basis.

There are many ways in which protein chains fold. However, only a few of these forms are very stable. In nature, the most common forms that proteins take are the α helix as well as the β sheet. These structures can be described by the bond angles ψ (psi), and φ (phi) of the amino acid residues.

Diagram and model of balls and rods of the alpha helix of proteins (secondary structure). Taken and edited from: Alejandro Porto.

The interactions that are established between the side chains of the amino acid residues can help stabilize or, conversely, destabilize the secondary structure of proteins. The secondary structure can be observed in the constitution of many fibrous proteins.

History

In the 30s of the last century, William Atsbury, working with X-rays, found that the protein of the hair, as well as that of the porcupine quills, had segments in their structure that were regularly repeated.

Based on these results, and with the knowledge of the importance that hydrogen bonds represent in the orientation of the polar groups of peptide bonds, William Pauling and collaborators, consequently, hypothetically determined the possible regular conformations that proteins could possess.

Pauling and his collaborators, in the decade of the 50s, established several postulates that had to be fulfilled in the bonds of polypeptide chains, among them, and in the first place, that two atoms cannot approach each other at a distance less than that of their respective radios of Van der Waals.

They also indicated that non-covalent bonds are needed to stabilize the folding of the chains.

Based on these postulates and previous knowledge, and using molecular models, they were able to describe some regular conformations of proteins, including those that were later shown to be the most frequent in nature, such as the α helix and the β sheet..

Α helix

It is the simplest secondary structure, where the polypeptide chain is arranged in a rolled and compacted form around an imaginary axis. Furthermore, the side chains of each amino acid protrude from this helical backbone.

The amino acids, in this case, are arranged so that they have bond angles ψ of -45 ° to -50 °, and φ of -60 °. These angles refer to the bond between the α-carbon and the oxygen of the carbonyl and the bond between the nitrogen and the α-carbon of each amino acid, respectively.

Additionally, scientists have determined that for each turn of the α helix 3.6 amino acid residues are present and that this turn is always dextrorotatory in proteins. In addition to being the simplest structure, the α-helix is ​​the predominant form in α-keratins, and about 25% of the amino acids in globular proteins adopt this structure.

The α helix is ​​stabilized due to its numerous hydrogen bonds. Thus, in each turn of the helix, three or four links of this type are established.

In hydrogen bonds, the nitrogen of a peptide bond and the oxygen atom of the carbonyl group of the subsequent fourth amino acid interact, in the direction of the amino-terminal side of that chain.

Scientists have shown that an α-helix can be formed with polypeptide chains made up of L- or D-amino acids, provided that all amino acids have the same stereoisomeric configuration. In addition, natural L-amino acids can form α-helices with both right and left turn.

However, not all polypeptides can form stable α-helices, since their primary structure affects its stability. The R chains of some amino acids can destabilize the structure, preventing the conformation of the α helices.

Β sheet

In the β sheet, or β folded sheet, each one of the amino acid residues has a 180 ° rotation with respect to the preceding amino acid residue. In this way, the result is that the skeleton of the polypeptide chain remains extended and in a zigzag or accordion shape.

Accordion-folded polypeptide chains can be placed adjacent to each other and produce linear hydrogen bonds between both chains.

Two adjacent polypeptide chains can be arranged in parallel, that is, both can be oriented in the amino-carboxyl direction, forming the parallel β-sheet; or they may be located in opposite directions, the antiparallel β sheet then being formed.

Side chains of adjacent amino acid residues protrude from the chain backbone in opposite directions, resulting in an alternating pattern. Some protein structures limit the amino acid types of the β structures.

For example, in densely packed proteins, short R chain amino acids, such as glycine and alanine, are more frequent at their contact surfaces.

The β sheet of the secondary structures of proteins. Taken and edited from: Preston Manor School + JFL.

Other conformations of the secondary structure

Propeller 3

This structure is characterized by presenting 3 amino acid residues per turn, instead of the 3.6 presented by the α helix and a hydrogen bonding loop made up of 10 elements. This structure has been observed in some proteins, but it is not very common in nature.

Π helix

This structure, on the other hand, presents 4.4 amino acid residues per spiral turn and a 16-membered loop of hydrogen bonds. Although this configuration is sterically possible, it has never been observed in nature.

The possible cause of this may be its hollow center, too large to allow the Van der Waals forces to act, which would help stabilize the structure, and yet it is too small to allow the passage of water molecules.

Super secondary structure

Supersecondary structures are combinations of secondary structures of α-helices and β-folded sheets. These structures can occur in many globular proteins. There are different possible combinations, each of which has its own characteristics.

Some examples of supersecondary structures are: the βαβ unit, in which two parallel β sheets are joined by an α-helix segment; the αα unit, characterized by two successive α-helices but separated by a non-helical segment, associated by compatibility of their side chains.

Several β sheets can be folded on itself giving a β barrel configuration, while an antiparallel β sheet folded on itself constitutes a super-secondary structure called a Greek key.

References

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