Secondary structure of proteins

A 3D representation of the protein structure of mioglobin: alpha helices are shown in color and the white random coil; no folded leaves are shown. This protein was the first to have its structure solved by X-ray crystallography, thanks to Max Perutz and Sir John Cowdery Kendrew in 1958, which meant to receive the Nobel Prize in Chemistry in 1962.

The secondary structure of proteins is the local regular folding between nearby amino acid residues of the polypeptide chain. This type of protein structure is adopted thanks to the formation of hydrogen bonds between the carbonyl (-CO-) and amino (-NH-) groups of the carbons involved in the peptide bonds of nearby amino acids in the chain. These are also found in the form of a flattened spiral. There are different models of secondary structures (motifs), the most frequent being the alpha helix and the beta conformation or folded sheet.

Classification

Physical characteristics of the three major protein helices

The most common secondary forms are alpha helices and beta sheets. Other helices, such as the 310 and the π helix, have been postulated to possess energetically favorable hydrogen bonding patterns, but are rarely seen naturally, except for their presence at the ends of alpha helices. Other extended structures such as the polyproline helix and the alpha sheet are rare in the proteinaceous form but are believed to be important intermediates in protein folding.

• Helice alpha: In this structure the polypeptide chain develops in spiral over itself due to the spins produced around the alpha carbon of each amino acid. This structure is maintained thanks to intracatenary hydrogen links formed between the group -C=O of the amino acid "n" and the -NH of the "n+4" (four amino acids later in the chain).

• Beta Folded Sheet: When the main chain is stretched to the maximum that their covalents allow, a spatial configuration called beta chain is adopted. Some protein regions adopt a zigzag structure and partner with each other by establishing intercatenary hydrogen links. All the peptide links participate in these cross links, thus conferring great stability to the structure. The form in beta is a simple conformation formed by two or more parallel polypeptide chains (which run in the same sense) or anti-parallel (which run in opposite directions) and are joined closely by hydrogen bridges and various arrangements between amino acid free radicals. This conformation has a laminar and folding structure, like a accordion.

• Collagen propeller: a particular variety of the secondary structure, characteristic of collagen, protein present in tendons and connective tissue.

• There are other types of propellers: Propeller 3₁₀ (hydrogen poles between the amino acids "n" and "n+3") and propeller κ (genic sources between the amino acids "n" and "n+5"), but are much less common.

• Beta Giros: Sequences of the polypeptide chain with alpha or beta structure, are often connected to each other by so-called beta spins. They are short sequences, with a characteristic conformation that imposes a gross turning of 180 degrees to the main chain of a polypeptide.

Linus Pauling used X-ray crystallography to deduce the secondary structure of proteins. Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang at Stanford University in 1952.

DSSP Algorithm

There are several methods to define the secondary structure of a protein (for example STRIDE, DEFINE), but the Dictionary of Protein Structure (DSSP) method is the most widely used to describe these structures, which uses protein codes. one letter. There are eight types of structures that the DSSP defines:

• G = propeller 3 laps (3₁₀). Minimum length of 3 wastes.
• H = propeller of 4 (alpha propeller). Minimum length of 4 waste.
• I = propeller of 5 turns (Hélice π). Minimum length of 5 waste.
• T = hydrogen union turn (3-4-5)
• E = extended strand in parallel sheet shape and/or anti-parallel. Minimum length of 2 waste.
• B = residue in isolated beta point.
• S = bent (does not have hydrogen unions).
• C = roll (residues that are not part of that mentioned above).