Proteins are biological polymers composed of amino acids. Amino acids linked by peptide bonds form a polypeptide chain. One or more polypeptide chains twisted into a 3D shape to form a protein.

There are four distinct levels of protein structure. The four levels of the protein structure are distinguished from one another by the degree of complexity in the polypeptide chain.

The different levels of the protein structure are known as primary, secondary, tertiary, and quaternary structure.

The alpha helix and the beta sheet are the most common types of secondary structure of protein. On the other hand, Protein loops are patternless regions which connect two regular secondary structures.

The Constitution of Secondary Structure of Proteins

Secondary structure refers to the regular, repeating spatial arrangement of adjacent amino acid residues in a polypeptide chain. This is maintained by hydrogen bonds between the amide hydrogen and the carbonyl oxygen of the peptide backbone. The major secondary structures are Alpha Helixes and Beta Sheets.

The hydrogen bonds always occurs between C=O and H-N groups but the exact pattern of them is different in an alpha helix and a beta sheet.

Alpha Helix

Alpha helix is a right handed coil of amino acid residues on a polypeptide chain, typically ranging between 4 and 40 residues. This coil held together by hydrogen bonds between the oxygen of C=O on top coil and the hydrogen of N-H on the bottom coil. Such hydrogen bonds are formed exactly every 4 amino acid residues, and each complete turn of the helix is ​​composed of only 3.6 amino acid residues. This regular pattern gives the alpha helix a very definite features with regards to the thickness of the coil and the length of each complete turn along the helix axis.

The structural integrity of an alpha helix is in part dependent on correct steric configuration. Amino acids whose R-groups are too large (tryptophan, tyrosine) or too small (glycine) destabilize alpha helixes. Proline also destabilizes alpha helixes because of its irregular geometry.

Another factor that affects the stability of the alpha helix is ​​the overall dipole moment of the entire helix by the individual dipoles of the C = O group involved in hydrogen bonding. Stable alpha helixes typically end with a charged amino acid to neutralize the dipole moment.

Importance of Alpha Helix

Alpha helixes makes the most efficient use of hydrogen bonding, which is the stickiness between the hydrogen in amino groups and oxygen in the carboxyl groups. It is very stable because all of the peptide groups take part in two hydrogen bonds, one up and one down in the helix axis. It is found in many globular protein.

Beta Sheet

Beta sheet is a regular element of secondary structure in proteins, in which two or more extended strands of the polypeptide chain lie side by side, held together by a regular array of hydrogen bonds between backbone N-H and C=O groups, to form a ridged planar surface.

This can happen in a parallel arrangement or in an anti-parallel arrangement.

In anti-parallel arrangement, the C-terminus end of one segment is on the same side as the N-terminus end of the other segment. In the parallel arrangement, the C-terminus end and the N-terminus end are on the same sides for both segments. The “pleat” occurs because of the alternating planes of the peptide bonds between amino acids; the aligned amino and carbonyl group of each opposite segment alternate their orientation from facing towards each other to facing opposite directions.

The parallel arrangement is less stable because the geometry of the individual amino acid molecules forces the hydrogen bonds to occur at an angle, making them longer and thus weaker. Contrarily, in the anti-parallel arrangement the hydrogen bonds are aligned directly opposite each other, making for stronger and more stable bonds.

Importance of Beta Sheet

Beta sheets consist of extended polypeptide strands (beta strands) connected by a network of hydrogen bonds and occur widely in proteins. The importance of beta sheet interactions in biological processes makes them potential targets for intervention in diseases such as AIDS, cancer, and Alzheimer’s disease.

Loops

Many residues in a given protein will form regions of regular structure, in alpha helixes and beta sheets. The segments of the protein that join these secondary structure elements together, that do not have easily observable regular patterns in their structure, are referred to as loops.

This does not mean, that loops are only a minor component of a protein structure. On average, half of the residues in a protein are found in loops and they are typically found on the surface of the protein, which is largely responsible for its shape, dynamics and physiochemical properties.

Importance of Loops

Connecting different secondary structures together is often not the only purpose of a loop. Loops are vital for the antibodies function. They are often vitally important to a proteins function. For example, they are known to play a vital role in protein-protein interactions, recognition sites, signaling cascades, ligand binding, DNA binding, and enzyme catalysis.