One of the most common type of secondary structure found in proteins is the α-helix. Existence of this type of structure was first predicted by Linus Pauling. Linus Carl Pauling was an American chemist, biochemist, peace activist, author, educator, and husband of American human rights activist Ava Helen Pauling.
But after several years of his prediction and was confirmed when the first three-dimensional structure of a protein, myoglobin (by Max Perutz and John Kendrew) was determined by X-ray crystallography.
To give you a better impression of how a helix looks like, only the main chain of the polypeptide (a linear organic polymer consisting of a large number of amino-acid residues bonded together in a chain, forming part of (or the whole of) a protein molecule) is show in the figure, no side chains. There are 3.6 residues/turn in an α-helix, which means that there is one residue every 100 degrees of rotation (360/3.6). Each residue is translated 1.5 Å along the helix axis, which gives a vertical distance of 5.4 Å between structurally equivalent atoms in a turn (pitch of a turn). The α-helix is the major structural element in proteins.
An example of an α-helix is shown on the figure below, such type of representation of a protein structure is called sticks representation.
In figure-2, When looking at the helix in the figure below, we notice how the carbonyl oxygen atoms C=O (shown in red) point in one direction, towards the amide NH groups 4 residues away (i, i+4). Together these groups form a hydrogen bond, one of the main forces in the stabilization of secondary structure in proteins. The hydrogen bonds are shown on the right figure as dashed lines. It is found that most of the alpha helices in protein are right handed
The second major type of secondary structure in proteins is the β-sheet. β-sheets consist of several β-strands, stretched segments of the polypeptide chain kept together by a network of hydrogen bonds.he β-sheet (also β-pleated sheet) is a common motif of regular secondary structure in proteins. Beta sheets consist of beta strands (also β-strand) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. A β-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation. The supramolecular association of β-sheets has been implicated in formation of the protein aggregates and fibrils observed in many human diseases, notably the amyloidoses such as Alzheimer’s disease.
An example of a β-sheet with the stabilizing hydrogen bonds shown as dashed lines is shown on the figure below:
The figure shows how hydrogen bonds link different segments of the polypeptide chain. These segments do not need to follow to each other in the sequence and may be located in different regions of the polypeptide chain.
The same β-sheet is shown on the figure below, this time in the context of the 3D structure to which it belongs and in a so-called “ribbon” representation (the coloring here is according to secondary structure – β-sheets in yellow and helices in magenta). In the figure each β−strand is represented by an arrow, which defines its direction starting from the N-terminus to the C-terminus. When the strand arrows point in the same direction, we call such β-sheet parallel:
When the strand arrows point in opposite directions, the sheet is anti-parallel. In the next figure you can see an example of a protein structure with an anti-parallel β-sheet:
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