Secondary structure in biochemistry and structural biology refers to the general three-dimensional structure of local segments of biopolymers like proteins and nucleic acids (DNA/RNA). It does not give the exact specifications of atomic positions in three-dimensional space, which are well thought-out in the tertiary structure. Secondary structure finds its format definition by the hydrogen bonds of the biopolymer, as observed in an atomic-resolution structure. In case of proteins, the patterns of hydrogen bonds between backbone amide and carboxyl groups define the secondary structure .In nucleic acids; the hydrogen bonding between the nitrogenous bases defines the secondary structure.
In case of proteins, on the other hand, the secondary structure has a less formal definition because of the fact that hydrogen bonding is associated with other structural features.
Alpha-helix is the most commonly occurring secondary structure in proteins. Alpha-helix structure was first predicted by Linus Pauling and was later confirmed by the determination of the first three-dimensional structure of myoglobin by Max Perutz and John Kendrew. An example of an alpha-helix is shown on the figure below.
The alpha helix (α-helix) basically is a right-handed coiled or spiral conformation, where every backbone N-H group contributes a hydrogen bond to the backbone C=O group of the amino acid four residues earlier. This secondary structure is also occasionally known by the name classic Pauling-Corey-Branson alpha helix. α-helices are the most common protein structural element that crosses biological membranes), it is assumed because of the fact that the helical structure can suit all backbone hydrogen-bonds internally, parting no polar groups uncovered to the membrane if the side chains are hydrophobic
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The β sheet (also β-pleated sheet) is the second type of regular secondary structure in proteins; only to some extent is less common in comparison to alpha helix. Beta sheets is made up of beta strands which are connected in lateral direction by the means of minimum two or three backbone hydrogen bonds, thereby giving a formation of a normally twisted, pleated sheet. An extension of polypeptide chain which is characteristically 3 -10 amino acids long with backbone in an approximately fully extended conformation is called a beta strand. In many human diseases such as amyloidoses (for e.g. Alzheimer’s disease) there has been formation of protein aggregation by means of higher-level association of β sheets.
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