Elementary Idea of Secondary Structure of Protein

Proteins fold into different three-dimensional structures in the vast majority of cases. A protein’s natural conformation is the shape into which it folds spontaneously. Because of the chemical properties of their amino acids, many proteins can fold on their own, while others require the aid of molecular chaperones to fold in their natural forms.

A protein structure is characterized as a polymer of amino acids linked together by peptide bonds. Protein structures are formed by the condensation of amino acids, which create peptide bonds. The primary structure of a protein is its sequence of amino acids. The dihedral angles of the peptide bonds determine the secondary structure, while the folding of protein chains in space determines the tertiary structure.

The formation of a quaternary structure occurs when folded polypeptide molecules bind to complex functional proteins. Proteins fold into different three-dimensional structures in the vast majority of cases. A protein’s natural conformation is the shape into which it folds spontaneously. Because of the chemical properties of their amino acids, many proteins can fold on their own, while others require the aid of molecular chaperones to fold in their natural forms.

Also Check: Denaturation of Proteins and its Causes 

Secondary Structure Of The Protein

The interaction between the repeating peptide unit’s hydrogen bond donor and acceptor residues is referred to as a secondary structure. Linus Pauling, an American scientist, predicted the two most essential secondary structures of proteins, the alpha helix, and the beta-sheet, in the early 1950s.

Pauling and his colleagues discovered that, among other things, the folding of peptide chains should retain the bond angles and planar shape of the peptide bond, as well as keep atoms from coming together so tightly that they repelled each other via van der Waal’s interactions.

Finally, Pauling anticipated that hydrogen bonds must be capable of stabilizing peptide backbone folding. The conditions are met by two secondary structures: the alpha helix and the beta-pleated sheet. Pauling’s prognosis was right. The majority of identified secondary structures observed in proteins are of one of two types.

• Secondary protein structure refers to local folded structures that arise inside a polypeptide as a result of interactions between backbone atoms.
• Proteins aren’t just long polypeptide chains.
• The interaction of the peptide link’s amine and carboxyl groups enables these polypeptide chains to fold.
• The structure refers to the various shapes that a long polypeptide chain might adopt.
• They have been discovered to occur in two different sorts of structures: helix and pleated sheet forms.
• This structure results from the regular folding of the polypeptide chain’s backbone caused by hydrogen bonding between the peptide bonds -CO and -NH groups.

However, parts of the protein chain can develop their own local fold, which is simpler and typically takes the form of a spiral, an expanded shape, or a loop. These local folds are known as secondary elements, and they contribute to the protein’s secondary structure.

Alpha helix (α-helix)

1. The Helix is one of the most frequent ways for a polypeptide chain to create all potential hydrogen bonds by twisting into a right-handed screw and hydrogen-bonding the -NH group of each amino acid residue to the -CO of the adjacent turn of the helix. The polypeptide chains twisted together to form a right-handed screw.
2. The alpha helix is made up of H-bonds that are uniformly spaced between residues along a chain. A peptide bond’s amide hydrogen and carbonyl oxygens are H-bond donors and acceptors, respectively.
3. When the chain is traced from the amino to the carboxyl direction, the alpha helix is righthanded. (The helical nomenclature is easiest recognized by pointing the thumb of the right hand upwards—this is the helix’s amino to carboxyl orientation.)
4. The helix then curves in the same direction as the right hand’s fingers.) As the helix twists, the peptide bond’s carbonyl oxygens point upwards toward the downward-facing amide protons, forming the hydrogen bond. The amino acid R groups point away from the helix.
5. The number of residues per turn characterizes helices. The alpha helix does not have an integral number of amino acid residues each turn. The alpha helix has 3.6 residues per turn; in other words, the helix will repeat itself every 36 residues, with ten twists in that interval.

Also Check: MCQs on Amino Acids

Beta-sheet (β-pleated sheet)

1. The polypeptide chains are stretched out next to one another and then connected by intermolecular H-bonds in this configuration.
2. All peptide chains in this structure are stretched to nearly maximum extension and then arranged side by side, bound together by intermolecular hydrogen bonds. Because the structure mimics the pleated folds of draperies, it is known as the β-pleated sheet.
3. The beta-sheet is formed by H-bonding between neighbouring chains’ backbone residues. A single chain establishes H-bonds with neighbouring chains in the beta-sheet, with the donor (amide) and acceptor (carbonyl) atoms facing sideways rather than along the chain as in the alpha helix.
4. Beta sheets can be either parallel, with the chains pointing in the same direction when depicted in the amino to carboxyl-terminal, or antiparallel, with the neighbouring chains pointing in opposite ways.
5. Various amino acids promote the formation of alpha helices, beta-pleated sheets, or loops. Over 1,000 distinct proteins have known primary sequences and secondary structures. Correlation of these sequences and structures indicated that some amino acids are more commonly found in alpha helices, beta sheets, or neither.
6. Alanine, cysteine, leucine, methionine, glutamic acid, glutamine, histidine, and lysine are helix formers. Valine, isoleucine, phenylalanine, tyrosine, tryptophan, and threonine are all beta formers. Serine, glycine, aspartic acid, asparagine, and proline are the most common amino acids found in turns.