α- Helix (Secondary structure of proteins)
Shape of the helix: The α-helix is a right-handed coiled strand resembles a curled ribbon.
(L-aminoacids cause steric problems in left handed helix)
α – helices found in proteins are right-handed.
“Core” of α-helix does not have an empty space(atoms in the centre are in close contact)
Formation of α – helix: Hydrogen bonds form within the polypeptide chain in order to create a helical structure.
Bonds: It contains internal hydrogen bonding between aminoacid residues
Within an α – helix hydrogen bonding is between carbonyl oxygen of nth aminoacid and amide hydrogen of (n+4)th aminoacid towards the C terminus of the helix.
The hydrogen bonds make this structure especially stable. The amino acids side – chain substituents fit in next to the N – H groups
Bonding exception: The three amino groups at one end of the helix and the three carbonyl groups at the other end not involved in hydrogen bond formation.
- All helical structures can be described by an nN notation where
- n is the number of residues in one turn of a helix (3.6 for thea-helix)
- N is the number of atoms in the hydrogen bonded loop (13 for the α-helix)
- Alpha helix is a 3.613 Helix
Each hydrogen bond closes a loop containing 13 atoms: The carbonyl oxygen, 11 backbone atoms, and the amide hydrogen.
This α – helix can also be called a 3.613 helix, based on its pitch and hydrogen-bonded loop size.
Orientation of hydrogen bonds in the helix: The hydrogen bonds that stabilises the helix are nearly parallel to the long axis of the helix.
R groups of aminoacids in the α-helix: The R group of the amino acid in an α-helix extend to the outside, where they are free to interact.
Measurements in an α-helix (parameters): In an ideal α helix
The number of amino acid residues required for one complete turn = 3.6 aminoacids
(i.e., approximately 3 2/3 residues: one carbonyl group, three N—Cα—C units, and one nitrogen).
Pitch of a helix = distance along helix axis for 1 full turn = 0.54 nm (5.4 angstroms) / turn
Rise of a helix = distance along helix axis per residue = pitch / n = 0.15 nm (1.5 angstroms) / residue
Aminoacid preference: Certain amino acids are more or less likely to be found in α-helices.
- The amino acid proline posess an unusual R group (which bonds to the amino group to form a ring) which creates a bend in the chain and is not compatible with helix formation. So sometimes proline is called as a “helix breaker
- Proline lacks a hydrogen atom on its amide nitrogen. Proline cannot fully participate in intra helical hydrogen bonding. For these reasons, proline residues are found more often at the ends of α helices than in the interior.
- Proline is typically found in bends.
- Alanine residues are prevalent in the α helices of all classes of proteins. Alanine has a small, uncharged side chain and fits well into the α-helical conformation.
- Tyrosine and asparagine with their bulky side chains are less common in α helices.
- Glycine, whose side chain is a single hydrogen atom, destabilizes α-helical structures since rotation around its α-carbon is so unconstrained. This is the reason why many helices begin or end with glycine residues.
- Gly occurs infrequently as it is very flexible and takes coiled structure different from α-helix.
- Polypeptide with long block of Glu residues will not form an alpha helix at pH 7.
- Bulk shape of Cys, Ser, Thr can destabilize the helix if they are close together in the chain.
Strong Helix formers (Ha): Glu, Ala, Leu, Met
Strong Helix breakers (Ba): Gly, Pro
Positively charged amino acids are often found three residues away from negatively charged amino acids favoring the formation of an ion pair
Two aromatic amino acids are often similarly placed to allow hydrophobic interaction.
Helix dipole: Electric dipole of a peptide bond is transmitted through the hydrogen bonds along an alpha helix resulting in an overall helix dipole.
Negatively charged aminoacids near the amino terminal end stabilizes the helix. Positively charged aminoacid near the end terminal destabilizes the helix.