alpha helix

Secondary Protein Structures

Alph-Helix:

Predicted by Linus Pauling and Core in 1951. Alpha-Helix contains 3.6 amino acid residues per turn, 5.4 Angstroms per turn. The helix is held together by hydrogen bonds between Oxygens and Amines, such that the Amine of the n-th residue is hydrogen bonded to the n-4th residue’s oxygen. This configuration makes the R-groups stick out away from the center of the helix. 

The hydrogen bonding through the length of an Alpha-Helix produces an electric dipole inducing partial positive charge at the N-terminus and a partial negative charge at the C-terminus. The hydrogen bonding pattern makes the four amine-groups closest to the N-terminus and the four carbonyl oxygens closest to the C-terminus not hydrogen bonded, therefore the partial charges are distributed amongst these residues. This buildup of partial charge causes irregular or more strained Alpha-Helix conformations at the opposing termini. 

Some residues are not favored in Alpha-Helices. Polar residues ( Serine Ser S, Asparagine Asn N, Aspartate Asp D, Threonine Thr T) disrupt the structure of the helix by forming hydrogen bonds with the peptide backbone. Bulky residues ( Tryptophan Trp W, Histidine His H) would cause steric issues. Glycine Gly G is unfavorable because of its flexibility, while on the other hand, Proline Pro P is unfavorable due to its inflexibility.

There are favorable amino acid residue patterns that stabilizes Alpha-Helices, too. Closely-packed residues of opposite charge form ion pairs. Aromatic R-groups spaced 4 residues produce stabilizing hydrophobic interactions. When amino acids are close to ends of the helix, having charge opposite to that of the terminus they reside in stabilizes the helix.

The diameter of the Alpha-Helix is roughly 12 angstroms, the same size as the major groove of DNA. This makes Alpha-Helices useful for DNA binding.