Chemistry

From amino acid to protein


Tutorial: α-Helix

The helix shown here comes from the protein myohaemerythrin (PDB code: 2MHR), an oxygen-binding protein in worms. It is essentially made up of a 4-helix bundle motif, the second helix was cut out for the illustration here.

In the case of the α-helix, the Peptide chain helical arranged. In eukaryotic naturally occurring peptides and proteins, the helix is ​​always clockwise, as this is sterically and energetically more favorable.

The helix is ​​going through Hydrogen bridges stabilized, which further develop four positions between the carbonyl oxygen of an amino acid and the amide hydrogen of the amino acid.

The representation of a helix in the direction of the longitudinal axis is also called helical wheel (helicalwheel). In the case of an α-helix, the CαAtoms along the longitudinal axis by 0.15 nm in relation to the previous Cα-Atom offset and rotated 100 degrees so that one full turn of the helix corresponds to 3.6 amino acid residues. The so-called pitch is 0.54 nm (= 3.6 x 0.15).

With an ideal helix structure, the Cα-Atoms come back to coincide after 5 turns (= 18 amino acids), which is not quite the case in our example (as in many real proteins). the distance between amino acid 1 (Ala 41) and amino acid 19 (Glu 59) should be 2.7 nm (18 x 0.15), which in turn is almost exactly correct (2.7 nm = 27 Å).

the Pages leftovers protrude outwards, whereby the β-carbon atoms do not extend radially, but rather like spiral arms (pinwheel) are bent (clockwise, looking from the N-terminal end).

the tubeformed by the helix is ​​about 0.5 nm in diameter. However, in reality it is not hollow, but is filled by the atoms of the peptide backbone, as in the Van der Waals representation becomes clear.