A Protein Alpha Helix
The alpha helix — Linus Pauling's Nobel-winning discovery — is the most common secondary structure of proteins. Watch it move in molecular dynamics.
An alpha helix is a sequence of amino acids in a protein that are twisted into a coil. It is the most common secondary structure of proteins. The discovery of the alpha helix was considered as a key contribution of Linus Pauling that led to his Nobel Prize in chemistry in 1954. This page shows a molecular dynamics simulation of an alpha helix. The helix is shown in the Cartoon mode with temperature coloring that represents the average kinetic energy of the residues.
A Coil Held by Hydrogen Bonds
A protein is a chain of amino acids linked by peptide bonds into a backbone. In an alpha helix, this backbone twists into a tight right-handed coil that makes one full turn roughly every 3.6 residues. What holds the coil together is a regular pattern of hydrogen bonds: the carbonyl oxygen of each amino acid bonds to the amide hydrogen of the residue four positions further along the chain. This repeating i → i+4 pattern runs the length of the helix, making it remarkably stable.
Side Chains Point Outward
While the backbone forms the inner coil, the distinctive side chains of the amino acids project outward from the helix. This arrangement lets an alpha helix present different chemical surfaces to its environment — some helices have water-loving residues on one face and water-avoiding residues on the other, which helps proteins fold correctly and anchor into cell membranes. The same simple coil can thus play very different roles depending on its sequence.
A Building Block of Proteins
The alpha helix is one of the two dominant forms of secondary structure, alongside the beta sheet. Real proteins string together many such elements, folding them into intricate three-dimensional shapes that determine their function. Alpha helices appear everywhere in biology — from the keratin in hair and nails to the DNA-binding regions of proteins that switch genes on and off.
Watching It Move
In this simulation the helix is drawn in Cartoon mode with temperature coloring, where the colors represent the average kinetic energy of the residues. Running molecular dynamics reveals that the helix is not a rigid rod but a flexible, breathing structure — constantly wiggling from thermal motion while its hydrogen-bond network keeps the overall coil intact. This balance between flexibility and stability is exactly what proteins rely on to do their jobs.
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