New to secondary structure? You might want to read a brief Introduction

To explore the helix, you can take a "guided tour" through it by clicking the buttons below. You can also explore the molecule on your own using the mouse and a pull-down menu (see Help).

Section 1: The Underlying Structure of an Alpha-Helical Peptide.

Show the skeleton of the peptide. This reveals a complex pattern of covalent bonds.

Simplify the pattern by removing the hydrogen atoms:

Hydrogen atoms off/on.

The alpha carbons (dark gray) are the central atom of each amino acid in the peptide chain.

Remove sidechains to reveal the backbone of this short chain of amino acids; it is helical, resembling the shape of a spiral staircase.

The simplest representation of an alpha-helix is a trace of the alpha carbons.

The sidechain of each amino acid projects out from the alpha carbon, away from the helix.

Sidechains off/on.

Any single turn around the "staircase" is completed by a length of the chain that is just under four amino acids long (3.6, to be exact).

Section 2: Why does the peptide remain in a helical shape?

When a peptide folds into an alpha-helix, the backbone atoms are brought near each other. Two important interactions occur to stabilize helical folding:

1. Hydrogen bonds form between the backbone oxygens and nitrogens. The amine hydrogen is "shared" by the nitrogen and the electronegative oxygen.

Hydrogen bonds occur at regular intervals along an alpha helix, due to the regular spacing of the amine and carbonyl groups along the chain. Hydrogen bonds provide an effective stabilizing force only when many act together, as they do here.

2. Hydrophobic interactions are another source of stability for the alpha-helical shape. The helix folds so as to minimize the contact of hydrophobic carbons with the watery medium.

The close packing of the backbone atoms excludes water and other molecules. If not for this packing, the backbone oxygens and amines would hydrogen bond to water molecules instead of each other.

View: End-on Side view

Take cross-sections: In Out

Section 3: Some helices are both hydrophobic and hydrophilic

Is this helix amphipathic?

Color the hydrophilic side chains purple.

Click and drag on the molecule to rotate it to see the distribution of hydrophilic side chains yourself.

Color the hydrophobic side chains light gray.

Click and drag the molecule to get the best view.

How do you think an amphipathic helix would fold with the rest of the protein in a watery environment, such as in the cytosol? What if the part of the protein containing the helix was embedded in a lipid environment, such as a membrane?
Answers discussed.

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