- In this initial view we can see a short fragment of a polypeptide chain in order to analyze some features of its primary structure. Atoms forming the chain backbone are disposed in zig-zag, as required by geometry of its bonding orbitals. Side chains of amino acid residues (or R groups) protrude outwards either side of backbone.
- Let's go now to a peptide bond between two amino acid residues. Because phenomenon of resonance, peptide bond shows some features of a double bond, which prevents free rotation of atoms on either bond side. So, six atoms marked in rectangle on model window are always confined to the same rigid flat. We can test it by activate rotation.
- Polypeptide chain backbone consist in a monotonous succession in wich the following sequenze repeats: alpha carbon, carboxyl group carbon, amino group nitrogen. Minding the restrictions to free rotation in peptide bond, we can visualize the polypeptide chain as a succession of rigid flats. Each of these rigid flats can freely rotate respect each other.
- Secondary structure.- In most proteins there are two main types of secondary structure.
- Alpha helix.- It is a helical structure with a thread pitch of 0.56 nm. Let's go to a polar view. Now let's hide hydrogen atoms. The polypeptide chain backbone is coiled and placed at the center of structure, while amino acid side chains protrude outward from this backbone. Let's hide side chains for a better understanding. Now, let's back to a side view. A ribbon model highlights the helical folding of the backbone. Using again a ball and stick model we recover side chains, now highlighted with a spectral color series. Alpha helix structure becomes stabilized by many hydrogen bonds. All peptide groups in the chain are involved in these hydrogen bonds. Zoom in to a better understanding.
- Primary structure specifies secondary structure, i.e., is the amino acid sequence which determines that a polypeptide chain folds resulting in an alpha helix or other secondary structure. Let's consider the effects of electrical charged residues of either sign and the side chains size.
- Beta sheet.- Polypeptide chain is folded in zigzag arrangement. Let's hide hydrogen atoms and side chains for a better understanding. Notice that a polypeptide chain can have several linear fragments separated by curvatures called beta turns. Now let's recover side chains and highlight the hydrogen bonds between different linear sections of the chain. This hydrogen bonds give stability to the structure. Let's look now the polypeptide chain represented by a ribbon model.
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An protein alpha helix in different representations by Marius Mihasan
