1. Introduction


The most common in proteins, thus the most well-known, repetitive secondary structure elements are alpha-helix, beta-sheet and 3(10)-helix, although any allowed and repeating Phi,Psi (and Omega) dihedral angle would result in a repeating (and helical) structure. Some authors described a few stereochemically allowed helices (pi-helix, left-handed alpha-helix), but all of them are rarely found in proteins. (You can find information about the basics of peptide geometry in Section 3 , and about the above secondary structure elements in Section 8 of the Principles of Protein Structure 97 course material.)

In the middle of the 50s, the structure of the fibrous protein collagen has been determined, and found to contain a left-handed triple-helical structure (Phi= -75 , Psi= 155 , n= -3.3). These left-handed helical sequences are rich in proline and hydroxi-proline residues. (Some more about collagen structure in Section 11 of the Principles of Protein Structure 97 course material.)

Theoretical calculations showed, that proline has two conformational energy minimum, one of them corresponding to trans-proline (Omega=180), and resulting in a left-handed helix, similar to the collagen-like helix (Phi= -75 , Psi= 145 , n= -3.0). This structure is called polyproline II (PPII) helix. The other minimum has cis-proline (Omega=0) in a right-handed helical structure (Phi= -75 , Psi= 160 , n= 3.3). This is the polyproline I (PPI) helix.

In the case of synthetic peptides both PPI (especially in apolar solvents) and PPII (especially in polar medium) has been found experimentally.

The PPII structure has proved to occur in a number of proteins, and seems to be a critical structural element for protein-protein interaction with SH3 domains.

The PPII helix has a preference to proline, but almost any natural amino-acid residue can be found in this conformation. (The formation of PPI helix is possible only by Pro residues, because of the cis conformation).

From the above, it is clear, that the polyproline helix is an important secondary structural element, and should be introduced in secondary structure analysis besides the other common elements, and it has been proved that a large fraction of protein segments earlier assigned to 'random', 'unordered' or 'other' groups, have the PPII helix conformation.

Next: Conformational properties of proline

by Zoltan Szabo, 1997