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2. Conformational properties of proline


See Section 3 of the Principles of Protein Structure 97 course material for conventions and basics of peptide geometry if you are not familiar with for example dihedral angles Phi, Psi, Omega, n (number of residues per turn).

It is well known, that proline, being an imino-acid with a five-member ring, is sterically restricted in rotation around the N-C(alpha) bond, thus has a limited Phi value of about -63 ±15 degrees. Because of this, proline can not be found in all the known main conformations, and proline disrupt regular secondary structural elements ( helix kinks, etc.).
And proline is the only amino-acid, which can be found in cis conformation (Omega=0 degree), because of the smaller energy difference of proline (it has two carbons bound to the N) between cis and trans states compared to other amino-acid residues (which have a H and a C atom bonded to the peptide N).

Thus proline is a conformationally important peptide:
  it can disrupt regular secondary structures
  it can induce (start) secondary structure
  it can stabilize the secondary structure, if it coincides with the allowed geometry of proline
  and there are geometries wich can be found only with proline ( see cis-proline).

So there may be geometries preferred by poline residues.

The conformational energy minimums of proline have been calculated, and found to be
Phi= -75 degrees Psi= 145 degrees for trans-proline (Omega=180 degrees)
 which is the repeating unit of the PPII (polyproline type II) helix and
Phi= -75 degrees Psi= 160 degrees for cis-proline (Omega=0 degrees)
 which is the repeating unit of the PPI (polyproline type I) helix.

These conformations are presented in Fig. 1. , which shows di-prolines in PPII and PPI conformation.

Di-proline in PPII and PPI conformation

Fig 2.1. Di-proline in PPII (Phi= -75 , Psi= 145 , Omega=180 ) and PPI (Phi= -75 , Psi= 160 , Omega=0 ) conformation.
One can see the difference between trans- and cis-proline, which results in left- or right-handedness of the helix, with these building units.
Here is a PDB coordinate file of this picture, for better visualization.

Next: Description of polyproline helices

by Zoltan Szabo , 1997