Left-handed polyproline II helix formation is (very) locally driven.
The left-handed polyproline II helix (PPII) is believed to be the preferred conformation for proline-rich regions of sequence in proteins. Such regions have been postulated to be protein-protein interaction domains. The formation of this structure is studied here using simple Monte Carlo computer simulations employing the hard sphere potential. It is found that polyproline sequences adopt only the PPII structure in the simulations. Non-proline, non-glycine residues inserted as guests into polyproline host peptides are conformationally restricted by the following proline residues and tend to be part of the PPII helix. It is found through insertion of two alanine residues into polyproline that the PPII structure is not propagated through more than one non-proline residue. This finding calls into question the hypothesis that proline-rich regions will preferentially adopt this structure since many such sequences are comprised of less than 50% proline residues.
Creamer
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Kentucky Center for Structural Biology, Department of Biochemistry, University of Kentucky, Lexington 40536-0298, USA. trevor@euripides.gws.uky.edu
D000595:Amino Acid Sequence; D003198:Computer Simulation; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation
D010455:Peptides; C011083:polyproline