Stereospecific interactions of proline residues in protein structures and complexes

J Mol Biol. 2003 Aug 22;331(4):925-40. doi: 10.1016/s0022-2836(03)00759-9.

Abstract

The constrained backbone torsion angle of a proline (Pro) residue has usually been invoked to explain its three-dimensional context in proteins. Here we show that specific interactions involving the pyrrolidine ring atoms also contribute to its location in a given secondary structure and its binding to another molecule. It is adept at participating in two rather non-conventional interactions, C-H...pi and C-H...O. The geometry of interaction between the pyrrolidine and aromatic rings, vis-à-vis the occurrence of the C-H...pi interactions has been elucidated. Some of the secondary structural elements stabilized by Pro-aromatic interactions are beta-turns, where a Pro can interact with an adjacent aromatic residue, and in antiparallel beta-sheet, where a Pro in an edge strand can interact with an aromatic residue in the adjacent strand at a non-hydrogen-bonded site. The C-H groups at the Calpha and Cdelta positions can form strong C-H...O interactions (as seen from the clustering of points) and such interactions involving a Pro residue at C' position relative to an alpha-helix can cap the hydrogen bond forming potentials of the free carbonyl groups at the helix C terminus. Functionally important Pro residues occurring at the binding site of a protein almost invariably engage aromatic residues (with one of them being held by C-H...pi interaction) from the partner molecule in the complex, and such aromatic residues are highly conserved during evolution.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Conserved Sequence
  • Evolution, Molecular
  • Hydrogen Bonding
  • Macromolecular Substances
  • Models, Molecular
  • Proline / chemistry*
  • Proline / metabolism
  • Protein Binding
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Proteins / metabolism

Substances

  • Macromolecular Substances
  • Proteins
  • Proline