The effect of the polyproline II (PPII) conformation on the denatured state entropy

Protein Sci. 2003 Mar;12(3):447-57. doi: 10.1110/ps.0237803.


Polyproline II (PPII) is reported to be a dominant conformation in the unfolded state of peptides, even when no prolines are present in the sequence. Here we use isothermal titration calorimetry (ITC) to investigate the PPII bias in the unfolded state by studying the binding of the SH3 domain of SEM-5 to variants of its putative PPII peptide ligand, Sos. The experimental system is unique in that it provides direct access to the conformational entropy change of the substituted amino acids. Results indicate that the denatured ensemble can be characterized by at least two thermodynamically distinct states, the PPII conformation and an unfolded state conforming to the previously held idea of the denatured state as a random collection of conformations determined largely by hard-sphere collision. The probability of the PPII conformation in the denatured states for Ala and Gly were found to be significant, approximately 30% and approximately 10%, respectively, resulting in a dramatic reduction in the conformational entropy of folding.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Alanine / chemistry
  • Animals
  • Binding Sites
  • Caenorhabditis elegans / chemistry
  • Caenorhabditis elegans Proteins / chemistry*
  • Caenorhabditis elegans Proteins / genetics
  • Entropy
  • Humans
  • Magnetic Resonance Spectroscopy
  • Mice
  • Models, Molecular
  • Mutation / genetics
  • Peptide Fragments / chemistry*
  • Peptides / chemistry*
  • Peptides / metabolism
  • Proline / chemistry
  • Protein Binding
  • Protein Conformation
  • Protein Denaturation
  • Protein Folding
  • Son of Sevenless Proteins / chemistry*
  • src Homology Domains*


  • Caenorhabditis elegans Proteins
  • Peptide Fragments
  • Peptides
  • Sem-5 protein, C elegans
  • Son of Sevenless Proteins
  • polyproline
  • Proline
  • Alanine