Thermodynamics of binding to SH3 domains: the energetic impact of polyproline II (PII) helix formation

Biochemistry. 2004 Jun 22;43(24):7787-97. doi: 10.1021/bi049752m.


Although numerous biophysical studies have focused on elucidating the structural and thermodynamic determinants that govern the free energy of binding between various SH3 domains and their putative recognition sequences, a quantitative accounting of the energetics of this interaction has proven enigmatic. Specifically, the binding results in a large and negative change on the standard enthalpy and entropy functions, a result which is inconsistent with the positive values for these quantities that is expected from the hydrophobic nature of the binding pocket. Here, the binding of the C-terminal SH3 domain of Sem-5 to its putative recognition peptide on the Sos (Son of Sevenless) protein is investigated using isothermal titration calorimetry under a variety of temperature and pH conditions. In addition, the energy associated with folding the Sos peptide into the binding competent polyproline II conformation is quantitatively evaluated. These results provide a rationale for the observed discrepancy between the experimental and predicted behavior and indicate that the determinants of binding in this system cannot be ascertained from a static structural representation of the binding process.

Publication types

  • 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

  • Amino Acid Sequence
  • Entropy
  • Models, Molecular
  • Peptides / chemistry*
  • Protein Binding
  • Protein Conformation
  • Son of Sevenless Proteins / chemistry
  • Thermodynamics
  • src Homology Domains*


  • Peptides
  • Son of Sevenless Proteins
  • polyproline