J. Davidson, O.Y. Lubman, T. Rose, G. Waksman, and S.F. Martin.
Calorimetric and structural studies of 1,2,3-trisubstituted cyclopropanes
as conformationally constrained peptide inhibitors of Src SH2 domain
binding.
Isothermal titration calorimetry and X-ray crystallography have been used to determine
the structural and thermodynamic consequences associated with constraining the pTyr
residue of the pYEEI ligand for the Src Homology 2 domain of the Src kinase (Src SH2
domain). The conformationally-constrained peptide mimics that were used are
cyclopropane-derived isosteres whereby a cyclopropane ring substitutes to the N-Calpha-Cbeta
atoms of the phosphotyrosine. Comparison of the thermodynamic data for the binding of
the conformationally-constrained peptide mimics relative to their equivalent flexible
analogues as well as a native tetrapeptide revealed an entropic advantage of 59 cal mol-1
K-1 for the binding of the conformationally-constrained ligands. However, an unexpected
drop in enthalpy for the binding of the conformationally-constrained ligands relative to
their flexible analogues was also observed. To evaluate whether these differences
reflected conformational variations in peptide binding modes, we have determined the
crystal structure of a complex of the Src SH2 domain bound to one of the
conformationally-constrained peptide mimics. Comparison of this new structure with that
of the Src SH2 domain bound to a natural 11-mer peptide (Waksman et al. (1993) Cell
72:779-790) revealed only very small differences. Hence, cyclopropane-derived peptides
are excellent mimics of the bound state of their flexible analogues. However, a rigorous
analysis of the structures and of the surface areas at the binding interface, and subsequent
computational derivation of the energetic binding parameters, failed to predict the
observed differences between the binding thermodynamics of the rigidified and flexible
ligands, suggesting that the drop in enthalpy observed with the conformationally-
constrained peptide mimic arises from sources other than changes in buried surface areas,
though the exact origin of the differences remains unclear.
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