Thermodynamics of single peptide bond cleavage in bovine pancreatic trypsin inhibitor (BPTI)

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Abstract
A major goal of this paper was to estimate a dynamic range of equilibrium constant for the opening of a single peptide bond in a model protein, bovine pancreatic trypsin inhibitor (BPTI). Ten mutants of BPTI containing a single Xaa→Met substitution introduced in different parts of the molecule were expressed in Escherichia coli. The mutants were folded, purified to homogeneity, and cleaved with cyanogen bromide to respective cleaved forms. Conformation of the intact mutants was similar to the wildtype, as judged from their circular dichroism spectra. Substantial conformational changes were observed on the chemical cleavage of three single peptide bonds—Met46-Ser, Met49-Cys, and Met53-Thr—located within the C-terminal helix. Cleavage of those peptide bonds caused a significant destabilization of the molecule, with a drop of the denaturation temperature by 56.4°C to 68°C at pH 4.3. Opening of the remaining seven peptide bonds was related to a 10.8°C to 39.4°C decrease in Tden. Free energies of the opening of 10 single peptide bonds in native mutants (ΔGop,N) were estimated from the thermodynamic cycle that links denaturation and cleavage free energies. To calculate those values, we assumed that the free energy of opening of a single peptide bond in the denatured state (ΔGop,D) was equal to −2.7 kcal/mole, as reported previously. Calculated ΔGop,N values in BPTI were in the range from 0.2 to 10 kcal/mole, which was equivalent to a >1 million–fold difference in equilibrium constants. The values of ΔGop,N were the largest for peptide bonds located in the C-terminal helix and significantly lower for peptide bonds in the β-structure or loop regions. It appears that opening constants for single peptide bonds in various proteins span across 33 orders of magnitude. Typical equilibrium values for a single peptide bond opening in a protein containing secondary structure elements fall into negligibly low values, from 10−3 to 10−8, and are efficient to ensure stability against proteolysis.