Interaction energy, terminal residue

The cystatins, which are a superfamily of proteins that inhibit papain-like cysteine proteases, are a classic example of these inhibitors. The cystatins (Fig. 3) insert a wedge-hke face of the inhibitor that consists of the protein N-terminus and two hairpin loops into the V-shaped active site of a cysteine protease. The N-terminal residues bind in the S3-S1 pockets in a substrate-like manner, but the peptide then turns away from the catalytic residues and out of the active site. The two hairpin loops bind to the prime side of the active site, which provides most of the binding energy for the interaction. Thus, both the prime and the nonprime sides of the active site are occupied, but no interactions are actually made with the catalytic machinery of the enzyme (23). 

Figure 38 Representation of the equilibrium between the cyclic and acyclic forms of a hexapeptide. The N- and C-terminal blocking groups, CH3CO— and —NHCH3, respectively, are not shown.233 The standard free energy change for this process depends on the intrinsic chemistry to form a disulfide bond from two sulfhydryl groups, the tendency of Pro-Giy (or any other dipeptide in this position) to form a P turn, and the tendencies of residues X and Y to adopt the extended conformation (and interact with each other). Table 5 of Reference 234 illustrates the range of standard free energy changes for a family of such hexapeptides.

The secondary site of eco binds to the protease over 20 A away from the active site and forms up to 30 van der Waals interactions and up to five additional hydrogen bonds. An additional important source of binding energy and association, the secondary site is composed of the 60 s and lOO s loops of eco and a hydrophobic patch near the protease residues 91 to 94 and the C-terminal a helix amino acids 236 to 242. This patch and helix separated from the 80 s loop accounts for the fold specificity of eco. Each inhibitor molecule forms an interaction with both proteases of the tetramer in a clamp configuration that can be adapted to fit most serine proteases. 

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