Coordination topology and stability for the native and binding conformers of chymotrypsin inhibitor 2

We demonstrate that the stabilization of the binding region is accomplished at the expense of a loss in the stability of the rest of the protein. A no vel molecular mechanics (MM) approach is introduced to distinguish residue stabilities of proteins in a given conformation. As an example, the relativ e stabilities of folded chymotrypsin inhibitor 2 (CI2) in unbound form, and CI2 in complex with subtilisin novo is investigated. The conformation of t he molecule in the two states is almost identical, with an similar to0.6-An gstrom root-mean-square deviation (RMSD) of the C alpha atoms. On binding, the packing density changes only at the binding loop. However, residue fluc tuations in the rest of the protein are greatly altered solely due to those contacts, indicating the effective propagation of perturbation and the pre sence of remotely controlling residues. To quantify the interplay between p acking density, packing order, residue fluctuations, and residue stability, we adopt an AM approach whereby small displacements are inserted at select ed residues, followed by energy minimization; the displacement of each resi due in response to such perturbations are organized in a perturbation-respo nse matrix L. We define residue stability lambda (i) = Sigma L-j(ij)/Sigma L-j(ji) as the ratio of the amount of change to which the residue is amenab le, to the ability of a given residue to induce change. We then define the free energy associated with residue stability, DeltaG(lambda) = -RT In lamb da. DeltaG(lambda) intrinsically selects the residues that are in the foldi ng core. Upon complexation, the binding loop becomes more resistant to pert urbation, in contrast to the alpha -helix that favors change. Although the two forms of CI2 are structurally similar, residue fluctuations differ vast ly, and the stability of many residues is altered upon binding. The decreas e in entropy introduced by binding is thus compensated by these changes. (C ) 2001 Wiley-Liss, Inc.