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 novel molecular mechanics (MM) approach is introduced to distinguish residue stabilities of proteins in a given conformation. As an example, the relative stabilities of folded chymotrypsin inhibitor 2 (CI2) in unbound form, and CI2 in complex with subtilisin novo is investigated. The conformation of the molecule in the two states is almost identical, with an approximately 0.6-A root-mean-square deviation (RMSD) of the Calpha atoms. On binding, the packing density changes only at the binding loop. However, residue fluctuations in the rest of the protein are greatly altered solely due to those contacts, indicating the effective propagation of perturbation and the presence of remotely controlling residues. To quantify the interplay between packing density, packing order, residue fluctuations, and residue stability, we adopt an MM approach whereby small displacements are inserted at selected residues, followed by energy minimization; the displacement of each residue in response to such perturbations are organized in a perturbation-response matrix L. We define residue stability lambda(i) = summation operator((j)L(ij))/ summation operator((j) L(ji)) as the ratio of the amount of change to which the residue is amenable, to the ability of a given residue to induce change. We then define the free energy associated with residue stability, DeltaG(lambda) = -RT ln lambda. DeltaG(lambda) intrinsically selects the residues that are in the folding core. Upon complexation, the binding loop becomes more resistant to perturbation, in contrast to the alpha-helix that favors change. Although the two forms of CI2 are structurally similar, residue fluctuations differ vastly, and the stability of many residues is altered upon binding. The decrease in entropy introduced by binding is thus compensated by these changes.
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Laboratory of Computational Biology, Faculty of Engineering and Natural Sciences, Sabanci University, Orhanli, Tuzla, Istanbul, Turkey. canan@sabanciuniv.edu
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D001696:Biomechanical Phenomena; D007700:Kinetics; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism*; D010940:Plant Proteins; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D013329:Structure-Activity Relationship; D013816:Thermodynamics
D010455:Peptides; D010940:Plant Proteins; C093336:chymotrypsin inhibitor 2