Principles of Protein Structure - G. Schulz 1982

Mechanisms of polypeptide chain folding and association
Aggregates of globular proteins
Specificity of protein-protein interactions

Surface complementarity is essential. Summarizing the calculation results from the previous section, several Conclusions can be drawn regarding Protein-Structure/156.html">Protein Interactions. First of all, we confirmed that burying non-polar surfaces away from Water yields the greatest Free energy gain (Table 5.6); furthermore, the entropic factor makes a critical contribution. The absolute magnitude of this contribution depends on the complementarity of the contacting surfaces: the contact surface area decreases significantly if water molecules can access it. The packing density (Sec. 3.6) across all such interfaces studied to date is as high as that in the interior of a protein [267].

The interface resembles the protein interior in terms of Hydrogen Bonds as well, which are formed by almost all of its polar groups [266]. In addition, all charged groups are linked by salt bridges. Recall that Fig. 3.3, which shows that the value of ∆G_пepeнос for polar groups is approximately equal to ∆G_пepeнос for non-polar groups, is based on data regarding The formation of efficient Hydrogen bonds and salt bridges in the protein interior.

Specificity is achieved through the complementarity of contact surface profiles, as well as the structural matching of Hydrogen bond Donors and acceptors and the residues forming salt bridges. For biological processes, not only the interaction efficiency is important, but also its specificity. How is specificity achieved in protein-protein interactions? As noted above, to achieve a large value of ∆G_пepeнoc, the contacting surfaces must be complementary. In addition, hydrogen bond donors and acceptors must be brought into close spatial proximity and properly oriented; otherwise, the association energy is sharply reduced. This applies to an even greater extent to buried salt bridges. Although their "active" contribution is small, they exhibit a large "passive" effect: if the charges are not compensated, the binding energy is weakened so severely (Sec. 3.5) that the protein loses its ability to associate. Thus, surface specificity is determined by its shape, The Nature of hydrogen bond donors and acceptors, and the charges. Judging by the number of different antigen-binding sites in IMMUNOGLOBULINS, a surface area of 100 Ų can adopt on the order of a thousand Conformations exhibiting different binding properties.