[Stereochemical theory of the 3-dimensional structure of globular proteins. I. Highly helical intermediate...

The authors analyze the physical prerequisites on which the proposed stereochemical theory of the three-dimensional structure of globular proteins is based. The theory represents a stereochemical modelling of the mechanism of protein self-organization suggested earlier by one of the authors. According to this mechanism, a highly helical intermediate structure(s) is formed at first and then it passes into the native one. In the highly-helical intermediate structure the arrangement of the polypeptide chain in space is the same as in the native structure. These two structures differ mainly by the secondary structure of the chain. The transition into the native structure proceeds under the effect of long-range interactions which transform the excess alpha-helices into beta-structural and irregular conformations. The so-called s-helices are considered (the alpha-helix, whose hydrophobic groups form a separate cluster on its surface). s-Helices can be obtained on the greater part of the polypeptide chain of any globular protein. In the unfolded protein chain they are the most stable and rapidly formed structures. It has been shown that namely s-helices are the initial blocks for the formation of the highly-helical intermediate structure. Stereochemical principles of the s-helix packing that permit to predict the three-dimensional structure of highly helical proteins have been found. According to these principles the highly helical structure represents the packing of hydrophobic surfaces and s-helices. In their turn, hydrophobic surfaces are formed as a result of complementary interaction of borders of hydrophobic clusters of two s-helices according to the "knob-hole" principle.