Theory of protein molecule self-organization. I. Thermodynamic parameters of local secondary structures in the unfolded protein chain

This paper presents the results of a stereochemical analysis of local interactions in unfolded protein chains (sterical repulsions, hydrogen, and hydrophobic bonds, etc.) by means of space-filling modeles. On the basis of this analysis, an evaluation is made of thermodynamic parameters controlling the building-in of all the 20 natural amino acid residues in all the physically possible position of local secondary structures (α-helices, including α-helices with short fragments of helices 3₁₀ at the C-terminus; β-bends of different types, helices 3₁₀, and their combinations) as well as thermodynamic parameters of separate hydrogen bonds of polar side groups with the neighbor peptide groups (“local contacts”). The accuracy of the obtained results is discussed.