[Use of multiple structural alignment for recognizing the type of protein spatial architecture].

A new approach to the inverse folding problem is proposed, which is based on the analysis of multiple structural alignments of protein families. The incorporation of multiple structure information allows one to take into account the variability of structural characteristics amongst protein structures of the same fold. The new method was tested on two highly populated structural families.

[A new approach to the thermodynamic role of imino acids in collagen. Solution of a thermodynamic paradox].

The dependence of denaturation transition thermodynamic parameters in various collagens from imino acid compositions has been analysed. Computational and experimental data suggest independence of the collagen molecule hydration on imino acid composition and sequence in the polypeptide chain. The continuous net of hydrogen bonds is interrupted, if imino acid residues occur in the sequence of amino acid residues, as follows from Monte Carlo computations, because the hydrogen of NH-group plays sufficient role in water shell formation for this conformation.

[Hydration of the left spiral of the poly-L-proline type. Study by the Monte Carlo method].

The paper exhibits results of hydration shell Monte Carlo calculations in poly-L-proline II and extended helix conformation and in alpha-helical and beta-structural conformations for comparison. It was found that left-handed helix of poly-L-proline II type as well as epsilon-helix are characterized by very favorable hydration. Therefore this conformation has preference as compared to other standard conformations of the main polypeptide chain.

[Conformation of a triple collagen spiral as a function of primary structure].

It has been shown by the method of conformational analysis that conformation of the polypeptide chain of a collagen molecule varies from one type of sequence to another, but in all the sequences the only two types of conformations can be characterized by minimal conformational energy. The collagen molecule as a whole is a combination of the single-bond Rich and Crick model and new double-bonded structure. Rigorous comparison with "thick" conformations obtained by Scheraga and coworkers was undertaken using precise calculations with flexible proline.