[The specificity in promoter recognition by the Bacillus subtilis RNA polymerase deltaA and deltaH holoenzymes is connected with periodicities in the promoter nucleotide sequences].

Promoters recognized by deltaA-RNA and deltaH-RNA polymerase have different periodic patterns their nucleotide disposition. By using the special method of Fourier analysis for symbolic sequences. Fourier spectra of the primary structure of promoters transcribed bv deltaA-RNA and deltaH-RNA polymerase were obtained. For two data sets, a small one and a big one, a stepwise discriminant analysis with jackknife test based on the spectral characteristics of each of the promoters was performed. It was shown that it is possible to classify the data with the accuracy of 100% sets into classes: promoters that are recognized by the deltaA-RNA polymerise and promoters that are recognized by the deltaH-RNA polymerase. Significant correlations between the promoter strength and the characteristics of their Fourier spectra were obtained. Thus, the periodicity in nucleotide distribution along the polynucleotide chain is the attribute sufficient for promoter recognition by RNA polymerase holoenzyme.

[Computation of the structure of collagen molecule fragments]. / Raschet struktury fragmentov molekuly kollagena.

Step-by-step computations of octapeptide structures was performed for human collagens I and III. It was shown that computational results (coordinates of atoms) practically coincide with X-ray data for the collagen fragment.

[Analysis of side group conformations in molecular mechanics. Possibility of reduction of the side group conformation library in alpha-helical proteins]. / K probleme analiza konformatsii bokovykh radikalov v metodakh molekuliarnoi mekhaniki. O vozmozhnostiakh reduktsii biblioteki konformatsii bokovykh radikalov dlia al'fa-spiral'nykh belkov.

A new reduced library of side-chain conformations in proteins has been formed with the aim to apply it as a start point in the molecular mechanics calculations. The adequacy of this library was demonstrated by computation of X-ray determined a-helical protein (PDB code 1BB1) as example.

[Structure of collagen with a new net of hydrogen bonds]. / Struktura kollagena s novoi setkoi vodorodnykh sviazei.

A conformational variability of the collagen triple helix was studied with the methods of molecular mechanics. The Rich-Crick model with one hydrogen bond per tripeptide fragment or the model with two hydrogen bonds per tripeptide fragment were used for tripeptides forming the primary structure of the protein. Imino acid and amino acid residues were located in the second position of the tripeptide fragments in the first and second cases, respectively. Conformations on domain boundaries, which had alternating structures with one and two hydrogen bonds per tripeptide, were particularly studied. Essentially all types of collagen backbone composed of amino acid residues most frequently occurring in this protein were considered. A new model was suggested that combined elements of the Rich-Crick model and our new approach. This was shown to be stereochemically valid, energetically advantageous, and consistent with the experimental data. It was conclusively demonstrated that the primary structure of collagen determines its tertiary structure.