[Evolutionary aspects of protein structure and folding]. / Evoliutsionnye aspekty struktury i foldinga belkov.

Four basic stages of evolution of protein structure are described based on recent work of the authors targeted specifically on reconstruction of the earliest events in the protein evolution. According to this reconstruction, the initial stage of short peptides of, probably, only few amino-acid residues had been followed by formation of closed loops of the size 25-30 residues, which corresponds to the polymer-statistically optimal ring closure size for mixed polypeptide chains. The next stage involved fusion of the respective small linear genes and formation of protein structures consisting of several closed loops of the nearly standard size, up to 4-6 loops (100-200 amino acid residues) in a typical protein fold. The last, modern stage began with combinatorial fusion of the presumably circular 300-600 bp DNA units and, accordingly, formation of multidomain proteins.

[Double and bifurcated hydrogen bonds in alpha-helices of globular proteins]. / Dvoinye i vilochkovye vodorodnye sviazi v al'fa-spiraliakh globuliarnykh belkov.

The statistical analysis of hydrogen bonds distribution in space structures of globular proteins has been done. The parameters of H-bonds in the different secondary structures of globular proteins were collected. In alpha-helices besides the canonical 1-5 H-bonds (the mean length 3 A), 1-4 H-bonds were observed (the mean length 3.2 A). The histograms of length and angular distributions of the bonds are presented. It was found on the basis of quantum chemistry calculations that most H-bonds in alpha-helices are double or bifurcated.

[The distribution of direct interactions in the spatial structures of globular proteins]. / Raspredelenie napravlennykh vzaimodeistvii v prostranstvennykh strukturakh globuliarnykh belkov.

The hydrogen bond distributions in 123 protein structures with the atom coordinates established at a resolution of less than 2 A were analyzed. The peculiarities of hydrogen bond distributions with respect to the lengths and remoteness of contacting residues in the primary structure were established. A hierarchy of H-bond energy distribution in the spatial structure of protein globules was demonstrated. The role of hydrogen bonds in the formation of domain structure and their special properties in proteins with different types of secondary structure are discussed.

[A new approach to calculation of the energy from van der Waals interactions in macromolecular proteins. Dielectric permeability as a physical parameter for calculations]. / Novyi podkhod k raschetu énergii van der Vaal'sovykh vzaimodeistvii v makromolekulakh belkov. Diélektricheskaia pronitsaemost' kak fizicheskii parametr dlia raschetov.

The problem in the calculation of Van der Waals interactions in protein globules based on the theory of condensed media was considered. The Van der Waals interactions are represented as energies of interaction of regions with a uniform density distribution. A definition of the local dielectric constant as a function of coefficients of absorption of molecular groups with a particular conformation was introduced. The applicability of this approach was estimated. The theory enables one to circumvent the problems arising in calculations based on pairwise additive approximation. The methods provides a high accuracy in determining the local features of spatial structures of globular proteins and physicochemical characteristics of their constituent amino acids and molecular groups.

[Determination of energetically significant parts of globulins and hierarchy of domain structure in macromolecules of proteins]. / Vydelenie energeticheski znachimykh uchastkov globuly i ierarkhiai domennoi struktury makromolekuly belka.

We have justified a Van der Waals approach for the problem of domains structure in globular proteins. A method for isolation of hierarchy of Van der Waals interactions in the space of protein globule has been found out. The definition of hierarchy's levels in the spatial structure of macromolecules is effected by the position of maxima in the distribution of potential energy of interactions. Multilevels system for domain structure organization of globular proteins and method for isolation of domains on different levels of energetical hierarchy has been established. Using this method we have revealed regions of different stability in 15 proteins globule.

[An objective method for isolating globular protein domains]. / Ob''ektivnyi metod vydeleniia domenov globuliarnykh belkov.

Regions of more stability and nearest environs were localized on the basis of the calculation of intramolecular interactions in the frame of pair-wise approach. A criterium for definition of domains boundary in globular proteins is establishing if residues from k to l are included into one domain and residues from l+1 to l+1+m are included into another domain. According to this criterium, the boundary between two domains is set between two residues in the case when the interaction energy is minimal when first residue is included into the first domain and the second one into another. Structural domains are founded and probability of existing of domains boundary is studied for the binase, barnase, and complex of barnase with dioxy-dinucleotide inhibitor. It is determinated that the biggest structural interaction between domains coinsiders with location of domains at 1-43, 44-110 residues correspondently.