[Simulated modeling of biopolymer molecular structure]. / Imitatsionnoe modelirovanie struktury molekul biopolimerov.

A simple approach for simulation of structure of biopolymers and their complexes is developed, including methods for conformational analysis "in vacuum" and methods for estimation of free energy of transfer between organic phase and water, evaluating hydrophobic interactions. The possibilities of the described methods are demonstrated by the simulation of the structure of C60-hydrocarbon polymer and glycine and alanine peptides.

[Structure and dynamics of proteins]. / O strukture i dinamike belkov.

The basic structural and dynamical properties of globular proteins are reviewed. The knowledge of these properties is necessary for understanding the molecular evolution. Special affection is devoted to physical modelling of proteins. Special attention is payed to the glassy model.

[Molecular drive]. / Molekuliarny'i draiv.

The review of the concept of molecular drive developed by Dover is presented. The ideas on the possible role of non-coding DNA are described and the duplication of genes as the fundamental factor preceding the appearance of the gene, which possesses a new function are characterized. The non-Mendelian processes--the non-equal crossing-over and the conversion of genes are considered. Molecular drive includes both these phenomena and the transposition of genes. The examples of drive are presented. Drive can be considered as the fundamental molecular mechanism of speciation and macroevolution. Evolution at molecular level is directly connected with the non-constancy of the genome and is non-Mendelian and non-Darwinian. Both the coding and non-coding DNA can serve as material for evolution.

[Molecular bases of evolution]. / Molekuliarnye osnovy évoluiutsii.

The general notions of the theory of evolution are listed. The unity of the "engineering principles" of the living nature is emphasized. The generalists and specialists species are discussed. The estimation of their evolution rates must be different if it is expressed by the number of species or by the morphological changes. The principles of "protein engineering" of the organisms and the role of metals in protein evolution are discussed. It is suggested that in the presence of ions of transition metals and zinc the Fox's proteinoids can possess more specific forms of enzymatic activity. In the evolution of language the horizontal transfer plays a much more important role than in the biological evolution. However in this case also the initial basis of the language remains. The random drift is considered and it is shown that in concordance with the neutralist theory there are no grounds to replace the calculation of the rates of mutational changes per time unity by the calculation per generation. The molecular drive is the main source of the evolutionary novelties. The drive is connected with drift. The synonymic mutations and the mutations in non-functional DNA are evolutionary important. The future mathematical theory of evolution must be based on the theory of Markov's chains with the stochastic matrix changing along the chain and containing the set of the non-diagonal members equal to zero. The results obtained in the theory of ontogeny are presented. The evolution of species is the evolution of ontogenies, the formation of the molecular theory of evolution can be possible only on the basis of the molecular theory of ontogeny. The internal causes of extinction of species reduce the accumulation of neutral and pseudo-neutral mutations.

[Conformational analysis of anti-arrhythmia agents of the lidocaine series and a model for the mechanism of their action]. / Konformatsionnyi analiz antiaritmikov lidokainovogo riada i model' mekhanizma ikh deistviia.

After conformation analysis of a number of lidocaine-like antiarrhythmic molecules a simple model of their mode of action is suggested. It is proposed that the hydrophobic antiarrhythmic molecules after their absorption on cytoplasmic membranes concentrate due to polar interactions close to ionic channel proteins, then bind to these proteins and allosterically influence the process of ionic conductance.

[Neutral mutations and interference-stability of the genetic code]. / Neitral'nye mutatsii i pomekhoustoichivost' geneticheskogo koda.

The fundamental suggestions of the neutral theory of evolution are discussed. It is shown that the safety of the genetic code is expressed also in the thermostability of proteins, i.e. in their conformational mobility. There is no contradiction between the mutational changes of the protein thermostability and the neutral theory.

[The effect of side radicals on the peptide structure. Surface of potential energy of model alanine and phenylalanine dipeptides]. / Vliianie bokovykh radikalov na strukturu peptidov. Poverkhnosti potentsial'noi énergii model'nykh dipeptidov alanina i fenilalanina.

The problem of stabilization of different dipeptide conformations is discussed within the fragment-fragment interactions method. It is shown, that the introduction of a CH3-group in glycine is a weak perturbation and for Ala-dipeptide the preferential structure remains C7 (like for glycine). On the contrary the introduction of a C6H5CH2-group in glycine is a strong perturbation and for Phe-dipeptide C5 becomes the preferential structure.

[Characteristics of nucleotide blocks in coding and non-coding DNA sequences from different organisms]. / Zakonomernosti sblochennosti nukleotidov v kodiruiushchikh i nekodiruiushchikh posledovatel'nostiakh DNK iz razlichnykh organizmov.

A statistical analysis of occurrence of particular nucleotide runs (1 divided by 10 nucleotides long) in DNA sequences of different species has been carried out. There are considerable differences in run distributions in DNA sequences of prokaryotes, invertebrates and vertebrates. Distribution of various types of runs has been found to be different in coding and non-coding sequences. There is an abundance of short runs 1 divided by 2 nucleotides long in coding sequences, and there is a deficiency of such runs in the non-coding regions. However, some interesting exceptions from this rule exist: for run distribution of adenine in prokaryotes and for distribution of purine-pyrimidine runs in eukaryotes. This may be stipulated by the fact that the distribution of runs are predetermined by structural peculiarities of the entire DNA molecule. Runs of guanine or cytosine of three to six nucleotides long occur predominantly in the non-coding DNA regions in eukaryotes, especially in vertebrates.

[The role of Hpi-hydrogen bonds in the stabilization of spiral structures of oligopeptides]. / Rol' Hpi-vodorodnykh sviazei v stabilizatsii spiral'nykh struktur oligopeptidov.

Different possibilities of H-bonds formation for formamide-water complexes and dimers of formamide were studied. Potential energy maps were calculated for di-, tri- and tetrapeptides. The maps provide necessary data to explain the relative stability of different oligopeptide conformers and Ramachandran maps for peptides.

[Molecular biology, darwinism and nomogenesis]. / Molekuliarnaia biologiia, darvinizm i nomogenez.

The theory of nomogenesis put forward by L. S. Berg in 1922 is discussed. It is shown that side by side with some erroneous anti-darwinian ideas the theory contains a series of important suggestions which anticipate the further development of the synthetic theory of evolution. Berg has foreseen the development of molecular biology. Thus he was the fore-teller of our branch of science. The theory of nomogenesis emphasized the limitations of natural selection which determine the directionality of evolution. Berg treated the speciation as a kind of phase transition. Even the most conscientious critics of Berg have misrepresented the real sense of his works. It is totally groundless to treat nomogenesis as an idealistic of Lamarkian theory. Berg was superior to his critics. However the enthusiasm about nomogenesis in our time shows the inability to separate "the grains from weeds".

[Stability of the alpha-helix structure of oligopeptides]. / Stabil'nost' alpha-spiral'noi struktury oligopetidov.

The problem of stabilization of oligopeptide alpha-helix conformation is discussed. The stabilizing role of intramolecular H-bonds and coulombic interactions for single molecules was shown. The influence of media results in the competition for formation of inter and intramolecular H-bonds and for coulombic interactions. High competitive media, eg. water, diminishes alpha-helix stability.

[Enzymatic mechanisms of compensation of deleterious mutations]. / O fermentativnykh mekhanizmakh kompensatsii vrednykh mutatsii.

Mechanisms of stabilization and compensation, that occur in biochemical systems with enzymes modified by harmful mutations are considered. The compensation of such mutations can result in their evolutionary neutralism. The stabilization is considered due to kinetic signals of metabolites which form the direct and feedback connections with enzymes (temporal stabilization), and also the compensation in enzymatic aggregates determined by the changes of conformation (spatial stabilization). Examples of the stabilization in one or several steady states of enzymatic systems are presented. The neutralism of the distortion of inhibitory and catalytic properties of enzymes is shown in the region of stabilization of these properties.

[Conformation analysis and structure-activity correlations of various lidocaine-like anti-arrhythmia agents]. / Konformatsionnyi analiz i korreliatsionnoe sootnoshenie struktura-aktivnost' nekotorykh potentsial'no aktivnykh antiaritmikov lidokainovogo riada.

Structure-activity correlationship of some potential-activity antiarrhythmic agents of lidocaine-like substances is found. Conformational properties of molecules of the substances are studied.