Govorun D. Physico-chemical mechanisms of biomolecular recognition

The dissertation is devoted to the study of the most general physico-chemical mechanisms of a protein- nucleic acid and nucleic acid-nucleic acid recognition. It was established that the NA bases with aminogroup are molecules with non-rigid structure, dipole-active interconversion of which occurs via three energetically and topologically non-equivalent ways - the "over-barrier" large amplitude inverse vibration of amino fragment and two essentially anisotropic "under-barrier" rotations of aminogroup. It was shown, that stacking of the NA bases and their Watson-Crick pairs does not boil down to non- specific interactions of static planar-parallel structures: contribution of specific Coulomb contacts of amino nitrogen atoms' lone-pairs with hydrogen atoms of adjacent (upper or lower) bases - so called vertical H-bonds - are substantial. Implying molecular regulation it was suggested to consider the NA bases' aminogroup as "a molecular joint", non-linear mobility of which could be controlled by H-bonds b oth directly and at a distance. The Watson-Crick base pairs were established to be extremely soft as to "propeller-twist" and "sharp bend" angles and capable of adoption non-planar conformation under influence of small external perturbations, as it takes place in DNA. There are developed microstructural models of spontaneous semiopen states of DNA and its premelting, long-range action in DNA and its spatial curvature, genotoxic effects of UV irradiation. Microstructural sources of a DNA structural-dynamic heterogeneity which dominates in protein-nucleic acid recognition were considered. The conclusion was made that leading stereochemical principle of DNA spatial structure is not isomorphism of Watson- Crick pairs but their structural-dynamical conformity. It was shown that the NA bases like NA themselves accumulate uniquely whole gamma of mutually conjugated forms of structural changeability - prototropic tautomerism, structural non-rigidity, geometric isomerism, capability to accept or to give a proton, the ir spontaneous deamination or oxidation under the contact with water and so on. It was demonstrated that prototropic tautomerism is far not confined to point mutagenesis. Biological significance of high energy tautomers, inaccessible to direct physico-chemical detection, so called "latent structures", is discussed. It is noted, that their biological importance is not directly connected with their energetic stability. A complete multitude of point H-contacts of the "a nucleotide base - an amino acid residue" type, stabilised by two H-bonds, were investigated. It was shown, that already at this level the recognition occurs according to scenario of mutual structural- dynamical adaptivity with participation of essentially interdependent intra- and intermolecular H-bonds capable not only of forming and breaking but also of switching over in a way of bifurcations. A structural non-rigidity of the bases is believed to be a security of unerring and expeditious recognition in conditions of the free volume deficit whic h is characteristic part for a living cell. The low-frequency Raman spectra of successively complicated NA components, as well as cocrystallizates of the "a base - an amino acid derivative" type are presented. Dynamic and energetic features of torsional tunnel junction of methyl group of Thy and the bases substituted at glycosidic nitrogen atoms are determined. An adequacy of the classical Maleev's model is confirmed: low-frequency qualitative mode observed in DNA Raman spectra is interpreted as collective extensional optical oscillations, exactly - librations of paired bases around glycosidic bond, which effectively interact with both acoustic extensial phonons and collective inverse vibrations of amino groups, are accompanied by collective torsional tunnel junction of the Thy methyl groups. A biological applications of this mode are discussed. An energetics and cooperative properties of H-bonds in crystals and cocrystals of nucleotide bases - model of nucleic acid-nucleic acid recognition - are investigated .