[Electronic and spacial structure of orthophosphate and dimethylorthophosphate].

The applicability of a number of semiempirical CNDO variants for the computations of the electronic structure of different conformations for all possible ionic forms of dimethylorthophosphate and orthophosphate has been considered. The Boyd-Whitehead variant of CNDO approximation (CNDO/BW) with the original parameters we chose for the P-O bond gives the best qualitative and sometimes quantitative correspondence with ab initio methods. We have utilized this approximation to compute the dependences of energies and P-O bond strengths in P-O-CH3 (P-O-H) fragments of dimethylorthophosphate and orthophosphate versus the angles of rotation of these fragments about the P-O bonds. It is shown that, during the rotation, the increase in the strength of one P-O bond is accompanied by the labiality of another one. The energy minima of dimethylorthophosphate and orthophosphate anions correspond to conformations with approximately equal strengths of the P-O bonds. Thus, none of these bond strengths achieves a minimum. The protonation of dimethylorthophosphate and orthophosphate results in a strengthening of P-O bonds and decreases the dependence of their strength on the variation of torsion angles. Di- and three-anionic derivatives of dimethylorthophosphate and orthophosphate are also discussed. It is shown that the strength of P-O bond diminishes as the negative charge of dimethylorthophosphate and orthophosphate grows. It the case of dianion, the dependence of bond rigidity on the torsion angle is less pronounced than in the case of monoanione. Our theoretical results are compared with the experimental data known from literature. The importance of our data for elucidating some essential features of functioning of enzymes accomplishing the breakdown and formation of P-O bonds is also discussed.

[A method of automatic determination of "reference" spectra of CD elements of circular structure of proteins with the "aromatic contribution"]. / Metod avtomaticheskogo opredeleniia "repernykh" spektrov KD élementov vtorichnoi struktury belkov s uchetom "vklada aromatiki".

An algorithm (with appropriate application package) which enables automatic determination of "reference" CD spectra of different protein secondary structure elements from set of CD spectra of proteins with known contents of the elements with taking into account of "aromatic contribution" is elaborated. By means of these spectra one can determine contents of secondary structure elements in arbitrary proteins and polypeptides.

[Study of the form of bacteriophage T7 RNA polymerase containing point substitutions in the region of functionally important amino acid residues]. / Issledovaniia forma RNK-polimerazy bakteriofaga T7, soderzhashchikh tochechnye zameny v oblasti funktsional'no bazhnykh aminokislotnykh ostatkov.

A study was carried out on the influence of point mutations of the functional amino acid residues on the secondary and ternary structure of bacteriophage T7 RNA polymerase as well as on the activity of the enzyme. A change in residue 631 is accompanied by significant changes in secondary structure (alpha-->beta transition). The substitution Lys-172 Leu changes both the secondary and ternary structures whereas the deletion of residues 172-173 does not lead to such changes. Changes in residues 631-632 do not affect the ability of the enzyme to bind the promoter and/or the synthesis of a full-length transcript but disturbs phosphodiester bond formation.

[Acid-base, tautomeric and isomeric equilibrium of pyridoxal oximes, pyridoxal-5'-phosphate and some of their analogs]. / Kislotno-osnovnye, tautomernye i izomernye ravnovesiia oksimov piridoksaliia, piridoksal'-5'-fosfata i nekotorykh ikh analogov.

Success has been achieved in detailed understanding of tautomeric and isomeric equilibria and search for the new tautomeric and isomeric forms of oximes of pyridoxal, pyridoxal-5'-phosphate and some of their analogs, their presence is explained. This is due to a careful deconvolution of absorption spectra of different ionic forms of oximes into bands corresponding to separate electronic transitions. The spectroscopical data and the results of quantum-chemical calculations are compared for all the forms of compounds under investigation. As it has been found to be valid for other vitamin B6 derivatives as well, quantum-chemical calculations can be used for analytical purposes.

[Principles of dissociation of complex spectra of biologically active substances into bands corresponding to separate electron transitions]. / Printsipy razlozheniia slozhnykh spektrov biologicheski aktivnykh soedinenii na polosy, sootvetstvuiushchie otdel'nym élektronnym perekhodam.

General principles of spectroscopic deconvolution of complex spectra into bands that correspond to separate electronic transitions are considered. Any spectroscopic deconvolution should be based on a physical model. The absence of the physical model makes the deconvolution senseless. The methods of postulation of physical models and their refinement resulting from self-consistent deconvolutions are discussed. We have performed deconvolutions of absorption spectra of different ionic and tautomeric forms of pyridoxamine, pyridoxamine-5'-phosphate, pyridoxal, pyridoxal-5'-phosphate, common nucleic bases and their nucleosides. The results of the above-mentioned deconvolutions, as well as the serviceable program that allows to carry out such deconvolutions and recommendations for its usage are presented.

[A model of enzymatic decarboxylation of glutamic acid]. / Model' fermentativnogo dekarboksilirovaniia glutaminovoi kisloty.

Interaction of glutamate decarboxylase with its adequate substrate and some quasi-substrates was studied by spectrokinetic, quantum-chemical and some other approaches. It was shown that in the course of decarboxylation an abortive transamination of pyridoxal-5'-phosphate leading to the enzyme inactivation does occur. Identification of intermediate coenzyme-substrate complexes allowed to formulate a model of enzymatic decarboxylation taking into account both the main and abortive reactions. The analysis of electronic structure of the intermediates revealed some of the factors determining the functional specificity of the reaction under study.

[Electron spectroscopy and the electron structure of molecules]. / Elektronnaia spektroskopiia i élektronnoe stroenie molekul.

The experimental-theoretical approach to the study of physico-chemical, in particular, spectroscopic and photochemical properties of groups of related molecules is considered. The problem of physically correct spectral decompositions of complex electronic spectra into bands corresponding to separate electronic transitions and of the information obtained therefrom is discussed. Concrete examples of revealing photo- and enzymatic reaction mechanisms by combined spectroscopic and theoretical studies of molecular electronic structure and spectra are given. Special attention is paid to the connection of electronic structure of molecules with their physico-chemical, in particular, spectroscopic properties.

[Interrelation of the electronic structure of nucleic acid components and their ability and specificity in template synthesis]. / Vzaimosviaz' élektronnoi struktury komponentov nukleinovykh kislot s vozmozhnost'iu i spetsifichnost'iu ikh uchastiia v matrichnom sinteze.

A hypotesis suggesting that the specificity of polynucleotide template synthesis is based not on complementarity but on the correspondence of the electronic structure of the precursor and the enzyme active site (EAS), the latter being formed by the template, enzyme, and, possibly, by the polynucleotide synthesized is described. Comparison of the electronic structure of natural nucleic bases and their analogs allows to suppose that the EAS discriminates between adenine and cytosine, and uracil (thymine) and guanine, by electrostatic features: sign of the potential in the region of exocyclic substituents at C(4) of pyrimidines and C(5) of purines. For adenine and cytosine this sign is positive while for uracil (thymine) and guanine it is negative. The second feature allowing to discriminate between purines and pyrimidines is connected with general difference of their electronic structure. The total charge of N-glycoside center, more negative for pyrimidines, can serve as an index of this difference. According to the hypothesis the compounds unable to form complementary pairs can be functionally active in the polynucleotide template synthesis and can show ambiguous functional specificity due not only to the presence of different ionic and/or tautomeric species but also to the potential in the aforementioned region being close to zero or the charge of N-glycoside center being intermediate. It can be assumed that for the formation of EAS the same features of the electronic structure of the nucleotide residues of the template are used, which are important for the interaction of the precursor with the EAS (recognition of the precursor).