[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.

[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.

Comparative study of binase and barnase: experience in chimeric ribonucleases.

Chimeric enzymes were constructed to elucidate the differences in physicochemical properties of two related bacterial RNases, barnase and binase. Chimeras (Ba26Bi, Ba73Bi, Ba26Bi73Ba and Bi73Ba) contain six to thirteen residue substitutions relative to barnase, which are beyond the active site. The catalytic activity of RNases toward GpU, GpC and poly(I), as well as conformational distinctions and heat denaturation parameters, were studied. Thermal denaturation of binase, barnase and chimeric RNases is a two-state transition. The mutation-induced changes in the free energy of unfolding of barnase deduced from thermal and urea denaturation nearly coincide. The kinetic parameters for GpU and GpC demonstrate that the chimeras fall into two groups: barnase-like and binase-like. This division is determined by the origin of their C-terminal part (residues 73-110) which is also responsible for their thermostability at pH 2.4. An inverse linear dependence was found between kcat for poly(I) and denaturation temperature of RNases at pH 5.5, which points out that certain lability of the protein molecule appears to be necessary for efficient polynucleotide cleavage.

[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.

[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.

[Spatial structure of secretin molecule]. / Prostranstvennoe stroenie molekuly sekretina.

By conformational analysis and circular dichroism the structure of peptide hormone secretin and its shortened N-terminal fragments in different solvents (water, aqueous solutions of alpha-L-phosphatidic acid and sodium dodecyl sulfate) have been studied. The results obtained by the two methods are compared.

[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.

[Determination of protein secondary structure from circular dichroism spectra. III. Protein-derived base spectra of circular dichroism for antiparallel and parallel beta-structures]. / opredelenie vtorichnoi struktury belkov iz spektrov krugovogo dikhroizma. III. Belkovye repernye spektry dlia antiparallel'noi i parallel'noi beta-struktur.

Protein-derived basic CD spectra for alpha-helix, antiparallel and parallel beta-structures, beta-bends and irregular form of proteins have been determined from the experimental CD spectra of six (myoglobin, lysozyme, ribonuclease A, papain, lactate dehydrogenase, subtilisin BPN') or seven (glyceraldehyde-3-phosphate dehydrogenase added) reference proteins and the analysis of the X-ray data. The secondary structures of thirteen proteins (seven reference and six additional ones) have been analysed using the basic CD spectra thus obtained. The data obtained have been compared with the results of the X-ray data analysis. It is shown that the accuracy of determination of the beta-structure and beta-bends contents using our basic CD spectra is about 2-3 times better than using the basic spectra reported by Chang et al. (Analyt. Biochem. 91, 13-31, 1978).

[Determination of the secondary structure of proteins from their circular dichroism spectra. II. Estimation of the contribution of beta-pleated sheets]. / Opredelenie vtorichnoi struktury belkov iz spektrov krugovog dikhroizma. II. Uchet vklada beta-izgibov.

Protein-derived basic CD spectra for alpha-helical, beta-structural, beta-bends and irregular regions of the proteins have been determined from the experimental CD spectra of five reference proteins (myoglobin, lysozyme, ribonuclease A, papain, lactate dehydrogenase) with the knowledge of the fractions of the residues in the corresponding conformation. The alpha-helical and beta-structural regions of the reference proteins have been isolated from the X-ray data using the common "rigid" criteria for all the proteins, as proposed by Finkelstein and Ptitsyn. The residues in the beta-bend have been isolated using the data of Chou and Fasman and also three assumptions formulated in the present paper. The basic CD spectra thus obtained have been used for the analysis of secondary structures of 10 proteins (5 reference and 5 additional ones). There is a good agreement between the results of the X-ray data and those obtained from the CD spectra.

[Determination of the secondary structure of proteins from their circular dichroism spectra. I. Protein reference spectra for alpha-, beta- and irregular structures]. / Opredelenie vtorichnoi struktury belkov iz spektrov krugovogo dikhroizma. I. Belkovye repernye spektry dlia alpha-, beta- i nereguliarnoi struktur.

It is shown that to obtain the protein-derived basic CD spectra for alpha-helical, beta-structural and irregular regions it is necessary to use a common criterion for isolation of secondary structures for all the reference proteins. Using the "rigid" criterion proposed by Finkelstein, Ptitsyn, Kozytsyn and the "mild" one (as proposed by Levitt and Greer) isolation of the alpha- and beta-structural regions for 5 reference proteins (myoglobin, lysozyme, ribonuclease A, papain, lactate dehydrogenase) has been carried out. Using the f alpha, f beta and f irregular thus obtained and the experimental CD spectra of these proteins, the basic CD spectra for alpha-helical, beta-structural and irregular regions in the proteins have been calculated. It is shown that the use of criterions common for all the proteins leads to good agreement between the calculated basic CD spectra for alpha-helical, beta-structural and irregular forms and the CD spectra of polylysine in the corresponding conformations. The secondary structure of the proteins studied has been analysed using the new protein-derived basic spectra and fairly good quantitative agreement with the X-ray data was achieved.

[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).