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V G Dashevskiĭ

Publications and source records attributed to V G Dashevskiĭ.

8 recordsLinked to original sources
PubMed1980

[Lattice model for globular protein three-dimensional structure].

A discrete, completely determined model is proposed which allows rough evaluation of the polypeptide chain folding in globular proteins with given amino acid sequence. The growth of a self-avording chain begins from the N terminal and is confined by the diamond lattice with prohibition of contacts in the neighbouring junctions of the lattice. The aim function is calculated as the sum of the contributions due to the contacts through the junction as well as the contributions connected with beta sheets. The optimal conformation is found by maximizing the aim function using the cut off method. The model is applied to the trypsin inhibitor and ribonuclease S, provided that the contributions of contacts through the lattice junction are caused by hydrophobic interaction between residues. The results of calculations are shown to depend on the depth of looking over as well as on the parametrization of the aim function. A parametrization is proposed which gives the radia of gyration and matrices of interresidue contacts on agreement with experimental data. The limitations of the lattice model are discussed in connection with the results obtained.

Amino Acid Sequence↗
PubMedDate not supplied

[Internal rotation potentials in polynucleotides].

An empirical potential function for internal rotation around P-O bonds in polynucleotides is suggested. Its parameters have been determined taking into account the result of quantum mechanical calculations for dimethylphosphate.

Molecular Conformation↗
PubMedDate not supplied

[Refinement of the A- and B-forms of DNA by the atom-atomic potential founctions method].

Structures of poly(dA). poly(dT), poly[d(A-T)].poly[d(T-A)], and poly (dG). poly (dC) were refined by an empirical method, taking into account flexible sugar moieties and simmetry conditions of DNA. The energetical optimal forms were found using Arnott's forms as starting points. These forms were shown to depend only slightly on the polynucleotide type and sequence, and characterized by C(2') endo-C(3') endo and the polynucleotide type and sequence, and characterized by C(2') endo-C(3') endo and C(3') endo and C(3') endo-C(2') endo sugar conformations. The resulting structures have the helix parameters corresponding to X-ray findings and characterized by augment resemblance between structural parameters (dichedral angles and sugar conformation) of A- and B-basic DNA forms.

DNA↗
PubMedDate not supplied

[Study of the relationship between secondary DNA strucure and base sequence by the technic of theoretical conformational analysis].

An investigation of double-stranded polynucleotide conformations using the algorithm for exclusion of redundant dihedral angles and flexible sugar unit has been performed. The fragment of DNA including three nucleotide pairs was taken into account for polynucleotides poly[d(A--T)].poly[d(T--A)], poly[d(G--C)].poly[d(C--G)], poly(dA).poly(dT) and poly(dG).poly(dC). The resulting structures being energetically optimal have helical parameters corresponding to X-ray experimental values for A- and B-forms. It was revealed that B-form is the most energetically favorable structure, therefore the earlier conception that water is of importance for B-form stabilisation may be revised. Relative stabilities of B- and A-forms depend upon base sequence because unequal contributions of the stacking and backbone energy in whole potential energy of the structrues with different sequences.

Base Sequence↗
PubMedDate not supplied

[B-form as the absolute energy minimum for DNA. Entropy nature of the B--A transition].

The B-form is characterizing by lower potential energy than A-form, especially if electrostatic term is added. For realistic values of epsilon (4; 1) spontaneous A--B-transition occurs during minimization procedure. The conclusion arises about entropy mechanism of A-form stabilization. The B--A-transition is impossible lower certain temperature for certain salt concentrations. The strong and mobile dehydratant must stimulate the A-form realization. The strong and polymeric dehydrant must stimulate the compactization of macromolecule on the basis of B-form.

Chemical Phenomena↗
PubMedDate not supplied

[Calculation of the conformation of stereo-regular, double-spiral polynucleotides].

By the step-by-step selection method energetically optimal conformation of double-stranded polynucleotides were calculated proceeding from the conformations of mono-and dinucleotides. These structures were found to belong to the families of DNA A and B forms. The dependence of six torsion angles of the polynucleotide chain on the glycosidic angle chi was investigated. As a result certain areas admitting of double-helix polynucleotides with sugar C3-endo with chi = -80 degrees were established.

DNA, Single-Stranded↗