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Biomedical subjects

Iu D Nechipurenko

Publications and source records attributed to Iu D Nechipurenko.

At least 19 recordsLinked to original sources
PubMedDate not supplied

[Analysis of distribution of ligands adsorbed on DNA fragments].

The effect of finite fragment length on the distribution pattern of bound protein along the DNA fragment is considered. If the size of the binding site for a ligand on DNA is comparable with the length of the DNA fragment fluctuations in the amount of ligand bound to the fragment create some difficulties for evaluating the distribution pattern of ligand on DNA. A mathematical approach is developed which enables one to calculate the distribution pattern of ligand on DNA provided that the number of bound ligand on the DNA fragment is known. Expression are also obtained to treat the effects of fluctuations in the number of ligand molecules bound to the DNA fragment on the distribution pattern of ligand. A new procedure is proposed which may be useful for locating the preferable binding sites for ligand on DNA on the basis of footprinting experiments.

Adsorption↗
PubMedDate not supplied

[The effect of long-range interactions between adsorbed ligands on the DNA helix-coil transition].

The influence of different types of long-range interaction of ligands adsorbed on DNA on the helix-coil transition was theoretically considered. The contact interaction was shown to differ significantly from the long-rang one. It was shown also that even weak dependence of a long-range potential on a degree of helicity resulted in the strong changes of a DNA melting curve. This result allowed to understand the different experimental data on DNA melting in the presence of different substances which reduced AT-and GC-base pairs thermostability difference.

Adsorption↗
PubMedDate not supplied

[Binding of small molecules with nucleic acids having tertiary structure].

A model has been developed which allows description of the binding of antibiotics and dyes to a nucleic acid in which different regions are involved in the formation of a certain tertiary structure. Interactions between different segments of nucleic acid may contribute to the internal overall energy of the macromolecule. We consider the case when the tertiary structure and the internal energy of the macromolecule are altered upon binding of small molecules. These structural changes affect the shape of the binding isotherm of ligand to the nucleic acid. We obtain relations which permit to determine the dependence of the internal energy on the degree of binding of ligand to nucleic acid.

DNA↗
PubMedDate not supplied

[Anticooperative interactions between the nearest neighbor chromatosomes].

A model which permits the description of chromatosomes distribution along the DNA were developed. The experimental data on the spacing of chromatosomes on rat liver chromatin were analysed. It was shown that chromatosomes dimers spaced at less than 40 base pairs are encountered more rarely than might be expected on the basis of a random distribution of chromatosomes along DNA. We propose that between nearest neighbor chromatosomes in the fibre there exist interactions which hinder the rapprochement of chromatosomes. The data analysis put forth in this paper permits us to determine the energetic parameters of such anticooperative interactions.

Animals↗
PubMedDate not supplied

[Characteristics of nucleotide blocks in coding and non-coding DNA sequences from different organisms].

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.

Animals↗
PubMedDate not supplied

[Interaction of substrates and substrate-like inhibitors with the peptidyltransferase center from Escherichia coli ribosomes].

The binding isotherms of CACCA(3'NHPhe----Ac) and CACCA(3'NHPhe) to E. coli ribosomes and 50S subunits were measured. A theoretical model of adsorption for the case of cooperative interaction between two ligands adsorbed on a ribosome was designated. The analysis of the experimental binding isoterms leads to the following conclusions. A ribosome (or subunit) binds one CACCA (3'NHPhe----Ac) molecule to donor site of the peptidyl transferase center, but two CACCA (3'NHPhe) molecules to both donor and acceptor sites. The binding of CACCA (3'NHPhe) to ribosomes (or subunits) is a cooperative process, characterized by the cooperativity coefficient tau = 40 +/- 5 or more. When model substrates CACCA-Phe, CACCA-Leu and CACCA-Val were taken instead of CACCA (3'NHPhe) in the incubation mixture with ribosomes, dipeptides were obtained even in the case, when ratio [model substrate]: [ribosome] (in moles) was much lower than 1. Puromycin binding to acceptor site with constant (1-2) X 10(4) M-1 also stimulates CACCA(3'NHPhe----Ac) adsorption to the donor site of ribosomes with cooperativity coefficient being equal to 1.5-2.5. It is also shown that cytidine 5'-phosphate binding to the donor site increases kappa cat of the reaction of minimal donors with CACCA-Phe by 1.5 orders of magnitude but has no effect on Km of this reaction. These facts point out that cytidine 5'-phosphate being adsorbed on the corresponding area of the donor site leads to the conversion of low-productive complex [ribosome + minimal donor substrate + acceptor substrate] into high-productive complex [ribosome + minimal donor substrate + acceptor substrate + cytidine 5'-phosphate].

Acyltransferases↗
PubMedDate not supplied

[Cooperative effects during the binding of large ligands with DNA. Non-contact interaction between adsorbed ligands].

Equations are derived to describe the cooperative binding of large ligands to DNA. A mathematical approach is developed which enables one to give a simple probabilistic interpretation of binding equations and to solve them in the general case when long-range interactions are allowed between bound ligands. These interactions can be mediated by conformation changes induced in the DNA in the course of binding process and transformed over some distances beyond the DNA region immediately covered by a bound ligand molecule (allosteric effect of DNA). Interactions between ligand molecules can be formally described in terms of model potential characterizing pairwise interactions between bound ligands. A procedure is developed which allows one to determined the form of such potential from experimentally measured binding isotherms. It is based on a comparison of experimental binding isotherms with the appropriate curves calculated for the case of non-interacting ligands.

Adsorption↗
PubMedDate not supplied

[Cooperation effects in binding of large ligands to DNA. II. Contact interactions between adsorbed ligands].

Cooperative effects arising upon binding of biologically active ligands to DNA are considered. Equations are derived which enable one to describe the binding of two different ligands to DNA. We also consider the case when ligand can form two type of DNA complexes. The cooperative binding of the ligand in the vicinity of saturation level of binding can be described with a good accuracy by equation derived for the non-cooperative adsorption of the same ligand with some effective binding constant Keff. It is shown that cooperative effects arising upon binding of proteins and other ligands to DNA can be divided into two groups depending on the symmetry of interactions between the bound ligand molecules. In particular, if such interactions favor the formation of dimeric ligand species on the DNA, Keff approximately a1/2, where a is the ligand-ligand interaction constant. If cooperative interactions favor the formation of aggregates of unrestricted size, then Keff approximately aL+Y, where L is the size of the binding site for the ligand on DNA.

Adsorption↗
PubMedDate not supplied

[Interactions between distamycin A analogs bound to DNA].

The experimental binding isotherms of the distamycin A analog to 8 natural and synthetic DNAs were analyzed. The shapes of binding isotherms suggest that the bound ligand molecule induces transitions of DNA (B-form) into two perturbated conformation states. These transitions are responsible for the existence of positive and negative cooperative effects on binding of distamycin analogs to DNA. At low levels of binding positive cooperative effects play a dominating role whereas at high levels of binding negative cooperative effects are observed. These cooperative effects can be described by the aid of a potential of pairwise interactions between nearest neighbour bound antibiotic molecules. A detailed analysis of experimental binding isotherms shows that characteristic distances over which these interactions are extended depend on the AT content of DNA. The energetical and structural parameters characterising the allosteric transitions of DNA to the perturbated states are obtained.

Allosteric Regulation↗
PubMedDate not supplied

[Thermodynamic parameters characterizing interaction between ligand molecules adsorbed on a polymer].

Procedure was elaborated for recognizing potentials of paired interactions between ligand molecules adsorbed on the polymer. A method is proposed for describing such interactions by means of the potentials of simplest shapes, rectangular and trapezoidal ones. It is shown that when the interactions cover the distances much larger than the mean ones between the adsorbed molecules, the adsorption is described by the expression specific for noncooperative binding of the ligands. On this basis the method for analysing the experimental isotherms of adsorption is developed. It permits estimation of the interaction energy between the ligand adsorbed molecules and specific distance to which these interactions are distributed. This method is applied for analysing experimental isotherms of adsorption of antibiotic distamycin A on poly (dG) . poly (dC).

Biopolymers↗