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2016 A model of complementary interaction of short peptides with the DNA double helix

Comparison of the spatial arrangement of functional groups of the nucleic bases on the surface of the major groove of DNA double helix and the functional groups of short peptides shows that these polyampholyte structures have the possibility of complementary multi-point interaction. As an example, presents a model of complementary binding of synthetic pineal tetrapeptide Ala-Glu-Asp-Gly sequence nucleotide ACTS in the composition of the leading chains of the DNA double helix, which is repeated on promoterin areas telomere genes and RNA polimerai II. It is shown that regulatory peptides and complementary to them blocks in the composition of double-strand DNA can be bound proton-donor and proton-acceptor interactions involving the molecules of hydration water.

As you know, a normal cell responds to external or internal changes by changes in the intensity of transcription of active genes and RNA synthesis, One of the factors pathological condition is a slowing of these processes, in particular, a violation of the processes of initiation of transcription [12]. At the same time there were reports that some of the proteins that control the cell cycle, can be active as transcription factors [16].

The question about the mechanism of initiation of transcription is solved by the study of the structures of transcription factors and determination of their binding sites with the DNA double helix on promotera (non-coding) region of the gene. Since the appearance of the first works in this area in the early 80-ies of the structural motifs in the structure of the transcription factors of some genes and their complexes with defined sequences of nucleotide pairs of the DNA double helix on promoterin the sites of genes [34, 35]. It is established that, in nucleated cells the activation of chromatin and control of transcription are carried out by a complex system of agonists and transcription factors, including high molecular weight proteins and low molecular weight peptides and short peptides [22, 37].

Then it seemed that the specific activity of many macromolecular transcription factors localized on relatively short sections of the peptide chain, consisting of 30-100 amino acid residues [31]. These observations highlighted a new problem of pharmacology and medicine. You need to find out what is the minimum length and amino acid sequence of a short peptide, directly and selectively contacting with promoterin a portion of a gene and is able to mimic the action of the transcription factor. In more detail the molecular mechanisms of initiation of transcription in the cells presented in the monograph [27. R. 341-403].

The usual approach to finding a binding site in a protein structure is to use immunospecificity methods. So, for example, was determined by plot-chain of laminin consisting of 14 amino acid residues responsible for adhesion of epithelial cells. Further research showed that this peptide can be shortened to five amino acid residues the selectivity of binding to the receptor [19]. A similar problem was posed and solved practically for the peptide hormone erythropoietin. The hormone erythropoietin (MM 46000) promotes the proliferation, differentiation and survival of progenitor cells of erythrocytes. The library of peptides by means of breeding has been found short peptides (14 amino acid residues) exhibiting activity similar to the native hormone [41].

At the same time was isolated and investigated by endogenous regulatory peptides of the person that showed tissue-specific activity when used in ultra-low concentrations. Study of the products of hydrolysis of hemoglobin and peptides contained in the nutrient medium during the cultivation of human erythrocytes, showed that short segments of the chains of globins are active, unusual original hemoglobin: they bind to opiate receptors potentiate the action of bradykinin [24]. Regulatory peptides were also isolated from the living culture of bone marrow cells, examined in relation to specific regulatory activity and called myelopeptide [6].

Experiments in recent years have shown that natural peptide preparations and synthetic analogues - tetrapeptide a certain structure — exhibit tissue-specific activity, participating in the activation of chromatin, and normalizing the rhythm of protein synthesis in tissue culture [1, 4, 5, 9] and at the level of the whole organism [10, 13, 26, 32]. It is possible to assume that short peptides that support autocrine regulation, are mimetikom and high-molecular agonists of transcription factors.

Mechanisms of penetration of short peptides in the cell and in the cell nucleus can be different. According to I. P. ashmarina, the mechanism of penetration of neuropeptides in the cell and into the genome of a neuron is similar to the mechanism of penetration of steroid hormones. More hydrophilic short peptides, in contrast to steroid hormones to overcome lipid membranes in contact with hydrophilic groups of phospholipids on the outer side of the membranes are grouped and enter into a cell using a mechanism close to pinocytosis [2]. The formation of complexes "protein-protein" and dissociation — a common mechanism of intracellular transport processes. In the cytoplasm are steroid receptors, containing in the structure domain "C4 zinc finger". In the absence of this steroid hormone receptor is associated with protein hsp 90 (heat stock protein), which is always present in the cytoplasm. With the appearance of a steroid hormone the inactive complex dissociates and the steroid hormone binds to the receptor, forming an active complex, which goes to the nucleus where it binds to regulatory site of the target gene and activates (or represses) the transcription [31].

Modern ideas about the permeability of the cytoplasmic and nuclear membranes show that for penetration through these membranes exist in the diffusion path.

In addition to the previously known ion channels and processes of pinocytosis, open channels formed by a family of transmembrane proteins Parinov present in mitochondrial and cytoplasmic membranes [25]. These proteins are composed of up to 50% hydrophilic amino acids and structural motifs amphiphilic a-helix. However, most of the peptide chain is in the R-conformation. Several transmembrane chains Parinov form a barrel-shaped (barrel-shaped) pores, which are permeable for small hydrophilic and amphiphilic molecules (urea, glycerin, tryptophan, etc.). For example, when the difference of the concentrations of tryptophan 0.001 M diffusion flux through the membrane is 600 molecules per second across 1 µm2 of membrane surface [12. R. 509].

Parinov family includes the subfamily of aquaporins — proteins that control the flow of water into the cell and out of cells depending on small changes in pH of the environment [17].

Membrane of the nucleus also have a developed system of transport pores formed by protein complexes nucleoporins that control the transport nucleoprotein complexes in the nucleus and from the nucleus [33]. Inner diameter nucleopore is about 42 n. m so that they are permeable to the diffusing molecules with molecular weight up to 5000 Da [27. R, 69].

Thus, the possibility of penetration of short peptides in the cell and in the cell nucleus does not cause any fundamental doubts. Our experiments are consistent with the views on the penetration of short peptides into the cell and its nucleus, as after adding the peptide into the cell culture revealed changes in the status of chromatin, In [1, 8, 13] on the cells in tissue culture it has been proven that short synthetic peptides not only enter a cell through cytoplasmic and nuclear membranes, but also participate in the activation of some genes, in particular gene telomerase [5].

In [9], we studied the influence of short synthetic peptides to changes in the heterochromatin in leukocytes and detected activation of ribosomal genes, decondensation densely Packed fibrils of chromatin and release of genes repressed in the result of age-related condensation euchromatin areas of cells.

To date, however, there is an obvious gap between the numerous observations of the regulatory influences of neurohormones and synthetic oligopeptides on the state of chromatin and the understanding of the molecular mechanisms of selective binding of these peptides with premodernity portions of genes.

Among short synthetic peptides, studied by us earlier in relation to the activation of chromatin, the greatest efficiency was shown by the synthetic pineal tetrapeptide (Ala-Glu-Asp-Gly) [1, 4, 8, 9]. This peptide is also of particular interest, since he has a high geroprotective activity. We investigated the structural features of this peptide to find the parameters of correspondence between specific for the peptide amino acid sequence and the sequence of nucleotides in the double helix structure of DNA. A model of the specific binding peptide with the recognition site on promotera the portion of a gene, based on the principle of geometrical and electrochemical complementarity pravostoronnikh two molecules of the peptide and of the DNA double helix.