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V A Kulichkov

Publications and source records attributed to V A Kulichkov.

32 records · Page 2Linked to original sources
PubMedDate not supplied

[Complexity analysis of a genome. II. Extensive homology zones in bacteriophage lambda].

The suggested earlier complexity approach for detecting structural regularities in primary structures of nucleic acids is illustrated by using lambda phage as an example. Among the most interesting regularities detected in the lambda phage genome are the following: (a) the presence of "extended homology zones" i.e. fragments in which block transpositions of duplicative type predominate explicitly; (b) the abundance of palindrome-hairpin structures and duplications in the origins and termini of many genes; (c) the hierarchy in the repeats and inversions organization.

Bacteriophage lambda↗
PubMedDate not supplied

[Complexity analysis of genomes. I. Complexity and classification methods of detected structural regularities].

A new computer method for detecting local structural regularities in genomes of different microorganisms is described. The method is based on the concepts of complexity and complexity profile of a finite sequence. The complexity measure taking into account the specificity of genetic texts (presence of repeats, symmetries, inversions) is proposed. The genomes of different viruses and bacteriophages contained in Genbank were processed. The classification and interpretation of structural regularities were carried out.

Bacteriophages↗
PubMedDate not supplied

[Molecular-biological study of vaccinia virus genome. II. Localization and nucleotide sequence of vaccinia virus genes coding for proteins 36K and 12K].

Genes encoding virus-specific late proteins with molecular mass 36 kDa and 12 kDa were mapped in HindIII-P DNA fragment of vaccinia virus strain L-IVP by hybrid selection of RNA to cloned DNA fragments followed by in vitro translation. RNA origin site of the 36K protein was detected in HindIII-J fragment. Nucleotide sequences of these genes were determined. Amino acid sequences of the 36K and 12K polypeptides were compared with the protein bank PIR.

Amino Acid Sequence↗
PubMedDate not supplied

[The effect of distribution of adjacent amino acids in primary structures on the possibility of mutation substitutions in globular proteins].

Frequency distributions of adjacent ARs in the primary structures of 320 globular proteins out of different superfamilies were investigated. ARs of every type were compared with the occurrence frequencies of 20 canonic residues at the distances of 1-20 residues according to their primary structure. Amino acid residues were found to be divided into groups of interchangeable residues in the course of globular protein evolution according to the distribution kinds and in terms of Euclidean distances. The use of pancreatic RNases of mammals showed that the approximate preservation of frequency adjacent (1-4 residues according to their primary structure) and characteristics in 5-15 residues mid-interactions may be used in studying the supposed amino acid substitutions in globular protein.

Amino Acid Sequence↗
PubMedDate not supplied

[Development of rules for vaccine engineering based on the variability of peptide fragments in closely related proteins].

Based on the protein sequence data bank (PIR), the "variable fragment" bank, comprising pairs of closely related proteins, containing one or more strongly differing sites of primary structures was formed. The bank includes 465 "variable fragments" of 383 protein pairs. Amino acid residues composition of "variable fragments" was examined and indexes of potential amino acid residues variability was formed. An analysis of amino acid fragments replaceability was carried out by substituting the N-, C-terminal, or middle part of a chain), the fragments length differences and physico-chemical properties of residues, such as volume, hydrophobicity, polarity, isoelectric point, etc. Some general empirical rules of peptide insertions in carrier-proteins were created based on these analyses. The rules are directed for performing modifications maintaining the common structure and function of the carrier-protein molecule. The selection scheme for determining the regions suitable for modification and the criteria for defining the width of acceptable modifications in this regions were suggested. The use of potential variability profile for detecting regions suitable for peptide insertion was considered on the model of hepatitis B surface protein.

Amino Acid Sequence↗
PubMedDate not supplied

[The nature of amino acid substitution in antigenic drift of hemagglutinin N3 and neuraminidase N2 from the influenza virus].

The nature of amino acid replacements in 16 drift variants of hemagglutinin H3 subtype and 5 drift variants of neuraminidase N2 subtype of the influenza A virus were studied. The dependences of relative replacement frequencies and relative quantities of frequent replacements upon differences of properties of substituted residues are plotted. In contrast to most of the known proteins, amino acid replacements in hemagglutinin and neuraminidase depend weakly on the physico-chemical parameters of amino acids. For the antigenic determinants studied the replacement frequencies were compared to those calculated according to two models: one for conservative replacements and the other for accidental mutation of the genetic code. The differences in the nature of amino acid replacements are found in four antigenic determinants of hemagglutinin. The replacements in experimentally selected proteins are shown to go beyond limitations of natural variants. The explanations of the reasons of low epidemicity of some strains and ineffective attempt to imitate the natural antigenic drift of viruses by using experimental selection are proposed. The causes of time-limited circulation of H3N2 influenza virus subtype are discussed.

Amino Acid Sequence↗
PubMedDate not supplied

[A method of calculatiing immunochemical cross-reactions between homologous proteins].

The effects of amino acid substitutions within the antigenic sites, within the residues close to these sites and within other parts of the molecule on the cross-reaction with the antisera to homologous protein were considered. The method for calculus the values of cross-reactions, based on using primary structures data, X-ray coordinate of one of the homologues and the locations of the antigenic sites is proposed. The values obtained by this method for the cross-reactions of ten myoglobins from various species with antisperm-whale myoglobin sera have a good correlation with the known experimental data. The possibility of using the method to make the location of protein antigenic sites more precise is discussed.

Amino Acids↗
PubMedDate not supplied

[Structural and physico-chemical properties of amino acids of functionally important regions of proteins].

A correlation of the localization of functionally important regions with places having low and high values on twelve profiles built on a basis of amino acid sequences was analysed using a broad set of proteins. The profiles of hydrophilicity, resemblance to the sequences of human proteins, flexibility, mutability and others were considered. The resemblance profile was plotted by the program fixing short similar fragments in the testing protein and 92 human ones. The active centres were shown to be located in the primary structure regions having relatively low values on the resemblance profiles. Similar effect was observed in the mutability and alpha-helicity profiles. The potential functionally important sites of the human leukocyte interferon and interleukin-2 isolated on the basis of the analysis of this profiles were in accord with the available literary data.

Amino Acids↗
PubMedDate not supplied

[Effect of spatial coupling of amino acid residues on the possibility of mutational substitution in globular proteins].

Amino acid residues can be divided into similar groups by frequencies of interreplacements in the evolutionary pathway and by trends to spatial contacts at the tertiary structures of globular proteins. Each residue was compared to the cluster of spatial surrounding--the totality of residues spacially drawn together. 5210 clusters in 32 unhomologous proteins with established tertiary structure and 6447 clusters formed only by variables amino acid residues were analysed. Spatial contacts among residues were studied depending on the secondary structure and the amount of residues in a cluster. It was assumed that functionally admissible mutations may be defined, first of all, by the degree of neighboring of amino acid residues in the spatial surrounding.

Amino Acid Sequence↗
PubMedDate not supplied

[Use of marker genes located on X-chromosomes to analyze lens development in Arctic fox/fox hybrids].

Glucose-6-phosphate dehydrogenase (G6PD) isozymes were studied in the lens and some tissues of Arctic fox x fox female hybrids at different developmental stages. During the embryonic and early postnatal (till the 2nd day of life) development the lens is characterized by a high degree of individual variation of the ratio between parental G6PD forms. The number of stem cells for the lens was determined to be equal to six by means of binomial method of description of this variation. Taking into account the similarity of G6PD spectra in the right and left lenses, a suggestion was put forward that both the lenses develop from the common pool of stem cells. After the 4th day of postnatal life a hemizygote-like phenotype of maternal type was observed in the lenses of all hybrid females. It is suggested that the formation of pseudohemizygote phenotype is due to the posttranslation chemical modification of G6PD isozymes.

Animals↗
PubMedDate not supplied

[Preferential retention of the mink chromosome group in somatic cell hybrids of Chinese hamster and American mink].

The chromosomal complement was studied in 57 independent clones of hybrid cells obtained in six experiments for fusion of Chinese hamster and American mink cells. Various mink chromosomes in hybrids of concern are lost. It is shown when a small number of mink chromosomes are retained in hybrid clones, chromosomes 6, 9, 10, 12, 13, 14 and X segregate in a similar way and are preferentially retained in these clones. When a considerable number of mink chromosomes are detained in hybrid clones, the segregation mode is close to a random one.

Animals↗
PubMedDate not supplied

[A bank of protein family images Prof-Image for rapid determination of possible functions of random amino acid sequences].

A bank of images of protein families (PROF IMAGE bank) is developed using early published method and amino acid sequences of 24-th release SWISS-PROT bank (27752 sequences). The method relies on physical-chemical and structural properties of amino acids and on the choice of fragments of protein families for the most discriminate distinction of amino acid sequences of a family from representatives of other families or random sequences. Specifications of the algorithms of building the images, principles of amino acid sequences selection to form protein families, the structure of the bank, and characteristics of images of 163 protein families are described. The data are illustrated by the image of alpha-interferon precursors family. The results of the images comparison with all proteins of the SWISS-PROT bank and ways to use the PROF IMAGE bank for determination of possible functions of amino acid sequences are discussed.

Algorithms↗
PubMedDate not supplied

[Samples of the protein family for comparing amino acid sequences].

A method to develop images of protein families for fast comparison with any amino acid sequences is proposed. The method is based on physico-chemical properties of amino acids and on the choice of fragments of amino acid sequences of protein families that maximally distinguish the sequences from members of other families or random sequences. The efficiency of the method is demonstrated on comparison of images developed for protein families of alpha-interferons, alpha-hemoglobins, long neurotoxins, and DNA polymerases with the SWISS-PROT data bank.

DNA-Directed DNA Polymerase↗