Biomedical subjects

V V Lobzin

Publications and source records attributed to V V Lobzin.

6 recordsLinked to original sources

PubMed2006

Anticodons, frameshifts, and hidden periodicities in tRNA sequences.

Fourier analysis of the short-range periodicities for the complete set of sequences coding for tRNA genes in genome of Bacillus subtilis proves that periodicities with periods p = 2, 3, 4, and 6 sites are the inherent properties of tRNAs. The related periodicities should be understood in a broad statistical sense and their identifying needs the elaborate statistical methods. To improve the statistics, the analysis of significant periodicities was performed for the binary R-Y, S-W, and K-M sequences. Generally, such short-range periodicities are produced via biased positioning of particular nucleotides rather than via the tandem multiplication and subsequent modifications of repeats, though the latter mechanism may also be realized. Quasi-coherently piercing long segments of tRNA, the short-range periodicities create the effective long-range structural coupling between the acceptor stem and the anticodon loop and may participate in the mechanisms of molecular recognition. The periodicities with p = 2 and 4 provide the natural ground for the translation with spontaneous or programmed frameshifting and are present in tRNAs decoding the most frameshift-prone codons. The observation of short-range periodicities suggests that the mechanisms of amino-acylation of tRNAs and codon-anticodon pairing are not independent. Their study may also provide the important information related to the origin and evolution of the genetic code.

Anticodon↗

PubMed2003

DNA polymorphism in the beta-Esterase gene cluster of Drosophila melanogaster.

We have analyzed nucleotide polymorphism within a 5.3-kb region encompassing the functional Est-6 gene and the psiEst-6 putative pseudogene in 28 strains of Drosophila melanogaster and one of D. simulans. Two divergent sequence types were detected, which are not perfectly associated with Est-6 allozyme variation. The level of variation (pi) is very close in the 5'-flanking region (0.0059) and Est-6 gene (0.0057), but significantly higher in the intergenic region (0.0141) and putative pseudogene (0.0122). The variation in the 3'-flanking region is intermediate (0.0083). These observations may reflect different levels of purifying selection in the different regions. Strong linkage disequilibrium occurs within the region studied, with the largest values revealed in the putative pseudogene and 3'-flanking region. Moreover, recombination is restricted within psiEst-6. Gene conversion is detected both within and (to a lesser extent) between Est-6 and psiEst-6. The data indicate that psiEst-6 exhibits some characteristics that are typical of nonfunctional genes, while other characteristics are typically attributed to functional genes; the same situation has been observed in other pseudogenes (including Drosophila). The results of structural entropy analysis demonstrate higher structural ordering in Est-6 than in psiEst-6, in accordance with expectations if psiEst-6 is indeed a pseudogene. Taking into account that the function of psiEst-6 is not known (but could exist) and following the terminology of J. Brosius and S. J. Gould, we suggest that the term "potogene" may be appropriate for psiEst-6, indicating that it is a potential gene that may have acquired some distinctive but unknown function.

Animals↗

PubMed1999

Characterization and comparison of protein structures. Part I-characterization.

The quantitative criteria characterizing the regularity of Calpha-backbones in the protein structures are presented. A technique is based on the Fourier remapping of the Cartesian coordinates for the Calpha-chain. The Fourier spectra identify the hidden periodicities and symmetries in protein structures, while the integral regularity is assessed via the spectral structural entropies. The formal unification of digitizing and the similarities in statistics for the random counterparts allow study of the direct correlations between the distribution of physico-chemical characteristics along the amino acid sequence and the spatial conformation of the polypeptide chain. The significant correlations are found for both hydrophobicity and side-chain volumes, though, as expected, the effects for hydrophobicity turn out essentially stronger. A scheme is illustrated by the set of 120 protein structures comprising the representatives from the main superfamilies and superfolds.

Amino Acid Sequence↗

PubMed1999

Characterization and comparison of protein structures. Part II-comparison.

The Fourier methods are applied to the pairwise comparison of Calpha-backbones in protein structures. The technique allows to assess both the general similarity and the main origins of resemblance (coincident periodicities, similarity of fragments, or large-scale semblance of folding). The analogous methods can be extended to the study of correlations between the structural characteristics for the Calpha-backbone of one protein and the distribution of physico-chemical parameters along the primary amino acid sequence for the other. Finally, we discuss the problem of clusterization of pairwise data into tree-like hierarchical system.

Amino Acid Sequence↗

PubMed1998

Study of correlations in segmented DNA sequences: application to structure coupling between exons and introns.

A technique for the study of correlations in segmented DNA sequences is developed. Within this approach the effects of compositional patchiness are separated from the beginning, allowing us to display the refined effects of structural coupling between different segments. The mutual analysis of Fourier structure spectra and pair correlation functions identifies both the main ranges (long, short, or intermediate) and the sources (coincident periodicities, large scale density variations, short-memory coupling, or coherent point mutations) of correlations. A scheme is applied to the study of structural coupling between exons and introns in fragmented genes of eukaryotes. The molecular, genetic, and evolutionary aspects of the features observed are discussed.

Animals↗

PubMed1998

Nucleosome units and hidden periodicities in DNA sequences.

The relationship between the hidden periodicities in DNA sequences and the nucleosome units is investigated. It is shown that in the vicinity of lengths of about 200 bases there are statistically significant periodicities which remain approximately universal for exon-intron sequences both in the different genes and the different eukaryotic species. The additional analysis displays, nevertheless, that these approximately coincident universal periodicities can be generated by a variety of mechanisms. The relevance of the features observed to the structure of chromatin is discussed.

Animals↗