Vesna Skerl

Vinča Institute of Nuclear Sciences, Beograd, Central Serbia, Serbia

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Publications (8)27.02 Total impact

  • Vesna Skerl
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    ABSTRACT: A pool of 110 randomly selected/generated amino acids sequences was used to perform specific local sequence similarity alignment analysis with the pool of 279 reported sequences of human T-cell receptor (TCR) V-regions. The 110 analyzed sequences were divided, according to their origin and nature, into six protein groups, as: human intracellular (hi), extracellular/transmembrane (he) and extracellular adhesive matrix (ha) proteins, 'average' human proteins (hum), proteins of non-human origin (nhum) and randomly generated quasi-protein sequences (r). These sequences were decomposed into all their overlapping 11-mer segments, generating a total of 56,836 derived peptides (at least 8000 per group). Each derived peptide was aligned with the 279 human TCR V-regions and assigned to the category (alpha-like, beta-like, gamma-like or delta-like) corresponding to the class (V alpha, Vbeta, Vgamma or Vdelta) of the V-region encompassing the most similar segment, as determined by the performed similarity-search. The six protein groups were found to differ significantly in their distribution of derived peptides among the four categories. According to the binomial tests results, human proteins from the extracellular compartment (he, ha) comprise a higher proportion of delta-like segments (P = 2.3 x 10(-2) and P < 10(-8), respectively) than the 'average' human proteins (hum). In addition, and in accordance with this finding, proteins that are normally not found in that topological compartment comprise a lower proportion of delta-like peptides (P = 1.4 x 10(-5) and P < 10(-8) for groups nhum and hi, respectively) than the 'average' human proteins (hum). In contrast, these proteins comprise a higher proportion of gamma-like segments (P = 8.3 x 10(-3), P = 1.4 x 10(-3) and P = 1.7 x 10(-4), for groups r, nhum and hi, respectively) than the 'average' human proteins (hum). These findings indicate significant differences between proteins encountered in the extracellular compartment--that are normally immunologically tolerated--and those the presence of which is usually non-tolerated. The results suggest that the discrimination and the reaction of the human immune network to proteins found in the extracellular compartment correlate with the proteins' pattern of preferential local sequence similarity with the Vgamma and Vdelta classes of human TCR V-regions, implying a specific and an important role of gammadelta-cells in the maintenance of the immune homeostasis. Whether this implication represents a rule associated with self-tolerance, will be investigated by future analyses.
    No preview · Article · Mar 1998 · Immunology Letters
  • R Metlas · V Skerl · V Veljković · S Pongor
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    ABSTRACT: Twenty-five V3 loops of envelope gp 120 extracted from 30 HIV-1 isolates were compared with T-cell receptor (TCR) subunits variable (V) portions using pairwise alignments of 11-residue peptides. The results indicate that, in comparison with random sequences, the analyzed V3 loops, unlike control (unrelated) sequences, display highly significant local similarity with TCR V delta (p approximately 10(-20)). However, pattern-matching searches were performed on a much larger number of V3 loops (484). In particular, selective pattern TR * * * NT * K * I is shared by V delta from human T-cell line KT19E and 230 HIV-1 V3 loops (N-terminal portion). Pattern RA * YT * * * I * G is common for V delta chain isolated from T-cell line DS6 of an immunodeficient patient and 69 V3 loops (C-terminal portion). The presented delta-chain portions of sequence similarity with the V3 loops overlap the putative complementarity-determining region (CDR3), thus possibly indicating functional similarity too.
    No preview · Article · Jul 1995 · Immunology Letters

  • No preview · Article · Dec 1994 · AIDS Research and Human Retroviruses
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    ABSTRACT: SBASE 3.0 is the third release of SBASE, a collection of annotated protein domain sequences. SBASE entries represent various structural, functional, ligand-binding and topogenic segments of proteins as defined by their publishing authors. SBASE can be used for establishing domain homologies using different database-search tools such as FASTA, and BLAST3 which is especially useful in the case of loosely defined domain types for which efficient consensus patterns can not be established. The present release contains 41,749 entries provided with standardized names and cross-referenced to the major protein and nucleic acid databanks as well as to the PROSITE catalogue of protein sequence patterns. The entries are clustered into 2285 groups using the BLAST algorithm for computing similarity measures. SBASE 3.0 is freely available on request to the authors or by anonymous 'ftp' file transfer from . Individual records can be retrieved with the gopher server at and with a www-server at <http://www.icgeb.trieste.it>. Automated searching of SBASE by BLAST can be carried out with the electronic mail server <[email protected] /* */>. Another mail server <[email protected] /* */> assigns SBASE domain homologies on the basis of SWISS-PROT searches. A comparison of pertinent search strategies is presented.
    Full-text · Article · Sep 1994 · Nucleic Acids Research
  • Z. Hatsagi · V. Skerl · S. Pongor
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    ABSTRACT: Identification of biologically important motifs in protein sequences requires the parallel handling of the structural and biological data of proteins given in sequence databases. We approach this problem with a generalized data model, in which both kinds of data are included in one representation consisting of substructures (entities), relationships, and hierarchical classification schemes containing the semantic definitions of these. A consistent implementation of this model is not attempted because of the lack of standardized semantic classification schemes. However, we use the model to design simple approximate strategies that can identify patterns in current (partially standardized) databases. Application examples to prediction of functional domains from sequence are given.< >
    No preview · Conference Paper · Feb 1994
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    ABSTRACT: By examining sequence similarity between the V3-loop of gp120 from various HIV-1 isolates and human proteins, we found that the V3 loop portion KKGIAIGPGR in strain New York 5 (HIV-1NY5) shares 70% identical residues with the collagen-like region (CLR) of human complement component C1q-A. C1q CLR was found to react with autoantibodies from several autoimmune disorders. Thus, we assumed that it would be of interest to find out the C1q reactivity with antibodies from AIDS sera. The results obtained show that the V3 loop-derived synthetic peptide KKGIAIGPGRTLY reacts both with AIDS patients sera and with antibodies purified on the V3 loop peptide-affinity column. The same affinity-purified antibodies bind also to C1q molecules. Since, according to our previous results, HIV-1 V3 loops and immunoglobulin heavy chain variable regions (Ig VH) share several common features, we suggest that the envelope of HIV-1NY5 bears a functional internal image of the C1q-A CLR epitope. Therefore, gp120 could manipulate the immune network and contribute to HIV-induced autoimmunity.
    No preview · Article · Feb 1994 · Viral Immunology
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    ABSTRACT: SBASE 2.0 is the second release of SBASE, a collection of annotated protein domain sequences. SBASE entries represent various structural, functional, ligand-binding and topogenic segments of proteins [Pongor.S. et al. (1993) Prof. Eng., in press]. This release contains 34,518 entries provided with standardized names and it is cross-referenced to the major protein and nucleic acid databanks as well as to the PROSITE catalog of protein sequence patterns [Bairoch.A. (1992) Nucl. Acids Res., 20 suppl, 2013–2018]. SBASE can be used for establishing domain homologies using different database-search tools such as FASTA [Lipman and Pearson (1985) Science, 227, 1436–1441], FASTDB [Brutlag et al. (1990) Com p. Appl. Blose I., 6, 237–245] or BLAST3 [Altschul and Lipman (1990) Proc. Natl. Ac ad. Scl. USA, 87, 5509–5513] which is especially useful in the case of loosely defined domain types for which efficient consensus patterns can not be established. SBASE 2.0 and a set of search and retrieval tools are freely available on request to the authors or by anonymous ‘ftp’ file transfer from .
    Full-text · Article · Aug 1993 · Nucleic Acids Research
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    ABSTRACT: SBASE is a database of annotated protein domain sequences representing various structural, functional, ligand binding and topogenic segments of proteins. The current release of SBASE contains 27 211 entries which are provided with standardized names in order to facilitate retrieval. SBASE is cross-referenced to the major protein and nucleic acid databanks as well as to the PROSITE catalog of protein sequence patterns [Bairoch, A. (1992) Nucleic Acids Res., 20, Suppl., 2013–2118]. SBASE can be used to establish domain homologies through database search using programs such as FASTA [Lipman and Pearson (1985) Science, 227, 1436–1441], FASTDB [Brutlag et al. (1990) Comp. Appl. Biosci., 6, 237–245] or BLAST3 [Altschul and Lipman (1990) Proc. Natl. Acad. Sci. USA, 87, 5509–5513], which is especially useful in the case of loosely defined domain types for which efficient consensus patterns cannot be established. The use of SBASE is illustrated on the DNA binding protein Brain-4. The database and a set of search and retrieval tools are freely available on request to the authors or by anonymous ‘ftp’ file transfer from .
    Full-text · Article · Jun 1993 · Protein engineering