V Skerl

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

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Publications (7)24.41 Total impact

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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.
    Immunology Letters 01/1995; 47(1-2):25-8. · 2.34 Impact Factor
  • AIDS Research and Human Retroviruses 12/1994; 10(11):1425-6. · 2.71 Impact Factor
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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 [Lipman and Pearson (1985) Science, 227, 1436-1441], and 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 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 < ftp.icgeb.trieste.it >. Individual records can be retrieved with the gopher server at < icgeb.trieste.it > 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 < sbase@icgeb.trieste.it >. Another mail server < domain@hubi.abc.hu > assigns SBASE domain homologies on the basis of SWISS-PROT searches. A comparison of pertinent search strategies is presented.
    Nucleic Acids Research 09/1994; 22(17):3610-5. · 8.81 Impact Factor
  • 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.< >
    System Sciences, 1994. Proceedings of the Twenty-Seventh Hawaii International Conference on; 02/1994
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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.
    Viral Immunology 02/1994; 7(4):215-9. · 1.75 Impact Factor
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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) Prot. 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) 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 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 mean value of ftp.icgeb.trieste.it.
    Nucleic Acids Research 08/1993; 21(13):3111-5. · 8.81 Impact Factor
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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 < ftp.icgeb.trieste.it >.
    Protein engineering 06/1993; 6(4):391-5.

Publication Stats

97 Citations
24.41 Total Impact Points

Institutions

  • 1995
    • Vinča Institute of Nuclear Sciences
      Beograd, Central Serbia, Serbia
  • 1994
    • University of Chicago
      • Department of Computer Science
      Chicago, IL, United States
  • 1993–1994
    • International Centre for Genetic Engineering and Biotechnology
      Trst, Friuli Venezia Giulia, Italy