Structural criteria of biologically active RGD-sites for analysis of protein cellular function - a bioinformatics study.
Med Sci Monit
; 8(8): BR301-12, 2002 Aug.
Article
em En
| MEDLINE
| ID: mdl-12165734
ABSTRACT
BACKGROUND:
Cell adhesion involves interactions of integrins and extracellular proteins, often facilitated by the RGD motif. Only presence of the RGD in a sequence of a protein may be not sufficient for the biological activity (binding to an integrin) and additional biochemical and/or structural studies are essential. MATERIAL/METHODS:
Structural criteria that would allow identification biologically active RGD-sites on the base of a spatial structure may assist analysis of function of a protein in the cell. For the first time, computational analysis of RGD-sites in a large non-redundant set of protein structures was done.RESULTS:
Out of 3819 protein chains sequences of about 100 contained RGDs. Analysis of the structures of the RGD-'native' proteins has allowed establishing main determinants of the biologically active conformations of the RGD sites surface accessibility of the whole RGD-sequence and the secondary structure. The criteria, applied to the remaining proteins of the set, identify 23 proteins ( approximately 25%) with potentially active RGD-sites. The results strongly suggest that RGD has a high propensity for being involved in protein-protein interactions and this may explain occurrence of RGDs in intracellular proteins. Results of the analysis suggest (in some cases, confirm) novel integrin-related activities for 7 membrane/extracellular proteins, as well as confirm RGD-facilitated cell attachment for 5 viral proteins.CONCLUSIONS:
Only presence of RGD in a sequence is not sufficient to propose biological activity of this site. The results also suggest that the method can be used on large scale for example, for identifying potential integrin-interacting proteins in an animal genome.
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Base de dados:
MEDLINE
Assunto principal:
Oligopeptídeos
/
Conformação Proteica
/
Proteínas
/
Biologia Computacional
Tipo de estudo:
Prognostic_studies
Limite:
Animals
/
Humans
Idioma:
En
Revista:
Med Sci Monit
Assunto da revista:
MEDICINA
Ano de publicação:
2002
Tipo de documento:
Article
País de afiliação:
Federação Russa