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- Title
BIOINFORMATIC LOOKUP FOR METALLOPROTEINASES AND THEIR NATURAL INHIBITORS. STRUCTURAL RELATIONSHIPS.
- Authors
Petreu, T.; Cotrutz, Carmen Elena; irbu, P. D.; Neamtu, Monica; Maria Filioreanu, Ana; Badescu, L.; Neamtu, A.
- Abstract
Matrixins or matrix metalloproteinases (MMPs) represent a class of structural and functional related enzymes responsible for altering the natural elements of the extracellular matrix. EnzymeDB database and SWISS-PROT databases was used for MMP and TIMP structures search. For a comparative investigation of the aminoacid sequence in the MMP catalytic site we have used an online application, MUSCLE (MUltiple Sequence Comparison by Log-Expectation). We have used BLAST application to investigate sequence similarities. Structural analysis for MMPs in current protein databases, was performed on DALI server (Distance-matrix ALIgnment). DALI is able to search proteins that are using the same packing pattern as the template introduced in the search module. For hominids we have found 148 MMPs in UniProtKB database from which 143 are human-type. We have performed a database search for TIMP element in UniProtKB database. We have obtained a number of 605 results, whose taxonomy included 10 bacterial elements and 595 elements in eukaryotes. In hominids, we found 90 TIMPs from which 86 are human type. We have observed a poor structural correlation between the 4 human TIMPs. From DALI results, from the 161 aminoacids in the catalytic domain file, only 58 were conserved (36.02%). We have performed a thorough bioinformatic investigation regarding MMP and their natural inhibitors structures. For human MMPs we have described 23 structures for which we have performed a pairwise alignment and also a structural alignment in the available protein structure databases; we have remarked a high conservation degree for both type of alignments in the area of the catalytic site. This supposes that investigations must be extended toward potential allosteric inhibition sites on the enzyme in order to explain various failures of synthetic inhibitos action on the MMP extracellular matrix degrading activity.
- Subjects
BIOINFORMATICS; METALLOPROTEINASES; EXTRACELLULAR matrix; AMINO acid sequence; ALLOSTERIC enzymes
- Publication
Annals of the Romanian Society for Cell Biology, 2011, Vol 16, Issue 1, p175
- ISSN
2067-3019
- Publication type
Article