SitCon: binding site residue conservation visualization and protein sequence-to-function tool

Kairys, Visvaldas; Fernandes, Miguel X.

http://hdl.handle.net/10400.13/5004

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Authors

Kairys, Visvaldas

Fernandes, Miguel X.

Abstract(s)

We introduce SitCon (SITe CONservation), a program designed to explore conservation of functionally important sites in a series of hypothetically homologous candidate protein structures, given amino acid sequence as an input. This can especially be useful when looking for an unknown function of a protein. SitCon exploits the fact that binding sites of proteins are preserved better than the overall residue sequence conservation. To test the capability of unknown function prediction, we randomly chose known function proteins from Caenorhabditis elegans genome. To imitate a behavior of an unknown function target, only the low homology proteins with 0.01 E-score 100 were analyzed as templates. Out of 29 enzyme targets, SitCon was able to provide various hints about their function in at least 69% of the cases. For the eight nonenzyme targets, the predictions matched in only 25% of the cases. SitCon was also tested for a capability to predict presence or absence of metal-containing heterogroups in the target enzymes with 80% success rate. Because this algorithm is not based on specific protein signatures, it may allow detection of overlooked relationships between proteins. SitCon is also very effective as a tool allowing visual comparison of binding site residue conservation between the target and homologous templates side-by-side.

Keywords

Genome Sequence-to-function Protein function prediction Binding site Amino acid residue conservation . Faculdade de Ciências Exatas e da Engenharia

URI

http://hdl.handle.net/10400.13/5004

Citation

Kairys, V., & Fernandes, M. X. (2007). SitCon: Binding site residue conservation visualization and protein sequence‐to‐function tool. International Journal of Quantum Chemistry, 107(11), 2100-2110.