Protein Repeats: from Structure to Function

Andrey Kajava,  Structural Bioinformatics and Molecular Modelling, CNRS, France

ABSTRACT - A significant portion of proteins carrying fundamental functions contain arrays of tandem repeats. Furthermore, over the last years a number of evidences has been accumulated about the high incidence of tandem repeats in the virulence proteins of pathogens, toxins and allergens. Genetic instability of these regions can allow a rapid response to environmental changes and thus can lead to emerging infection threats.   Thus, discovery of these domains and their structure-function study promise to be a fertile direction for research leading to the identification of targets for new medicaments and vaccines. Andrey Kajava, in collaboration with Gaurav Sablok and Nicola La Porta, is going to developed an online database FungProSec, which will give a systematic and curated information on the presence of these protein homorepeats in fungal proteomes and secretomes. A preliminary demo for this database will be shown during the presentation.  The present version of the FungProsec contains 58 sequenced fungal proteomes from JGI and NCBI and 51 secretomes. The threshold in the present analysis was kept as 7 consensus amino acid repeats, for any protein repeat to be considered as a true repeat pattern and to avoid false positive. The web-interface allows the user to select the proteome and secretome. The repeat statistics interface gives the user, the information on several repeat statistics including the repeat unit and length, number of repetitions of the repeat unit and position of the repeat in the protein. The user can also select the amino acid on the basis of the physio-chemcial properties (non-polar, aliphatic residues, aromatic residues, polar, non-charged residues, positively charged residues, negatively charged residues) and can view its repeat statistics in the proteomes and secretomes.

Andrej Kajava

ANDREY V. KAJAVA is the Head of Structural Bioinformatics and Molecular Modelling, CNRS, France. His main research interests are protein structures and biomolecular interactions. The obtained knowledge is applied for prediction of protein structures and functions, drug design, as well as for de novo design of proteins with deliberately chosen functions. In the past, AK conducted research in prestigious laboratories in Russia, Germany, Belgium, Switzerland and United States. Andrej Kajava published over 95 peer-reviewed papers in scientific journals and 4 patents (ISI citations: over 3200; h-index: 28).

Host: Gaurav Sablok and Nicola La Porta