Development and application of sequence based approaches for recognition and functional characterization of protein kinases

Abstract

Protein kinases, the third most populous protein family, are a major class of enzymes that regulate a wide range of cellular processes by phosphorylating multiple cellular proteins. There are many conserved sequence motifs within the catalytic domain that are essential for the regulation of the proteins, and the catalytic core is commonly shared across all typical protein kinases. In this thesis, we present identification and comprehensive analyses of Ser/Thr or Tyr (STY) protein kinases encoded in many pathogenicity causing organisms. The role of kinases in causing pathogenicity has been elucidated in many of the previous studies. With the emergence of diverse pathogenic species in the last few decades, the protein kinases of the pathogens and the respective hosts might have evolved to adapt to the hostile environment and tolerate stress response. Hence, it is essential to even perform a comparative study of kinases within pathogens against those encoded in their host species. Protein kinases can be identified using sequence-based approaches. However, some of the kinase subfamilies have highly diversified, and one requires sensitive homology detection approaches for their identification. Therefore, we developed a fresh protocol named quotMaster Blasterquot for the detection of distantly related proteins. The performance of Master Blaster is evaluated by comparing against widely-used profile based and hidden Markov model-based methods. An improvement in fold coverage using Master Blaster is reported. We also used artificially designed sequences for detecting distantly related proteins using Master Blaster. Use of the designed sequences was found to be useful in connecting protein families that are highly diverged at sequence level. We applied the developed protocol to identify protein kinases encoded in Candida albicans and performed an extensive analysis of these kinases using sequence-based methods. A comparative study of kinases within C. albicans, pathogenic and non-pathogenic non-albicans Candida species, ...