Central Theme

Our major goal is to determine how proteins adapt to perform specific functions, and in particular, how they co-operate with each other to carry out their biological roles efficiently. A knowledge based computational approach is particularly appropriate to address complex problems in biology involving protein architecture, interactions and biosynthesis.

Terpenoid Diversity in Plants

The focus of this work is an analysis of plant terpenoid biosynthetic diversity based on a comprehensive computational study of the literature and available data on genes, proteins, and regulators of the terpene biosynthetic pathways. Despite the diversity in function and structure, all isoprenoids derive from the universal C5 precursors, isopentenyl pyrophosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP). The cytoplasmic mevalonate pathway (MVA) and plastidial methyl erythritol pathway (MEP) together contribute to the formation of isoprene units (IPP) which are in turn, the precursors of numerous terpenoid compounds made by the terpene synthase enzymes (TPS). Terpenoids play a variety of crucial roles, such as in defense, and as components of membranes (sterols), pigments (carotenoids), hormones (gibberellins, abcissic acid, cytokinins), in the electron transport chain (quinines), and in the attraction of pollinators (volatile terpenes) as well. Key molecular features of terpene diversity are being investigated at the center through a detailed in-silico analysis of the terpene synthase enzymes and pathway interactions

Analysis of Molecular Interaction Networks

Biomolecular network comparisons have been carried out for Saccharomyces cerevisiae since it has the largest and most comprehensive amount of interaction data available. Superimposition of the physical protein interaction network over expression and regulatory networks (preliminary data) have revealed interesting clues towards understanding the mechanism of complex genetic interactions between superficially unrelated genes, mediated by long distance physical connections. Further analysis currently underway involves extraction of mRNA co-expression information for the pathway genes by microarray data normalization and multi-dimensional clustering techniques. A preliminary map of terpene pathways and its regulators is currently under construction. The interactors of various enzymes involved in isoprenoid pathways have been identified using information available in public interaction databases whereby putative interlogs are being extracted and verified using various strategies, from plant genomes.