TATA INSTITUTE OF FUNDAMENTAL RESEARCH
GKVK, BELLARY ROAD, BANGALORE
Date: Friday, June 19, 2009
Time: 10:15 a.m.
Dr. Arun Krishnan
Lead-Data Mining Group
Monsanto Research Center
Protein Structure Networks: Understanding the organization of protein structures
Ground floor Lecture Hall (LH1)
The architectural organization of protein structures has been the focus of intense research since it can hopefully lead to an understanding of how proteins fold. Despite the difference in models dealing with the way proteins fold into their tertiary structures, it is recognized that small regions of proteins tend to fold independently and are then stabilized by interactions between these distinct subunits. However, there are a number of different definitions of what comprises an independent subunit.
In our work, we looked at the organization of protein structures from the smallest unit in sequence space, viz., six-letter "words" to modules that interact with each other in 3D space all the way up to protein domains. We used network representations of proteins wherein the amino acids are the nodes and interactions between them are represented as edges. We identified invariants in protein structures which hold regardless of protein fold or family. Modules identified through our technique were shown through molecular dynamics simulations of the unfolding of ubiquitin to be those that formed early on during the folding process.
Co-ordinator: Prof. R. Sowdhamini (firstname.lastname@example.org)