Network biology: Understanding relationship among sequence, structure and dynamics of proteins through structural network

Research Group

N. Srinivasan and Nagasuma Chandra

Molecular Biophysics Unit, IISc and Department of Biochemistry, IISc

Understanding inter-relationship among protein sequences, three-dimensional (3-D) structures and dynamics is essential to interpret mechanistic basis of protein functions. While the sequence determines 3-D structure, knowledge of structures profoundly influences our understanding of protein function. As atoms in a protein are not absolutely stationary, it is essential to understand the dynamics associated with the atoms, chemical groups and residues in order ti interpret structural and mechanistic basis of protein function.

3-D structure of a protein is quite complex. However, such a complex 3-D entity can be represented as two-dimensional network with, for example, residues as nodes and join of interacting residues as edges. Such a graphical representation of proteins allows one to use analytical tools developed in this field for the network analysis.

We would like to address a number of questions using structural network approach: How far the structural networks similar for two proteins with same fold? Is there a relationship between extent of sequence divergence and similarity of structural network between two proteins of same fold? Is there any systematic pattern in the dynamics associated with the structural network of proteins of same fold? How similar is the structural network at the functional site and dynamics associated with the functional sites of proteins with same or similar function? What is the structural pathway of allosteric communication in proteins?

Addressing such questions is expected to enhance our understanding of sequence, structural, mechanistic and evolutionary basis of protein functions.

Queries on the project can be directed to iiscsrinivasan@gmail.com