March 1st, 2.00pm - 3.00pm / Room 117
Macromolecular Structure and Function: Insights from Network
Approaches
Prof. Saraswathi Vishveshwara, MBU, IISc
Abstract:
Understanding the structure and function of macromolecules like
proteins and DNA is crucial to decipher the functioning of living
systems as well as to learn about the molecular basis of diseases.
Last two decades have witnessed an exponential growth in the
biological data such as genome sequences and the structures of
proteins, nucleic acids and their complexes. The challenge is to
extract meaningful, valuable information from this vast amount of
data. Computational methods, as well as computing power, have
also increased enormously during this period. Consequently,
computational biology has become an active area of inter-
disciplinary research involving the investigation of problems
ranging from system biology to atomistic simulations.
Today network approaches are employed to explore a variety of
fields including electrical communication, computer networking,
finance, social networks, and biological networks. In the present
talk, I shall describe the network approach adopted to study the
structure and function of proteins. The three dimensional
co-ordinates of the atoms of proteins are used to represent the
structure in a network form, in which the amino acid residues of
the polymer chain are represented as nodes and non-covalent
interactions among them in the 3- D structure are represented as
edges. A graph, thus constructed, is examined for emergent global
properties such as the nodes of high connectivity (hubs),
collection of nodes with high inter-connectivity (cliques,
communities), paths of communication between selected terminal
nodes and so on. Many of these parameters find biological
significance, such as the hotspots for holding the structure and
protein-protein interaction, paths of long-distance communication
(allosteric communication), etc. Further, the function is a
dynamical property that is captured by molecular dynamics (MD)
simulations. And the network analyses of the trajectories provide
a dynamical picture of the function.
The concepts and methods outlined above will be elucidated and the
biological insights will be discussed with specific examples.
About the speaker:
Prof. Saraswathi Vishveshwara is an emeritus professor at Molecular
Biophysics Unit (MBU), IISc. She obtained her Ph.D in Quantum
chemistry of Biomolecules,
from City University of New York. She was a post doctoral fellow at
Carnegie Mellon University, Pittsburgh. She has worked in Quantum
chemistry with Late Sir John Pople, a Nobel Prize winner for his
contributions to the field of quantum chemistry. She was a
post-doctoral fellow at Molecular Biophysics Unit (MBU), IISc from
1977 to 1980. She was a faculty in Molecular Biophysics Unit (MBU),
IISc from 1981 to 2011. She is a fellow of the Indian Academy of
Sciences Bangalore and the National Academy of Science, Allahabad.
She has been associated with the IISc Mathematical Biology Project.
She had served as the Chairperson of Bioinformatics Centre and
served on various committees of Supercomputer Education and
Research Centre (SERC), IISc.
Her area of research is Computational Biology. She has taken an
interdisciplinary approach by applying the concepts of
physics/chemistry and various mathematical/computational techniques
to understand the structure, function and folding of proteins and
nucleic acids. She has extensively developed the concepts of graph
theory and network parameters to the problems related to protein
structure and function. She has developed methods to integrate
molecular dynamics simulations and graph theory to understand the
dynamical properties of macromolecules. Her scientific findings are
reported in more than 100 research articles.