Dr. Ashutosh Srivastava
We use integrative modeling involving computational methods such as molecular dynamics simulations, structural modeling and network analysis to study macromolecular complexes. This entails using structural information from multiple experiments such as Cryo-Electron Microscopy, X-ray crystallography, NMR, SAXS, FRET, Mass spectrometry etc. to develop comprehensive models of biological macromolecules. The research has been particularly focused on exploring macromolecular complexes involved in the mammalian circadian clock regulation. By way of collaborations with fellow experimental chemists and biologists, we also aim to contribute in discovery and development of biologically active small molecules that modulate circadian clock and could have implications in targeting sleep disorders, seasonal affective disorder, jet lag and cancer. Another research area where we are focusing is modeling intrinsically disordered regions in clock proteins and studying the role of their conformational dynamics in regulation of circadian rhythms.
● Integrative modeling of macromolecular complexes.
Integrative modeling entails using computational methods to combine data from multiple different biophysical experiments such as Cryo- Electron Microscopy, X-ray crystallography, NMR, etc. in order to study the structure and dynamics of biological macromolecules. Although applicable to any biological system, currently we are using integrative modeling to explore the structure and dynamics of macromolecular complexes involved in regulation of mammalian circadian clock.
● Network analysis of protein structures.
Representing three-dimensional structure of proteins as networks provides simple but powerful way of analyzing protein structure and function. We have previously used this formalism to study functional differences in proteins associated with small or negligible structural changes. We are currently using this method to understand the dynamics of proteins and how the network architecture evolves with conformational changes in proteins.
● Dynamics driven drug discovery.
The role of protein dynamics in drug discovery is being increasingly explored. We are interested in studying the dynamics of drug targets using computational methods such as molecular dynamics simulations and structural modeling to explore the transient or cryptic novel binding pockets.
● Modeling and conformational analysis of disordered regions.
Despite being crucial to several cellular functions, intrinsically disordered regions of the proteins form some of the toughest entities to explore the conformation and dynamics, both experimentally as well as computationally. Using some of the recent advances in computational modeling of such regions we are exploring the role of disordered regions in clock proteins and their role in regulation of circadian rhythms.
Background and Experience:
Assistant Professor, Biological Engineering, IIT Gandhinagar: Jan 2021 -
Postdoctoral Researcher, Nagoya University, Institute of Transformative Biomolecules, Japan 2016-2020
Postdoctoral Researcher, Nagoya University, Dept of Physics, Japan 2015-16
PhD, CSIR - CCMB Hyderabad, 2015
BTech (Hons), Amity University, 2009
Vidya Sundaram (Postdoctoral Researcher)
Sayantoni Chaudhuri (Ph.D Student )
Shashank Kumar Singh (Ph.D Student )
Shriyansh Srivastava (Ph.D. Student )
Rakesh Thakur (M. Tech Student)