Dr.  Monika Sharma
INSPIRE Faculty, Chemical Sciences

I am primarily interested in application of computational methods to study conformational dynamics of biomolecules and interactions among them.

In the real living world, each complex biological process/function breaks down to the interacting behavior between proteins, nucleic acids, lipids, and metabolites. Understanding each interaction thus, requires knowledge at the level of structure, stability, and dynamics of the macromolecules involved. Undoubtedly, advanced state-of-the-art biophysical and biochemical experiments provide invaluable insights into the structure, stability, and function of these molecules. However, most of these sophisticated experimental techniques are complex and time consuming, apart from being expensive. Also, they do not always directly provide an atomistic picture of macromolecular dynamics in situ with sufficient time resolution. In current scenario of enhanced computing power, computer simulations have emerged as a useful tool to not only better interpret experimental results; in several ways they complement experimental investigations. Atomistic molecular dynamics (MD) simulations present a convenient way to derive information by sampling dynamic molecular processes and can provide atomic level description of structural stability and function which are difficult to be obtained from the experimental studies.

I have used both conventional and enhanced molecular dynamics techniques, such as umbrella sampling, free energy perturbations, targeted MD, steered MD, and replica exchange MD to understand the conformational dynamics of proteins, nucleic acids, and their large complexes. Currently, I am carrying out in silico studies to understand the underlying mechanism of RNA complexation by signal transducer and activator proteins. These interactions have direct implications in various developmental and physiological processes such as mammalian spermatogenesis, metazoan central nervous system development, sperm-to-oogenesis in hermaphrodites, or Drosophila wing development. In addition to this, they have also been reported to be associated with numerous human pathologies like cancers and neurological disorders such as human inherited ataxia, multiple sclerosis, or schizophrenia.

Selected Publications

• Monika Sharma, Alexander V Predeus, Nicholas Kovacs, and Michael Feig . 2014. Differential Mismatch Recognition Specificities of Eukaryotic MutS Homologs, MutSα and MutSβ. Biophysical Journal. 106:2483-2492.

• 2. S. Michielssens, Jan H. Peters, David Ban, Supriya Pratihar, Daniel Seeliger, Monika Sharma, Karin Giller, Thomas Michael Sabo, Stefan Becker, Donghan Lee, Christian Griesinger, Bert L. de Groot. 2014. A designed conformational shift to control protein binding specificity. Angewadte Chemie. 53(9):10367-10371.

• Asli Yildirim, Monika Sharma, Bradley Varner, Liang Fang and Michael Feig. 2014. Conformational preferences of DNA in reduced dielectric environment. The Journal of Physical Chemistry B. 118(37): 10874-10881.

• Monika Sharma, Alexander V Predeus, Shayantani Mukherjee and Michael Feig. 2013. DNA Bending Propensity in the Presence of Base Mismatches: Implications for DNA Repair. The Journal of Physical Chemistry B. 117(20): 6194-6205.

• Monika Sharma, Gopalakrishnan Bulusu and Abhijit Mitra. 2009. MD simulations of ligand- bound and ligand-free aptamer: Molecular level insights into the binding and switching mechanism of the add A-riboswitch. RNA. 15: 1673-1692.