Non-Equilibrium Models inspired by RNA-Protein Specific Binding and Recognition

Sriram, Vedanth (2022) Non-Equilibrium Models inspired by RNA-Protein Specific Binding and Recognition. Masters thesis, Indian Institute of Science Education and Research Kolkata.

Text (MS dissertation of Vedanth Sriram (17MS078)) 17MS078_Thesis_file.pdf - Submitted Version Restricted to Repository staff only Download (2MB)

Abstract

RNA-Protein interactions play a vital role in Biology today. Not only are they central to numerous cellular functions such as transcription, translation and viral replication but their interactions may also have played a role in primordial life forms during the ’RNA World’. Earlier, due to limited structural information, studies elucidating exact RNA-Protein interaction pathways were limited. More recently, however, using the power of molecular dynamics and other simulation methods, more information about these pathways; both from a thermodynamic and kinetic perspective is available. This thesis aims to model the RNA-protein binding pathway inspired by the TAR-TAT system, which is common in viruses such as the Human Immunodeficiency Virus (HIV). Using tools from non-equilibrium statistical mechanics, we develop a minimal physical model to understand if and how domain-domain fluctuation anti-correlations could help direct specific recognition and binding processes in such RNA-Protein systems.

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