Dynamic Effect of Chelated Ion Environment in Stabilizing Viral RNA Pseudoknot

R, Vysakh (2021) Dynamic Effect of Chelated Ion Environment in Stabilizing Viral RNA Pseudoknot. Masters thesis, Indian Institute of Science Education and Research Kolkata.

Text (MS Dissertatio of Vysakh R (16MS201)) 16MS201_Thesis_file.pdf - Submitted Version Restricted to Repository staff only Download (10MB)

Abstract

Pseudoknots (PK) are most prevalent structural motif functioning in various biological processes in virus and cellular gene expressions including programmed –1 ribosomal frameshifting controlling optimal level of protein and enzyme translation. PK unit comprises of two helical segments connected by single-stranded regions or loops. However, it also forms other compact states through a variety of stem-loop interactions defying the strong electrostatic repulsion of negatively charged phosphodiester backbone. To stabilize such compact RNA structure optimal metal ions and hydration environment are needed to make them functionally active. K+ and Mg2+ are the prevalent ions which are preferentially activate PK in the cellular environment. Many experiments and computational studies have already shown the importance of divalent Mg2+ ion on RNA folding, but the specific functional role of monovalent ion, K+, and water (if any, other than their role as functional buffer) have been overlooked despite their presence being significant. My thesis work involves extensive molecular dynamics simulation study at atomistic resolution of the RNA PK considering a classic case of viral PK present in Beet western yellow virus in a physiological K+ salt environment and also, in mixed salt environment of K+ and Mg2+. My thesis results covers four chapters such chapter 4,5,6, and 7 :

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