Developing a multi-basin 3SPN model of highly-charged flexible polymers focusing on RNA

Agarwal, Sanchay (2023) Developing a multi-basin 3SPN model of highly-charged flexible polymers focusing on RNA. Masters thesis, Indian Institute of Science Education and Research Kolkata.

Text (MS dissertation of Sanchay Agarwal (18MS130)) Thesis_18MS130.pdf - Submitted Version Restricted to Repository staff only Download (6MB)

Abstract

RNA is a fundamental biomolecular unit essential for several biological processes, including gene expression, regulation, and catalysis. Exploring the structural dynamics and interactions of RNA molecules is crucial for advancing our understanding of cellular processes, viral mechanisms, and the development of novel therapeutics, among other applications. This is even more apparent in light of the recent global pandemic and the rapid structure resolution in monitoring the investigation to combat it. Indeed, biomolecular simulations, such as molecular dynamics (MD) simulations, have become an indispensable tool for RNA research. However, the complexity and magnitude of RNA systems present significant modeling challenges, as the dynamics of RNA are associated with large length scales and long time scales. Part of the complexity can be attributed to RNA’s high flexibility and strong intramolecular electrostatic forces owing to its highly charged nature. Coarse-graining (CG) is a powerful method that overcomes these obstacles by simplifying the representation of biomolecules, thereby facilitating the investigation of larger systems and extended timescales. However, apart from structural coarse-graining, RNA simulations call for the coarse-graining of electrostatic interactions. This is because the ion atmosphere around the RNA plays a major role in the formation and stability of secondary and tertiary structural motifs in RNA. Interesting phenomena such as counterion condensation occur in the presence of an ionic environment that results in the collapse of RNA despite its highly charged nature. In the work leading up to this thesis, we have developed a novel structure-based coarse-grained model for RNA, wherein each nucleotide is represented by three interacting beads. The model treats the local and non-local interactions within RNA molecules by developing a multigaussian Hamiltonian. The interaction in these sites is achieved via harmonic bonds and angle parameters alongside dihedrals treated with cosines. Using the concept of the energy landscape and the statistical mechanics of biopolymer collapse, RNA folding is achieved by defining native contact terms in the form of 10–12 potentials. The model has employed a multi-gaussian approach using parameters retrieved from the P-P radial distribution function (RDF). This has been done through explicit solvent simulations in various RNA molecules to contrast the degree of order in the presence and absence of an ionic atmosphere. We propose that the bulk of tertiary structure stabilization in RNA can be attributed to electrostatics. The model has been tested against small-angle X-ray scattering experiments alongside analyses against well-established theoretical models. At such a degree of coarse-graining, we aim to gain a structural understanding of biophysical phenomena associated with RNA without being limited to small systems but by aptly using small-scale atomistic simulations as a complementary method. This thesis has been divided into four chapters: In Chapter I, we discuss the counterion condensation phenomenon and various experimental and theoretical approaches to understanding it. Experimental techniques such as SAXS and theoretical approaches such as the classical and generalized counterion condensation models have been discussed. The methodology is contained in the second chapter. Here, the details of the explicit solvent simulations and dynamic counterion condensation (DCC) model simulations are discussed, along with the analysis techniques used in the project. In the third chapter, we motivate the study of structural parameters and present some results to show that differential treatment of counterion condensation on each phosphate is required to reproduce experimental data on the persistence length of ssDNA and RNA. In Chapter IV, the development of the novel 3SPN approach is elaborated upon. Validation of the model is achieved by comparing the RDF and RMSF in two different RNA fragments (SAMI riboswitch aptamer and BWYV pseudoknot) against well-established explicit solvent and DCC model-based simulations. Experimental validation is also provided with SAXS data from BWYV RNA fragments. With this model, the computational cost of simulating RNA molecules is significantly reduced, and we are able to achieve high computational speeds while being able to obtain relevant structural information.

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