Metal Ion Mediated Riboswitch Folding and Cognate Ligand Sensing

Ph.D. THESIS COLLOQUIUM 

Presenter Name:             Sunil Kumar

Ph.D Supervisor:             Prof. Govardhan P. Reddy

Date & Time:                  25 July, 2022, Monday at 4:00 pm through MICROSOFT TEAMS 

Title:                                Metal Ion Mediated Riboswitch Folding and Cognate Ligand Sensing

Meeting Link:

https://teams.microsoft.com/l/meetup-join/19%3a95b3dfced9714083b3ea8ab65a1c6082%40thread.tacv2/1658145300176?context=%7b%22Tid%22%3a%226f15cd97-f6a7-41e3-b2c5-ad4193976476%22%2c%22Oid%22%3a%224c6b5723-c199-451e-b247-7bb8bb66d531%22%7d

Abstract:

Riboswitches are noncoding RNA molecules that can control gene expression upon cognate ligand binding [1]. Riboswitches are primarily present in bacteria and are crucial for bacteria’s survival, which makes riboswitches attractive targets for discovering new antimicrobials [2]. Designing drugs that target a riboswitch function can be accelerated by understanding the effect of physicochemical factors (like ions, temperature, pressure, cosolvents, and pH) on the riboswitch folding and cognate ligand binding. The magnesium (Mg2+) ions possess the unique capability to exhibit site-specific binding along the RNA chain and modulate the population of functionally relevant RNA tertiary structures [3-5]. In this thesis, I will discuss the effect of Mg2+ on the folding thermodynamics and kinetics of the riboswitches and how cations assist riboswitches in attaining specific tertiary structures [4]. I will also provide insight into how the anionic cognate ligands bind to the polyanionic RNA backbone. Further, I will discuss the properties that contribute to cations’ binding in specific riboswitch sites. Finally, I will discuss how riboswitch responds to the cognate ligand binding and transmits the ligand binding information to the gene expression machinery.

References:

[1] Mandal, M.; Breaker, R., R. Gene regulation by riboswitches. Nat. Rev. Mol. Cell Biol. 2004, 5.6, 451-463.

[2] Blount, K., F.; Breaker, R., R. Riboswitches as antibacterial drug targets. Nat. Biotechnol. 2006, 24.12, 1558-1564.

[3] Misra, V.; Draper, D. On the role of magnesium ions in RNA stability. Biopolymers 1998, 48, 113–135.

[4] Kumar, S.; Reddy, G. TPP riboswitch populates holo-form-like structure even in the absence of cognate ligand at high Mg2+ concentration. J. Phys. Chem. B 2022, 126, 2369–2381.

[5] Halder, A.; Kumar, S.; Valsson, O.; Reddy, G. Mg2+ sensing by an RNA fragment: Role of Mg2+ -coordinated water molecules. J. Chem. Theory Comput. 2020, 16, 6702–6715