IIIT Hyderabad Publications
The Structure and Dynamics of Purine Riboswitches Addressing some generic questions using the Worm Like Chain model
Author: Shriyaa Mittal
Report no: IIIT/TH/2016/1
This work investigates some interesting questions arising out of mechanistical studies of purine riboswitches. As in any other riboswitch, the purine riboswitch has an aptamer domain linked to the expression platform of mRNAs. Discriminative ligand binding by the aptamer domain is known to regulate the mRNA expression. The aptamer domain of the purine (adenine, guanine and their variants) riboswitches con- sists of three helices P1, P2 and P3 which form a ‘Y’-shaped three-way junction (3WJ). The junction loops are J1-2, J2-3 and J3-1 which connect the corresponding helices. Loops L2 and L3 cap the helical stems P2 and P3, respectively. The helices P1 and P3 are collinear - forming a coaxial stack. Each of the stems P2 and P3 usually consist of 7 base-pairs. Helix P2 is adjacent to P3 and the two are held in parallel arrangement by interactions between the terminal loops L2 and L3. Complementary base pairs between nucleotides of the two loops have been found to form a kissing loop interaction. Earlier work carried out in our group on the study of the add adenine (A) riboswitch ap- tamer. It has provided insightful answers to the question how the recognition of the adenine by the ligand free APO form of the riboswitch is communicated to the downstream region via a conformational change in the downstream expression platform which is responsible for gene regulation , . These ideas, as understood from computational studies as well as from biochemical and biophysical experiments conducted in vivo or in vitro have been discussed in the first chapter. Crucial to this mechanism were (i) involvement of kissing loop interactions in facilitating the stabilization of the binding pocket, and (ii) ligand binding mediated stabi- lization of a helix which is involved in the switching event. In the second chapter we have reviewed single-molecule experiments carried out with sim- ple hairpin, hairpins involving kissing loops and aptamer domain of the adenine riboswitch, both in the presence as well as the absence of the ligand. It has been shown that a detailed understanding of the mechanism of helix stabilization due to tertiary interactions may be ob- tained using computational models of these motifs. The third chapter explores the standard worm-like chain (WLC) model for semi-flexible poly- mers. Extensive simulations of the WLC models have been carried out to observe the variation of the end-to-end distances of the polymer at different stiffness of the polymer using a bead- spring and a bending potential. The fourth chapter applies the WLC model to the problem of understanding the behaviour of RNA hairpins by suitably assigning the bond stiffness, base-pair strength, base-pair breaking threshold and strand stiffness under external pulling force in an attempt to simulate some of the observations in Chapter 2. In addition to this, extensive work was done in implementing a querieable database which relates the occurrence frequencies of different base pairs in RNA with their crystal and ground state optimized geometries (calculated at different levels of QM theory) and corresponding intrinsic interaction energies, RNABP COGEST, which was published. Since it is work that is distinct from the rest of the study, the work is reported as an Appendix titled ‘RNA Base Pair Count Geometry and Stability (RNABP COGEST) - Database Development and Imple- mentation of Useful Features’.
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Centre for Computational Natural Sciences and Bioinformatics
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