Analysis of the Passage Times for Unfolding/Folding of the Adenine Riboswitch Aptamer.

ABSTRACT: The conformational transitions of the adenosine deaminase A-riboswitch aptamer both with and without ligand binding are investigated within the tenets of the generalized Langevin equation in a complex viscoelastic cellular environment. Steered molecular dynamics (SMD) simulations are performed to evaluate and compare the results of the first passage times (FPTs) with those obtained from the theory for the unfold and fold transitions of the aptamer. The results of the distribution of Kramers's FPT reveal that the unfold-fold transitions are faster and hence more probable as compared to the fold-unfold transitions of the riboswitch aptamer for both ligand-bound and -unbound states. The transition path time is lower than Kramers's FPT for the riboswitch aptamer as the transition path times fo

SUBMITTER: Sharma S 

PROVIDER: S-EPMC9955275 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature