About the Talk
Presenter
Pavlína Pokorná: Postdoctoral Fellow, CNR-IOM, Italy
Pavlína Pokorná received her PhD in Biomolecular Chemistry and Bioinformatics from Masaryk University, Czech Republic, under the supervision of Jiří Šponer. Since 2023 she has been a postdoctoral fellow in the group of Alessandra Magistrato at CNR-IOM, Italy. Her research focuses on multi-scale computational studies of nucleic acids and RNA–protein complexes, with particular emphasis on modelling dynamic systems and processes involving RNA conformational changes; recently she has worked mainly on splicing-related systems.
Abstract
RNA conformational changes are pivotal to many biological processes. Yet, owing to RNA’s high flexibility, capturing its structural dynamics presents a challenge for both experimental and computational techniques. An example of such a system is guanine quadruplexes (G4s), whose folding–unfolding dynamics contribute to the regulation of gene expression. Using all-atom enhanced-sampling MD simulations, we simulated the folding of three-quartet RNA G4 structures. Our trajectories capture G4 folding as a multi-pathway process, devoid of simplistic, well-structured intermediates. Instead, the RNA molecule first collapses into a compact, coil-like ensemble, from which the G4 gradually forms through a series of small, incremental steps, often proceeding via a two-quartet G4 before the final rearrangements leading to the three-quartet form take place. The length of the loops connecting the guanine tracts appears to influence the population of different folding intermediates, with longer loops stabilizing triplex structures more effectively. On the other hand, our simulations also revealed challenges and limitations of enhanced-sampling methods and of current state-of-the-art force fields. These challenges are shared among other RNA systems with complex dynamics, whose reliable modeling requires careful simulation setup and critical evaluation of the results.
Date: October 21st, 2025
Language: English
