Biophysical Society Thematic Meeting | Trieste 2024

Emerging Theoretical Approaches to Complement Single-Particle Cryo-EM

Poster Abstracts

12-POS Board 12 OVERCOMING SLOW MG²⁺ DYNAMICS IN RNA SIMULATIONS Olivier Languin-Cattoën 1 ; Elisa Posani 1 ; Mattia Bernetti 2,3 ; Giovanni Bussi 1 ; 1 Scuola Internazionale Superiore di Studi Avanzati, Molecular and Statistical Biophysics, Trieste, Italy 2 University of Bologna, Department of Pharmacy and Biotechnology, Bologna, Italy 3 Fondazione Istituto Italiano di Tecnologia, Computational and Chemical Biology, Genova, Italy Magnesium ions have a crucial role in shaping RNA structural and catalytic properties [1]. Unfortunately, identification of Mg²⁺ binding sites using X -ray crystal diffraction and Cryo-EM is notably challenging, and has been shown to be biased [2]. Additionally, RNA folding and ion binding are coupled, highly dynamical processes that are not easily captured by standard refinement procedures, which generally aim at inferring a static molecular model.Molecular Dynamics (MD) simulations are an ideal complementary tool for studying the interplay between ions and nucleic acids, but they greatly suffer from the slow binding kinetics and overall low diffusivity of divalent cations. In his work, we develop a methodological approach to accelerate Mg²⁺ dynamics while m aintaining the system’s exact thermodynamics. We optimize a set of Mg²⁺ Lennard -Jones parameters to accelerate Mg-water and Mg-RNA binding kinetics while maximizing overlap with the original ensemble, allowing the direct use of Hamiltonian Replica Exchange methods as already available in most MD softwares. Additionally, we implement a simulated-tempering variant that bypasses the need for a ladder of replicas, and replaces it with an appropriate re-weighting of the simulated trajectory. This allows to scale up the method to a large number of ions without requiring a large number of replicas. Moreover, this procedure can be seamlessly combined to other strategies relying on multiple replicas, such as Metainference [3], in order to incorporate available experimental information and investigate the intricate relationship between Mg²⁺ ions and RNA structural dynamics.[1] Bowman et al., Curr. Opin. Struct. Biol., 22:262-272 (2012)[2] Auffinger et al., RNA, 27:243-252 (2021)[3] Bonomi et al., Sci. Adv., 2(1): e1501177 (2016)

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