Structural bioinformatics of RNA folding, interactions, and modifications

In this lecture, Prof. Bujnicki presented an in-depth overview of structural bioinformatics approaches to understanding RNA folding, molecular interactions, and chemical modifications. He emphasized the central role of RNA as a regulator of cellular processes, highlighting how its three-dimensional structure, dynamics, and interactions with proteins, small molecules, and ions underpin gene regulation and catalysis. The lecture discussed current experimental challenges in determining RNA structure and dynamics, particularly for flexible or partially disordered regions, and demonstrated how computational modeling provides a powerful complementary strategy.

Prof. Bujnicki presented hybrid and coarse-grained modeling approaches developed in his laboratory to study:

• RNA folding,
• RNA–protein interactions,
• Structural consequences of RNA modifications.

These methods, combined with experimental data from cryo-electron microscopy, X-ray crystallography, and biochemical techniques, enable efficient prediction, evaluation, and analysis of RNA 3D structures across diverse biological systems, bridging experimental and theoretical perspectives and opening new avenues for RNA-targeted drug discovery.

References

1. Boniecki M. et al., Nucleic Acids Res. 44, e63 (2016)
2. Mukherjee S. et al., Structure 32(11):1860-1876 (2024)
3. Loureiro RJ et al., Curr Opin Struct Biol. 94:103137 (2025) Janusz M. Bujnicki is a Professor of Biology and leads a research group at IIMCB in Warsaw, Poland. His group integrates bioinformatics with structural biology, focusing on understanding how RNA molecule sequences encode their 3D structures, and determine the interactions and biological functions.