Exploring molecular interactions between yeast topoisomerase I and RNA polymerase III subunit, Rpc82 using an in-silico approach

Abstract

The process of DNA transcription leads to the generation of torsional stress, which must be resolved for smooth progression of the transcription machinery. In Saccharomyces cerevisiae, DNA topoisomerase I (Top I), a type IB topoisomerase, plays a critical role in relaxing supercoils and mitigating the topological strain associated with transcription. While several proteins from the transcription machinery have been reported to interact with yeast Top I, the precise structural domains involved and the detailed features of the interaction interfaces remain largely unexplored. This gap is partly due to the absence of a complete three-dimensional structure of the full-length enzyme, which hinders structure-based computational analyses of its interactome. A full-length model of yeast Top I was generated using a domain-based modeling approach and evaluated using structural validation metrics and comparative analyses with homologous structures. Leveraging this model, we investigated a potential interaction between Top I and Rpc82, a key subunit of RNA polymerase III involved in transcription of small non-coding RNAs such as tRNAs and 5S rRNA. The interaction was evaluated using an integrative computational approach combining molecular docking, binding free-energy calculations, and molecular dynamics simulations. The analyses identified a putative interaction interface involving the WH2–WH3 region of Rpc82 and primarily the D1 and D3 domains of Top I. Molecular dynamics simulations indicated that the predicted Top I–Rpc82 complex remained structurally stable under the simulated conditions. The calculated binding energy-to-surface-area ratio of the complex was comparable to benchmark values for biologically relevant heterodimeric protein interfaces, supporting the plausibility of the predicted interaction. Overall these findings provide a structural framework for future experimental validation of Top I interactions, paving the way for mechanistic insights into its regulatory functions and contribution to genome maintenance and stability.