Integrative structural modelling of fission yeast contractile ring and analysis of actin-protein interactions

Abstract

Cytokinesis in eukaryotes includes assembly, constriction, and disassembly of the contractile ring (CR). Failure in any of these can lead to polyploidy and tumour formation. Fission yeast has been widely used as a model organism to study the process of cytokinesis; much about the protein composition and spatial distribution in the fission yeast CR is known. However, the lack of structural information about these proteins has limited the mechanistic understanding of the process. We used a recently developed structure prediction tool, AlphaFold, to predict the structures of protein complexes in fission yeast CR. Additionally, we used MSA manipulation strategies to model the actin crosslinkers, α-actinin (Ain1) and fimbrin (Fim1) in multiple conformations. Based on the analysis, we hypothesise that the Fim1 might be a more flexible crosslinker than the Ain1. Despite single actin being present in fission yeast, its involvement in various cytoskeletal networks and many interactors prompted us to look at the actin structures in the PDB to identify the structure-function correlation between actin and actin-binding proteins. Using heatmap visualisation of the actin-protein interfaces coupled with agglomerative clustering methods, we observed that cofilin-bound actin filaments show altered actin-actin interfaces and myosin-bound actin filaments occupy two different clusters on the interface heatmap. By calculating helical parameters of actin filaments from the PDB, outliers were observed- Plasmodium falciparum actin-1 and cofilin-bound actin, in terms of helical twist; human β and γ-actin isoforms along with a phalloidin-bound rabbit actin filament, in terms of helical rise; pointed-end of actin having bent filament axis. This project provides a first step in modelling the fission yeast contractile ring and a workflow for comprehensive analysis of actin structures in the PDB.