Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy

Abstract

The condensin protein complex compacts chromatin during mitosis using its DNA-loop extrusion activity. Previous studies proposed scrunching and loop-capture models as molecular mechanisms for the loop extrusion process, both of which assume the binding of double-strand (ds) DNA to the hinge domain formed at the interface of the condensin subunits Smc2 and Smc4. However, how the hinge domain contacts dsDNA has remained unknown. Here, we conducted atomic force microscopy imaging of the budding yeast condensin holo-complex and used this data as basis for coarse-grained molecular dynamics simulations to model the hinge structure in a transient open conformation. We then simulated the dsDNA binding to open and closed hinge conformations, predicting that dsDNA binds to the outside surface when closed and to the outside and inside surfaces when open. Our simulations also suggested that the hinge can close around dsDNA bound to the inside surface. Based on these simulation results, we speculate that the conformational change of the hinge domain might be essential for the dsDNA binding regulation and play roles in condensin-mediated DNA-loop extrusion.

Author summary

Condensin is a protein which plays important roles in proper chromosome condensation and segregation. Recent studies have suggested that the chromosome condensation is driven by a DNA loop extrusion activity of condensin and that binding of the condensin hinge domain to DNA underlies this activity. However, the structural model of the hinge/DNA complex has not been available, which has limited our understanding of how condensin extrudes DNA loops. In this study, we performed high speed atomic force microscopy (AFM) imaging of budding yeast condensin complexes, conducted molecular dynamics simulations with constraints derived from the AFM image, and modeled the structures of the hinge domain with the open conformation and the hinge/DNA complex. The simulation results suggest that opening and closing of the hinge domain regulate its binding to DNA. This regulation might be relevant to the molecular mechanisms of DNA-loop extrusion.