Obstacle bypassing and intrinsically asymmetric loop extrusion in the segment-capture model of Structural Maintenance of Chromosomes complexes

Abstract

Structural Maintenance of Chromosomes (SMC) complexes are large protein assemblies that play a central role in chromosomal organization across all domains of life by acting as molecular motors that extrude DNA loops. Although the molecular architecture of SMCs has been characterized in considerable detail, their mechanistic mode of action remains actively debated. One proposed mechanism is the segment-capture model, in which SMC complexes undergo an asymmetric conformational change upon ATP binding and hydrolysis, effectively "pumping" short DNA segments through the SMC ring and thereby enlarging loops. While this model accounts for several experimentally observed features of loop extrusion, it has been questioned in light of experiments showing that SMC complexes can traverse large nanoparticle-sized obstacles on DNA. Moreover, recent experimental advances have provided new insights that extend beyond the original formulation of the model. Here we show that, contrary to previous criticisms, the segment-capture model can naturally account for key features of recent experiments, including the bypass of large obstacles when the SMC hinge acts as a bypass gate. Furthermore, we outline a set of targeted experiments designed to critically test the models predictions, providing a clear path toward resolving outstanding questions about the mechanistic basis of loop extrusion.