DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations

Abstract

Structural Maintenance of Chromosomes (SMC) complexes play essential roles in genome organization across all domains of life. To determine how the activities of these large (≈50 nm) complexes are controlled by ATP binding and hydrolysis, we developed a molecular dynamics model that accounts for conformational motions of the SMC and DNA. The model combines DNA loop capture with an ATP-induced ‘power stroke’ to translocate the SMC complex along DNA. This process is sensitive to DNA tension: at low tension (0.1 pN), the model makes loop-capture steps of average 60 nm and up to 200 nm along DNA (larger than the complex itself), while at higher tension, a distinct inchworm-like translocation mode appears. By tethering DNA to an experimentally-observed additional binding site (‘safety belt’), the model SMC complex can perform loop extrusion (LE). The dependence of LE on DNA tension is distinct for fixed DNA tension vs. fixed DNA end points: LE reversal occurs above 0.5 pN for fixed tension, while LE stalling without reversal occurs at about 2 pN for fixed end points. Our model matches recent experimental results for condensin and cohesin, and makes testable predictions for how specific structural variations affect SMC function.

A joint-ParB interface promotes Smc DNA recruitment

“…ParB may bind on the same side as ScpAB (''front'') or approach from the opposite side (''back''). According to the DNA-segment-capture model, in the latter scenario, subsequent DNA translocation (without prior conversion to a topological DNA-Smc association-''loading'') would shrink the newly captured DNA loop from the Smc complex and would thus be counterproductive (Diebold-Durand et al, 2017;Marko et al, 2019;Nomidis et al, 2022). However, results obtained with engineered asymmetric Smc dimers were not fully conclusive, possibly indicating that both scenarios may contribute to Smc targeting (Figures S7A and S7B).…”

Can pseudotopological models for SMC-driven DNA loop extrusion explain the traversal of physical roadblocks bigger than the SMC ring size?

“…According to the models of Shaltiel et al 12 and Nomidis et al 13 , SMC complexes entrap DNA pseudo-topologically, i.e., the two DNA strands that form the base of a loop pass through the ring structure formed by the SMC and kleisin subunits of these complexes. In view of the clear observation of the passage of roadblocks bigger than the SMC ring size into extruded loops in our experiments, the authors of these papers attempted to explain our observations within the context of their models.…”

“…First, let us summarize the alternative model that Shaltiel et al and Nomidis et al proposed 12,13 . We focus on the model of Shaltiel et al who most explicitly pointed out the dynamics involved in the roadblock passage, according to their model, but the same considerations apply to the model by Nomidis et al Without explicitly commenting on the detailed SMC conformational changes involved in these models (which also differ between these models), we describe how these authors attempt to explain the passage of roadblocks bigger than the ring size of SMCs.…”

“…Below, we evaluate this alternative explanation in the light of our experimental observations. First, let us summarize the alternative model that Shaltiel et al and Nomidis et al proposed 12,13 . We focus on the model of Shaltiel et al who most explicitly pointed out the dynamics involved in the roadblock passage, according to their model, but the same considerations apply to the model by Nomidis et al…”

“…After these data appeared on bioRxiv in July 2021 11 , two new pseudotopological models were proposed by Shaltiel et al (“hold-and-feed mechanism” 12 ) and by Nomidis et al (“segment-capture model” 13 ). In the light of the roadblock experiments, the authors of these models attempted to explain the passage of the huge roadblocks within the context of their models.…”