# Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion

## TL;DR

This study uses molecular simulations to identify DNA binding sites in the cohesin complex and their roles in DNA loop extrusion, a key process in genome organization.

## Contribution

The study identifies experimentally testable DNA binding sites in cohesin subunits and highlights the roles of STAG1 and NIPBL in DNA loop extrusion.

## Key findings

- Molecular dynamics simulations predicted DNA binding patches on cohesin subunits SMC1, SMC3, STAG1, and NIPBL.
- Multiple DNA binding patches form a clamping group that facilitates DNA bending and loop extrusion.
- The accessory subunits STAG1 and NIPBL are shown to be essential for DNA binding and chromatin organization.

## Abstract

The SMC complex cohesin mediates interphase chromatin structural formation in eukaryotic cells through DNA loop extrusion. Here, we sought to investigate its mechanism using molecular dynamics simulations. To achieve this, we first constructed the amino-acid-residue-resolution structural models of the cohesin subunits, SMC1, SMC3, STAG1, and NIPBL. By simulating these subunits with double-stranded DNA molecules, we predicted DNA binding patches on each subunit and quantified the affinities of these patches to DNA using their dissociation rate constants as a proxy. Then, we constructed the structural model of the whole cohesin complex and mapped the predicted high-affinity DNA binding patches on the structure. From the spatial relations of the predicted patches, we identified that multiple patches on the SMC1, SMC3, STAG1, and NIPBL subunits form a DNA clamping patch group. The simulations of the whole complex with double-stranded DNA molecules suggest that this patch group facilitates DNA bending and helps capture a DNA segment in the cohesin ring formed by the SMC1 and SMC3 subunits. In previous studies, these have been identified as critical steps in DNA loop extrusion. Therefore, this study provides experimentally testable predictions of DNA binding sites implicated in previously proposed DNA loop extrusion mechanisms and highlights the essential roles of the accessory subunits STAG1 and NIPBL in the mechanism.

The study explores the molecular dynamics of human cohesin, a protein complex crucial for the structural organization of chromosomes in eukaryotic cells. Using molecular dynamics simulations, we identified specific DNA-binding sites within cohesin’s subunits, including SMC1, SMC3, STAG1, and NIPBL. These sites play a pivotal role in cohesin’s ability to mediate DNA loop extrusion—a process essential for genome organization and gene regulation. By constructing structural models of the cohesin complex, we uncovered cooperative interactions among DNA-binding patches. These interactions stabilize DNA and facilitate its bending, vital for forming chromatin loops. The study also highlights the indispensable roles of the accessory proteins STAG1 and NIPBL, whose absence may disrupt DNA binding. This work provides new insights into the mechanisms underpinning DNA loop extrusion, validating previously proposed models and suggesting novel sites for experimental investigation. These findings deepen our understanding of cohesin’s role in genome architecture and open avenues for further studies into chromatin dynamics and gene expression regulation.