Regensburg 2025 – scientific programme
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BP: Fachverband Biologische Physik
BP 3: Computational Biophysics I
BP 3.2: Talk
Monday, March 17, 2025, 09:45–10:00, H44
Symmetry of loop extrusion by dimeric SMC complexes is DNA-tension-dependent — Biswajit Pradhan1, •Adrian John Pinto2, Peter Virnau2, and Eugene Kim1 — 1Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany — 2Institut für Physik, Staudingerweg 9, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany
Structural maintenance of chromosome (SMC) complexes are involved in genome organization and regulation via DNA loop extrusion. During extrusion SMC proteins reel DNA from one or both sides and a loop forms and increases. At low DNA tension (< 0.1pN), Smc5/6 and Wadjet extrude DNA from both sides of the loop. At higher tension, however, they transition to a behavior akin to one-sided extruders, yet still capable of extruding from one or the other side thereby switching the direction of extrusion [1]. In order to model this process in simulations, we propose a coarse-grained model for DNA loop extrusion using a Kratky-Porod chain as a basis for DNA and a handcuff for SMC proteins. By matching stalling forces, we are able to simulate loop extrusion on experimental time and length scales. We find that the observed switching from two- to one-sided behavior does not require a change in motor activity, but can be explained as a complex interplay of extrusion, stalling and thermal fluctuations.
[1] Pradhan, B., Pinto, A., Kanno, T., et al. (2024). Symmetry of loop extrusion by dimeric SMC complexes is DNA-tension-dependent. bioRxiv. https://doi.org/10.1101/2024.09.12.612694
Keywords: DNA loop extrusion; coarse-grained model; SMC proteins