Exploring protein-mediated compaction of DNA by coarse-grained simulations and unsupervised learning.

ABSTRACT: Protein-DNA interactions and protein-mediated DNA compaction play key roles in a range of biological processes. The length scales typically involved in DNA bending, bridging, looping, and compaction (≥1 kbp) are challenging to address experimentally or by all-atom molecular dynamics simulations, making coarse-grained simulations a natural approach. Here, we present a simple and generic coarse-grained model for DNA-protein and protein-protein interactions and investigate the role of the latter in the protein-induced compaction of DNA. Our approach models the DNA as a discrete worm-like chain. The proteins are treated in the grand canonical ensemble, and the protein-DNA binding strength is taken from experimental measurements. Protein-DNA interactions are modeled as an isotropic binding pote

SUBMITTER: de Jager M 

PROVIDER: S-EPMC11427786 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature