2024/03/20 by Francesco Borando, Guido Tiana, Borando, Francesco +1 · 1 citation
Biochemistry, Genetics and Molecular Biology · #Biomolecules (q-bio.BM) #FOS: Biological sciences #FOS: Physical sciences #Genomics and Chromatin Dynamics #Protein Structure and Dynamics #Soft Condensed Matter (cond-mat.soft) #Viral Infectious Diseases and Gene Expression in Insects
paper · pdf · doi:10.48550/arxiv.2403.13569
openalex publication_date 2024/03/20 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show through molecular--dynamics simulations of a polymer surrounded by binders that the strength of the binder-polymer interaction separates an equilibrium from a non-equilibrium regime. In the equilibrium regime, the system can be efficiently described by an effective model in which the binders are traced out. Even in this case, the polymer display features that are different from those of a standard homopolymer interacting with two-body interactions. We then extend the effective model to deal with the case where binders cannot be regarded as in equilibrium and a new phenomenology appears, including local blobs in the polymer. Providing an effective description of the system can be useful in clarifying the fundamental mechanisms governing chromatin structuring.