ICTS:29648

Video URL

Protein search processes mediated by chromatin topology

Protein search processes mediated by chromatin topology

(2024). Protein search processes mediated by chromatin topology. SciVideos. https://youtu.be/dK2ZtS8-vdc

Protein search processes mediated by chromatin topology. SciVideos, Sep. 17, 2024, https://youtu.be/dK2ZtS8-vdc 

          @misc{ scivideos_ICTS:29648,
            doi = {},
            url = {https://youtu.be/dK2ZtS8-vdc},
            author = {},
            keywords = {},
            language = {en},
            title = {Protein search processes mediated by chromatin topology},
            publisher = {},
            year = {2024},
            month = {sep},
            note = {ICTS:29648 see, \url{https://scivideos.org/icts-tifr/29648}}
          }
Shuvadip Dutta
Talk numberICTS:29648
Source RepositoryICTS-TIFR
Source EventInterdisciplinary aspects of chromatin organization and gene regulation
Collection

Abstract

We investigate the role of compaction of chromatin domains in modulating search kinetics of proteins. Collapsed conformations of chromatin, characterised by long loops which bring distant regions of the genome into contact, and manifested structurally as Topologically Associated Domains (TADs) affect search kinetics of DNA associated transcription factors and other proteins. In this study, we investigate the role of the compactness of chromatin on the dynamics of proteins using a minimal model. Using analytical theory and simulations, we show that an optimal compaction exists for which the residence time of proteins on a chromatin-like polymer backbone is minimum. We show that while bulk diffusion is an advantageous search strategy for extended polymers, for highly folded polymer domains, intersegmental transfers allow optimal search. We extend these results to more detailed polymer models - using the Freely Rotating Chain model, a Lennard-Jones bead-spring polymer model, which approxi...