Explicit ion modeling predicts physicochemical interactions for chromatin organization.

ABSTRACT: Molecular mechanisms that dictate chromatin organization in vivo are under active investigation, and the extent to which intrinsic interactions contribute to this process remains debatable. A central quantity for evaluating their contribution is the strength of nucleosome-nucleosome binding, which previous experiments have estimated to range from 2 to 14 k_BT. We introduce an explicit ion model to dramatically enhance the accuracy of residue-level coarse-grained modeling approaches across a wide range of ionic concentrations. This model allows for de novo predictions of chromatin organization and remains computationally efficient, enabling large-scale conformational sampling for free energy calculations. It reproduces the energetics of protein-DNA binding and

SUBMITTER: Lin X 

PROVIDER: S-EPMC10945522 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature