Decoding dissociation of sequence-specific protein-DNA complexes with non-equilibrium simulations.

ABSTRACT: Sequence-specific protein-DNA interactions are crucial in processes such as DNA organization, gene regulation and DNA replication. Obtaining detailed insights into the recognition mechanisms of protein-DNA complexes through experiments is hampered by a lack of resolution in both space and time. Here, we present a molecular simulation approach to quantify the sequence specificity of protein-DNA complexes, that yields results fast, and is generally applicable to any protein-DNA complex. The approach is based on molecular dynamics simulations in combination with a sophisticated steering potential and results in an estimate of the free energy difference of dissociation. We provide predictions of the nucleotide specific binding affinity of the minor groove binding Histone-like Nucleoid Structur

SUBMITTER: van Heesch T 

PROVIDER: S-EPMC10711434 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature