Protein target search diffusion-association/dissociation free energy landscape around DNA binding site with flanking sequences.

ABSTRACT: In this work we present a minimal structure-based model of protein diffusional search along local DNA amid protein binding and unbinding events on the DNA, taking into account protein-DNA electrostatic interactions and hydrogen-bonding (HB) interactions or contacts at the interface. We accordingly constructed the protein diffusion-association/dissociation free energy surface and mapped it to 1D as the protein slides along DNA, maintaining the protein-DNA interfacial HB contacts that presumably dictate the DNA sequence information detection. Upon DNA helical path correction, the protein 1D diffusion rates along local DNA can be physically derived to be consistent with experimental measurements. We also show that the sequence-dependent protein sliding or stepping patterns along DNA are regul

SUBMITTER: Wan B 

PROVIDER: S-EPMC11900189 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature