What Are the Molecular Requirements for Protein Sliding along DNA?

• Published in: The journal of physical chemistry. B 2021-04, Vol.125 (12), p.3119-3131
• Main Authors: Bigman, Lavi S, Greenblatt, Harry M, Levy, Yaakov
• Format: Article
• Language: English
• Subjects: B: Biophysical and Biochemical Systems and Processes; Diffusion; DNA - metabolism; DNA-Binding Proteins - metabolism; Molecular Dynamics Simulation; Protein Binding; Static Electricity
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/acs.jpcb.1c00757

DNA-binding proteins rely on linear diffusion along the longitudinal DNA axis, supported by their nonspecific electrostatic affinity for DNA, to search for their target recognition sites. One may therefore expect that the ability to engage in linear diffusion along DNA is universal to all DNA-binding proteins, with the detailed biophysical characteristics of that diffusion differing between proteins depending on their structures and functions. One key question is whether the linear diffusion mechanism is defined by translation coupled with rotation, a mechanism that is often termed sliding. We conduct coarse-grained and atomistic molecular dynamics simulations to investigate the minimal requirements for protein sliding along DNA. We show that coupling, while widespread, is not universal. DNA-binding proteins that slide along DNA transition to uncoupled translation–rotation (i.e., hopping) at higher salt concentrations. Furthermore, and consistently with experimental reports, we find that the sliding mechanism is the less dominant mechanism for some DNA-binding proteins, even at low salt concentrations. In particular, the toroidal PCNA protein is shown to follow the hopping rather than the sliding mechanism.