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• W3138488698 abstract "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." @default.
• W3138488698 created "2021-03-29" @default.
• W3138488698 creator A5050606685 @default.
• W3138488698 creator A5054904960 @default.
• W3138488698 creator A5087176858 @default.
• W3138488698 date "2021-03-23" @default.
• W3138488698 modified "2023-10-11" @default.
• W3138488698 title "What Are the Molecular Requirements for Protein Sliding along DNA?" @default.
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• W3138488698 doi "https://doi.org/10.1021/acs.jpcb.1c00757" @default.
• W3138488698 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/8041311" @default.
• W3138488698 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/33754737" @default.
• W3138488698 hasPublicationYear "2021" @default.
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