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

Abstract

Proteins including transcription factors (TFs) and regulating enzymes search DNA for specific sites by alternating 3D diffusion in cell nucleus space and 1D diffusion on DNA. The search dynamics and free energy landscape of the protein along DNA depend essentially on the protein-DNA interactions, which simultaneously determine the protein-DNA association strength and relative population profiling along DNA, e.g., measured from protein binding microarray (PBM) to genome-wide mapping. Here we present a minimal structure-based model of protein diffusional search along 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 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 regulated by collective interfacial HB dynamics, which also determines the ruggedness of the 1D diffusion free energy landscape. In comparison, protein association or binding with DNA are generically dictated by the protein-DNA electrostatic interactions, with an interaction zone of nanometers around DNA. Extra degrees of freedom (DOFs) of the protein such as rotations and conformational fluctuations can be well accommodated within the electrostatic interaction zone. As such we demonstrate that the protein binding or association free energy profiling along DNA smoothens over the 1D diffusion free energy landscape, which leads to population variations for an order of magnitude upon a marginal free energetic smoothening around the specific or consensus sites. We further show that the protein unbinding or dissociation from a comparatively high-binding affinity DNA site is dominated by lateral diffusion to the flanking low-affinity sites. The results suggest that experimental characterizations on the relative protein-DNA binding affinities or population profiling on the DNA are systematically and physically impacted by the extra DOFs of protein motions aside from translation as well as from flanking DNA sequences due to protein 1D diffusion and non-specific binding/unbinding.