Protein mediated bridging motifs: A key mechanism in biopolymer organization

Abstract

The protein-mediated bridging motif is ubiquitous and essential for shaping cellular structures in all organisms. In this paper, we dissect the bridging motif for a model system: the Heat-stable Nucleoid-Structuring protein (H-NS). We present data from two complementary single-molecule assays that probe the H-NS-DNA interaction: a dynamic optical-trap-driven unzipping assay and an equilibrium H-NS-mediated DNA looping assay. To quantitatively analyze and compare these assays, we develop a general theoretical framework for describing the bridging motif. The interplay between these experiments and our theoretical model not only infers the effective interaction free energy, the bridging conformation and the duplex-duplex spacing, but also reveals a second, unresolved, cis-binding motif that challenges our current understanding of the role of bridging proteins in chromatin structure. The theoretical framework we have developed is generally applicable to the description of protein-mediated bridging motifs in chromatin and cytoskeletal organization.