Mechanical Properties of DNA Binding Proteins: Tales in Silico

Abstract

A variety of proteins work as molecular machines; their motion is coupled with the function, hence their mechanical properties are important. In the nucleus, many of them interact with DNA. Their mechanisms to recognize and bind to specific DNA sequences, and the underlying mechanical properties, are particularly interesting. To elucidate such mechanisms, we started with a small example, namely transcription activator-like effector (TALE), and studied its structural properties by molecular dynamics. TALE is a protein in helical shape. Its crystallographic structures with and without DNA bound suggest that it shrinks and wraps a double-strand DNA. It consists of 34 amino-acid long repeats; each repeat has a nucleotide recognition site called RVD, so that the entire repeats can specifically bind to a DNA sequence. It is widely used for TALE nucleases (TALEN) in gene editing, and some improved mutants are known. Interestingly, non-RVD mutations, which do not directly contact with DNA, can enhance the activity of TALEN (e.g. Platinum TALEN by Sakuma et al., Sci. Rep. 2013). Recent coarse-grained studies showed that TALE is soft and can be stretched much to the direction of the helical axis (Flechsig, PLOS ONE 2014). These results implies that not only the DNA binding sites but also structural and mechanical properties of the rest of the molecule may determine the performance. We investigated such properties by all-atom molecular dynamics simulations. TALE without DNA, starting from the DNA-bound conformation, elongated within nanoseconds, suggesting that it is strongly compressed when bound to DNA. We conjectured that structures easy to shrink effectively bind to DNA. Some non-RVD mutants, including that used in Platinum TALEN, indeed showed shorter equilibrium distances between RVDs, which must fit the nucleotide positions. Possible mechanisms of positioning and wrapping around DNA will be also discussed.