Linker Histone-Nucleosome Interactions : A Modelling and Simulation Study

Abstract

In the cell nucleus, DNA wraps around histone proteins, forming nucleosome particles, and packs into a highly negatively charged structure, the chromatin fiber. The linker histone is a protein that binds to the nucleosome and determines how the nucleosomes are linked to each other. To simulate the nucleosome-linker histone interactions, a Brownian Dynamics (BD) technique together with normal mode analysis (NMA) was applied. NMA of the nucleosome revealed the most prominent modes of motion of its two linker DNAs. The results were used to generate conformations of the linker DNAs which were used in BD simulations of the rigid-body docking of a linker histone and its mutants to the nucleosome. From the simulations, two distinct binding sites and one non-binding site on the linker histone were identified. The amino acids found to be most important for binding in the simulations with the linker histone mutants are consistent with experimental data. Moreover, a dominant binding mode of the linker histone to the nucleosome was found for a wide range of conformations of the linker DNAs. The association kinetics of the linker histone to the nucleosome was modeled using the results obtained by the BD docking. The obtained high association rates close to the diffusional limit (10^9 M^{-1} s^{-1}) were attributed to electrostatic steering between both biomolecules. A new method accounting for molecular flexibility during BD simulation was developed. One of the binding partners is treated as a discrete set of structural conformations representing its flexibility. The transition between the conformations is described by a Markovian process with probability following four different selection algorithms: three are based on the interaction energy between the molecules and the fourth is based on random selection. The method was successfully applied to the linker histone-nucleosome system, where the nucleosome was modeled as a flexible molecule. The result suggests that the linker histone preferentially binds to more open nucleosome conformations. Following the BD results obtained, the encounter complex dynamics was modeled by atomic detail Molecular Dynamics (MD), taking into account all degrees of freedom in classical mechanics on $sim 10:ns$ time scale. The simulation resulted in a stable biomolecular complex with a conformational change on the loop region of the linker histone, which could be attributed to an induced fit effect. As well as providing insights into the determinants of linker histone-nucleosome binding, the results are expected to be valuable for higher order modelling of the chromatin fiber.