Probing the Function of Chromatin Remodeling Factors with Biomolecular Simulations

Abstract

Eukaryotes package and maintain their genetic code in chromatin fibers. The fundamental unit of chromatin is the nucleosome, a complex of approximately equal mass of protein and DNA molecules.  By altering the physical and biochemical properties of the nucleosome, the cell regulates the structure and stability of chromatin and thus tunes gene expression. 

 In this talk, I will discuss efforts by our group to use molecular dynamics simulations in conjunction with data from NMR, SAXS, and Cryo-EM experiments to understand the processes by which chromatin remodeling factors alter the structure and dynamics of single and poly-nucleosomal arrays.  I will focus on the effects of histone variants, post-translational modifications, and linker histones. 

In addition, I will discuss how we can use Bayesian inference to rigorously determine a minimal ensemble of states of flexible biomolecular complexes to describe the results of small angle X-ray scattering experiments from enhanced sampling simulations.