UMD Theses and Dissertations

Permanent URI for this collectionhttp://hdl.handle.net/1903/3

New submissions to the thesis/dissertation collections are added automatically as they are received from the Graduate School. Currently, the Graduate School deposits all theses and dissertations from a given semester after the official graduation date. This means that there may be up to a 4 month delay in the appearance of a given thesis/dissertation in DRUM.

More information is available at Theses and Dissertations at University of Maryland Libraries.

Browse

Filters

20151

Settings

Author: search.filters.author.Winogradoff, DavidSubject: search.filters.subject.CENP-A

Search Results

Now showing 1 - 1 of 1
  • Thumbnail Image
    Item
    Molecular Dynamic Simulations of Nucleosomes and Histone Tails: The Effects of Histone Variance and Post-Translational Modification
    (2015) Winogradoff, David; Papoian, Garegin; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The packaging of genomic information and the regulation of gene expression are both fundamentally important to eukaryotic life. Meters of human DNA must fit inside the micron-diameter nucleus while still rapidly becoming available for templated processes such as transcription, replication, and repair. Therefore, the DNA-protein complex known as chromatin must dynamically transition between more compact, closed states and more accessible, open ones. To fully understand chromatin structure and dynamics, it is necessary to employ a multifaceted approach, integrating different general philosophies and scientific techniques that include experiment and computation. Since the DNA in chromatin is organized into arrays of nucleosomes, we take a bottom-up approach in this dissertation, striving first to understand the structure and dynamics of an individual nucleosome and subdomains thereof. Atomistic computational methods have provided useful tools to study DNA and protein dynamics at the nanosecond, and recently microsecond, timescale. In this dissertation, we present recent developments in the understanding of the nucleosome though atomistic molecular dynamics (MD) simulations. By applying different all-atom MD computational techniques, we demonstrate that replacing the canonical H3 histone with the centromere-specific variant CENP-A translates to greater structural flexibility in the nucleosome, that replacing H3 with CENP-A increases the plasticity of an individual histone dimer, and that the effects of acetylation on the H4 histone tail are cumulative and specific to lysine 16 mono-acetylation.