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.

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2010 - 20182

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Subject: search.filters.subject.PROTEIN FOLDING

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    UNCOVERING THE BIOPHYSICAL MECHANISMS OF HISTONE COMPLEX ASSEMBLY
    (2018) Zhao, Haiqing; Papoian, Garegin A.; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    At the most basic level, inheritance in living beings occurs by passing the genomic information such as the DNA sequences from the parent generation to the offspring generation. Hence, it is a fundamental goal for every generation to efficiently express the genomic information and safely pass it on to the next generation. In human and other eukaryotic species, this mission is mediated via chromatin, a macromolecule with intricate hierarchical structure. The fundamental unit of chromatin is called a nucleosome, a complex of histone proteins wrapped around with DNA. To carry out diverse biological functions such as transcription and DNA replication, the DNA-protein complex must dynamically transition between more compact, closed states and more accessible, open ones. To fully understand the chromatin structure and dynamics, it is essential to comprehend the basic structural unit of chromatin, nucleosome. In this dissertation, I present my doctoral research in the exploration of the nucleosome dynamics problem, focusing on the assembly process of histone proteins. From histone monomer to dimer, then to tetramer, octamer, and nucleosome, I used different computational modeling theories and techniques, together with different experimental collaborations, to investigate the overall thermodynamics and specific mechanistic details of nucleosome dynamics at different levels. My work has shed light on the fundamental principles governing the histone protein folding and histone complex assembly, in particular, highlighting similarities and differences between the canonical and variant CENP-A histones.
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    THERMODYNAMIC PROPERTIES OF THE UNFOLDED ENSEMBLE OF PROTEINS
    (2010) DESAI, TANAY MAHESH; MUNOZ, VICTOR; Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    A random coil, whose size is determined by its excluded volume, and net energetic interactions with its environment, has served as a representation of the unfolded ensemble of proteins. The work in this thesis involves equilibrium, nuclear magnetic resonance and time-resolved kinetics spectroscopic studies on the unfolded ensemble of BBL, a globally downhill folding 40-residue protein involved the Krebs cycle of E. coli, in its acid-denatured state, and on a sequence-randomized version of this protein. The effect of variability in thermodynamic conditions, such as temperature and the presence of added chaotropes or kosmotropes, on the equilibrium properties and reconfiguration dynamics of the unfolded state, have been deduced in the absence of competition with folding events at low pH. The unfolded ensemble experiences expansion and collapse to varying degrees in response to changes in these conditions. Individual interactions of residues of the protein with the solvent and the cosolvent (direct interactions), and the properties of the solution itself (indirect interactions) are together critical to the unfolded chain's properties and have been quantitatively estimated. Unfolded, protonated BBL can be refolded by tuning the properties of the solvent by addition of kosmotropic salts. Electrostatic interactions turn out to be essential for folding cooperativity, while solvent-mediated changes in the hydrophobic effect can promote structure formation but cannot induce long-range thermodynamic connectivity in the protein. The effect of sequence on the properties of heteropolymers is also tested with a randomized version of BBL's sequence. Chain radii of gyration, and the degree and rate of hydrophobic collapse depend on the composition of the sequence, viz. hydrophilic versus hydrophobic content. However, the ability to maximize stabilizing interactions and adopt compact conformations is more evident in naturally selected protein sequences versus designed heteropolymers. Chain reconfiguration of unfolded BBL takes place in ∼1/(100 ns), in agreement with theoretical estimates of homopolymer collapse rates. The refolding dynamics of salt-refolded BBL in the range of 1/(6 μs) at 320 K, emerge as being independent of the degree of folding or protonation of the chain, a result in keeping with the description of dynamics in BBL as oscillations in a single, smooth harmonic potential well, which only varies in its position and curvature with varying thermodynamic conditions.