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You searched for +publisher:"Clemson University" +contributor:("Stuart , Steve J."). Showing records 1 – 2 of 2 total matches.

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Clemson University

1. Brice, Allyn. A THEORETICAL INVESTIGATION EXAMINING DNA CONFORMATIONAL CHANGES AND THEIR EFFECTS ON GLYCOSYLASE FUNCTION.

Degree: PhD, Physical Chemistry, 2011, Clemson University

Glycosylase enzymes initiate the process of base excision repair (BER) in order to prevent the irreversible modification of the genome. In the BER process a damaged DNA base is recognized, removed from the DNA sequence, and then the remaining abasic site is repaired. Glycosylase enzymes are responsible for the base recognition mechanism and catalysis of the base excision. One of the most studied glycosylase superfamilies is uracil DNA glycosylase (UDG). The UDG superfamily has demonstrated specificity for excising uracil, which is the deamination product of cytosine, from DNA sequences of prokaryotes and eukaryotes. Mismatch-specific uracil DNA glycosylase (MUG) is a member of the UDG superfamily, and interestingly has shown specificity for both uracil and xanthine bases. The following dissertation provides an anlaysis on the recognition mechanism of E. coli MUG for deaminated DNA bases. Glycosylase enzymes require the damaged base to be flipped out of the base stack, and into an active site for catalysis of the N-glycosidic cleavage. Typically, recognition of substrates by enzymes is characterized by binding affinities, but in the following work the binding of E.Coli MUG is broken down into contributions from the base flipping and enzyme binding equilibria. Since DNA conformational changes play a large role in UDG systems, the robustness of molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) free energy method was evaluated for a DNA conformational change. The A-form to B-form DNA conformational free energy differences were calculated using MM/PBSA, and compared with free energy differences determined with a more rigorous umbrella sampling method. MM/PBSA calculations of the free energy difference between A-form and B-form DNA are shown to be in very close agreement with the PMF result determined using an umbrella sampling approach. The sensitivity to solvent model and force field used during conformational sampling was also established for the MM/PBSA free energies. In order to determine the influence of base flipping conformational changes on the MUG recognition process, PMF profiles were generated for each of the damaged bases (uracil, xanthine, oxanine, inosine). Agreement was displayed between the base pair stability trends from the umbrella sampling, and the enzyme activities from experiment. Interaction energies and structural analyses were used to examine the MUG enzyme, which revealed regions of the active site critical for binding xanthine and uracil substrates. Site-directed mutagenesis experiments were performed on MUG to determine the role of specific amino acids in the recognition mechanism. Mutations were studied further through modeling and molecular dynamics (MD) simulations of the unbound and bound proteins. Advisors/Committee Members: Dominy, Brian N., Stuart , Steve J., Arya , Dev P., McNeill , Jason.

Subjects/Keywords: Base Flipping; CHARMM; Generalized Born; Glycosylase; MM/PBSA; Umbrella Sampling; Physical Chemistry

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Brice, A. (2011). A THEORETICAL INVESTIGATION EXAMINING DNA CONFORMATIONAL CHANGES AND THEIR EFFECTS ON GLYCOSYLASE FUNCTION. (Doctoral Dissertation). Clemson University. Retrieved from https://tigerprints.clemson.edu/all_dissertations/845

Chicago Manual of Style (16th Edition):

Brice, Allyn. “A THEORETICAL INVESTIGATION EXAMINING DNA CONFORMATIONAL CHANGES AND THEIR EFFECTS ON GLYCOSYLASE FUNCTION.” 2011. Doctoral Dissertation, Clemson University. Accessed May 08, 2021. https://tigerprints.clemson.edu/all_dissertations/845.

MLA Handbook (7th Edition):

Brice, Allyn. “A THEORETICAL INVESTIGATION EXAMINING DNA CONFORMATIONAL CHANGES AND THEIR EFFECTS ON GLYCOSYLASE FUNCTION.” 2011. Web. 08 May 2021.

Vancouver:

Brice A. A THEORETICAL INVESTIGATION EXAMINING DNA CONFORMATIONAL CHANGES AND THEIR EFFECTS ON GLYCOSYLASE FUNCTION. [Internet] [Doctoral dissertation]. Clemson University; 2011. [cited 2021 May 08]. Available from: https://tigerprints.clemson.edu/all_dissertations/845.

Council of Science Editors:

Brice A. A THEORETICAL INVESTIGATION EXAMINING DNA CONFORMATIONAL CHANGES AND THEIR EFFECTS ON GLYCOSYLASE FUNCTION. [Doctoral Dissertation]. Clemson University; 2011. Available from: https://tigerprints.clemson.edu/all_dissertations/845

2. Wu, Peng. EQUILIBRIUM AND DYNAMIC CHARGE STORAGE IN NANOPORES WITH ROOM TEMPERATURE IONIC LIQUIDS.

Degree: PhD, Mechanical Engineering, 2014, Clemson University

Electrochemical capacitors store electrical energy physically in the electrical double layers at the electrode/electrolyte interfaces. In spite of their high power density and extraordinary cyclability, the widespread deployment of electrochemical capacitors is limited by their moderate energy density. The current surge in interest in electrochemical capacitors is driven by recent breakthroughs in developing novel electrode and electrolyte materials. In particular, electrodes featuring sub-nanometer pores and room-temperature ionic liquids are promising materials for next-generation electrochemical capacitors. To realize the full potential of these materials, a basic understanding of the charge storage mechanisms in them is essential. In this Dissertation, using atomistic simulations, we investigated the charge storage in sub-nanometer pores using room-temperature ionic liquids as electrolytes. These simulations of the equilibrium charge storage in slit-shaped nanopores in contact with room-temperature ionic liquids showed that the capacitance of the nanopores exhibits a U-shaped scaling behavior in pores with width from 0.75 to 1.26 nm. The left branch of the capacitance scaling curve directly corresponds to the anomalous capacitance increase and thus confirms prior experimental observations. The right branch of the curve indirectly agrees with experimental findings that so far have received little attention. We also found that the charge storage in sub-nanometer pores follows a distinct voltage dependent behavior. At low voltages, charge storage is achieved by swapping co-ions in the pore with counter-ions in the bulk electrolytes. As voltage increases, further charge storage is due mainly to the removal of co-ions from the pore, leading to a capacitance increase. The capacitance eventually reaches a maximum when all co-ions are expelled from the pore. At even higher electrode voltages, additional charge storage is realized by counter-ion insertion into the pore, accompanied by a reduction of capacitance. The molecular origins of these phenomena were elucidated by a new theoretical framework we developed specifically for the charge storage in nanopores using solvent-free electrolytes. These simulations of the charging dynamics of sub-nanometer pores in contact with room-temperature ionic liquids showed that the charging of ionophilic pores, of width comparable to the size of ion, is a diffusive process. Such a process is often accompanied by overfilling and followed by de-filling. In sharp contrast to conventional expectations, charging is fast because ion diffusion during charging can be an order of magnitude faster than in the bulk, and charging itself is accelerated by the onset of collective modes. Further acceleration can be achieved using ionophobic pores by eliminating overfilling/de-filling and thus leading to charging behavior qualitatively different from that in conventional, ionophilic pores. Overall, our studies indicated that electrodes with sub-nanometer pores and room-temperature ionic liquids can… Advisors/Committee Members: Qiao, Rui, Saylor, John R., Stuart, Steve J., Xuan, Xiangchun.

Subjects/Keywords: charging dynamics; electrochemcial capacitors; energy storage; room temperature ionic liquids; supercapacitors; Mechanical Engineering

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Wu, P. (2014). EQUILIBRIUM AND DYNAMIC CHARGE STORAGE IN NANOPORES WITH ROOM TEMPERATURE IONIC LIQUIDS. (Doctoral Dissertation). Clemson University. Retrieved from https://tigerprints.clemson.edu/all_dissertations/1279

Chicago Manual of Style (16th Edition):

Wu, Peng. “EQUILIBRIUM AND DYNAMIC CHARGE STORAGE IN NANOPORES WITH ROOM TEMPERATURE IONIC LIQUIDS.” 2014. Doctoral Dissertation, Clemson University. Accessed May 08, 2021. https://tigerprints.clemson.edu/all_dissertations/1279.

MLA Handbook (7th Edition):

Wu, Peng. “EQUILIBRIUM AND DYNAMIC CHARGE STORAGE IN NANOPORES WITH ROOM TEMPERATURE IONIC LIQUIDS.” 2014. Web. 08 May 2021.

Vancouver:

Wu P. EQUILIBRIUM AND DYNAMIC CHARGE STORAGE IN NANOPORES WITH ROOM TEMPERATURE IONIC LIQUIDS. [Internet] [Doctoral dissertation]. Clemson University; 2014. [cited 2021 May 08]. Available from: https://tigerprints.clemson.edu/all_dissertations/1279.

Council of Science Editors:

Wu P. EQUILIBRIUM AND DYNAMIC CHARGE STORAGE IN NANOPORES WITH ROOM TEMPERATURE IONIC LIQUIDS. [Doctoral Dissertation]. Clemson University; 2014. Available from: https://tigerprints.clemson.edu/all_dissertations/1279

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