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You searched for +publisher:"University of Georgia" +contributor:("Robert J. Woods"). Showing records 1 – 3 of 3 total matches.

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University of Georgia

1. Austin, Berinyuy Yongye. Computational elucidation of the structural basis for the antigenicity of bacterial capsular polysaccharides: Neisseria meningitidis.

Degree: PhD, Chemistry, 2008, University of Georgia

Neisseria meningitidis (N. meningitidis) is the leading cause of bacterial meningitis in neonates. The capsule comprises of polysaccharides that serve as key virulence factors that mask vulnerable epitopes and impart antiphagocytic properties. Thirteen strains are known, based on antibody recognition of the capsular polysaccharides (CPS). Only five strains: A, B, C, W-135 and Y are responsible for meningococcal disease. Currently, CPS-conjugate vaccines are available only against types A, C, W-135 and Y. Type B is weakly immunogenic because its CPS, alpha.-(2,8)-linked polysialic acid, is a self-antigen present in the gangliosides of human neural cell-adhesion molecules. Attempts to boost the immunogenicity of CPSs from type B have involved chemical modifications, with the primary goal being the induction of cross-reactivities between antibodies raised against the modified CPS with the bacterial CPS. Herein, computational protocols are employed to elucidate the conformational properties of haptens from the CPS of N. meningitidis B, and to probe the effects of chemical group modifications on their conformational properties. A generalizable biomolecular force field, GLYCAM06, aimed at modeling neutral and charged carbohydrates, such as the N. meningitidis CPSs, has been developed. The force field is tested on its ability to reproduce the experimental and QM vibrational frequencies of carbohydrates, experimental rotational energy barriers and quantum mechanics (QM) rotational energy curves of small molecules. Solution phase tests determine whether explicit-solvent molecular dynamics (MD) simulations, employing 3GLYCAM06, can reproduce experimental NMR observables such homonuclear scalar J-coupling constants, nuclear Overhauser enhancement distances and the populations of rotational isomeric states. Explicit-solvent thermodynamic integration MD simulations are employed to determine whether GLYCAM06 can be utilized to predict the binding modes of carbohydrate-protein interactions. The experimental relative affinities of a monoclonal antibody for a series of trisaccharides from the capsule of Shigella flexneri variant Y are employed as benchmarks. For structural properties, a pentasaccharide is docked to crystal structures and to a comparative model of the antibody. The docking simulations underscore the importance of employing high quality protein structures in generating theoretical models of protein-carbohydrate complexes. Refining the theoretical complexes via explicit-solvent MD simulations, significantly improves quality in terms of reproducing experimental hydrogen bonds. Advisors/Committee Members: Robert J. Woods.

Subjects/Keywords: Neisseria meningitidis

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APA (6th Edition):

Austin, B. Y. (2008). Computational elucidation of the structural basis for the antigenicity of bacterial capsular polysaccharides: Neisseria meningitidis. (Doctoral Dissertation). University of Georgia. Retrieved from http://purl.galileo.usg.edu/uga_etd/austin_berinyuy_y_200805_phd

Chicago Manual of Style (16th Edition):

Austin, Berinyuy Yongye. “Computational elucidation of the structural basis for the antigenicity of bacterial capsular polysaccharides: Neisseria meningitidis.” 2008. Doctoral Dissertation, University of Georgia. Accessed July 15, 2020. http://purl.galileo.usg.edu/uga_etd/austin_berinyuy_y_200805_phd.

MLA Handbook (7th Edition):

Austin, Berinyuy Yongye. “Computational elucidation of the structural basis for the antigenicity of bacterial capsular polysaccharides: Neisseria meningitidis.” 2008. Web. 15 Jul 2020.

Vancouver:

Austin BY. Computational elucidation of the structural basis for the antigenicity of bacterial capsular polysaccharides: Neisseria meningitidis. [Internet] [Doctoral dissertation]. University of Georgia; 2008. [cited 2020 Jul 15]. Available from: http://purl.galileo.usg.edu/uga_etd/austin_berinyuy_y_200805_phd.

Council of Science Editors:

Austin BY. Computational elucidation of the structural basis for the antigenicity of bacterial capsular polysaccharides: Neisseria meningitidis. [Doctoral Dissertation]. University of Georgia; 2008. Available from: http://purl.galileo.usg.edu/uga_etd/austin_berinyuy_y_200805_phd


University of Georgia

2. Barnes, Jarrod Wesley. Molecular dynamics simulation of the endopolygalacturonase II – octagalacturonate complex.

Degree: MS, Biochemistry and Molecular Biology, 2004, University of Georgia

The endopolygalacturonase II enzyme from A. niger was studied with an octameric fragment of -1,4-D-polygalacturonic acid. We present an approach to modeling the complex using MD simulations and offer a structural in terpretation for the expe rimental data given by amide exchange mass spectrometry and site-directed mutagenesis studies. The detailed model predicts a conformational change in the linear fo rm of the bound substrate to an activated bent form, which is supported by the experimental data given. The bent conformation of the substrate partially transverses the primary binding cleft and occupies a newly proposed secondary binding region, thus giving insight into the cleavage pathway for the endopolygalacturonase II enzyme. Advisors/Committee Members: Robert J. Woods.

Subjects/Keywords: Molecular Dynamics

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

APA (6th Edition):

Barnes, J. W. (2004). Molecular dynamics simulation of the endopolygalacturonase II – octagalacturonate complex. (Masters Thesis). University of Georgia. Retrieved from http://purl.galileo.usg.edu/uga_etd/barnes_jarrod_w_200412_ms

Chicago Manual of Style (16th Edition):

Barnes, Jarrod Wesley. “Molecular dynamics simulation of the endopolygalacturonase II – octagalacturonate complex.” 2004. Masters Thesis, University of Georgia. Accessed July 15, 2020. http://purl.galileo.usg.edu/uga_etd/barnes_jarrod_w_200412_ms.

MLA Handbook (7th Edition):

Barnes, Jarrod Wesley. “Molecular dynamics simulation of the endopolygalacturonase II – octagalacturonate complex.” 2004. Web. 15 Jul 2020.

Vancouver:

Barnes JW. Molecular dynamics simulation of the endopolygalacturonase II – octagalacturonate complex. [Internet] [Masters thesis]. University of Georgia; 2004. [cited 2020 Jul 15]. Available from: http://purl.galileo.usg.edu/uga_etd/barnes_jarrod_w_200412_ms.

Council of Science Editors:

Barnes JW. Molecular dynamics simulation of the endopolygalacturonase II – octagalacturonate complex. [Masters Thesis]. University of Georgia; 2004. Available from: http://purl.galileo.usg.edu/uga_etd/barnes_jarrod_w_200412_ms


University of Georgia

3. Wittkopp, Sarah Margaret Tschampel. Derivation and application of a TIP5P-consistent force field.

Degree: PhD, Chemistry, 2005, University of Georgia

The inclusion of zero-mass point charges (commonly called lone-pairs or extended points) around electronegative atoms, such as oxygen, within force fields is known to improve hydrogen bonding directionality. In parallel, inclusion of lone-pairs in the TIP5P water modelincreased its ability to reproduce both gas-phase and condensed- phase properties over its non-LP predecessor, TIP3P.In general, force field parameters relevant for modeling solvent are developed independently of those for biomolecules, generally focusing on the ability of the parameters to reproduce bulk properties of the solvent. Such an approach is not generally extendible to solutes, which themselves never exist in the pure liquid phase. Therefore, a different ansatz has to be implemented to derive the most optimal lone-pair description for each type of solute, which is not always consistent with the solvent model. Currently, the partial charges for most biomolecular parameter sets are computed via fitting of the classical molecular electrostatic potential to the quantum molecular electrostatic potential. Application of this methodology to optimize lone-pair description is therefore consistent with current approaches of modeling electrostatics and is straightforward to implement. Here, we present an atom-type specific lone-pair model, which leads to the most optimal lone-pair placement for each atom-type, and notably, results in reproduction of the lone-pair description in TIP5P. Carbohydrates are rich in hydroxyl groups and development of a lone-pair inclusive carbohydrate parameter set for use with a lone-pair containing water model, such as TIP5P, ensures compatibility between these two models. Implementation of this lone-pair model into the GLYCAM series of parameter sets improves the geometry of a series of hydrogen bonded clusters over the non–lone-pair containing parameter set and is shown to reproduce crystalline and aqueous-phase properties for mono- and disaccharides. In addition, this methodology can easily be implemented to derive a general biomolecular parameter set and a preliminary investigation of this application to the protein segment, in conjunction with the carbohydrate segment, is examined. Advisors/Committee Members: Robert J. Woods.

Subjects/Keywords: force field

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

APA (6th Edition):

Wittkopp, S. M. T. (2005). Derivation and application of a TIP5P-consistent force field. (Doctoral Dissertation). University of Georgia. Retrieved from http://purl.galileo.usg.edu/uga_etd/wittkopp_sarah_m_200512_phd

Chicago Manual of Style (16th Edition):

Wittkopp, Sarah Margaret Tschampel. “Derivation and application of a TIP5P-consistent force field.” 2005. Doctoral Dissertation, University of Georgia. Accessed July 15, 2020. http://purl.galileo.usg.edu/uga_etd/wittkopp_sarah_m_200512_phd.

MLA Handbook (7th Edition):

Wittkopp, Sarah Margaret Tschampel. “Derivation and application of a TIP5P-consistent force field.” 2005. Web. 15 Jul 2020.

Vancouver:

Wittkopp SMT. Derivation and application of a TIP5P-consistent force field. [Internet] [Doctoral dissertation]. University of Georgia; 2005. [cited 2020 Jul 15]. Available from: http://purl.galileo.usg.edu/uga_etd/wittkopp_sarah_m_200512_phd.

Council of Science Editors:

Wittkopp SMT. Derivation and application of a TIP5P-consistent force field. [Doctoral Dissertation]. University of Georgia; 2005. Available from: http://purl.galileo.usg.edu/uga_etd/wittkopp_sarah_m_200512_phd

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