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Biochemistry, Biophysics, and Structural Biology Commons

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Retrospective Theses and Dissertations

Physical Sciences and Mathematics

Biophysics

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Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Understanding Protein Motions By Computational Modeling And Statistical Approaches, Lei Yang Jan 2008

Understanding Protein Motions By Computational Modeling And Statistical Approaches, Lei Yang

Retrospective Theses and Dissertations

Because of its appealing simplicity, the elastic network model (ENM) has been widely accepted and applied to study many molecular motion problems, such as the molecular mechanisms of chaperonin GroEL-GroES function, allosteric changes in hemoglobin, ribosome motions, motor-protein motions, and conformational changes in general. In this dissertation, the ENM is employed to study various protein dynamics problems, and its validity is also examined by comparing with experimental data. First, we apply principal component analysis (PCA) to identify the essential protein motions from multiple structures (X-ray, NMR and MD) of the HIV-1 protease. We find significant similarities between the first few ...


Molecular And Chemical Characterization Of Genes Involved In Maize Cuticular Wax Biosynthesis , M. Ann D. N. Perera Jan 2005

Molecular And Chemical Characterization Of Genes Involved In Maize Cuticular Wax Biosynthesis , M. Ann D. N. Perera

Retrospective Theses and Dissertations

The primary surfaces of the arial parts of plants, and the surfaces of reproductive organs are covered by an extra cellular layer called the cuticle. The cuticle provides the foremost protection to the plant in order to adapt to the terrestrial environment. The cuticle composed of a biopolymer (cutin), which is embedded in a coating of cuticular waxes. Understanding the biochemical, genetic and physiological mechanisms for the biosynthesis of these cuticular waxes is relatively poor. This body of work has established methods for the chemical analysis of the cuticular waxes of maize plants. I have used these methods to chemically ...


X-Ray Crystallographic Studies On Adenylosuccinate Synthetase From Escherichia Coli , Zhenglin Hou Jan 1998

X-Ray Crystallographic Studies On Adenylosuccinate Synthetase From Escherichia Coli , Zhenglin Hou

Retrospective Theses and Dissertations

Adenylosuccinate synthetase catalyzes the first committed step in de novo biosyntheses of AMP from IMP and aspartate, using GTP as the energy source. Metal cations, ligand-induced conformational transitions and metabolic effectors significantly influence the catalytic potential of the synthetase. The Mg2+, Mn2+, or Ca 2+ bind to the same site, coordinating alpha-, beta-, and gamma-phosphoryl groups of GTP. The level of catalysis supported by each cation is linked to its influence on the basicity of Asp13, a residue which abstracts the proton from N1 of IMP. Zn2+, a potent inhibitor of the synthetase, coordinates the beta- and gamma-phosphoryl groups of ...


Characterization Of Biomacromolecules By Nuclear Magnetic Resonance Spectroscopy , Wayne Robert Baker Jan 1996

Characterization Of Biomacromolecules By Nuclear Magnetic Resonance Spectroscopy , Wayne Robert Baker

Retrospective Theses and Dissertations

Two proteins were examined by Nuclear Magnetic Resonance (NMR) spectroscopy. The Emb-1 protein of Daucus carota was found to have few spectral characteristics indicative of a stable tertiary structure. In particular, line-widths were narrow, chemical shift dispersion was poor and nuclear Overhauser effect spectra were sparse. The NMR spectra of Ribonuclease A was examined at a range of pH values and the chemical shifts of a selected number of resonances was plotted as a function of the pH. From these titrations curves pKa values were determined and assigned to specific ionizing groups within the protein based, in part, on physical ...