Open Access. Powered by Scholars. Published by Universities.®

Biochemistry, Biophysics, and Structural Biology Commons

Open Access. Powered by Scholars. Published by Universities.®

Articles 1 - 8 of 8

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

Identification Of Interface Residues Involved In Protein-Protein And Protein-Dna Interactions From Sequence Using Machine Learning Approaches , Changhui Yan Jan 2005

Identification Of Interface Residues Involved In Protein-Protein And Protein-Dna Interactions From Sequence Using Machine Learning Approaches , Changhui Yan

Retrospective Theses and Dissertations

Identification of interface residues involved in protein-protein and protein-DNA interactions is critical for understanding the functions of biological systems. Because identifying interface residues using experimental methods cannot catch up with the pace at which protein sequences are determined, computational methods that can identify interface residues are urgently needed. In this study, we apply machine-learning methods to identify interface residues with the focus on the methods using amino acid sequence information alone. We have developed classifiers for identification of the residues involved in protein-protein and protein-DNA interactions using a window of primary sequence as input. The classifiers were evaluated using both ...


Distance-Based Nmr Structure Determination And Refinement, Feng Cui Jan 2005

Distance-Based Nmr Structure Determination And Refinement, Feng Cui

Retrospective Theses and Dissertations

Protein structures play a pivotal role in understanding protein functions. X-ray crystallography and nuclear magnetic resonance spectroscopy (NMR) are two main experimental approaches for protein structure determination. The structures determined by NMR are not as accurate as those by X-ray crystallography in general, due to limited distance data (e.g. NOEs) that can be generated from NMR experiments. The NMR modeling algorithms are not well developed either, to produce high-quality structures with desired accuracy and efficiency. To address the NMR modeling issues, a so-called geometric build-up approach for NMR modeling has been developed, which remarkably reduces computing time in determining ...


Probing Carbohydrate Biocatalysis Through The Use Of Electrospray Ionization Mass Spectrometry And Isothermal Titration Calorimetry , Corbin James Zea Jan 2005

Probing Carbohydrate Biocatalysis Through The Use Of Electrospray Ionization Mass Spectrometry And Isothermal Titration Calorimetry , Corbin James Zea

Retrospective Theses and Dissertations

Electrospray ionization mass spectrometry,(ESI-MS)-based assays have been newly developed to study three classes of enzymes (sugar nucleotidyltransferases, glycosyltransferases, and phosphorylases) from the three distinct families of life: archaea, eukaryotes, and prokaryotes. These three classes of enzymes play vital roles in carbohydrate storage, degradation and synthesis. The sugar nucleotidyltransferases from Escherichia coli and yeast that biosynthesize UDP-glucose and ADP-glucose respectively were studied using the first ESI-MS assay. Nonlinear regression of the kinetic data was comparable to those determined from the traditional UDP-glucose dehydrogenase coupled assay. This technique allowed us to determine that the yeast sugar nucleotidyltransferase has one binding ...


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 ...


Cell Envelope Constituents Of Pseudomonas Putida Contributing To Growth And Survival In Low-Water-Content Habitats , Martinus Franciscus Maria Van De Mortel Jan 2005

Cell Envelope Constituents Of Pseudomonas Putida Contributing To Growth And Survival In Low-Water-Content Habitats , Martinus Franciscus Maria Van De Mortel

Retrospective Theses and Dissertations

The ability of bacteria to respond to the ever changing environmental conditions they encounter requires the utilization of a broad range of colonization and survival strategies. One of the most important and probably least understood factors determining bacterial activity in terrestrial habitats is water availability. The goal of this dissertation research was to identify traits that contribute to maintaining a functional cell envelope when cells are dehydrated, which will help us to assess the scope of physiological changes necessary for growth in low-water-content habitats. The primary objective was to identify genes that are specifically regulated by dehydration (matric stress), and ...


Subunits Of Highly Fluorescent Protein R-Phycoerythrin As Probes For Cell Imaging And Single-Molecule Detection , Dragan Isailovic Jan 2005

Subunits Of Highly Fluorescent Protein R-Phycoerythrin As Probes For Cell Imaging And Single-Molecule Detection , Dragan Isailovic

Retrospective Theses and Dissertations

R-phycoerythrin (R-PE) subunits and enzymatic digests were characterized by high-performance liquid chromatography (HPLC), capillary and gel electrophoresis, and HPLC-electrospray ionization mass spectrometry. Subunits were isolated from R-PE by HPLC and detected as single molecules by total internal reflection fluorescence microscopy (TIRFM). Favorable spectroscopic characteristics of R-PE subunits and digest peptides in the visible region of spectrum originate from phycoerythrobilin (PEB) and phycourobilin (PUB) chromophores. High absorption coefficients and fluorescence (even under denaturing conditions), broad excitation and emission fluorescence spectra, and low molecular weights make these molecules suitable for fluorescence labeling of biomolecules and cells.;Fluorescent proteins were further formed both ...


Real-Time Monitoring And Manipulation Of Single Bio-Molecules In Free Solution , Hung-Wing Li Jan 2005

Real-Time Monitoring And Manipulation Of Single Bio-Molecules In Free Solution , Hung-Wing Li

Retrospective Theses and Dissertations

The observation and manipulation of single biomolecules allow their dynamic behaviors to be studied to provide insight into molecular genetics, biochip assembly, biosensor design, DNA biophysics.;In a PDMS/glass microchannel, a nonuniform electroosmotic flow (EOF) was created. By using a scanning confocal fluorescence microscope and total internal-reflection fluorescence microscope (TIRFM), we demonstrated that negatively charged DNA molecules were focused by the nonuniform EOF into a thin layer at the glass surface. This phenomenon was applied to selectively detect target DNA molecules without requiring the separation of excessive probes and can be applied continuously to achieve high throughput.;A variable-angle-TIRFM ...


Exploring Statistical Methods For Analysis Of Microarray Data , Tanzy Mae Tallapoosa Paz Love Jan 2005

Exploring Statistical Methods For Analysis Of Microarray Data , Tanzy Mae Tallapoosa Paz Love

Retrospective Theses and Dissertations

The expansion of molecular biology in recent years has created an increasing amount of data and interest in specific tools to analyze them. Much of these data come from a class of high-throughput technology that measures hundreds or thousands of variables at the same time. One such high-throughput technology currently in use is microarray technology. The three major objectives in expression analysis are data preprocessing, identifying differential expression, and grouping genes by common behavior. Extracting the useful information on gene expression from the available output is not trivial. The data collection process is quite noisy in that non-biological bias may ...