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Articles 151 - 161 of 161

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

Generation And Statistical Modeling Of Active Protein Chimeras: A Sequence Based Approach, Nicholas Fico Oct 2013

Generation And Statistical Modeling Of Active Protein Chimeras: A Sequence Based Approach, Nicholas Fico

Open Access Dissertations

Generation of active protein chimeras is a valuable tool to probe the functional space of proteins. Statistical modeling is the next logical step, allowing us to build a model of gene fragment replaceability between species. In this thesis I begin to develop the statistical tools that are needed to systematically describe combinatorial protein libraries. I present three sets of diverse chimeric protein libraries developed using sequence information. The statistical model of the human N-Ras and human K-Ras-4B genes reveal a set previously unidetifed surface residues on the N-Ras G-Domain that may be involved in cellular localization. Statistical modeling of a …

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Characterization Of The Specificity And Functions Of The Protein Phosphatase Cdc14, Christie Eissler Oct 2013

Characterization Of The Specificity And Functions Of The Protein Phosphatase Cdc14, Christie Eissler

Open Access Dissertations

Protein phosphorylation is perhaps the most ubiquitous posttranslational modification in eukaryotes and recent studies suggest that upwards of 75% of human proteins are phosphorylated. Many proteins are phosphorylated at multiple sites, often controlled by multiple kinases and phosphatases. Multisite phosphorylation can differentially affect the functional and regulatory cellular outcomes. For example, dephosphorylation of a protein at a particular site may inhibit nuclear localization of a protein while dephosphorylation of a different site may be necessary for enzymatic activation of a protein. Thus, multisite protein phosphorylation can complicate our understanding of the biological significance and the functional consequences of protein phosphorylation. …

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Structural And Functional Characterization Of The Endosome-Associated Deubiquitinating Enzyme Amsh, Christopher Williamson Davies Oct 2013

Structural And Functional Characterization Of The Endosome-Associated Deubiquitinating Enzyme Amsh, Christopher Williamson Davies

Open Access Dissertations

The endosomal sorting complexes required for transport (ESCRT) machinery is a ubiquitin-dependent molecular mechanism made of up of four individual complexes: ESCRT-0, -I, -II, III, that is necessary for regulating the degradation of cell surface receptors directed towards the lysosome. Not only are the ESCRTs implicated in endosomal sorting and trafficking of proteins, its members also have roles in other important biological processes such as: cytokinesis, HIV budding, transcriptional regulation, and autophagy. As a function of its involvement in several processes throughout the cell, the ESCRT machinery is implicated in a wide variety of diseases including cancer, neurological disease, bacterial …

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Biochemistry / Histone Protein Modification - Purdue University, Jake R. Carlson, Katherine Beavis Aug 2013

Biochemistry / Histone Protein Modification - Purdue University, Jake R. Carlson, Katherine Beavis

Data Curation Profiles Directory

The researcher is conducting research on the brain cells of drosophila larvae. Specifically, the goal is to sort nuclei from glial and neuronal cells from the brains of mutant and wild type drosophila larvae. She will do transcriptome and high throughput ChIP-seq analysis on the cell nuclei to examine the distribution of complexes that modify histones and how loss of those complexes affects transcription. The stages of her research involve a long period of methodology development, a shorter data collection period, and then data analysis. The lab notebook contains written documentation of all experiments and trials and links to data, …

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Function And X-Ray Crystal Structure Of Escherichia Coli Yfde, Elwood Mullins, Kelly L. Sullivan, T. Joseph Kappock Jul 2013

Function And X-Ray Crystal Structure Of Escherichia Coli Yfde, Elwood Mullins, Kelly L. Sullivan, T. Joseph Kappock

Department of Biochemistry Faculty Publications

Many food plants accumulate oxalate, which humans absorb but do not metabolize, leading to the formation of urinary stones. The commensal bacterium Oxalobacter formigenes consumes oxalate by converting it to oxalyl- CoA, which is decarboxylated by oxalyl-CoA decarboxylase (OXC). OXC and the class III CoA-transferase formyl- CoA:oxalate CoA-transferase (FCOCT) are widespread among bacteria, including many that have no apparent ability to degrade or to resist external oxalate. The EvgA acid response regulator activates transcription of the Escherichia coli yfdXWUVE operon encoding YfdW (FCOCT), YfdU (OXC), and YfdE, a class III CoA-transferase that is ~ 30% identical to YfdW. YfdW and …

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Biology And Ecology Of Glyphosate-Resistant Giant Ragweed, Kabelo Segobye Jan 2013

Biology And Ecology Of Glyphosate-Resistant Giant Ragweed, Kabelo Segobye

Open Access Theses

Giant ragweed (Ambrosia trifida L.) is a competitive annual plant found in disturbed landscapes and is the most troublesome weed in Indiana and the US Corn Belt. It is one of the most common and problematic weeds in corn and soybean production. The introduction of herbicide glyphosate, N-(phosphonomethyl) glycine in early 1970's provided farmers with a better and low-cost tool to control weeds. The use of glyphosate drastically increased after the development of glyphosate resistant agronomic crops in 1996 and was use as a post-emergence selective herbicide. This led to overreliance and repeated use of glyphosate for weed control especially …

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Development Of A Starch-Based Mussel-Mimetic Adhesive Polymer, Jeffrey Kazimir De Kozlowski Jan 2013

Development Of A Starch-Based Mussel-Mimetic Adhesive Polymer, Jeffrey Kazimir De Kozlowski

Open Access Theses

Mussel-mimetic adhesive polymers have gained lots of attention for their strong adhesive strength, moisture resistance, and unique ability to crosslink. These properties are mainly attributed to the high content of catecholic 3,4-dihydroxyphenylalanine (DOPA) in mussel adhesive proteins. While there has been success in creating mussel-mimetic synthetic polymers, less effort has been given to create a renewable, green, biocompatible counterpart. This thesis explores the possibilities of starch-based mussel-mimetic adhesives. Carboxymethyl starch of various molecular weights and degree of substitution was synthesized and subsequent conjugation of dopamine to these polymers by 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide was investigated. The polymers suffered from very low substitution (DScatechol …

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Interaction Between Maltose Binding Protein And Escherichia Coli Maltose Transporter, Yan Huang Jan 2013

Interaction Between Maltose Binding Protein And Escherichia Coli Maltose Transporter, Yan Huang

Open Access Theses

The ATP-binding cassette (ABC) transporter superfamily is one of the largest families of transport proteins. The ABC transporters are responsible for selective permeability of solute across membranes energized by ATP hydrolysis, which occurs in all domains of life. Maltose transporter is an ABC importer that mediates maltose/maltodextrin uptake in bacteria and archaea. It is identified as an essential virulence factor in pathogenic species of Streptococcis pyogenes and Vibrio cholera (1, 2). Escherichia coli maltose transporter is a well-characterized system with crystal structures and exclusive biochemical studies available. Knowledge of the E. coli maltose transport mechanism will lead to a better …

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Interaction Between Centromeric Histone H3 Variant And Shugoshin, Visarut Buranasudja Jan 2013

Interaction Between Centromeric Histone H3 Variant And Shugoshin, Visarut Buranasudja

Open Access Theses

Precise and faithful segregation of chromosome segregation during mitosis depends on the ability of the cell to regulate chromosome bi-orientation on the mitotic spindle. Shugoshin (Sgo1), the protector of meiotic centromeric cohesin, is required for proper establishment of chromosome bi-orientation. Sgo1 plays a crucial role as part of a mitotic tension sensor between sister chromatids. Recently, Sgo1 has been reported to interact with histone H3 at the pericentromere region, as an important factor for tension sensing and chromosome segregation. However, the role of Sgo1 in tension sensing at centromere is still elusive. The centromere is the region of attachment of …

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3d Picture Of The Syk-Vav1 Protein Complex: Tracking The B-Cell Signal One Complex At A Time, Dan I. Piraner Jul 2011

3d Picture Of The Syk-Vav1 Protein Complex: Tracking The B-Cell Signal One Complex At A Time, Dan I. Piraner

The Journal of Purdue Undergraduate Research

Protein signaling is the key method by which cells recognize a stimulus from their environment and convert it into a response. Signaling occurs in many forms: hormones, growth factors, and even proteins may act as signals from the environment. The response to their detection must be carried from the cell surface, where the signal is detected, to the nucleus, where the cell alters its DNA expression. This study analyzes one component in the signaling pathway of Spleen Tyrosine Kinase (Syk). The Syk protein receives a signal from B-cell receptors and amplifies it, resulting in an adaptive immune response and the …

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Combating Bioterrorism: Purification And Structural Analysis Of The E3 Proteins Of The Venezuelan Equine Encephalitis Virus And The Chikungunya Virus, Tyshia Gwin Jul 2011

Combating Bioterrorism: Purification And Structural Analysis Of The E3 Proteins Of The Venezuelan Equine Encephalitis Virus And The Chikungunya Virus, Tyshia Gwin

The Journal of Purdue Undergraduate Research

Outbreaks of the Venezuelan Equine Encephalitis Virus (VEEV) and the Chikungunya Virus (CHIKV) continue to emerge in Central and South America, Africa, and Asia, but there are currently no vaccines or anti-virals for these viruses. Given their ease of transmission, debilitating symptoms, and genetic alterability, VEEV and CHIKV have great potential for development into biological weapons. Therefore, there is an urgent need to determine possible methods of treatment or prevention. One possibility of prevention lies in determining the structure and biological function of the E3 protein that plays a key role in the infectivity of the viruses. In this research, …

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