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Full-Text Articles in Molecular Biology

New Strategies To Reveal Protein Candidates In Protein-Protein Interactome Study, Meng-Chieh Chen Oct 2014

New Strategies To Reveal Protein Candidates In Protein-Protein Interactome Study, Meng-Chieh Chen

Open Access Theses

Comprehensive protein-protein interaction network analysis can help reveal protein functions in a system-wide manner. A reliable knowledgebase of interaction networks is not only important for selecting the candidates for drug therapies, but also for evaluating the disease risk. In current interaction databases, 322579 interactions comprised of 56460 proteins have been reported (statistical analysis from APID: Agile Protein Interaction DataAnalyzer; http://bioinfow.dep.usal.es/apid/index.htm). The huge datasets are contributed mainly by yeast -two -hybrid (Y2H) screening and affinity-purification followed by mass spectrometry (AP-MS). High false positive rates and failing to cover certain interaction categories are the limitations ...


Interactions Of Eukaryotic Translation Initiation Factors And 3' Untranslated Region Of Barley Yellow Dwarf Virus Mrna During Protein Synthesis: A Study Of Equilibrium Binding, Kinetics And Thermodynamics, Bidisha Banerjee Jun 2014

Interactions Of Eukaryotic Translation Initiation Factors And 3' Untranslated Region Of Barley Yellow Dwarf Virus Mrna During Protein Synthesis: A Study Of Equilibrium Binding, Kinetics And Thermodynamics, Bidisha Banerjee

All Dissertations, Theses, and Capstone Projects

Eukaryotic initiation factor (eIF) 4F binding to mRNA is the first committed step in cap-dependent protein synthesis. Barley Yellow Dwarf Virus (BYDV) employs a cap-independent mechanism of translation initiation which is mediated by a structural element BTE (BYDV translation element) located in the 3’ UTR of its mRNA. eIF4F bound the BTE and a translational inactive mutant with high affinity; thus questioning the role of eIF4F in translation of BYDV. To examine the effects of eIF4F in BYDV translation initiation, BTE mutants with widely different in vitro translation efficiencies ranging from 5-164% compared to WT were studied. Using fluorescence anisotropy ...


Identification Of Molecular Determinants That Shift Co- And Post-Translational N-Glycosylation Kinetics In Type I Transmembrane Peptides: A Dissertation, Heidi L. H. Malaby Apr 2014

Identification Of Molecular Determinants That Shift Co- And Post-Translational N-Glycosylation Kinetics In Type I Transmembrane Peptides: A Dissertation, Heidi L. H. Malaby

GSBS Dissertations and Theses

Asparagine (N)-linked glycosylation occurs on 90% of membrane and secretory proteins and drives folding and trafficking along the secretory pathway. The N-glycan can be attached to an N-X-T/S-Y (X,Y ≠ P) consensus site by one of two oligosaccharyltransferase (OST) STT3 enzymatic isoforms either during protein translation (co-translational) or after protein translation has completed (post-translational). While co-translational N-glycosylation is both rapid and efficient, post-translational N-glycosylation occurs on a much slower time scale and, due to competition with protein degradation and forward trafficking, could be detrimental to the success of a peptide heavily reliant on post-translational N-glycosylation. In evidence, mutations ...


Pharmaceuticals And Personal Care Products: Emerging Contaminants In Aquatic Ecosystems, Jenny E. Zenobio Apr 2014

Pharmaceuticals And Personal Care Products: Emerging Contaminants In Aquatic Ecosystems, Jenny E. Zenobio

Open Access Theses

In recent years, the presence of pharmaceuticals and personal care products (PPCPs) in aquatic systems has led to research on their fate and effects. PPCPs have been found in mixture in wastewater effluents, surface, ground, and drinking water at low concentrations from areas of intense urbanization. Although adverse effects to human health from the current environmental concentrations are unlikely, the impacts to ecological receptors are not clear. We performed field and laboratory studies to quantify and evaluate effects of PPCPs on fish. First, a field study was conducted at the Baca National Wildlife Refuge, Colorado (2010-2012) because a portion of ...


Inducible Protein Dimerization: New Tools And Applications To Understanding The Mitotic Checkpoint, Edward Raymond Ballister Jan 2014

Inducible Protein Dimerization: New Tools And Applications To Understanding The Mitotic Checkpoint, Edward Raymond Ballister

Publicly Accessible Penn Dissertations

Cellular processes such as growth, migration, signaling and cell division require choreographed interactions between dozens or hundreds of proteins carefully organized in time and space. In order to test hypotheses about complex cellular functions, it is desirable to experimentally perturb the interactions of individual proteins that perform these functions with a level of spatial and temporal control commensurate with the time and space scales over which the system is naturally organized. Inducible protein dimerization offers the ability to experimentally control protein-protein interactions. Inducible dimerization can be used to test the immediate effects of dimerizing two proteins, or it can be ...


Dephosphorylation Of Iqg1 By Cdc14 Temporally Regulates Actin Ring Formation, Daniel Patrick Miller Jan 2014

Dephosphorylation Of Iqg1 By Cdc14 Temporally Regulates Actin Ring Formation, Daniel Patrick Miller

Masters Theses

"Cytokinesis is the final step in cell division when the cell separates the cytoplasm by contracting a ring composed of filamentous actin (F-actin) and type II myosin. Iqg1, an IQGAP family member, is an essential scaffolding protein in budding yeast (S. cerevisiae) required for actin recruitment to, and contraction of, the actomyosin ring. Actin is recruited by the calponin homology domain (CHD) in anaphase after Iqg1 is localized to the bud neck. Consensus sites for the cyclin-dependent kinase (CDK) Cdc28 were identified flanking the CHD. This led us to the hypothesis that phosphorylation of Iqg1 by Cdc28 negatively regulates actin ...


Studies Of Integrins' Lateral Dynamics At A Single Particle Level, Dipak Mainali Jan 2014

Studies Of Integrins' Lateral Dynamics At A Single Particle Level, Dipak Mainali

Graduate Theses and Dissertations

One of the important factors in controlling the dynamics, structure, and functioning of the cell membrane is the lateral diffusion of membrane proteins and lipids. Integrins are one of the ubiquitous transmembrane proteins that are vital for numerous cellular functions. Integrins' lateral mobility and rearrangement is essential for integrins primary function of cell-extracellular matrix adhesion, cell-cell adhesion, and signaling. Lateral movement allows integrins to associate with extracellular ligand and other cytoplasmic and membrane proteins to incite biological activity such as signaling and downstream effects. This thesis describes the role of both downstream and upstream effectors, such as extracellular ligand, selected ...