Biochemistry Commons^™

A Novel Transmembrane Ligand Inhibits T Cell Receptor Activation, Yujie Ye

Doctoral Dissertations

T lymphocytes (T cells) play essential roles in the adaptive immune system. Each mature T cell expresses one type of functional T cell receptor (TCR). The TCR recognizes antigens bound to the major histocompatibility complex (MHC) in antigen presenting cells. The resulting stimulation signal crosses the transmembrane domain of TCR and initiates downstream signaling cascades. The human immune system relies on TCRs to recognize a variety of pathogens. Normally, TCR can distinguish the self-antigens from pathogenic antigens. However, dysfunction or aberrant expression of TCRs causes different inflammatory and autoimmune diseases, which afflict millions of people annually (Chapter I). Current treatments …

Computer Simulations Of Biological Systems: From Protein Dynamics To Drug Discovery, Rupesh Agarwal

Doctoral Dissertations

Computational biophysics methods such as molecular dynamics (MD) simulations are often used in combination with experimental techniques like neutron scattering, NMR, and FTIR to explore protein conformational landscapes. With the improvements in experimental techniques, there is also a need to continually optimize the MD forcefield parameters to make precise predictions that match experimental results. To complement many of these experiments, an accurate model of deuteration is frequently required, but has been elusive. In our work, we developed a novel method to capture isotope effects in classical MD simulations by re-parameterization of the bonded terms of the CHARMM forcefield using quantum …

Pinpointing The Molecular Basis For Metal Ion Effects On Plasminogen Activator Inhibitor-1 (Pai-1), Joel Cullen Bucci

Doctoral Dissertations

Plasminogen activator inhibitor type-1 (PAI-1) specifically inhibits the proteases tissue type plasminogen activator and urokinase plasminogen activator to control the activation of fibrinolysis. Vitronectin interacts with PAI-1 primarily through the somatomedin B (SMB) domain to stabilize and localize PAI-1 to sites of injury. Our laboratory observed that transition metals such as copper²⁺ have VN dependent, reciprocal effects on how long PAI-1 remains active. We aim to determine the molecular basis for effects of copper²⁺ on PAI-1 activity. We employed a computational algorithm (MUG) to predict metal binding clusters, and introduced mutations hypothesized to create metal binding deficiency. We …

Understanding The Molecular Mechanism Underlying The Great Thermal Stability Of Thermophilic Enzymes Using Aminoglycoside Nucleotidyltransferase 4' As A Model, Xiaomin Jing

Doctoral Dissertations

The aminoglycoside nucleotidyltransferase 4' (ANT) is a homodimeric enzyme that detoxifies antibiotics by nucleotidylating at the C4'-OH site. Two thermostable variants T130K and D80Y generated by direct evolution in laboratory differ by only a single residue replacement compared to the wild type mesophilic enzyme. Both variants display enhanced melting temperatures and execute catalysis at temperatures the wild type would be inactive. However, T130K variant still keeps molecular properties of mesophilic enzyme. T130àK130 does not trigger significant change in enzyme’s local flexibility or thermodynamics of ligand binding while D80Y variant has distinct properties in ligand recognition and dynamics. We hypothesize that …

Engineering Photosystem I Complexes For Use In Bio-Hybrid Dye-Sensitized Solar Cells, Richard Franklin Simmerman

Doctoral Dissertations

Increasing global population, growing per capita energy needs, diminishing fossil fuels, and climate change collectively will require new, innovative, and sustainable alternatives to meet the world’s growing energy needs. One of the most promising yet simple approaches are dye-sensitized solar cells (DSSCs). However, conventional DSSCs use semi-conductor anodes sensitized with complex synthetic organometallic dyes. Most dyes utilize ruthenium complexes to absorb photons, which upon excitation, inject electrons into the anode, while holes migrate to the cathode via liquid electrolyte. However, these dyes are expensive, difficult to make, and resource-limited. This dissertation focuses on replacing synthetic dyes with the naturally occurring, …

Pore Selectivity And Gating Of Arabidopsis Nodulin 26 Intrinsic Proteins And Roles In Boric Acid Transport In Reproductive Growth, Tian Li

Doctoral Dissertations

Plant nodulin-26 intrinsic proteins (NIPs) are members of the aquaporin superfamily that serve as multifunctional channels of uncharged metabolites and water. They share the same canonical hourglass fold as the aquaporin family. The aromatic arginine (ar/R) selectivity filter controls transport selectivity based on size, hydrophobicity, and hydrogen bonding with substrates. In Arabidopsis thaliana, NIP II subclass proteins contain a conserved ar/R “pore signature” that is composed of Alanine at the helix 2 position (H2), Valine/Isoleucine at the helix 5 position (H5), and an Alanine (LE1) and an invariant Arginine (LE2) at the two loop E positions. In this study, …

Applications And Improvements In The Molecular Modeling Of Protein And Ligand Interactions, Jason Bret Harris

Doctoral Dissertations

Understanding protein and ligand interactions is fundamental to treat disease and avoid toxicity in biological organisms. Molecular modeling is a helpful but imperfect tool used in computer-aided toxicology and drug discovery. In this work, molecular docking and structural informatics have been integrated with other modeling methods and physical experiments to better understand and improve predictions for protein and ligand interactions. Results presented as part of this research include:

1.) an application of single-protein docking for an intermediate state structure, specifically, modeling an intermediate state structure of alpha-1-antitrypsin and using the resulting model to virtually screen for chemical inhibitors that can …

Understanding The Origins Of Product Specificity Of Protein Methyltransferases From Qm/Mm Md And Free Energy Simulations, Yuzhuo Chu

Doctoral Dissertations

Protein lysine methyltransferases (PKMTs) catalyze the methylation of certain lysine residues on histone tails using S-adenosyl-L-methionine (AdoMet) as the methyl donor. Regulation of chromatin structure and gene expression through histone lysine methylation depends on the degree of methylation. Therefore, it is of importance to understand the features of PKMTs that control how many methyl groups would be added to the target lysine (product specificity). In my dissertation, I have applied quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) and free energy simulations to understand the origin of the product specificities of SET8, GLP and their mutants. The relative free energy barriers …

Soybean Nodulin 26: A Channel For Water And Ammonia At The Symbiotic Interface Of Legumes And Nitrogen-Fixing Rhizobia Bacteria, Jin Ha Hwang

Doctoral Dissertations

During the infection and nodulation of legume roots by soil bacteria of the Rhizobiaceae family, the invading endosymbiont becomes enclosed within a specialized nitrogen-fixing organelle known as the "symbiosome". In mature nodules the host infected cells are occupied by thousands of symbiosomes, which constitute the major organelle within this specialized cell type. The symbiosome membrane is the outer boundary of this organelle which controls the transport of metabolites between the symbiont and the plant host. These transport activities include the efflux of the primary metabolic product of nitrogen fixation and the uptake of dicarboxylates as an energy source to support …

Investigating The Flexibility Of Intrinsically Disordered Proteins In Folding And Binding, Amanda Leilah Debuhr

Chancellor’s Honors Program Projects

No abstract provided.

Dynamics Of The Toc Gtpases: Modulation By Nucleotides And Transit Peptides Reveal A Mechanism For Chloroplast Protein Import, Lovett Evan Reddick

Doctoral Dissertations

The chloroplast is the green organelle in the plant cell responsible for harvesting energy from sunlight and converting it into sugars and ATP. Origins of this organelle can be traced back to an endosymbiotic event in which a primitive eukaryotic cell capable of oxidative phosphorylation engulfed a free-living cyanobacterium capable of photosynthetic respiration (1). Immediately following this event the details are not clear, however what is known is that over the course of evolution, the engulfed cyanobacteria relinquished approximately 97% of its protein coding sequences to the host cell nucleus, thus making the newly formed chloroplast reliant on its host …