Other Biochemistry, Biophysics, and Structural Biology 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 …

Erecta Family Genes Regulate The Shoot Apical Meristem And Organ Formation, Daniel A. Degennaro

Doctoral Dissertations

Plants are sessile and must adjust their organ growth to their environments. A reservoir of stem cells in the shoot apical meristem (SAM) supplies cells for differentiation into organs. The SAM must balance organ production with stem cell maintenance. The ERECTA family (ERfs) encodes the leucine-rich repeat receptor-like kinases ERECTA (ER), ERECTA-LIKE 1 (ERL1), and ERL2. ERf signaling regulates organ initiation and stem cell maintenance. Results presented in this work include the following:

1) WUSCHEL (WUS) and CLAVATA3 (CLV3) make up a negative feedback loop to maintain SAM size. WUS and CLV3 expression localization is critical for …

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 …

Bioinformatic And Experimental Approaches For Deeper Metaproteomic Characterization Of Complex Environmental Samples, Ramsunder Mahadevan Iyer

Doctoral Dissertations

The coupling of high performance multi-dimensional liquid chromatography and tandem mass spectrometry for characterization of microbial proteins from complex environmental samples has paved the way for a new era in scientific discovery. The field of metaproteomics, which is the study of protein suite of all the organisms in a biological system, has taken a tremendous leap with the introduction of high-throughput proteomics. However, with corresponding increase in sample complexity, novel challenges have been raised with respect to efficient peptide separation via chromatography and bioinformatic analysis of the resulting high throughput data. In this dissertation, various aspects of metaproteomic characterization, including …

Electron Transport To Photosystem I By Soluble Carriers: Evolution Of The Interacting Pair, Khoa Dang Nguyen

Doctoral Dissertations

Oxygenic photosynthesis is driven via sequential action of Photosystem II (PSII) and (PSI) reaction centers via the Z-­‐scheme. Both of these pigment– membrane protein complexes are found in cyanobacteria, algae, and plants. PSI, unlike PSII, is remarkably stable and does not undergo limiting photo-­‐damage. This stability, as well as other fundamental structural differences, makes PSI the most attractive reaction centers for applied photosynthetic applications. These applied applications exploit the efficient light harvesting and high quantum yield of PSI where the isolated PSI particles are redeployed providing electrons directly as a photocurrent or, via a coupled catalyst to yield H2. Here, …

Complex Non-Equilibrium Structural Dynamics In Globular Proteins, Xiaohu Hu

Doctoral Dissertations

Internal structural motions in proteins are essential to their functions. In this present dissertation, we present the results from an extensive set of molecular dynamics simulations of three very different globular proteins and demonstrate that the structural fluctuations observed are highly complex, manifesting in non-ergodic and self-similar subdiffusive dynamics with non-exponential relaxation behavior. The characteristic time of the motion observed at a given timescale is dependent on the length of the observation time, indicating an aging effect. By comparing the simulation results to the existing single-molecule fluorescence spectroscopic data on other globular proteins, we found the characteristic relaxation time for …

Computer Simulations Of Enzymes, Jianzhuang Yao

Doctoral Dissertations

Enzymes are important catalysts in living systems, and understanding catalytic mechanisms of enzymes is an important task for modern biophysics and biochemistry. Computer simulations have emerged as very useful tools for understanding how enzymes work. In this dissertation, QM/MM MD simulations were applied to study the catalytic mechanisms of several enzymes, including sedolisin, S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases, and salicylic acid binding protein 2. For sedolisin, we focus on the acylation and deacylation reactions catalyzed by the enzymes. We proposed a general acid/base mechanism involving the Glu/Asp residues at the active site. MD and QM/MM free energy simulations on pro-kumamolisin show that …

Comparative Genomics Of Microbial Chemoreceptor Sequence, Structure, And Function, Aaron Daniel Fleetwood

Doctoral Dissertations

Microbial chemotaxis receptors (chemoreceptors) are complex proteins that sense the external environment and signal for flagella-mediated motility, serving as the GPS of the cell. In order to sense a myriad of physicochemical signals and adapt to diverse environmental niches, sensory regions of chemoreceptors are frenetically duplicated, mutated, or lost. Conversely, the chemoreceptor signaling region is a highly conserved protein domain. Extreme conservation of this domain is necessary because it determines very specific helical secondary, tertiary, and quaternary structures of the protein while simultaneously choreographing a network of interactions with the adaptor protein CheW and the histidine kinase CheA. This dichotomous …

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 …

Acceleration And Verification Of Virtual High-Throughput Multiconformer Docking, Sally Rose Ellingson

Doctoral Dissertations

The work in this dissertation explores the use of massive computational power available through modern supercomputers as a virtual laboratory to aid drug discovery. As of November 2013, Tianhe-2, the fastest supercomputer in the world, has a theoretical performance peak of 54,902 TFlop/s or nearly 55 thousand trillion calculations per second. The Titan supercomputer located at Oak Ridge National Laboratory has 560,640 computing cores that can work in parallel to solve scientific problems. In order to harness this computational power to assist in drug discovery, tools are developed to aid in the preparation and analysis of high-throughput virtual docking screens, …

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 …

Development Of An Electrochemical Technique For Oxidative Surface Mapping To Investigate Solution-Phase Protein Dynamics With High Performance Mass Spectrometry And Advanced Informatics, Carlee Suzanne Patterson Mcclintock

Doctoral Dissertations

Oxidative protein surface mapping has gained popularity over recent years within the mass spectrometry (MS) community for gleaning information about the solvent accessibility of folded protein structures. The hydroxyl radical targets a wide breadth of reactive amino acids with a stable mass tag that withstands subsequent MS analysis. A variety of techniques exist for generating hydroxyl radicals, with most requiring sources of radiation or caustic oxidizing reagents. The purpose of this research was to evaluate the novel use of electrochemistry for accomplishing a comparable probe of protein structure with a more accessible tool. Two different working electrode types were tested …