Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
Results
Showing 1 to 20 of 20 for “"Protein Model"”.
-
Machine Learning Methods for Protein Model Quality Estimation
In my research, I developed protein model quality estimation methods aimed at evaluating the reliability of computationally predicted protein models in the absence of experimentally solved ground truth structures. These methods specifically focus on estimating errors within the protein models to …
-
Design and manufacture of a large-scale collagen protein model for educational use
A meter-scale model of the fibrous 1CGD molecule, a synthetic collagen-like peptide, was modeled and manufactured for educational use. We chose to model and manufacture the 1CGD molecule because collagen is of biological importance, the molecular coordinates are well-established, and because the …
-
Computer-aided design and manufacturing feasibility of a large-scale collagen protein model for educational use
… for use in classroom setting. The collagen model was modeled with the SolidWorks and Catia software packages. One chain of space-filled Collagen 1CGD was modeled with SolidWorks, and the entirety of space-filled Collagen 1BKV and 1CGD was modeled with Catia. The feasibility of manufacturing …
-
Engineering Myoglobin Into Both a Structural and Functional Model of Nitric Oxide Reductase
To date, FeBMb is the first protein model of the FeB site of NOR and provides the first evidence, from an NOR model, that the identity of the metal in analogous non-heme metal binding sites of HCO (i.e., CuB) and NOR (i.e., FeB) can tune NO activity. In summary, FeBMb is both a structural and …
-
Engineering the interface of cytochrome b5 and myoglobin for in vitro and in vivo applications
Heme-copper oxidases (HCOs) are large membrane proteins found in both bacteria and in eukaryotes. They catalyze about 90% of oxygen reduction in the atmosphere. They utilize a heme-copper center, which is comprised of a heme and a copper ion coordinated with three histidines, to catalyze the …
-
The Protein Redesign Approach to Modeling Manganese Peroxidase
… mutants. MnC cP(W51F,W191F) is the most active protein model of MnP constructed to date.
-
Metalloprotein Design
… as a template for the purpose of producing a protein model of cytochrome P450 (cyt P450), and both CcP and swMb have been used as templates for engineering metal-binding sites characteristic of the active site in cytochrome c oxidase (CcO). Spectroscopic characterization of the mutants will be …
-
Characterization and transcriptomic profiling of Arabidopsis thaliana under cellulose biosynthesis inhibitor treatment
… based on mutation location. A 3-D homology protein model of the cellulose synthases (CESAs) was generated to display our alleles. This model contradicted previous models and predicted a protein with seven-membrane spanning helices. Transcriptomic profiling of Arabidopsis thaliana in response …
-
Determining molecular conformation from distance or density data
… resolution. The second problem is building a protein model from the initial three dimensional electron density distribution (density map) from X-ray crystallography. This problem is computationally challenging because proteins are extremely flexible.
-
NIR hyperspectral imaging for animal feed ingredient applications
… a Corning NIR HSI instrument was used to predict protein and oil content in soybean meal and visualize predicted protein distribution over the entire soybean meal sample. Preprocessing by standard normal variate and Savitzky-Golay derivative was effective in improving calibration model …
-
Foam fractionation of biopolymers: studies of protein behaviour in analytical and preparative systems
… the effects of molecular interactions between proteins upon foam quality in batch and continuous operations, and to investigate foam fractionation as a method of protein recovery from real biological feedstocks. Foam stability studies of model protein solutions acted as engineering indicators …
-
Multiscale modeling and simulation of deformation and failure mechanisms of hierarchical alpha-helical protein materials
Alpha-helical (AH) protein structures are critical building blocks of life, representing the key constituents of biological materials such as cells, hair, hoof and wool, where they assemble to form hierarchical structures. AHs play an important mechanical role in biological processes such as …
-
Addition of flexible linkers to GPU-accelerated coarse-grained simulations of protein-protein docking
Multiprotein complexes are responsible for many vital cellular functions, and understanding their formation has many applications in medical research. Computer simulation has become a valuable tool in the study of biochemical processes, but simulation of large molecular structures such as proteins …
-
Elucidating protein stabilization with fluorescence techniques
Insulin is an important protein that controls blood glucose levels, but its function becomes ineffective during protein aggregation. Insulin readily undergoes protein aggregation and it contributes to hyperglycaemia. In long-term hyperglycaemia, glucose can alter the structure and stability of …
-
EXPLORING THE EFFECTS OF PHYSIOLOGICAL ENVIRONMENT ON AMYLOID AGGREGATION
… systems. Specifically, aggregation of protein molecules results in formation of amyloid deposits, that has been associated with neuronal dysfunction leading up to neurodegeneration. The protein aggregation is often influenced by several external physiological features, which can …
-
Phase Phenomena of Proteins in Living Matter
Proteins must fold and function in the immensely complex environment of a cell, i.e. the cytoplasm—this is far from the ideal test-tube setting of a dilute solution. Here, this thesis answers an important question at the interface of physics and biology: how does the crowded cellular environment …
-
Study Of Covalent And Non-Covalent Interactions In Ternary Systems Involving: Metal/DNA-RNA/Protein, Where Metal = Platinum(II), Palladium(II)
Ternary systems comprising DNA/RNA, proteins and one (or more) metal ion are generating increased interest due to its biological relevance. The knowledge gained from the study of these systems could provide important clues regarding the precise mechanism for transcription factors, repair proteins …
-
Metalloprotein engineering with unnatural amino acids: application in functional heme-copper oxidase and azurin
Metalloproteins, proteins with metal ion cofactors, are estimated to make up more than a third of total proteome. They involve in key biological processes such as photosynthesis, respiration, and nitrogen fixation. The important roles and potential applications of metalloprotein urges the need for …
-
Tracing history of protein domain organization, functional loops, and dipeptides with chronologies and networks
This Dissertation was approved for publication on 2022-07-14 at 09:55.
-
Stochastic and physical modeling of fundamental biological processes
Modeling is a necessary tool to understand the large volumes of data generated from quantitative experiments on biological systems. It combines our knowledge of a phenomenon into a succinct mathematical or computational description. In this dissertation, we first describe briefly two applications …