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.
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Showing 1 to 20 of 20 for “"protein conformational changes"”.
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Mesoscopic modeling of protein conformational changes
"The conformational changes of proteins are studied theoretically with the help of coarsegrained mesoscopic models of protein structure. The models explicitly incorporate the effects of the polarity of the peptide backbone and of the specificity of hydrophobic interactions. These two features are …
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Theoretical Approaches to the Characterization of Water, Aqueous Interfaces, and Improved Sampling of Protein Conformational Changes
<p>Methods to advance the understanding of water and other aqueous systems are devel- oped. This work falls into three areas: The creation of better interaction potentials for water, improved methods for sampling configurational space, and the applications of these methods to understand systems of …
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A molecular dynamics simulation based principal component analysis framework for computation of multi-scale modeling of protein and its interaction with solvent
… calculating the normal modes and interactions of proteins, macromolecular assemblies and surrounding solvents. The framework employs a combination of molecular dynamics simulation (MD) and principal component analysis (PCA). It enables the capture and visualization of the molecules' normal modes …
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Interactions between molecules and nanostructures using quartz crystal microbalance
The understanding of protein behaviour at the nanoscale is critical for the development of new therapies and biosensing. The assembly of peptides for new therapies are performed on the surface of a biosensor and because of the rough nature of this sample, the characterisation is usually performed …
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On The Development, Characterization, And Use Of Protein Fluorescence And Infrared Spectroscopic Probes
Proteins possess unique physical and chemical properties that allow them to carry out a wide variety of biological activities and functions. While it is generally understood that a protein’s function is dictated by its structure and dynamics, arriving at a molecule-level understanding of the …
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Bioanalytical methods for studies of homocysteine and novel cardiovascular disease indicators
… methods, which allowed rapid monitoring of protein oligomerization in PT-protein reaction mixtures. The results of these studies suggest that PT formation is a plausible mechanism for Hcy clearance. Moreover, PT formation was shown to protect proteins from post-translational modification by …
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Protein structure and interaction under environmental stress : from quality control recognition to evolution of collective behavior
A protein's function in the cell depends on its structure, which in turn depends on the intracellular environment. Stress like heat shock or nutrient starvation can alter intracellular conditions, leading to protein misfolding - i.e. the inability of a protein to reach or maintain its native …
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2D IR spectroscopy and computational modeling : application to protein folding and binding
… are developed that can be used to study protein conformational changes such as folding and binding. Every functional motion of a protein is inextricably linked to conformational dynamics. However, most of our insight into protein folding and binding is indirectly obtained through kinetics …
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Regulation of the Human Parainfluenza Virus (hPIV3) Fusion Protein
… of this work was to determine how the fusion (F) protein is regulated with a focus on the heptad repeat B (HRB) region of the F protein located in the ectodomain, directly adjacent to the transmembrane domain. This region has been suggested to play important roles in the initiation of fusion</p> …
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RCK Domain Model of Calcium Activation in BK Channels
… the transduction of the binding energy through protein conformational changes to the channel domain. The RCK domain model thus provides a framework for the study of Ca<sup>2+</sup> activation in BK channels.</p>
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Temperature-jump 2D IR spectroscopy to study protein conformational dynamics
… characterized, and applied to the study of protein folding and association. In solution, protein conformational changes span a wide range of timescale from nanoseconds to minutes. Ultrafast 2D IR spectroscopy measures time-dependent structural changes within the protein ensemble by probing …
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Structures of oxalate oxidoreductase : C₂ activation by a microbial TPP-dependent ferredoxin oxidoreductase
… these structures have revealed dramatic protein conformational changes in the active site that are likely to facilitate catalysis. As OOR is only the second OFOR to be structurally characterized, these structures have provided a wealth of information about the larger OFOR superfamily as …
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Learning the ABC's of Ribose Transport Using Biophysical Methods
… transporters comprise a large superfamily of proteins that are involved in a variety of biological phenomenon, from bacterial metabolism to cellular homeostasis, antigen-presentation, and drug resistance. These proteins are implicated in a variety of clinically relevant phenomenon, including …
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Deconstructing G Protein-Coupled Receptor Dimer Pharmacology: Case Studies in Dopamine D1 and D2 Receptors
… functions. At a molecular level, G protein coupling is considered the main activation mechanism for most of the receptor-mediated cellular processes. A number of studies using native tissue have supported the idea that receptors can interact to form dimers or higher order oligomers. …
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Mechanistic investigations of the radical transport pathway in fluorotyrosine-substituted class Ia ribonucleotide reductases
… are kinetically masked by rate-limiting protein conformational changes. Herein, the stable Y₁₂₂₈ is site-specifically replaced with a 2,3,5-trifluorotyrosyl radical (2,3,5-F₃Y*) that modulates the driving force for RT. This 2,3,5-F₃Y-substituted RNR perturbs PCET kinetics such that a …
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Mechanistic characterization of acetic acid resistance enzymes of Acetobacer aceti
… citryl-CoA (CitCoA), and CitCoA hydrolysis. Protein conformational changes that close the active site assemble a catalytically competent condensation active site. The 2.2 Å resolution crystal structure of CS from the thermoacidophile <em>Thermoplasma acidophilum</em> (TpCS) fused to a …
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Application of fluorescence spectroscopy for the in-vial investigation of protein solutions
Therapeutic protein formulations are subjected to various stressors during manufacturing, transport, and storage, causing destabilisation, in turn leading to deleterious effects such as immunogenic reactions or inefficacy upon administration. An essential part of this production and supply process …
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The Application of a Reporter Group to α-Chymotrypsin
… in order to obtain information about small changes in the environment at specific positions in protein molecules. In this method one environmentally sensitive group is introduced into a specific position in the protein so that small changes induced by substrates or modifiers can be followed. …
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Development and Application of Large-Scale Protein Folding Stability Analysis in Drug Target Identification and Disease Biomarker Discovery
… been developed for the large-scale analysis of protein folding stabilities. The main focus of this dissertation is to develop and apply these large-scale protein folding stability approaches in drug target identification and disease biomarker discovery. One goal of this work is to develop a …
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Mechanism and energetics of membrane transporters and channels
"Living cells have evolved specialized transport proteins called membrane transporters and channels that catalyze exchange of materials across the cell membrane. Membrane trans- porters couple the active transport of their specific substrates against their electrochemical gradient. On the other …