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 85 for “"conformational dynamics"”.
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Conserved Conformational Dynamics Control PTP1B Enzymatic Activity
… function also depends on intrinsic protein dynamics. Further, while sequence conservation is well-correlated with conservation of structure, it is unknown if sequence also conserves protein dynamics. To understand the role of dynamics, and its potential conservation, on enzyme function we …
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Simulations of carbohydrate conformational dynamics and thermodynamics
In this thesis, free energy calculations are employed to establish the conformation freedom of selected carbohydrates. The focus is on the biologically important (1-4)-linked glucans, although the α(1-1) α and α(1-6) linkages are also investigated. Two principal types of potential of mean force …
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Physical Studies of Actin Nucleation and Conformational Dynamics
Actin is a 42 kilodalton ATPase that exists ubiquitously in eukaryotic cells. Unlike other ATPases, however, actin, under suitable conditions, can polymerize, forming helical filaments. Cells, in orchestrating their myriad cellular processes, utilize actin's intrinsic capacity to polymerize, but do …
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Thermal adaptation of conformational dynamics in ribonuclease H
… thus a balance must be struck between the dynamics required for function and the rigidity required for maintaining a globular protein's characteristic folded structure. These relationships have been studied in detail through comparison of homologous proteins from organisms adapted to …
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The Conformational Dynamics of the Polymorphic Amyloid β Protofilaments
… conformations, we performed molecular dynamics simulations to further relax the protofilaments. We prepared the relaxed structures for simulations in the presence of coarse-grained bilayers. I self-assembled multiple coarse-grained lipid bilayers to study the effects of the …
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Insights into protein function from evolutionary and conformational dynamics
… solid tissue. We investigated the evolutionary dynamics of the cadherin superfamily of cell-cell adhesion proteins to infer a structural basis for their paradoxical mixture of pairwise binding specificity and promiscuity. Our analysis predicts a small set of specificity-determining residues …
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Temperature-jump 2D IR spectroscopy to study protein conformational dynamics
… 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 the frequency changes associated with amide I backbone …
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Efficient sampling of protein conformational dynamics and prediction of mutation effects.
Molecular dynamics (MD) simulation is a powerful tool enabling researchers to gain insight into biological processes at the atomic level. There have been many advancements in both hardware and software in the last decade to both accelerate MD simulations and increase their predictive accuracy; …
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Ubiquitin Conformational Dynamics and Hydration Shell Dynamics by Solid State NMR
Knowledge of protein dynamics is essential for understanding the enzyme catalysis, protein molecular recognition, and the entropy changes during protein-ligand binding. Nuclear Magnetic Resonance (NMR) is an ideal biophysical experimental tool for the study of protein dynamics because it can be …
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Probing the conformational dynamics of amyloid oligomers in biologically relevant microenvironments
… of the aggregation microenvironment on amyloid conformational dynamics remains a large confounding factor in our understanding of oligomeric species. Amyloidogenic peptides are typically intrinsically disordered, and their conformational landscape is highly sensitive to aggregation conditions, …
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Membrane protein conformational dynamics and ligand-binding interactions in bacterial glycoconjugate biosynthesis
… strategies to study membrane protein dynamics. This thesis presents a strategy that employs structural bioinformatics in Chapter 2, molecular dynamics simulation (MD) in Chapter 3, and single-molecule FRET microscopy (smFRET) in Chapter 4 to observe the ligand-dependent conformational …
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Conformational dynamics of polypeptides and the folding of miniproteins studied by fluorescence spectroscopy
Proteinfaltung beschreibt den Prozess, in dem eine unstrukturierte Aminosäurekette in eine dreidimensionale Proteinstruktur faltet, und zwar in Abhängigkeit von der Aminosäurensequenz. Der Übergang von der Aminosäurekette zum gefalteten Protein ist noch nicht vollständig verstanden, da viele …
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Conformational Dynamics of the Glutamate Receptors via single Molecule Förster Resonance Energy Transfer
… agonist presence and, when activated, undergo a conformational shift that allows calcium ion transport across the membrane. In a number of neurological diseases, genetic variants can cause mutations that disrupt the balance between fast binding response and desensitization resulting in over- or …
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Characterising the conformational dynamics of β₁-adrenergic receptor activation and G protein coupling
… binding into an orthosteric pocket induces conformational changes in a highly interconnected allosteric activation network which enables coupling to intracellular signalling partners, including selective coupling to specific G protein α-subtypes. Investigations in solution by nuclear …
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Characterizing Conformational Dynamics and Catalytic Activity of Enzymes by Hydrogen-Deuterium Exchange Mass Spectrometry
Determining the conformational dynamics of enzymes as they undergo catalysis has been challenging for decades due to the short timescale and limitations of traditional analysis, including techniques such as CPMG 2D NMR and X-ray crystallography. Herein is the study of two proteins: TEM-1 …
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Structure, conformational dynamics and formation of large amyloids: the case of alpha-synuclein fibrils
… to do a detailed structural characterization and conformational dynamics of AS fibrils using improved sample preparation and labeling schemes; These results show that the core of the fibrils extends for about 70 residues with a repeated secondary structure motif; Additionally, it demonstrates that …
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Conformational Dynamics of the Nuclear Pore Complex Studied With Coarse-Grained Modelling and Polarized Light Microscopy
… my thesis work, I explored the organization and dynamics of the nuclear pore complex (NPC) through coarse-grained modelling and polarized-total internal reflection fluorescence (pol-TIRF) microscopy. The NPC is a large (~120 MDa in humans) macromolecular assembly that controls the flow of …
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Conformational dynamics control catalysis in disparate systems : structural insights from DNA repair and antibiotic biosynthetic enzymes
… One such example of a system that relies on conformational flexibility is the human DNA repair protein alkyladenine DNA glycosylase (AAG). To efficiently repair DNA, AAG must search the million-fold excess of unmodified DNA bases to find a handful of DNA lesions. Such a search can be …
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Conformational Dynamics of K-Ras and H-Ras Proteins: Is There Functional Specificity At The Catalytic Domain?
… on lobe II of Ras catalytic domain alters dynamics and leads to differential preference for different effectors or modulators. In this work, we used all atom molecular dynamics to analyze the dynamics in the catalytic domain of H-ras and K-ras. We have also analyzed the dynamics of a …
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