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 19 of 19 for “"conformational landscape"”.
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The conformational landscape of RNA translational regulators and their potential as drug discovery targets
… ensemble of energetic minima along a free-energy landscape. Knowledge of this structural landscape has become an important goal for understanding its diverse biological functions. In this case, NMR spectroscopy has emerged as an important player in the characterization of RNA structural ensembles, …
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Characterisation of the conformational landscape of the β1-adrenergic receptor and development of a strategy towards NMR studies of the protease-activated receptor 1
… a comprehensive description of the dynamic and conformational landscape of the minimally thermostabilised avian β1-adrenergic receptor (tβ1AR) using solution state nuclear magnetic resonance (NMR) spectroscopy. The tβ1AR is a class A G-protein-coupled receptor (GPCR) and the human counterpart is …
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Elucidating the Structural and Dynamical Properties of the Intrinsically Disordered Protein Nrf2 Using Molecular Dynamics Simulations
… ineffective. The focus was to uncover the conformational landscape of Nrf2’s Neh4 and Neh5 domains, which participate in crucial interactions for complete transcriptional activation. Since Nrf2 is an intrinsically disordered protein (IDP), molecular dynamics simulations were employed to …
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Agonist-Induced Conformational Changes In The Nmda Receptor
… and glutamate molecules and undergo a series of conformational changes that results in the opening of a cation-permeable pore in the neuronal plasma membrane. Various aspects of NMDA receptor function are not fully understood, including the phenomenon of negative cooperativity between the …
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Structual Visualization of Cytoskeletal Force Tranduction
… In this thesis, I show that myosin forces elicit conformational transitions in actin filaments (F-actin) that modulate interactions between F-actin and the force-activated cell adhesion protein α-catenin.In vitro reconstitution and cryo-electron microscopy reveal myosin force-evoked superhelical …
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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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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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Structural and Functional Effect of Phosphorylation On Ampa Receptors
… We also indicate a strong shift in the domain’s conformational landscape using single molecule FRET. Using wild-type GluA1 receptors, as well as glutamate and alanine to mimic phosphorylation and dephosphorylation respectively, we show based on FRET measurements that the C-terminal segment moves …
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Light-induced modulation of DNA recognition by the Rad4/XPC damage sensor protein.
… a dose-dependent manner. In addition, NPOM-DNA conformational landscape is monitored by fluorescence lifetime technique and shows B-DNA-like conformations for NPOM adduct (despite its bulky modification) as verified by molecular dynamic studies. Further conformational analysis shows that …
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Emerging out of the “blur”: exploration, evaluation and significance of 3D N-glycans’ structure through molecular dynamic studies
… information and uniquely dictates the overall conformational landscape of any given N - glycan. With this expanded viewpoint of sequence-to-structure dependencies in complex N-glycans, we applie d this knowledge to glycoproteins, where variation of glycan composition affects its functiona l …
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Molecular basis of the evolution of new protein functions: Kemp elimination and phosphoryl transfer reactions
… and substrate binding site by modulating the conformational landscape of a protein; third, intramolecular epistasis, the way that mutations interact with each other and the sequence background that they are introduced to, can constrain evolutionary trajectories and make the evolutionary …
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Molecular basis of the evolution of new protein functions: Kemp elimination and phosphoryl transfer reactions
… and substrate binding site by modulating the conformational landscape of a protein; third, intramolecular epistasis, the way that mutations interact with each other and the sequence background that they are introduced to, can constrain evolutionary trajectories and make the evolutionary …
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Molecular recognition, in- and out- of equilibrium, in the actions of bacterial multidrug efflux nanomachines
… however, its allosteric nature and complex conformational landscape have presented challenges to achieve this aim. Using a combination of structural, computational and biochemical approaches, mechanistic insights have been gained into substrate recognition and non-equilibrium displacement …
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Lessons from Tau RT–QuIC: Structure, Kinetics, and Drug Discovery
… a single side chain substitution can steer the conformational landscape. Finally, the application of the platform was illustrated in various translational settings. It resolved an unclassified human tauopathy, distinguished seed–positive P301S from seed–negative S305N mutation and knock–in mice …
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Investigating the role of ICL3 in β1-adrenergic receptor activation
… GPCRs are dynamic and have a complex energy landscape as they regulate complex downstream signaling processes. The thermostable turkey β1-adrenergic receptor (tβ1AR) is a prototypical class A GPCR widely used in structural studies and is activated by catecholamine ligands, adrenaline, and …
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Structural Mechanisms of F-actin Mechanochemical Regulation and Flexible Network Assembly
… molecules and solvent could alter the energetic landscape of filament bending, producing structural differences in bent states which could be discriminated by ABPs. By developing a neural-network–based particle picking approach and using methods to handle flexible heterogeneity in cryo-electron …
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Brownian dynamics simulation of soft matter with hydrodynamics: methods for constrained systems and shear processing of 2D materials
… athermal sheets in shear flow. We find a rich conformational landscape of 4 different behaviors --- flat, tumbling, 1D folded, and 2D folded --- which are well-delineated by several dimensionless groups representing the ratios between shear strength and interaction strength, and bending …
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Interactions of Proteins with Membranes: Insights from Molecular Dynamics Simulations
… microscopy often struggle to capture the full conformational landscape of membrane proteins due to their complex interactions with lipid bilayers and their dynamic nature. These limitations make computational approaches, particularly molecular dynamics (MD) simulations, invaluable tools for …
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Modulation of The Receptor Gating Mechanism and Allosteric Communication In Ionotropic Glutamate Receptors
… mechanism and inadequate knowledge regarding the conformational dynamics of the receptors during channel gating mechanism have been some of the limiting factors in elucidating the structure-function relation of iGluRs. Thus, to understand the conformational dynamics of iGluR family and correlate …