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 21 for “"conformational ensemble"”.
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Inferring protein conformational ensemble using deep learning and evolutionary couplings
Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2024-05-01
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Primary Structure and Solution Conditions Determine Conformational Ensemble Properties of Intrinsically Disordered Proteins
… are intrinsically disordered, the nature of IDP conformational ensembles remains unclear. In this dissertation, we describe relationships connecting characteristics of IDP conformational ensembles to their primary structures and solution conditions.</p><p>Using molecular simulations and …
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Structural Biology in Cellular Environments Using Sensitivity Enhanced NMR
… and applying the technique to investigate the conformational ensemble of Tau. Chapter 1 provides an overview of in-cell NMR in biological systems and intrinsically disordered proteins. A brief primer of NMR, DNP and EPR is also provided in this chapter. Chapter 2 describes the development of …
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Investigations of Local Unfolding Like Conformational Excursions in the Native State of Adenylate Kinase
… to selectively perturb the excited state conformational repertoire, leaving the ground-state X-ray crystallographic structure unaffected. The results not only demonstrate that the conformational ensemble of AK is significantly populated by a locally unfolded state that is depopulated upon …
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The mechanism of collagenolysis : a substrate-centric view
… mechanism, particularly as it pertains to the conformational ensemble of collagen, using both experimental and computational methods. In particular, this work concentrates on: (1) devising a reaction scheme for this mechanism and verifying that it can explain existing experimental observations; …
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Probing Order within Intrinsically Disordered Proteins
… This folded state may be present within the ensemble of conformations sampled by the unbound protein, opening the question of what comes first: folding or binding? Protein engineering techniques were employed to alter the level of residual ‘bound-like’ structure within the free conformational …
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Physics-based predictions of RNA loop stability and structures
… helices. In the first project, we develop a new conformational entropy model for RNA structures consisting of multiple helices connected by cross-linked loops. The basic strategy of our approach is to decompose the whole structure into a number of three-body building blocks, where each building …
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Automated Parsing of Flexible Molecular Systems using Principal Component Analysis and K-Means Clustering Techniques
… a grand scientific challenge due to the size and conformational flexibility of these systems. The work requires parsing and analyzing thousands of conformations in each molecular state for meaningful chemical information and subjecting the ensemble to costly quantum chemical calculations. The …
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UNIQUE ALLOSTERIC MECHANISM REGULATING PROTEIN-PROTEIN INTERACTION THROUGH PHOSPHORYLATION: A CASE STUDY OF THE CONFORMATIONAL CHANGES IN THE SYK TANDEM SH2 PROTEIN
… to the domain-domain dynamics and the conformational ensemble of the tandem SH2. A picture in which the Syk-immunoreceptor interaction is regulated by a mechanism of dynamic allostery emerged.
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Efficient sampling of protein conformational dynamics and prediction of mutation effects.
… challenging to restrain simulations using ensemble-averaged experimental observables. Among various approaches to elucidate the kinetics of molecular simulations, Markov State Models (MSMs) have proven their ability to extract both kinetic and thermodynamic properties of long-timescale …
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XYLARIC ACID, D-ARABINARIC ACID (D-LYXARIC ACID), L-ARABINARIC ACID (L-LYXARIC ACID), AND RIBARIC ACID-1,4-LACTONE; SYNTHESIS AND ISOLATION - SYNTHESIS OF POLYHYDROXYPOLYAMIDES THEREFROM
… coupled to MM3(96) was employed to search the conformational space afforded the diamides. A Boltzmann distribution was applied to the resultant conformational ensemble which was analyzed for structural detail. Theoretical average 1H vicinal coupling constants were compared to experimental 1H …
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XYLARIC ACID, D-ARABINARIC ACID (D-LYXARIC ACID), L-ARABINARIC ACID (L-LYXARIC ACID), AND RIBARIC ACID-1,4-LACTONE; SYNTHESIS AND ISOLATION - SYNTHESIS OF POLYHYDROXYPOLYAMIDES THEREFROM
… coupled to MM3(96) was employed to search the conformational space afforded the diamides. A Boltzmann distribution was applied to the resultant conformational ensemble which was analyzed for structural detail. Theoretical average 1H vicinal coupling constants were compared to experimental 1H …
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Investigating the Electrostatic Properties and Dynamics of Amyloidogenic Proteins with Polarizable Molecular Dynamics Simulations
… 2) How do charge-altering mutations modulate the conformational ensemble and thermodynamic properties of Aβ? 3) How do charge-altering post-translational modifications of Aβ and tau modulate changes in the conformational ensembles? These studies establish that shifts in local microenvironments …
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Modeling Disorder in Proteins Yields Insights into the Evolution of Stability and Function
… Instead, these proteins form a disordered conformational ensemble of states. These proteins are known as Intrinsically Disordered Proteins (IDPs) and are both biologically functional and abundant. Recent advances in heteropolymer theory unveiled a powerful set of sequence patterning metrics …
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Leveraging Local Perturbations to Map Allosteric Networks of Phosphatases
… A deeper understanding of how redistributions of conformational states drive allostery in proteins could allow us to better grasp natural regulatory principles in cells and open new doors to therapeutic development. Conformationally dynamic human Protein Tyrosine Phosphatases (PTPs) exemplify the …
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Computational methods to design biophysical experiments for the study of protein dynamics
… simulations and Markov state models of protein conformational dynamics are utilized to rank sets of labeled residue-pairs in terms of their ability to capture the conformational dynamics of the protein. The applications of our experimental study design methodology called OptimalProbes on …
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Order, disorder, and protein aggregation
… elongation. In the first study, I present a conformational ensemble of a-synuclein, the culprit protein of Parkinson's disease, constructed using a Variational Bayesian Weighting algorithm in combination with NMR data collected by our collaborators. We find that the data fit a description in …
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Observing residual structure in disordered peptides with multidimensional infrared spectroscopy
… that one can measure the residual structure and conformational heterogeneity of a putatively disordered sequence. This methodology was first used to study the structure and dynamics of the tryptophan zipper 2 (TZ2) peptide. The TZ2 peptide is a 12 residue engineered sequence that employs the …
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Fantastic ribonucleoprotein complexes and how to study them. Architectural principles of regulatory assemblies in bacteria.
… X-ray solution scattering (SAXS) combined with conformational ensemble computation indicates that the truncated degradosome is a highly flexible system with extended scaffold domains but can adopt more compact conformations when 9S rRNA is bound. Complementary cryo-EM studies of the catalytic …
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Organised Chaos: defining different degrees of intrinsic disorder by molecular dynamics methods
… which results in an enrichment of the disordered conformational ensemble with secondary structure motifs that may act as molecular recognition features (MoRFs), or nucleation sites. According to this hypothesis, specific MoRFs are recognized by receptors and fold upon binding, within a scheme that …
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