No description available.

No description available.

No description available.

Protein folding pathways can be extraordinarily complex. In this study, circular dichroism (CD) and 19F NMR are used to investigate the folding network of calmodulin, a calcium-binding protein, which is biosynthetically enriched with 3-fluorophenylalanine. In calmodulin’s calcium-loaded state, CD experiments identify the existence of a folding intermediate along a heat-denaturation pathway. In comparison to the native state, 19F NMR solvent isotope shifts reveal decreased accessibility of water to hydrophobic core, whereas O2 paramagnetic shifts show increased hydrophobicity of this folding intermediate. 15N-1H and methyl 13C-1H HSQC NMR spectra demonstrate that this folding intermediate retains a near-native tertiary structure, whose hydrophobic interior is highly dynamic. 19F NMR CPMG relaxation dispersion measurements suggest that this near-native intermediate state is transiently adopted below the temperature associated with its onset. The folding network also involves an unproductive off-pathway intermediate. In contrast, calmodulin’s calcium-free state exhibits a simpler folding process which lacks discernible intermediates.

In order to rationally optimize a reaction, it is necessary to have a thorough understanding of its mechanism. Consequently, great effort has been made to elucidate a variety of reaction mechanisms. However, the fundamental ideas needed to understand reaction mechanisms are not yet fully developed. Throughout the literature, one encounters numerous examples of experimental observations that are not explainable by conventional mechanistic ideas and methods. The research described in this dissertation employs a unique approach towards the identification and analysis of systems whose observations cannot be explained by conventional transition state theory (TST). The nucleophilic substitution of 4,4-dichloro-but-3-en-2-one by sodium-para-tolyl-thiolate was explored. It was deduced that the reaction was concerted and consequently, the product selectivity observed in the reaction cannot be explained by TST. Dynamic effects play a major role in the observed selectivity and this is further supported by the results of dynamic trajectory simulations. Using computational studies, the ethanolysis of symmetric aryl carbonates was also shown to be concerted, provided that the substrate possesses good leaving groups. Furthermore, extensive precedence has been set by Gutthrie, Santos, Schelgel, and others, detailing concerted substitutions at acyl carbon. The Fujiwara hydroarylation is thought to occur by either a C-H activation mechanism or an electrophilic aromatic substitution (EAS). The KIEs associated with this reaction have been determined and provide strong support for the latter. Computational studies also displayed fair agreement with experimentally determined KIEs, further supporting the EAS mechanism. Isotopic perturbation of equilibria is invaluable in helping to determine whether a structure exists as a single structure or whether it is a time average of two equilibrating structures. The bromonium cation of tetramethylethylene and hydrogen pthalate have been wrongly reported as existing as equilibrating structures. The time averaged geometries have been determined in each case, via a variety of methods and the myth of equilibrating structures in the above cases has been debunked.

<p>We present a computational structure-based redesign of the phenylalanine adenylation domain of the non-ribosomal peptide synthetase (NRPS) enzyme gramicidin S synthetase A (GrsA-PheA) for a set of non-cognate substrates for which the wild-type enzyme has little or virtually no specificity. Experimental validation of a set of top-ranked computationally-predicted enzyme mutants shows significant improvement in the specificity for the target substrates. We further present enhancements to the methodology for computational enzyme redesign that are experimentally shown to result in significant additional improvements in the target substrate specificity. The mutant with the highest activity for a non-cognate substrate exhibits 1/6 of the wild-type enzyme/wild-type substrate activity, further confirming the feasibility of our computational approach. Our results suggest that structure-based protein design can identify active mutants different from those selected by evolution.</p><p>Knowledge about the structures of individual domains and domain interactions can further our redesign of the NRPS enzymes for new bioactive nature product. So far, little structure information has been available for the auxiliary domains such as the epimerization domains and how they interact with the NRPS modules. Solution structure studies by nuclear magnetic resonance (NMR) provide advantages for understanding the dynamics of the domains and reveal active conformations that sometimes are not represented by the crystal structures. However, the large size of the NRPS proteins present challenges for structure studies in solution. In chapter 3, we study the solution structure of the 56 kDa epimerization domain of GrsA (GrsA-PheE) by NMR. We use multidimensional backbone resonance experiments as well as specific labeling strategy to assign the backbone resonances of GrsA-PheE. Secondary structures are determined by sets of residual dipolar couplings (RDCs) measured in multiple alignment media. To determine the global fold of the protein, we obtain long-range distance restraints by measuring the paramagnetic relaxation enhancements (PREs) from 15 site-directed spin labeling samples. </p><p>In chapter 4, we investigate the redox regulation of phosphatases. The activity levels of protein tyrosine phosphatases (PTPs) in cells are highly regulated in various ways including by phosphorylation, localization and protein-protein interaction. Additionally, redox-dependent modification has emerged as a critical part in attenuating PTPs activity in response to cellular stimuli. The tandem Src homology 2 domain-containing PTPs (SHPs) belong to the family of nonreceptor PTPs. The activity level of SHPs is highly regulated by interaction of SH2 domain, phosphorylation level of C-terminal tail and by reversible oxidation. In vivo evidence has shown the reversible oxidation of catalytic cysteine inhibits SHPs activity transiently as a result, affecting the phosphorylation level of its target proteins. In this chapter, we investigate in vitro the reversible oxidation of full-length and catalytic domain of SHP-1 and SHP-2 by using kinetic measurements and mass spectrometry. We have confirmed the susceptibility of the active site cysteines of SHPs to oxidative inactivation, with rate constants for oxidation similar to other PTPs (2-10 M-1s-1). Both SHP-1 and SHP-2 can be reduced and reactivated with the reductants DTT and gluthathione, whereas only the catalytic domain of SHP-2 is subject to reactivation by thioredoxin. Unlike PTPs whose oxidation contains a catalytic cysteine disulfide bonding to a backdoor cysteine or forms a sulfenylamide bonding to nearby backbone nitrogen, we have found that in the reversibly oxidized SHPs, the catalytic cysteines is re-reduced while two conserved backdoor cysteines form a disulfide linkage. Knocking out either of the backdoor cysteine preserves the reversibility of the oxidized SHPs with a disulfide formation between the catalytic cysteine and the remaining backdoor cysteine. However, removal of both backdoor cysteines leads to irreversible oxidative inactivation, demonstrating that these two cysteines are necessary and sufficient for ensuring reversible oxidation of the SHPs. Our results extend the mechanisms by which redox regulation of PTPs is used to modulate intracellular signaling pathways.</p> / Dissertation

No description available.

Das Thema dieser Arbeit ist die Sensitivitätserhöhung der Kernspinmagnetresonanzspektroskopie (NMR-Spektroskopie) für die Anwendung an biologischen Systemen durch dynamische Kernspinpolarisation (DNP). Dementsprechend wurden die experimentellen Bedingungen möglichst ähnlich zu einer physiologischen Umgebung in Lösung gewählt. Unter diesen Voraussetzungen ist der Overhauser-Effekt der zentrale Mechanismus für DNP. Dieser ist von der relativen Diffusion zwischen den Kernspins des Zielmoleküls und dem polarisierenden Molekül, welchesein ungepaartes Elektron aufweist, abhängig. Als experimenteller Ansatz für diese Arbeit wurde ein Shuttle-DNP-Spektrometer mit Proben im flüssigen Zustand ausgewählt. Hierbei wurden die Kernspins bei einem Magnetfeld von 0,34 T polarisiert und für eine hoch auflösende NMR-Detektion in ein Magnetfeld von 14,09 T transferiert. Mehrere technische Anpassungen, welche zu einer Erhöhung der Stabilität und Reproduzierbarkeit der Messungen führten, wurden sukzessiv implementiert. Für die Signale der Protonen von L-Tryptophan wurde im Hochfeld eine DNP-Verstärkung εhf von bis zu -2,4 (H^η2) gemessen. Darauf aufbauend wurde ein allgemeiner Verstärkungsfaktor εglobal eingeführt. Dieser beinhaltete sowohl die Vorteile des Shuttle-DNP-Spektrometers, wie beispielsweise die schnellere Aufnahmerate der DNP-Experimente als auch die Nachteile, wie etwa die Linienverbreiterung der Signale durch die Gegenwart des polarisierenden Radikals. Anschließend wurde dieser Faktor schrittweise auf eindimensionale Messungen angewandt und an diese angepasst. Hierfür wurden die Aufbaurate der Polarisation und die Aufnahmezeit der Messungen mit DNP und Boltzmann-Polarisation optimiert, um das maximale Signal-zu-Rauschen-Verhältnis pro Messzeit zu erhalten. Diese Parameter basieren auf T1 bzw. T2∗. Das Ergebnis dieser Schritte war ein angewandter, allgemeiner Verstärkungsfaktor εapp von -4.0 für Hδ1 von L-Tryptophan. Des Weiteren wurden die Kernspineigenschaften von Protonen für DNP, wie z.B.die Relaxationsraten, gemessen und miteinander verglichen. Der daraus abgeleitete Kopplungsfaktor implizierte, dass die intermolekulare, dipolare Wechselwirkung zwischen den Kernspins des Zielmoleküls und dem Elektron des polarisierenden Radikals von der räumlichen Zugänglichkeit der Kernspins beeinflusst wurde. Zudem wurde gezeigt, dass diese Wechselwirkung am besten durch ein Model basierend auf translatorischer Diffusion beschrieben werden konnte. Mit diesem wurde der Abstand der dichtesten Annährung zwischen den Kernspins und dem ungepaartem Elektron bestimmt. Diese Abstände reichen entsprechend der Zugänglichkeit des jeweiligen Protons von 3 bis 5 Å. Darauf aufbauend wurden die DNP-Verstärkungen für Kohlenstoff gemessen. Für deuteriertes L-Tryptophan-d8,15N2,13C11 wurden Verstärkungen zwischen -0,3 und -2,5 erzielt. Durch weitere Berechnungen wurde gezeigt, dass diese Verstärkungen mit den zuvor berechneten Abständen der dichtesten Annäherung der Protonen übereinstimmten und dadurch den Ansatz des Models der translatorischen Diffusion untermauerten. In weiteren Messungen an protoniertem L-Tryptophan-15N2,13C11 wurde der Drei-Spin-Effekt erstmalig bei einem gelösten Molekül beobachtet. Dieser Effekt basierte auf der dipolaren Wechselwirkung zwischen den Spins der Protonen, Kohlenstoffkerne und Radikal-Elektronen. Er verursachte positive Signalverstärkungen von bis zu 2,3 für alle Kohlenstoffe außer dem Carbonyl-Kohlenstoff, welcher eine Signalverstärkung von -2,5 aufwies. Diese Ergebnisse waren in Übereinstimmung mit einem erweiterten Kopplungsfaktor, der die intramolekulare Wechselwirkung zwischen Kohlenstoff und Proton neben der zwischen Kohlenstoff und Elektron berücksichtigte. In einem abschließenden Schritt wurden DNP-Experimente an einem Protein (Ubiquitin-U-15N,U-13C) durchgeführt. Zu diesem Zweck wurden zweidimensionale Shuttle-DNP-1H-13C-HSQC-Spektren aufgenommen. Zum ersten Mal konnte ein DNP-Transfer zu der Oberfläche eines Proteins in Lösung nachgewiesen werden.

<p>Recent work has shown that hyperpolarized magnetic resonance spectroscopy (HP-MRS) can trace in vivo metabolism of biomolecules and is therefore extremely promising for diagnostic imaging. The most severe challenge this technique faces is the short signal lifetime for hyperpolarization, which is dictated by the spin-lattice (T1) relaxation. In this thesis we show with theory, simulation and experiment that the long-lived nuclear spin states in chemically equivalent or near equivalent spin systems offer a solution to this problem. Spin polarization that has lifetime much longer than T1 (up to 70-fold) has been demonstrated with pulse sequence techniques that are compatible with clinical imaging settings. Multiple classes of molecules have been demonstrated to sustain such long-lived hyperpolarization.</p> / Dissertation

Solid state ¹H MAS NMR spectroscopy was used to investigate the temperature and hydration dependance of water and hydroxyl proton spectra of hydrated mesoporous MCM-41. The NMR spectra show a complex peak structure, with hydroxyl proton resonances seen in dry MCM-41 disappearing as water is introduced into the pores, and new peaks appearing representing water and hydrated silanol groups. Until now the assignment of these peaks was unclear and the consensus was that magnetization exchange played an important role in the coalescence of the various peaks which appear in the spectra. It was found recently that magnetization exchange is not necessary to produce the spectral featured observed [Niknam, M., M.Sc. Thesis, University of Waterloo (2010)]. In the present study a simplified model, based on chemical shift averaging by the making and breaking of hydrogen bonds as water undergoes rotational motion and translational self-diffusion on the pore surface, has been developed to explain the NMR spectral results. The model is able to reproduce the experimental ¹H MAS NMR spectra for all hydrations and temperatures studied. For the first time, definitive spectral assignments for all hydroxyl and water protons in the sample has been achieved. Spectral features arising due to temperature change have been explained by using the known result that the proton chemical shift of a hydrogen atom involved in hydrogen bonding varies linearly with temperature. Furthermore, it is reported for the first time, that with increasing hydration, water molecules begin to favour forming two hydrogen bonds to the surface. This may represent the first step in the pore filling process.