No description available.

No description available.

Escherichia coli transcription termination factor Rho is a hexameric RNA/DNA helicase that terminates transcription using energy derived from the hydrolysis of ATP. The ATP binding sites of Rho are located at the interfaces of adjoining subunit Cterminal domains and have the Walker A and B motifs, characteristic of many ATPases (Skordalakes & Berger, 2003; Richardson 2002). Available Rho crystal structures capture the protein with its active site in an open configuration that must close to permit ATP hydrolysis. Because of this, the identities of active site residues predicted to mediate ATP hydrolysis are uncertain. To determine which amino acids activate water, stabilize transition state, sense the γ- phosphoryl group, and coordinate the magnesium ion of MgATP, we have carried out site-specific mutagenesis on candidate residues which are conserved across bacterial species, and characterized the relevant properties of the mutant proteins. The residues chosen were E211 as the water activator, R212 as the γ sensor, R366 as the arginine finger, and D265 as the residue that coordinates Mg2+. Each mutant protein was investigated for its ability to oligomerize as hexamers, assayed for ATPase activity, ATP and RNA binding, and pre-steady-state kinetics. The results show that the mutant proteins form hexamers similarly as to wild type Rho. The RhoE211 mutants display at least a 200-fold lower activity as ATPases, bind both ATP and RNA with similar affinities as the wild type protein, and display no burst in pre-steady-state kinetics. RhoR212A protein has 20-fold lower activity as an ATPase compared to wild type Rho, binds ATP with at least a 50-fold weaker affinity, and RNA with a 2-fold higher KD compared to wild type Rho. RhoR366A functions as an ATPase with 50-fold lower activity, binds RNA with similar affinity as wild type Rho and binds ATP with a 5- fold weaker affinity. RhoD265N displays 150-fold lower ATPase activity compared to the wild type enzyme, binds ATP with a 10-fold weaker affinity, and binds RNA with similar affinity as wild type Rho. Pre-steady-state kinetics studies indicate that the mutant proteins investigated show no burst kinetics, indicating a failure or a significantly slower rate of the hydrolysis (chemistry) step. It is possible that the rate-limiting step is the chemistry step in these mutant proteins, contrary to the wild type protein where the chemistry step is much faster (300/s). Together, the results obtained are consistent with the proposed roles for these residues: E211 is involved in activating a water molecule, R212 functions as the γ sensor, R366 functions as the arginine finger and D265 is involved in coordination of the Mg2+ ion. This study has elucidated the mechanism of ATP hydrolysis, by determining some of the key residues involved in the hydrolysis reaction. This study is only a part of the characterization of the active site residues. There might be other residues involved in one or all of the functions proposed. Utilizing the findings from this study, other experiments and models can be implemented to understand how Rho hydrolyzes ATP and utilizes the energy to move along the RNA molecule and functions as a helicase. / Biochemistry

Actin is one of the most abundant and highly conserved proteins in eukaryotic cells. The globular protein assembles into long filaments, which form a variety of different networks within the cytoskeleton. The dynamic reorganization of these networks - which is pivotal for cell motility, cell adhesion, and cell division - is based on cycles of polymerization (assembly) and depolymerization (disassembly) of actin filaments. Actin binds ATP and within the filament, actin-bound ATP is hydrolyzed into ADP on a time scale of a few minutes. As ADP-actin dissociates faster from the filament ends than ATP-actin, the filament becomes less stable as it grows older. Recent single filament experiments, where abrupt dynamical changes during filament depolymerization have been observed, suggest the opposite behavior, however, namely that the actin filaments become increasingly stable with time. Several mechanisms for this stabilization have been proposed, ranging from structural transitions of the whole filament to surface attachment of the filament ends. The key issue of this thesis is to elucidate the unexpected interruptions of depolymerization by a combination of experimental and theoretical studies. In new depolymerization experiments on single filaments, we confirm that filaments cease to shrink in an abrupt manner and determine the time from the initiation of depolymerization until the occurrence of the first interruption. This duration differs from filament to filament and represents a stochastic variable. We consider various hypothetical mechanisms that may cause the observed interruptions. These mechanisms cannot be distinguished directly, but they give rise to distinct distributions of the time until the first interruption, which we compute by modeling the underlying stochastic processes. A comparison with the measured distribution reveals that the sudden truncation of the shrinkage process neither arises from blocking of the ends nor from a collective transition of the whole filament. Instead, we predict a local transition process occurring at random sites within the filament. The combination of additional experimental findings and our theoretical approach confirms the notion of a local transition mechanism and identifies the transition as the photo-induced formation of an actin dimer within the filaments. Unlabeled actin filaments do not exhibit pauses, which implies that, in vivo, older filaments become destabilized by ATP hydrolysis. This destabilization can be identified with an acceleration of the depolymerization prior to the interruption. In the final part of this thesis, we theoretically analyze this acceleration to infer the mechanism of ATP hydrolysis. We show that the rate of ATP hydrolysis is constant within the filament, corresponding to a random as opposed to a vectorial hydrolysis mechanism. / Aktin ist eines der am häufigsten vorkommenden und am stärksten konservierten Proteine in eukaryotischen Zellen. Dieses globuläre Protein bildet lange Filamente, die zu einer großen Vielfalt von Netzwerken innerhalb des Zellskeletts führen. Die dynamische Reorganisation dieser Netzwerke, die entscheidend für Zellbewegung, Zelladhäsion, und Zellteilung ist, basiert auf der Polymerisation (dem Aufbau) und der Depolymerisation (dem Abbau) von Aktinfilamenten. Aktin bindet ATP, welches innerhalb des Filaments auf einer Zeitskala von einigen Minuten in ADP hydrolysiert wird. Da ADP-Aktin schneller vom Filamentende dissoziiert als ATP-Aktin, sollte ein Filament mit der Zeit instabiler werden. Neuere Experimente, in denen abrupte dynamische Änderungen während der Filamentdepolymerisation beobachtet wurden, deuten jedoch auf ein gegenteiliges Verhalten hin: Die Aktinfilamente werden mit der Zeit zunehmend stabiler. Mehrere Mechanismen für diese Stabilisierung wurden bereits vorgeschlagen, von strukturellen Übergängen des gesamten Filaments bis zu Wechselwirkungen der Filamentenden mit dem experimentellen Aufbau. Das zentrale Thema der vorliegenden Dissertation ist die Aufklärung der unerwarteten Unterbrechungen der Depolymerisation. Dies geschieht durch eine Kombination von experimentellen und theoretischen Untersuchungen. Mit Hilfe neuer Depolymerisationexperimente mit einzelnen Filamenten bestätigen wir zunächst, dass die Filamente plötzlich aufhören zu schrumpfen und bestimmen die Zeit, die von der Einleitung der Depolymerisation bis zum Auftreten der ersten Unterbrechung vergeht. Diese Zeit unterscheidet sich von Filament zu Filament und stellt eine stochastische Größe dar. Wir untersuchen daraufhin verschiedene hypothetische Mechanismen, welche die beobachteten Unterbrechungen verursachen könnten. Die Mechanismen können experimentell nicht direkt unterschieden werden, haben jedoch verschiedene Verteilungen für die Zeit bis zur ersten Unterbrechung zur Folge. Wir berechnen die jeweiligen Verteilungen, indem wir die zugrundeliegenden stochastischen Prozesse modellieren. Ein Vergleich mit der gemessenen Verteilung zeigt, dass der plötzliche Abbruch des Depolymerisationsprozesses weder auf eine Blockade der Enden, noch auf einen kollektiven strukturellen Übergang des gesamten Filaments zurückzuführen ist. An Stelle dessen postulieren wir einen lokalen Übergangsprozess, der an zufälligen Stellen innerhalb des Filaments auftritt. Die Kombination von weiteren experimentellen Ergebnissen und unserem theoretischen Ansatz bestätigt die Vorstellung eines lokalen Übergangsmechanismus und identifiziert den Übergang als die photo-induzierte Bildung eines Aktindimers innerhalb des Filaments. Nicht fluoreszenzmarkierte Aktinfilamente zeigen keine Unterbrechungen, woraus folgt, dass ältere Filamente in vivo durch die ATP-Hydrolyse destabilisiert werden. Die Destabilisierung zeigt sich durch die Beschleunigung der Depolymerisation vor der Unterbrechung. Im letzten Teil der vorliegenden Arbeit untersuchen wir diese Beschleunigung mit theoretischen Methoden, um auf den Mechanismus der ATP-Hydrolyse zu schließen. Wir zeigen, dass die Hydrolyserate von ATP innerhalb des Filaments konstant ist, was dem sogenannten zufälligen Hydrolysemechanismus entspricht und im Gegensatz zum sogenannten vektoriellen Mechanismus steht.

Cholera toxin (CT) moves from the cell surface to the endoplasmic reticulum (ER) where the catalytic CTA1 subunit separates from the holotoxin and unfolds due to its intrinsic thermal instability. Unfolded CTA1 then moves through an ER translocon pore to reach its cytosolic target. Due to the instability of CTA1, it must be actively refolded in the cytosol to achieve the proper conformation for modification of its G protein target. The cytosolic heat shock protein Hsp90 is involved with the ER-to-cytosol translocation of CTA1, yet the mechanistic role of Hsp90 in CTA1 translocation remains unknown. Potential post-translocation roles for Hsp90 in modulating the activity of cytosolic CTA1 are also unknown. Here, we show by isotope-edited Fourier transform infrared (FTIR) spectroscopy that Hsp90 induces a gain-of-structure in disordered CTA1 at physiological temperature. Only the ATP-bound form of Hsp90 interacts with disordered CTA1, and its refolding of CTA1 is dependent upon ATP hydrolysis. In vitro reconstitution of the CTA1 translocation event likewise required ATP hydrolysis by Hsp90. Surface plasmon resonance (SPR) experiments found that Hsp90 does not release CTA1, even after ATP hydrolysis and the return of CTA1 to a folded conformation. The interaction with Hsp90 allowed disordered CTA1 to attain an active state and did not prevent further stimulation of toxin activity by ADP-ribosylation factor 6, a host cofactor for CTA1. This activity is consistent with its role as a chaperone that refolds endogenous cytosolic proteins as part of a foldosome complex consisting of Hsp90, Hop, Hsp40, p23, and Hsc70. A role for Hsc70 in CT intoxication has not yet been established. Here, biophysical, biochemical, and cell-based assays demonstrate Hsp90 and Hsc70 play overlapping roles in the processing of CTA1. Using SPR we determined that Hsp90 and Hsc70 could bind independently to CTA1 at distinct locations with high affinity, even in the absence of the Hop linker. Studies using isotope-edited FTIR spectroscopy found that, like Hsp90, Hsc70 induces a gain-of-structure in unfolded CTA1. The interaction between CTA1 and Hsc70 is essential for intoxication, as an RNAi-induced loss of the Hsc70 protein generates a toxin-resistant phenotype. Further analysis using isotope-edited FTIR spectroscopy demonstrated that the addition of both Hsc70 and Hsp90 to unfolded CTA1 produced a gain-of-structure above that of the individual chaperones. Our data suggest that CTA1 translocation involves a ratchet mechanism which couples the Hsp90-mediated refolding of CTA1 with extraction from the ER. The subsequent binding of Hsc70 further refolds CTA1 in a manner not previously observed in foldosome complex formation. The interaction of CTA1 with these chaperones is essential to intoxication and this work elucidates details of the intoxication process not previously known.