Thesis (Ph. D.)--West Virginia University, 2004. / Title from document title page. Document formatted into pages; contains xv, 181 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references.

Thesis (Ph. D.)--University of Virginia, 1998. / Energy coupling in the F₀F₁ ATP synthase. Includes bibliographical references (p. 160-178). Also available online through Digital Dissertations.

Thèse (Ph. D.)--Université Laval, 2008. / Bibliogr.: f. [162]-185. Publié aussi en version électronique dans la Collection Mémoires et thèses électroniques.

Thesis (Ph. D.)--University of Washington, 2005. / Vita. Includes bibliographical references (leaves 101-112).

Thesis (Ph. D.)--University of Florida, 2004. / Typescript. Title from title page of source document. Document formatted into pages; contains 258 pages. Includes vita. Includes bibliographical references.

Les protéines de la famille des AAA+ ATPases sont présentes dans de nombreux complexes moléculaires. Ces protéines sont capables de s’assembler en anneaux héxamériques (homomères ou hétéromères) pour former des moteurs moléculaires. Au cours de ma thèse, je me suis particulièrement intéressé à deux complexes macromoléculaires à AAA+ ATPases présentant un grand intérêt thérapeutique contre différents cancers : la particule régulatrice du protéasome 26S et l’hélicase du réplisome, Mcm2-7. Le protéasome 26S est la principale machinerie moléculaire impliquée dans la dégradation régulée des protéines poly-ubiquitinées tandis que l’hélicase mcm 2-7 est responsable du désappariement des brins de l’ADN chromosomique lors de la réplication de l’ADN. Ces deux complexes comprennent un anneau hétérohéxamérique de sous-unités AAA+ ATPases appelé Rpt1 à Rpt6 dans le cas du protéasome 26S et Mcm2 à Mcm7 dans le cas de l’hélicase mcm2-7. J’ai focalisé mes travaux sur l’étude du rôle du chaperon Hsm3/S5b dans l’assemblage du protéasome 26S d’une part, et le rôle spécifique de la sous-unité Mcm2 dans le transfert intergénérationnel des histones d’autre part. Le chaperon Hsm3/S5b se lie avec la sous-unité Rpt1. L’étude des complexes de levure Hsm3-Rpt1 et humain S5b-Rpt1 par cristallographie aux rayons X m’a permis de proposer que le chaperon d’Hsm3/S5b pourrait jouer un rôle de médiateur entre les sous-unités Rpt1, Rpt2 et Rpn1 lors de l’assemblage de la particule régulatrice. De plus, ce chaperon pourrait jouer également un rôle d’inhibiteur pour l’assemblage entre la particule régulatrice 19S et la particule cœur 20S du protéasome 26S. Certaines sous-unités AAA+ ATPase, telles que celles du réplisome, possèdent des domaines additionnels, leur conférant un rôle secondaire spécifique et indépendant de leur rôle principal de moteur moléculaire. C’est le cas de Mcm2, qui lie les histones H3-H4 par son domaine N-terminal. J’ai mis en évidence et caractériser cette interaction par différentes techniques biophysiques, en particulier la cristallographie aux rayons X, la RMN et le SEC-MALS. Ces résultats m’ont permis de proposer un modèle pour le transfert intergénérationnel des histones dans lequel Mcm2 joue un rôle crucial de chaperon moléculaire des histones directement intégré dans la machinerie de réplication. / AAA+ ATPases are involved in numerous molecular complexes. These proteins form homomeric or heteromeric hexamers and constitute molecular motors. During my Ph. D., I focused my work on two macromolecular complexes composed of AAA+ ATPases: the 26S proteasome regulatory particle and the Mcm2-7 helicase of the replisome. These complexes are implicated in the development of cancers and constitute interesting therapeutic targets. The 26S proteasome is the main machinery responsible for the regulated degradation of poly-ubiquitinated proteins and the helicase Mcm2-7 is responsible for the unwinding of the DNA during replication. These two complexes are composed of a heterohexameric ring of six AAA+ ATPases called Rpt1 to 6 for the 26S proteasome regulatory particle and Mcm2 to 7 for the replisome. I have studied the role of Hsm3/S5b in the assembly mechanism of the proteasome and the specific role of the subunit Mcm2 in the intergenerational transfer of the epigenetic information. X-ray structures of the complexes Hsm3-Rpt1 and S5b-Rpt1 allowed us to elucidate the dual functions of the assembly chaperone Hsm3/S5b which mediates the assembly of the subcomplex Rpt1-Rpt2-Rpn1 during the assembly of the regulatory particle. In addition, hsm3/S5b inhibits the association of a premature regulatory particle onto the core particle and protects the HbYX motif of Rpt1. Other AAA+ ATPases, like the replisome subunits, possess additional domains which confer specific roles. I also studied the interaction between the N-terminal domain of Mcm2 and the tetrameric form of histones H3-H4 by several methods like X-ray crystallography, NMR and SEC-MALS. I propose a model of the intergenerational transfer of histones H3-H4 in which Mcm2 plays a crucial role of molecular histones chaperone directly integrated in the replication machinery.

The aim of the present investigation was to determine whether a plasma membrane high affinity Ca²+-ATPase plays an integral role in the maintenance of cytoplasmic free Ca²+ in pancreatic acinar cells. To achieve this, the Ca²+-transport and Ca²+-ATPase activities were characterized and their properties compared. Plasma membranes from guinea-pig pancreatic acini were shown to contain an ATP-dependent high affinity Ca²+-pump and a high affinity Ca²+-dependent ATPase activity. In addition, a low affinity ATPase activity was also observed. The high affinity Ca²+-ATPase activity as well as the Ca²+-transport were found to be dependent on Mg²+, whereas the low affinity ATPase activity appeared to be inhibited by Mg²+. The high affinity ATPase activity was 7-fold greater in magnitude than the Ca²+-transport. Whereas the Ca²+-transport was very specific for ATP as a substrate, the high affinity Ca²+-ATPase showed little specificity for various nucleotide triphosphates. These data would suggest that the Ca²+-transport and the high affinity Ca²+-dependent ATPase in guinea-pig pancreatic acinar plasma membranes may be two distinct activities To further investigate whether the two activities were related, we investigated how the Ca²+-transport and Ca²+-ATPase activities were regulated by intracellular mediators. Regulation of the two activities by calmodulin, cyclic AMP-dependent protein kinase, Protein kinase C and inositol phosphates was investigated. Calmodulin failed to stimulate either activity. In addition, calmodulin antagonists, trifluoperazine and compound 48/80 produced a concentration-dependent inhibition of Ca²+-transport. These data suggested the presence of endogenous calmodulin. Both antagonists failed to influence the Ca²+-dependent ATPase activity. Experiments using boiled extracts from guinea-pig pancreatic acinar plasma membranes and erythrocyte plasma membranes Ca²+-ATPase confirmed the presence of endogenous calmodulin. The catalytic subunit of cyclic AMP-dependent protein kinase stimulated Ca²+ transport, suggesting that cyclic AMP may have a role in the regulation of Ca²+-pump-mediated Ca²+ efflux from pancreatic acini. Ca²+-dependent ATPase activity, on the other hand, was not affected by the catalytic subunit. HA 1004, a specific inhibitor of cAMP-dependent protein kinase, failed to inhibit the Ca²+-transport and Ca²+-dependent ATPase activities. Since, this inhibitor was also ineffective at inhibiting the catalytic-subunit-stimulated Ca²+ transport, it may be concluded that HA 1004 is ineffective in blocking the actions of cAMP-dependent protein kinase in pancreatic acinar plasma membranes. In our studies, purified protein kinase C, the phorbol ester TPA and the diacylglycerol derivative, SA-DG, failed to stimulate the Ca²+-uptake activity. However, these agents produced stimulation of the Ca²+-dependent ATPase activity in the presence of phosphatidylserine. CGP 41 251, a potent and selective inhibitor of protein kinase C, did not inhibit the Ca²+-transport or Ca²+-dependent ATPase activities. These observations suggest that protein kinase C may not be involved in the regulation of the plasma membrane Ca²+-pump in guinea-pig pancreatic acinar cells. These results also point to another difference between Ca²+-transport and the Ca²+-ATPase activities in guinea-pig pancreatic acinar plasma membranes. Neither inositol trisphosphate nor inositol tetrakisphosphate produced a statistically significant effect on Ca²+-uptake, suggesting that IP₃- and/or IP₄-mediated Ca²+ releasing pathways may not operate in the isolated guinea-pig pancreatic acinar plasma membrane vesicles. In summary, the results presented here provide evidence to suggest that the high affinity Ca²+-ATPase is not the biochemical expression of plasma membrane Ca²+-transport in panreatic acini. Our results imply a role for calmodulin and cAMP-dependent protein kinase, but not protein kinase C, in the regulation of Ca²+ efflux from pancreatic acinar cells. / Medicine, Faculty of / Anesthesiology, Pharmacology and Therapeutics, Department of / Graduate

In this work, the evolutionary biophysics approach is applied to the two of the largest protein superfamilies present in human genomes, namely P-loop fold nucleoside triphosphatases (P-loop NTPases) and G-protein coupled receptors (GPCRs). This approach combines comparative analysis of protein structures and sequences with molecular modeling techniques in order to reveal not only the conservation of particular residues among proteins within each superfamily but also their role in the fundamental mechanisms underlying common functions. The study of the hydrolysis activation mechanism in P-loop NTPases started with the molecular dynamics simulations of Mg-NTP complexes (Mg-ATP and Mg-GTP) in the presence of K+, NH4+, and Na+ ions. These simulations showed that in the presence of large cations (K+ and NH4+), the conformation of the phosphate chain of ATP and GTP is extended, with large distances between alpha- and gamma-phosphates. This conformation is similar to the shape of ATP and GTP molecules (or their analogs) in the crystal structures of various P-loop NTPases. To clarify the role of monovalent cations in P-loop NTPases, MD simulations were conducted for two cation-dependent GTPases: tRNA modification GTPase MnmE and translation factor EF-Tu. MD simulations of Mg-GTP/EF-Tu complex bound to the tRNA and ribosome fragment in the presence of K+ ions have shown consistent binding of a potassium ion from the solution between alpha- and gamma-phosphates (AG site), similar to the cation binding in MnmE and other cation-dependent P-loop GTPases. In both proteins, binding of K+ ion in the AG site led to the rotation of gamma-phosphate, making this group more eclipsed with alpha-phosphate. The new rotated position of gamma-phosphate was stabilized by a novel H-bond with the backbone nitrogen of the K-3 residue (relative to the ubiquitously conserved Lys) of the P-loop motif. The activation mechanism observed in MD simulations of MnmE and EF-Tu could be envisioned as basic for P-loop NTPases, as these cation-dependent proteins are among the most ancient members of the P-loop superfamily. This mechanism was used as a basis for extensive comparative analysis of representative proteins from all major classes of P-loop NTPases. Based on the established conservation and presence of the key features in active sites of P-loop NTPases, the chain of events where rotation of gamma-phosphate triggers the nucleophilic attack and gamma-phosphate cleavage has been proposed as the basic universal activation mechanism of NTP hydrolysis in P-loop NTPases. The second part of this work explores the activation of GPCRs as sodium-translocating receptors. Crystal structures of the novel Na-pumping microbial rhodopsin along with the recent avalanche of GPCR structures provided the basis for comparative structure analysis, focused on investigating the similarities in the Na-binding sites of the two superfamilies. Structure superposition of GPCRs and microbial rhodopsins (MRs) based on comparison of their Na-binding sites was used to produce structure-guided sequence alignments of the two superfamilies. The only residue universally conserved between the two superfamilies was Trp in the helix 6/F (Trp6.48 in GPCRs). In both families, the signaling mechanism directly involves this residue, which is likely to be an ancient feature inherited from the common ancestor of MRs and GPCRs – the Na-pumping light-activated rhodopsin. The similarity of GPCRs with light-activated sodium pumps endorses the suggestion that GPCRs may also function as Na+ ion translocators. A model of GPCR activation accompanied by translocation of Na+ was constructed to demonstrate how this mechanism can explain the voltage sensitivity of certain Class A GPCRs. Two modes of activation were modeled – one where Na+ ion is transported into the cytoplasm and the one where Na+ ion is expelled to the intracellular space. The two modes quantitatively describe the behavior of voltage-activated and voltage-suppressed GPCRs, respectively. Finally, further structure scrutiny and rotamer analysis provided a plausible pathway of Na+ transmembrane translocation through the helical bundle of GPCRs.

Complex biosynthetic pathways are required for the assembly and insertion of iron-sulfur (Fe-S) cluster cofactors. The four cluster biogenesis systems that have been discovered require at least one ATPase, but generally the function of nucleotide hydrolysis is understudied. In the cytosolic iron sulfur cluster assembly (CIA) system, responsible for delivering [Fe4-S4] cluster cofactors for cytosolic and nuclear enzymes, the assembly scaffold comprises two homologous ATPases, called Nbp35 and Cfd1 in Saccharomyces cerevisiae. Genetic studies have discovered that the ATPase sites are required for scaffold function in vivo, but in vitro studies have failed to reveal why. The ATPase sites of the Nbp35 and Cfd1 contain a conserved P-loop nucleotide-binding protein fold with a deviant Walker A motif. Known metal trafficking P-loop NTPases’ metallochaperone mechanisms rely on both nucleotide binding and hydrolysis to properly assemble and deliver metal cargo. Furthermore, P-loop NTPases with a deviant Walker A motif commonly serve as central regulatory switches whose hydrolysis activity is modulated by small molecule cargos and/or protein partners. Therefore, it is proposed that the role of Nbp35-Cfd1’s ATPase sites is to direct Fe-S cluster movement by regulating protein and metal cargo interactions. The goal of this thesis is to better understand the scaffold reaction cycle by investigating the metallochaperone mechanism through Nbp35-Cfd1’s protein communications with its ATPase sites. To do this, the identification of at least one nucleotide-dependent partner protein must first be discovered. Herein, in vitro methods have been developed to uncover the scaffold’s ATPase site regulation of protein interactions. We describe a qualitative affinity copurification assay and a quantitative analysis for evaluating the dissociation constant and the kcat and Km values for ATP hydrolysis for the scaffold–partner protein complex. Additionally, the execution of these ATPase assays in an anaerobic environment can be applied to study nucleotide hydrolases involved in metallocluster biogenesis. These in vitro methods are applied to Nbp35-Cfd1 and it is discovered that ATP binding and hydrolysis regulates Nbp35-Cfd1 binding with two CIA factors: Dre2, a reductase proposed to assist in Fe-S cluster assembly, and Nar1, an adaptor between the early and late CIA factors. Although reconstitution of the scaffold’s Fe-S clusters results in a two-fold increase in its ATPase activity, the Dre2 and Nar1 ATP hydrolysis stimulation is dampened, demonstrating that both the Fe-S cargo and partner proteins regulate the scaffold’s ATPase reaction cycle. Next, the domains required for binding and ATPase stimulation were identified for Nbp35-Cfd1 with its partner proteins Dre2 and Nar1. The C-terminal Fe-S binding domain of Dre2 is sufficient for ATPase stimulation, while the Nar1 requires both its N- and C-terminal Fe-S binding domains to activate Nbp35-Cfd1’s ATP hydrolysis. The N-terminal Fe-S binding domain of Nbp35 is dispensable for binding and ATPase stimulation of both Dre2 and Nar1. The CIA targeting complex protein Cia1, which binds to Nar1, competes off Nbp35-Cfd1, indicating a shared binding domain. This data both validates and refines the current working model of the CIA system. To test whether the communication between the ATPase and Fe-S cluster binding domains of the CIA scaffold functions in an analogous manner across multiple species, a preliminary analysis was completed for whether Chaetomium thermophilum and Homo sapien Nbp35-Cfd1 exhibit similar ATPase characteristics and partner protein interaction as their S. cerevisiae ortholog. Human and fungal Nbp35-Cfd1 exhibit ATP binding and demonstrate nucleotide-dependent interactions with Dre2 and Nar1, suggesting that these interactions in a similar manner to effectively communicate in the CIA pathway. Overall, our study uncovers striking similarities between the CIA pathway and other systems which exploit a deviant Walker A NTPase to coordinate complex, multiprotein processes. Identification of the scaffold’s partner proteins significantly advances our understanding as to why the Nbp35/MRP-type Fe-S cluster biogenesis proteins are nucleotide hydrolases. This work provides some mechanistic insight into the functions of these proteins and provides a roadmap for how to investigate this large and widely distributed family and other P-loop NTPase metallochaperones. / 2024-09-19T00:00:00Z

Le spermatozoïde, afin d'être en mesure de féconder l'ovule, doit subir une série de modifications membranaires et biochimiques, regroupées sous le terme capacitation. De ces modifications, une augmentation de la phosphorylation en tyrosine de certaines protéines spermatiques spécifiques ainsi qu'une augmentation du Ca²⁺ intracellulaire sont observées. Il a été démontré que la phosphorylation sur résidu tyrosine associée à la capacitation des spermatozoïdes est sous le contrôle étroit du Ca²⁺, de la voie AMPc/PKA et des dérivés actifs de l'oxygène. De plus, il a été montré que la libération des réservoirs de Ca²⁺ par la thapsigargine, un inhibiteur spécifique des Ca²⁺ -ATPase du réticulum endoplasmique et sarcoplasmique (SERCA), pouvait provoquer l'augmentation de la phosphorylation en tyrosine et ce, dépendante des tyrosines kinases de la famille de src. Tous ces éléments suggèrent qu' il y a une Ca²⁺-ATPase sensible à la thapsigargine présente dans les spermatozoïdes permettant l'accumulation de Ca²⁺ dans les réservoirs et qu'au moins un membre de la famille de src dont l'activité est Ca²⁺ -dépendante est présente dans les spermatozoïdes. Dans un premier temps, j'ai identifié la Ca²⁺-ATPase SERCA2. C'est la première étude qui démontre que ce type de Ca²⁺ -ATPase est présente dans les spermatozoïdes de mammifères. La présence de SERCA2 au niveau de l'acrosome dans les spermatozoïdes humains, murins et bovins, suggère que cette Ca2+ -ATPase puisse contrôler la [Ca2+]i en accumulant le Ca²⁺ au niveau de l'acrosome. Puisque src est modulée positivement par le Ca²⁺, j'ai vérifié sa présence et son rôle dans les spermatozoïdes humains. Dans cette étude, j'ai clairement démontré que l'activité de src est Ca²⁺ dépendante et modulée positivement par la voie AMPc/PKA. De plus, la kinase src semble active tout au long de la capacitation et pourrait donc contribuer à l'augmentation de la phosphorylation associée à la capacitation. Enfin, j'ai tenté d' identifier des substrats de src par deux approches différentes. L'identification de ces protéines permettra de mieux comprendre le rôle de cette tyrosine kinase dans les fonctions Ca²⁺ -dépendantes du spermatozoïde.