ATPase

Summary

ATPases (, Adenosine 5'-TriPhosphatase, adenylpyrophosphatase, ATP monophosphatase, triphosphatase, SV40 T-antigen, ATP hydrolase, complex V (mitochondrial electron transport), (Ca2+ + Mg2+)-ATPase, HCO3−-ATPase, adenosine triphosphatase) are a class of enzymes that catalyze the decomposition of ATP into ADP and a free phosphate ion or the inverse reaction. This dephosphorylation reaction releases energy, which the enzyme (in most cases) harnesses to drive other chemical reactions that would not otherwise occur. This process is widely used in all known forms of life. Some such enzymes are integral membrane proteins (anchored within biological membranes), and move solutes across the membrane, typically against their concentration gradient. These are called transmembrane ATPases. Functions Transmembrane ATPases import metabolites necessary for cell metabolism and export toxins, wastes, and solutes that can hinder cellular processes. An important example is the sodium-potas

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Human tuberculosis (TB) is a frequently fatal lung disease mostly caused by Mycobacterium tuberculosis (M. tb), a slow-growing intracellular pathogen. M. tb utilizes the ESX-1 secretion system, classified as type VII, to export the virulence factors needed for host infection and pathogenesis. A functional ESX-1 pathway largely involves the proteins encoded by two gene clusters, esx-1 and espACD. These proteins are diverse in functions, such as cytolysis, immunogenicity, pore forming, stabilization and energization. Although many of the ESX-1 associated proteins were characterized individually, the overall mechanism of ESX-1 secretion is still far from clear. The main objective of my thesis is to better understand the structure and function of the ESX-1 secretion system in M. tb. To achieve this, an integrated approach which combines biochemistry, biophysics and genetics was applied. The experimental results are organized into three parts, in which I investigated EspC, EccCb1 and the effect of calcium on ESX-1 secretion. Firstly, the focus of this thesis is EspC, a secreted protein encoded in the espACD operon which is not linked to the esx-1 locus, but mediates ESX-1-associated virulence. Based on what I observed from a series of experiments, we propose a novel working model of the ESX-1 apparatus, in which EspC interacts with EspA in the cytosol and then translocates across the membrane to assemble into a channel in the outer membrane and spans the capsular layer of M. tb. This model could explain the mechanism by which the major virulence factors EsxA and EsxB (also named ESAT-6 and CFP-10) rely on EspC for secretion. Moreover, EspC is a potential outer membrane pore protein which has not been previously identified in M. tb. Secondly, the putative ATPase EccCb1 is another protein that was studied. EccCb1 is predicted as an ATPase that targets the EsxA/EsxB heterodimer during translocation. EccCb1 was overexpressed and purified in the form of a NusA- EccCb1 fusion protein due to its low stability. The protein was characterized as a hexamer with an ATPase activity. This result confirms that EccCb1 belongs to the FtsK/SpoIIIE ATPase family. Thirdly, we observed that ESX-1 secretion can be inhibited by a high concentration of calcium (~500 ÎŒM) in the culture medium. Moreover, bacterial persistence, rather than growth rate, decreased with the elevated calcium. RNA- seq was performed to evaluate the changes of global gene expression of M. tb in the presence of high calcium levels. Surprisingly, calcium dramatically repressed hypoxia response genes in the DevRS regulon, leading to reduced persistence. I also include a section that describes the additional work I was involved with, in which we investigated the activation of cGAS-dependent host response by ESX-1. Taken together, these findings provide new insights into the structural and functional aspects of ESX-1 secretion system, and will contribute to discovery of ESX-1 inhibitors with potential applications in TB therapy.

EPFL2016

Non-equilibrium kinetics and trajectory thermodynamics of synthetic molecular pumps

Cristian Pezzato

A major goal in the design of synthetic molecular machines is the creation of pumps that can use the input of energy to transport material from a reservoir at low chemical potential to a different reservoir at higher chemical potential, thereby forming and maintaining a chemical potential gradient. Such pumps are ubiquitous in biology. Some, including the Ca+2-ATPase of the sarcoplasmic reticulum, and the (Na+,K+)-ATPase found in the membranes of almost all cells, use energy from ATP hydrolysis to accomplish this task. Others, such as bacteriorhodopsin, use energy from light. Here, we examine in the context of recent artificial molecular pumps, the kinetics and thermodynamics of both light or externally driven pumps on the one hand and pumps driven by chemical catalysis on the other. We show that even for formally similar mechanisms there is a tremendous difference in the design principles for these two classes of pumps, where the former can function as energy ratchets, and the latter must operate as information ratchets. This difference arises because, unlike optically or externally driven pumps, the transition constants for pumps in which the required energy is provided by catalysis of a chemical reaction obey the principle of microscopic reversibility. We use cycle kinetics developed by Terrell Hill in the analysis of energy driven pumping. This approach is based on the trajectory thermodynamics of Onsager and Machlup. The recent "stochastic thermodynamic" approach is shown to be fundamentally flawed and to lead to incorrect predictions regarding the behavior of molecular machines driven by catalysis of an exergonic chemical reaction.

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Characterization of Coenzyme Q Biosynthesis Proteins through Integrative Modeling at the Protein-Membrane Interface

Deniz Aydin

Integral and peripheral membrane proteins account for one-third of the human proteome, and they are estimated to represent the target for over 50% of modern medicinal drugs. Despite their central role in medicine, the complex, heterogeneous and dynamic nature of biological membranes complicates the investigation of their mechanism of action by both experimental and computational techniques. Among the different membrane bound compartments in eukaryotic cells, mitochondria are highly complex in form and function, and they harbor a unique proteome that remains largely unexplored. A growing number of inherited metabolic diseases are associated with mitochondrial dysfunction, which necessitates the structural and functional elucidation of mitochondrial proteins. In this thesis, we combine experimental and computational methods to explore the activity of COQ8 and COQ9, two functionally elusive proteins of the biosynthetic complex that produces coenzyme Q, a redox-active lipid component of the mitochondrial electron transport chain. (i) Conserved Lipid Modulation of Ancient Kinase-Like UbiB Family Member COQ8. We demonstrate that COQ8 has an ATPase function that is activated when it specifically associates with cardiolipin-containing membranes. We identify its interaction surface with the inner mitochondrial membrane, which gives hints about the possible interaction surfaces with other members of the coenzyme Q synthesis machinery and has implications on how it mediates functional interactions with lipids. Collectively, this work reveals how the positioning of COQ8 on the inner mitochondrial membrane is key to its activation, and therefore advances our understanding of the COQ8 function. (ii) Membrane, Lipid, and Protein Interactions of Coenzyme Q Biosynthesis Protein COQ9. We explore the lipid binding activity of COQ9, and we reveal that COQ9 repurposes an ancient bacterial fold to selectively bind aromatic isoprenes, including CoQ intermediates that reside within the bilayer. We elucidate the mechanistic details of its membrane binding process, by which COQ9 warps the membrane surface and creates a tightly sealed hydrophobic region to access its lipid cargo. Finally, we establish a potential molecular interface between COQ9 and COQ7, the enzyme that catalyzes the penultimate step in CoQ biosynthesis, suggesting a model whereby COQ9 presents intermediates to CoQ enzymes to overcome the hydrophobic barrier of the membrane. Collectively, our results provide a mechanism for how a lipid binding protein might access, select, and extract specific cargo from a membrane and present it to a peripheral membrane enzyme. In conclusion, our work is a good illustration of the interplay between experiment and modeling in protein research and specifically in understanding how proteins perform their action in direct synergy with membrane environments. We anticipate our integrative methodologies and mechanistic findings will prove relevant to other membrane proteins, whose fine functional modulation at the membrane-water interface has been historically challenging to characterize.

EPFL2019

Characterization of Coenzyme Q Biosynthesis Proteins through Integrative Modeling at the Protein-Membrane Interface

Deniz Aydin

EPFL2019

EPFL2016