register interest

Dr Katharina Duerr

Research Area: Ion Channels and Disease (PROPOSED)
Technology Exchange: Crystallography, Drug discovery and Microscopy (EM)
Scientific Themes: Physiology, Cellular & Molecular Biology and Genetics & Genomics
Keywords: Membrane Protein Structural Biology

Membrane-embedded enzymes, receptors, channels and transporters are key regulators of essential cellular processes, such as metabolism, intercellular signalling and transport - making them prime targets for drug development. Despite their importance, structural information is limited, because membrane proteins are notoriously difficult to purify in large quantities and it is challenging to maintain their functional activity for structural studies.

The Membrane Protein Structure & Function (MPSF) group at the Structural Genomics Consortium (SGC) uses high-throughput screening methods to identify suitable candidates for structural studies from a large pool of human membrane proteins and their non-human homologues. After optimization of purification conditions in small-scale experiments and functional characterization, promising target proteins are produced in large quantities for structural studies, using X-ray crystallography or single-particle cryo-electron microscopy (cryo-EM). The molecular architecture determined by these methods can provide novel mechanistic insights into the function of membrane proteins and into their interactions with small molecule drugs, native ligands and substrates, and interacting proteins.

There are no collaborations listed for this principal investigator.

Chen L, Durr KL, Gouaux E. 2014. X-ray structures of AMPA receptor-cone snail toxin complexes illuminate activation mechanism Science, 345 (6200), pp. 1021-1026. | Read more

Dürr KL, Chen L, Stein RA, De Zorzi R, Folea IM, Walz T, Mchaourab HS, Gouaux E. 2014. Structure and dynamics of AMPA receptor GluA2 in resting, pre-open, and desensitized states. Cell, 158 (4), pp. 778-792. | Show Abstract | Read more

Ionotropic glutamate receptors (iGluRs) mediate the majority of fast excitatory signaling in the nervous system. Despite the profound importance of iGluRs to neurotransmission, little is known about the structures and dynamics of intact receptors in distinct functional states. Here, we elucidate the structures of the intact GluA2 AMPA receptor in an apo resting/closed state, in an activated/pre-open state bound with partial agonists and a positive allosteric modulator, and in a desensitized/closed state in complex with fluorowilliardiine. To probe the conformational properties of these states, we carried out double electron-electron resonance experiments on cysteine mutants and cryoelectron microscopy studies. We show how agonist binding modulates the conformation of the ligand-binding domain "layer" of the intact receptors and how, upon desensitization, the receptor undergoes large conformational rearrangements of the amino-terminal and ligand-binding domains. We define mechanistic principles by which to understand antagonism, activation, and desensitization in AMPA iGluRs.

Dürr KL, Tavraz NN, Spiller S, Friedrich T. Measuring Cation Transport by Na,K- and H,K-ATPase in <em>Xenopus</em> Oocytes by Atomic Absorption Spectrophotometry: An Alternative to Radioisotope Assays Journal of Visualized Experiments, (72), | Read more

Dürr KL, Tavraz NN, Friedrich T. Control of Gastric H,K-ATPase Activity by Cations, Voltage and Intracellular pH Analyzed by Voltage Clamp Fluorometry in Xenopus Oocytes PLoS ONE, 7 (3), pp. e33645-e33645. | Read more

Dürr KL, Seuffert I, Friedrich T. 2010. Deceleration of theE1P-E2P Transition and Ion Transport by Mutation of Potentially Salt Bridge-forming Residues Lys-791 and Glu-820 in Gastric H+/K+-ATPase Journal of Biological Chemistry, 285 (50), pp. 39366-39379. | Read more

Meier S, Tavraz NN, Dürr KL, Friedrich T. 2010. Hyperpolarization-activated inward leakage currents caused by deletion or mutation of carboxy-terminal tyrosines of the Na+/K+-ATPase α subunit The Journal of General Physiology, 135 (2), pp. 115-134. | Show Abstract | Read more

<jats:p>The Na<jats:sup>+</jats:sup>/K<jats:sup>+</jats:sup>-ATPase mediates electrogenic transport by exporting three Na<jats:sup>+</jats:sup>ions in exchange for two K<jats:sup>+</jats:sup>ions across the cell membrane per adenosine triphosphate molecule. The location of two Rb<jats:sup>+</jats:sup>ions in the crystal structures of the Na<jats:sup>+</jats:sup>/K<jats:sup>+</jats:sup>-ATPase has defined two “common” cation binding sites, I and II, which accommodate Na<jats:sup>+</jats:sup>or K<jats:sup>+</jats:sup>ions during transport. The configuration of site III is still unknown, but the crystal structure has suggested a critical role of the carboxy-terminal KETYY motif for the formation of this “unique” Na<jats:sup>+</jats:sup>binding site. Our two-electrode voltage clamp experiments on<jats:italic>Xenopus</jats:italic>oocytes show that deletion of two tyrosines at the carboxy terminus of the human Na<jats:sup>+</jats:sup>/K<jats:sup>+</jats:sup>-ATPase α<jats:sub>2</jats:sub>subunit decreases the affinity for extracellular and intracellular Na<jats:sup>+</jats:sup>, in agreement with previous biochemical studies. Apparently, the ΔYY deletion changes Na<jats:sup>+</jats:sup>affinity at site III but leaves the common sites unaffected, whereas the more extensive ΔKETYY deletion affects the unique site and the common sites as well. In the absence of extracellular K<jats:sup>+</jats:sup>, the ΔYY construct mediated ouabain-sensitive, hyperpolarization-activated inward currents, which were Na<jats:sup>+</jats:sup>dependent and increased with acidification. Furthermore, the voltage dependence of rate constants from transient currents under Na<jats:sup>+</jats:sup>/Na<jats:sup>+</jats:sup>exchange conditions was reversed, and the amounts of charge transported upon voltage pulses from a certain holding potential to hyperpolarizing potentials and back were unequal. These findings are incompatible with a reversible and exclusively extracellular Na<jats:sup>+</jats:sup>release/binding mechanism. In analogy to the mechanism proposed for the H<jats:sup>+</jats:sup>leak currents of the wild-type Na<jats:sup>+</jats:sup>/K<jats:sup>+</jats:sup>-ATPase, we suggest that the ΔYY deletion lowers the energy barrier for the intracellular Na<jats:sup>+</jats:sup>occlusion reaction, thus destabilizing the Na<jats:sup>+</jats:sup>-occluded state and enabling inward leak currents. The leakage currents are prevented by aromatic amino acids at the carboxy terminus. Thus, the carboxy terminus of the Na<jats:sup>+</jats:sup>/K<jats:sup>+</jats:sup>-ATPase α subunit represents a structural and functional relay between Na<jats:sup>+</jats:sup>binding site III and the intracellular cation occlusion gate.</jats:p>

Dürr KL, Abe K, Tavraz NN, Friedrich T. 2009. E2P State Stabilization by the N-terminal Tail of the H,K-ATPase β-Subunit Is Critical for Efficient Proton Pumping underin VivoConditions Journal of Biological Chemistry, 284 (30), pp. 20147-20154. | Read more

Dürr KL, Tavraz NN, Dempski RE, Bamberg E, Friedrich T. 2009. Functional Significance of E2State Stabilization by Specific α/β-Subunit Interactions of Na,K- and H,K-ATPase Journal of Biological Chemistry, 284 (6), pp. 3842-3854. | Read more

Dürr KL, Koepke J, Hellwig P, Müller H, Angerer H, Peng G, Olkhova E, Richter O-MH, Ludwig B, Michel H. 2008. A D-pathway mutation decouples the Paracoccus denitrificans cytochrome c oxidase by altering the side-chain orientation of a distant conserved glutamate. J Mol Biol, 384 (4), pp. 865-877. | Show Abstract | Read more

Asparagine 131, located near the cytoplasmic entrance of the D-pathway in subunit I of the Paracoccus denitrificans aa(3) cytochrome c oxidase, is a residue crucial for proton pumping. When replaced by an aspartate, the mutant enzyme is completely decoupled: while retaining full cytochrome c oxidation activity, it does not pump protons. The same phenotype is observed for two other substitutions at this position (N131E and N131C), whereas a conservative replacement by glutamine affects both activities of the enzyme. The N131D variant oxidase was crystallized and its structure was solved to 2.32-A resolution, revealing no significant overall change in the protein structure when compared with the wild type (WT), except for an alternative orientation of the E278 side chain in addition to its WT conformation. Moreover, remarkable differences in the crystallographically resolved chain of water molecules in the D-pathway are found for the variant: four water molecules that are observed in the water chain between N131 and E278 in the WT structure are not visible in the variant, indicating a higher mobility of these water molecules. Electrochemically induced Fourier transform infrared difference spectra of decoupled mutants confirm that the protonation state of E278 is unaltered by these mutations but indicate a distinct perturbation in the hydrogen-bonding environment of this residue. Furthermore, they suggest that the carboxylate side chain of the N131D mutant is deprotonated. These findings are discussed in terms of their mechanistic implications for proton routing through the D-pathway of cytochrome c oxidase.

Tavraz NN, Friedrich T, Dürr KL, Koenderink JB, Bamberg E, Freilinger T, Dichgans M. 2008. Diverse Functional Consequences of Mutations in the Na+/K+-ATPase α2-Subunit Causing Familial Hemiplegic Migraine Type 2 Journal of Biological Chemistry, 283 (45), pp. 31097-31106. | Read more

Dürr KL, Tavraz NN, Zimmermann D, Bamberg E, Friedrich T. 2008. Characterization of Na,K-ATPase and H,K-ATPase Enzymes with Glycosylation-Deficient β-Subunit Variants by Voltage-Clamp Fluorometry inXenopusOocytes† Biochemistry, 47 (14), pp. 4288-4297. | Read more

Vogler M, Dürr K, Jovanovic M, Debatin K-M, Fulda S. 2007. Regulation of TRAIL-induced apoptosis by XIAP in pancreatic carcinoma cells Oncogene, 26 (2), pp. 248-257. | Read more

Richter O-MH, Dürr KL, Kannt A, Ludwig B, Scandurra FM, Giuffrè A, Sarti P, Hellwig P. 2005. Probing the access of protons to the K pathway in the Paracoccus denitrificans cytochrome c oxidase FEBS Journal, 272 (2), pp. 404-412. | Read more

Chen L, Durr KL, Gouaux E. 2014. X-ray structures of AMPA receptor-cone snail toxin complexes illuminate activation mechanism Science, 345 (6200), pp. 1021-1026. | Read more

Dürr KL, Chen L, Stein RA, De Zorzi R, Folea IM, Walz T, Mchaourab HS, Gouaux E. 2014. Structure and dynamics of AMPA receptor GluA2 in resting, pre-open, and desensitized states. Cell, 158 (4), pp. 778-792. | Show Abstract | Read more

Ionotropic glutamate receptors (iGluRs) mediate the majority of fast excitatory signaling in the nervous system. Despite the profound importance of iGluRs to neurotransmission, little is known about the structures and dynamics of intact receptors in distinct functional states. Here, we elucidate the structures of the intact GluA2 AMPA receptor in an apo resting/closed state, in an activated/pre-open state bound with partial agonists and a positive allosteric modulator, and in a desensitized/closed state in complex with fluorowilliardiine. To probe the conformational properties of these states, we carried out double electron-electron resonance experiments on cysteine mutants and cryoelectron microscopy studies. We show how agonist binding modulates the conformation of the ligand-binding domain "layer" of the intact receptors and how, upon desensitization, the receptor undergoes large conformational rearrangements of the amino-terminal and ligand-binding domains. We define mechanistic principles by which to understand antagonism, activation, and desensitization in AMPA iGluRs.

Dürr KL, Abe K, Tavraz NN, Friedrich T. 2009. E2P State Stabilization by the N-terminal Tail of the H,K-ATPase β-Subunit Is Critical for Efficient Proton Pumping underin VivoConditions Journal of Biological Chemistry, 284 (30), pp. 20147-20154. | Read more

Dürr KL, Koepke J, Hellwig P, Müller H, Angerer H, Peng G, Olkhova E, Richter O-MH, Ludwig B, Michel H. 2008. A D-pathway mutation decouples the Paracoccus denitrificans cytochrome c oxidase by altering the side-chain orientation of a distant conserved glutamate. J Mol Biol, 384 (4), pp. 865-877. | Show Abstract | Read more

Asparagine 131, located near the cytoplasmic entrance of the D-pathway in subunit I of the Paracoccus denitrificans aa(3) cytochrome c oxidase, is a residue crucial for proton pumping. When replaced by an aspartate, the mutant enzyme is completely decoupled: while retaining full cytochrome c oxidation activity, it does not pump protons. The same phenotype is observed for two other substitutions at this position (N131E and N131C), whereas a conservative replacement by glutamine affects both activities of the enzyme. The N131D variant oxidase was crystallized and its structure was solved to 2.32-A resolution, revealing no significant overall change in the protein structure when compared with the wild type (WT), except for an alternative orientation of the E278 side chain in addition to its WT conformation. Moreover, remarkable differences in the crystallographically resolved chain of water molecules in the D-pathway are found for the variant: four water molecules that are observed in the water chain between N131 and E278 in the WT structure are not visible in the variant, indicating a higher mobility of these water molecules. Electrochemically induced Fourier transform infrared difference spectra of decoupled mutants confirm that the protonation state of E278 is unaltered by these mutations but indicate a distinct perturbation in the hydrogen-bonding environment of this residue. Furthermore, they suggest that the carboxylate side chain of the N131D mutant is deprotonated. These findings are discussed in terms of their mechanistic implications for proton routing through the D-pathway of cytochrome c oxidase.

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BackgroundPeriodontitis is the most common chronic inflammatory disease in humans worldwide. Its comorbidity with systemic diseases, such as type 2 diabetes, oral cancers and cardiovascular diseases, continues to generate considerable impact on healthcare and society. Porphyromonas gingivalis, one of the most studied organisms of the human oral microbiome, is the major causative agent in periodontitis. Surprisingly, this microorganism does not ferment carbohydrates, rather it uses proteinaceous ...

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