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The ubiquinol:cytochrome c oxidoreductase is a key component of several aerobic respiratory chains in different organisms. It is an integral membrane protein complex, made up of three catalytic subunits (cytochrome b, cytochrome c1 and Rieske iron sulphur protein) and up to eight additional subunits in mitochondria. The complex oxidizes one quinol molecules and reduces two cytochrome c during the Q cycle, originally described by Peter Mitchell. Electrons are split between the low and the high potential chain and protons are released on the positive side of the membrane, increasing the protonmotive force needed by the ATP-synthase for energy transduction. The cytochrome bc1 complex from P. denitrificans is a perfect model for structural and functional studies. Bacteria are easy to grow and the genetic material is readily accessible for genetic manipulation. Moreover, the P. denitrificans aerobic respiratory chain is very close to the mitochondrial one: the complexes involved in electron transfer resemble the ones found in mitochondria, but lack most of the additional subunits. As a unique feature, P. denitrificans has a strongly acidic domain at the N-terminal region of the cytochrome c1, a sequence of 150 aminoacids which does not correlate with any known protein. An analogous composition can be found in the eukaryotic cytochrome bc1 complex as a part of an accessory subunit, proposed to be involved in facilitating electron transfer between the complex and the electron acceptor cytochrome c. In order to study the function of this domain in the P. denitrificans cytochrome bc1 complex, a deletion mutant has been previously cloned and modified with an affinity tag as a C-terminal extension of cytochrome b. The complex is purified by affinity chromatography and characterized by steady-state kinetics using not only horse heart cytochrome c but also the endogenous electron acceptor, the membrane bound cytochrome c552, employed here as a soluble fragment. Steady–state kinetics indicate that the deletion of the long acidic domain had effects neither on the turnover rate nor on the apparent affinity for the substrate. To understand wether the deletion affects the reaction between the cytochrome bc1 complex and the substrate, laser flash photolysis experiments are performed, showing that the interaction observed was not changed in the complex missing the acidic domain. The results presented in this work confirm the ones previously obtained by Julia Janzon using soluble fragments of the same interaction partners. The deletion, however, affected the oligomerization state of the complex, as shown by LILBID (Laser Induced Liquid Bead Ion Desorption) analysis. The wild type complex has a tetrameric structure, better described as a “dimer of dimers”. The deletion of the acidic domain on the cytochrome c1 results in the separation of the two dimers, yielding the canonical dimer. Therefore, the complex deleted in the acidic domain is used for cloning and expression of a heterodimeric complex, containing an inactivating mutation in the quinol oxidation site in only one monomer, thus allowing a selective switch-off for half the complex. Such a complex is needed for the verification of an internal regulation mechanism, the half-of-the-sites reactivity. According to it, the dimeric structure of the cytochrome bc1 complex has functional implications, since the two monomers can communicate and work in a coordinated manner. This approach confirms that substrate oxidation does effectively take place only in one of the two monomers constituting the dimer, and that the binding of substrate at the Qo and Qi site regulates the switch between active and inactive monomer. Moreover, this mechanism works also as an effective protection against the reaction of quinone intermediates with oxygen and the formation of reactive oxygen species (ROS), responsable for cellular aging. The motion of the ISP head domain is also addressed in this work; in particular the mechanism which regulates the movements towards the cytochrome c1 and the electron bifurcation at the quinol oxidation site. Laser flash kinetics in presence of several inhibitors and the substrate allow studying the response of the ISP to the binding of different species at the quinol oxidation site. The binding of ligand at the Qo site in the complex triggers the conformational switch in the ISP head domain, supporting the mechanism proposed in the literature according to which the Qo site is able to “sense” the presence of substrate and transfer the information to the ISP, regulating its mobility. The internal electron pathway between the ISP and the cytochrome c1 has been analyzed also by stopped-flow kinetics, in presence and absence of inhibitors. The results indicate that two kinetic phases describe the reduction of cytochrome c1 by the ISP, and a model for the simulation of the data is proposed.
According to the World Health Organization (WHO) bacterial resistance to antibiotic drug therapy is emerging as a major public health problem around the world. Infectious diseases seriously threaten the health and economy of all countries. Hence, the preservation of the effectiveness of antibiotics is a world wide priority. The key to preserving the power of antibiotics lies in maintaining their diversity. Many microorganisms are capable of producing these bioactive products, the so called antibiotics. Specifically in microorganisms, polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS) produce these natural bioactive compounds. Besides being used as antibiotics these non-ribosomal peptides and polyketides display an even broader spectrum of biological activities, e.g. as antivirals, immunosuppressants or in antitumor therapy. The wide functional spectrum of the peptides and ketides is due to their structural diversity. Mostly they are cyclic or branched cyclic compounds, containing non-proteinogenic amino acids, small heterocyclic rings and other unusual modifications such as epimerization, methylation, N‐formylation or heterocyclization. It is has been shown that these modifications are important for biological activity, but little is known about their biosynthetic origin.
PKS and NRPS are multidomain protein assembly lines which function by sequentially elongating a growing polyketide or peptide chain by incorporating acyl units or amino acids, respectively. The growing product is attached via a thioester linkage to the 4’-phosphopantetheine (4’-Ppant) arm of a holo acyl carrier protein (ACP) in PKSs or holo peptidyl carrier protein (PCP) in NRPSs and is passed from one module to another along the chain of reaction centers. The modular arrangement makes PKS and NRPS systems an interesting target for protein engineering. More than 200 novel polyketide compounds have already been created by module swapping, gene deletion or other specific manipulations. Unfortunately, however, engineered PKS often fail to produce significant amounts of the desired products. Structural studies may faciliate yield improvement from engineered systems by providing a more complete understanding of the interface between the different domains. While some information about domain-domain interactions, involving the most common enzymatic modules, ketosynthase and acyltransferase, is starting to emerge, little is known about the interaction of ACP domains with other modifying enzymes such as methyltransferases, epimerases or halogenases.
To further improve the understanding of domain-domain interactions this work focuses on the curacin A assembly line. Curacin A, which exhibits anti-mitotic activity, is from the marine cyanobacterium Lyngbya majuscula. This outstanding natural product contains a cyclopropane ring, a thiazoline ring, an internal cis double bond and a terminal alkene. The biosynthesis of curacin A is performed by a 2.2 Mega Dalton (MDa) hybrid PKS-NRPS cluster. A 10-enzyme assembly catalyzes the formation of the cyclopropane moiety as the first building block of the final product. Interestingly, for these enzymes the substrate is presented by an unusual cluster of three consecutive ACPs (ACPI,II,III). Little is known about the function of multiple ACPs which are supposed to increase the overall flux for enhanced production of secondary metabolites.
The first task in this work was to elucidate the structural effect of the triplet ACP repetition by nuclear magnetic resonance (NMR). The initial data show that the excised ACPI, ACPII or ACPIII proteins resulted in [15N, 1H]-TROSY spectra with strong chemical shift perturbations (CSPs), suggesting an effect on the structure. The triplet ACP domains display a high sequence identity (93- 100%) making structural investigation using usual NMR techniques due to high peak overlap impossible. To enable the investigation of the triplet ACP in its native composition we developed a powerful method, the three fragment ligation. Segmental labeling allows incorporating isotopes into one single domain in its multidomain context. As a result we could prepare the triplet ACP with only one domain isotopically labeled and therefore assign the full length protein. In this way our method paved the way to study the structural effects of the triplet ACP repetition. We could show unexpectedly, that, despite the fact that the triplet repeat of CurA ACPI,II,III has a synergistic effect in the biosynthesis of CurA, the domains are structurally independent.
In the second part of this work, we studied the structure of the isolated ACPI domain. Our results show that the CurA ACPI undergoes no major conformational changes upon activation via phosphopantetheinylation and therefore contradicts the conformational switching model which has been proposed for PCPs. Further we report the NMR solution structures of holo-ACPI and 3-hydroxyl-3-methylglutaryl (HMG)-ACPI. Data obtained from filtered nuclear overhauser effect (NOE) experiments indicate that the substrate HMG is not sequestered but presented on the ACP surface.
In the third part of this work we focussed on the protein-protein interactions of the isolated ACPI with its cognate interaction partners. We were especially interested in the interaction with the halogenase (Cur Hal), the first enzyme within the curacin A sub-cluster, acting on the initial hydroxyl-methyl-glutaryl (HMG) attached to ACPI. Primarily we studied the interaction using NMR titration and fluorescence anisotropy measurements. Surprisingly no complex between ACPI and Cur Hal could be detected. The combination of an activity assay using matrix-assisted laser desorption/ionization (MALDI) mass spectroscopy and mutational analysis revealed several amino acids of ACPI that strongly decrease the activity of CurA Hal. Mapping these mutations according to their effect on the Cur Hal activity onto the structure of HMG-ACPI displays that these amino acids surround the substrate and form a consecutive surface. These results suggest that this surface is important for Cur Hal recognition and selectivity. Our research presented herein is an excellent example for protein-protein interactions in PKS systems underlying a specific recognition process.
Die Familie der Proteorhodopsine (PR) besteht aus Hunderten von PR Molekülen, die unter Lichteinwirkung Protonen pumpen und somit eine bedeutende Rolle für die Energiegewinnung spielen könnten. Da der pKa Wert des Proton Akzeptors der Schiff‘schen Base (SB) (~7.2) dem pH Wertes der Ozeane (~7.9) ähnelt, wird auch über eine regulatorische Funktion spekuliert. Wird in Erwägung gezogen, dass 24 000 PR Moleküle pro SAR86 Zelle vorhanden sind (Beja et al. 2001) und dass 13% der Bakterien der Meeresoberfläche PR besitzen (Sabehi et al. 2005) liefert dieses Protein wahrscheinlich einen bedeutenden Energiebeitrag neben der Photosynthese. Einblicke in den Mechanismus der Energieumwandlung erfordern sowohl die Untersuchung des Chromophores, welches die Lichtenergie absorbiert als auch der Struktur des Apoproteins, das durch die Generierung eines Protonengradienten zur Energiegewinnung beiträgt. Der Fokus der Doktorarbeit liegt auf dem Chromophor und seiner Umgebung. Eine erste Charakterisierung der SB und des Retinals erfolgt durch UV/VIS und NMR Messungen (Pfleger et al. 2008). Die 13C chemische Verschiebungen von 10,11-13C2 Retinal und die 15N chemische Verschiebung der protonierten SB, gebildet durch K231, zeigt eindeutig, dass im Grundzustand nur eine Konformation der Retinals, all-trans, vorliegt. Die 15N chemische Verschiebung weist außerdem auf eine starke Wechselwirkung der SB mit ihren Gegenionen hin. Desweiteren kann durch Messungen der 15N chemischen Verschiebung der SB bei verschiedenen pH Werten der pKa Wert der SB abgeschätzt werden, auf ~12. Diese Stabilisierung der positiv geladenen protonierten Form der SB weist auf die Existenz eines Wasserclusters hin, das durch die hohe Dielektrizitätskonstante die protonierte Form der SB stabilisieren könnte. Um zu überprüfen, ob Wasser an der SB gebunden ist, wird ein sogenanntes 15N-1H HETCOR Experiment durchgeführt. Der Bereich der 15N chemischen Verschiebung der SB korreliert mit einer Protonenresonanz bei ~5 ppm, welche im Bereich einer Wasserresonanz liegt und die durch D2O austauschbar ist. Dies indiziert eine wichtige Bedeutung von Wasser in der Nähe der SB für die Funktion von PR. Der Einfluss von Mutationen des Histidins H75 und des Aspartats D97 auf die 15N chemische Verschiebung der SB sowie die Auswirkung von Histidinmutationen auf das Chromophor deuten eine direkte Wechselwirkung von Aspartat 97 und der SB an, nicht aber eine direkte Wechselwirkung von H75 und der SB. Neben dem Chromophor ist außerdem das Signalpeptid Gegenstand der Untersuchung der Doktorarbeit. Motivation für die Untersuchung war die Inhomogenität der Proben, die im Zusammenhang mit ungleich prozessiertem PR stehen könnten. Ein zweiter Teil beschäftigt sich mit neuen Konzepten der Datenaufnahme, da das S/R in der Festkörper NMR ein limitierender Faktor darstellt. Diese beinhalten Verstärkung der Relaxation (RELOAD) sowie die Refokussierung von T2 bei Verwendung eines Prozessierungsschrittes, der „half echo alternating transformation“ (HEAT).
The enzyme quinol:fumarate reductase (QFR) from the anaerobic epsilon-proteobacterium Wolinella succinogenes is a membrane protein complex that couples the catalysis of the oxidation of menaquinol to menaquinone to that of the reduction of fumarate to succinate. This is the terminal step in fumarate respiration, a form of anaerobic respiration in which oxygen is replaced by fumarate as the terminal electron acceptor in many anaerobic microorganisms. In QFR, both the heme groups (low-potential distal and high-potential proximal heme b group in transmembrane subunit C) are part of the electron transport chain between the two catalytic sites of the redox enzyme. Although the reduction of fumarate by menaquinol is exergonic, it is not exergonic enough to support the generation of a transmembrane electrochemical proton potential delta p. Evidence has previously shown that this reaction is catalysed by a novel mechanism, involving the facilitation of transmembrane electron transfer by transmembrane proton transfer via an essential compensatory transmembrane proton transfer pathway ("E-pathway") which is inactive in the oxidized state of the enzyme. The two key constitutents of the the pathway are the amino acid residue Glu C180 of the transmembrane helix V (located in subunit C) and the ring C propionate of the distal heme bD. The aim of the project was to obtain, by employing a combination of time-resolved as well as static spectroscopic approaches, a detailed insight of the transmembrane electron coupled proton transfer mechanism. Minute changes in both the oxidized and reduced states of a redox protein system can be selectively and sensitively monitored by static Fourier Transformed Infrared (FTIR) difference spectroscopy. The technique employed in this context, electrochemically induced FTIR difference spectroscopy, is complemented by computer-based electrostatic calculations. In order to elucidate the catalytic mechanism of the important reactions in QFR, it is necessary to investigate these in a time-resolved manner. Rapid scan FTIR difference spectroscopy is a suitable technique that allows the course of the reaction to be monitored in a time dependent fashion. The techniques employed in this context are time-resolved (tr-FTIR) and transient absorption spectroscopy. In the following, the details of individual sub-projects are discussed in brief. ...
Mitochondrial complex I, the largest and most complicated proton pump of the respiratory chain, links the electron transfer from NADH to ubiquinone to the pumping of four protons from the matrix into the intermembrane space. In humans, defects in complex I are involved in a wide range of degenerative disorders. Recent progress in the X-ray structural analysis of prokaryotic and eukaryotic complex I confirmed that the redox reactions are confined entirely to the hydrophilic peripheral arm of the L-shaped molecule and take place at a remarkable distance from the membrane domain. While this clearly implies that the proton pumping within the membrane arm of complex I is driven indirectly via long-range conformational coupling, the molecular mechanism and the number, identity, and localization of the pump-sites remains unclear. Here, we report that upon deletion of the gene for a small accessory subunit of the Yarrowia complex I, a stable subcomplex (nb8m delta) is formed that lacks the distal part of the membrane domain as revealed by single particle analysis. The analysis of the subunit composition of holo and subcomplex by three complementary proteomic approaches revealed that two (ND4 and ND5) of the three subunits with homology to bacterial Mrp-type Na+/H+ antiporters that have been discussed as prime candidates for harbouring the proton pumps were missing in nb8m delta. Nevertheless, nb8m delta still pumps protons at half the stoichiometry of the complete enzyme. Our results provide evidence that the membrane arm of complex I harbours two functionally distinct pump modules that are connected in series by the long helical transmission element recently identified by X-ray structural analysis.
Host cell invasion by the facultative intracellular pathogen Listeria monocytogenes requires the invasion protein InlB in many cell types. InlB consists of an N-terminal internalin domain that binds the host cell receptor tyrosine kinase Met and C-terminal GW domains that bind to glycosaminoglycans (GAGs). Met binding and activation is required for host cell invasion, while the interaction between GW domains and GAGs enhances this effect. Soluble InlB elicits the same cellular phenotypes as the natural Met ligand hepatocyte growth factor/scatter factor (HGF/SF), e.g. cell scatter. So far, little is known about the central part of InlB, the B-repeat. Here we present a structural and functional characterization of the InlB B-repeat. The crystal structure reveals a variation of the β-grasp fold that is most similar to small ubiquitin-like modifiers (SUMOs). However, structural similarity also suggests a potential evolutionary relation to bacterial mucin-binding proteins. The B-repeat defines the prototype structure of a hitherto uncharacterized domain present in over a thousand bacterial proteins. Generally, this domain probably acts as a spacer or a receptor-binding domain in extracellular multi-domain proteins. In cellular assays the B-repeat acts synergistically with the internalin domain conferring to it the ability to stimulate cell motility. Thus, the B-repeat probably binds a further host cell receptor and thereby enhances signaling downstream of Met.
Using an electrophysiological assay the activity of NhaA was tested in a wide pH range from pH 5.0 to 9.5. Forward and reverse transport directions were investigated at zero membrane potential using preparations with inside-out and right side-out-oriented transporters with Na+ or H+ gradients as the driving force. Under symmetrical pH conditions with a Na+ gradient for activation, both the wt and the pH-shifted G338S variant exhibit highly symmetrical transport activity with bell-shaped pH dependences, but the optimal pH was shifted 1.8 pH units to the acidic range in the variant. In both strains the pH dependence was associated with a systematic increase of the Km for Na+ at acidic pH. Under symmetrical Na+ concentration with a pH gradient for NhaA activation, an unexpected novel characteristic of the antiporter was revealed; rather than being down-regulated, it remained active even at pH as low as 5. These data allowed a transport mechanism to advance based on competing Na+ and H+ binding to a common transport site and a kinetic model to develop quantitatively explaining the experimental results. In support of these results, both alkaline pH and Na+ induced the conformational change of NhaA associated with NhaA cation translocation as demonstrated here by trypsin digestion. Furthermore, Na+ translocation was found to be associated with the displacement of a negative charge. In conclusion, the electrophysiological assay allows the revelation of the mechanism of NhaA antiport and sheds new light on the concept of NhaA pH regulation.
Single crystals suitable for X-ray diffraction of (tBu2P)3Ga (monoclinic, space group Cc) were obtained from GaCl3 and two equivalents of Li[PtBu2] at room temperature in benzene. The phosphanylgallane (tBu2P)3Ga was also produced via a one-pot approach by reaction of GaCl3 with three or more than three equivalents of Li[PtBu2]. However, treatment of one equivalent of GaCl3 with one equivalent of Li[PtBu2] and subsequent protolysis yielded [tBu2PH2][tBu2P(GaCl3)2 - Li(Cl3Ga)2PtBu2]. Single crystals of this phosphonium salt (monoclinic, space group Cc) were obtained from benzene at room temperature.
To examine their luminescence behavior, two air-stable BN addition compounds were synthesized by the reaction of 5-fluoro-2-(2′-pyridyl)indole with 1,4- and 1,3-bis(bromo(methyl)boryl)benzene, respectively. Both BN adducts are luminescent. Their emission maxima (1,3-substituted BN adduct: 495 nm; 1,4-substituted BN adduct: 497 nm) are comparable with the value (490 nm) of the related mono-borylated benzene species, which is composed of a BPh2 fragment and a 5-fluoro-2-(2′-pyridyl) indole unit. The starting materials 1,4- and 1,3-bis(bromo(methyl)boryl)benzene were accessible by treatment of 1,4- or 1,3-bis(dibromoboryl)benzene with two equivalents of SnMe4. In addition, the results of the X-ray structure analyses of the B,B′-bis-5-fluoro-2-(2′-pyridyl)indolyl-complexed meta-bismethylborylbenzene fragment (9, triclinic, P1̅) as well as of 5-chloro-2-(2′-pyridyl)indole (2, monoclinic, P21/c) and 5-fluoro-2-(2′-pyridyl)indole (1, orthorhombic, Pca21) are reported. The pyridylindole derivatives of this approach were synthesized by an optimized two-step procedure from 2-acetylpyridine and 4-fluoro- or 4-chlorophenylhydrazine hydrochloride.
Virus-infected cells are eliminated by cytotoxic T lymphocytes, which recognize viral epitopes displayed on major histocompatibility complex class I molecules at the cell surface. Herpesviruses have evolved sophisticated strategies to escape this immune surveillance. During the lytic phase of EBV infection, the viral factor BNLF2a interferes with antigen processing by preventing peptide loading of major histocompatibility complex class I molecules. Here we reveal details of the inhibition mechanism of this EBV protein. We demonstrate that BNLF2a acts as a tail-anchored protein, exploiting the mammalian Asna-1/WRB (Get3/Get1) machinery for posttranslational insertion into the endoplasmic reticulum membrane, where it subsequently blocks antigen translocation by the transporter associated with antigen processing (TAP). BNLF2a binds directly to the core TAP complex arresting the ATP-binding cassette transporter in a transport-incompetent conformation. The inhibition mechanism of EBV BNLF2a is distinct and mutually exclusive of other viral TAP inhibitors.