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Proton-translocating NADH:ubiquinone oxidoreductase (complex I) transports two electrons from NADH to membranal ubiquinone: in this process protons are translocated across the membrane, producing 40% of the total proton gradient between matrix side and intermembrane space. Mitochondrial complex I contains at least 46 subunits in mammals, and has a molecular weight of around 1000 kDa. Electronic microscopy analysis showed that complex I has an L-form, which consists of two domains: a peripheral “arm” (hydrophilic domain) and a membrane “arm” (hydrophobic domain). The peripheral domain, which protrudes into the matrix, contains one non-covalently bound flavin mononucleotide (FMN) and the iron-sulfur clusters N1a, N1b, N2, N3, N4 and N5 as redox active groups. They transport electrons from NADH to ubiquinone. Cluster N2 is supposed to be the immediate electron donor to ubiquinone by virtue of its highest and pH dependent redox midpoint potential (Em,7 –150 mV). The exact location of the tetra-nuclear cluster N2 is still object of discussion. The TYKY and the PSST subunits contain three binding motifs for tetranuclear clusters which are formed by twelve cysteins. In an effort to investigate the “ubiquinone reduction module” of complex I, in the first part of this work site directed mutagenesis of the TYKY and PSST subunits has been carried out. Mutant strains were characterised in terms of complex I content, catalytic activity and EPR signature of cluster N2. The second part of this work was aimed at developing a substrate inducible version of the internal alternative NADH:ubiquinone oxidoreductase (NDH2i). A substrate inducible NDH2i is expected to offer a “switch” between complex I activity dependent (no NDH2i activity) and independent (NDH2i activity) cell growth, by changing between activating and non-activating substrates. This strategy would allow the screening for two types of complex I mutants, which is a prerequisite for realising a random PCR mutagenesis of single subunits of complex I, that allows the production of a high number of point mutations in relatively short time. Y. lipolytica complex I deficiency mutant strains could be easily identified, by virtue of their inability to survive under complex I dependent growth conditions (no NDH2i activity). By this way, amino acids that have an important role for complex I structure or function could be identified by subsequent sequence analysis. Each of the twelve cysteines that form the above mentioned three binding motifs for iron-sulfur cluster have been mutagenised. In mutant mitochondrial membranes, no assembled complex I could be detected. From these data one may conclude that the mutagenised 6 SUMMARY 92 cysteines play an important role for complex I stability, or that are a prerequisite for complex I assembly in Y. lipolytica, but there is not direct evidence indicating that any of the four mutagenised residues acts as a ligand. Two aspartates in the PSST subunit, Asp-99 and Asp-115, were found to be essential for complex I catalytic activity. EPR spectroscopic analysis indicated that the electron transfer to N2 cluster was not blocked and implied that this was not the reason for the loss of catalytic activity. From these data it can be concluded that D99 and D115 play a vital role for complex I NADH:ubiquinone reductase activity, but are not ligands for cluster N2 and that their position is not close enough to the cluster to influence directly its electromagnetic environment. Three mutations, identified in the PSST and TYKY homologous subunits of patients affected with Leigh syndrome (V119M in PSST, P78L and R101H in TYKY) were reconstructed in the obligate aerobic yeast Y. lipolytica. This approach may help to understand the aetiology of the Leigh syndrome, in terms of the ability of complex I to oxidize NADH and to transport electrons. In fact, all three mutations showed effects on electron transport, reducing the VMax by about 50%. Mutant V119M in the PSST subunit, which had a lethal effect in two patients that were homozygous for this mutation, affects a fully conserved residue. Overall, the results from site directed mutagenesis carried out so far support the theory that the “catalytic core ” (N2 cluster and quinone binding site) of complex I has been evolved from the electron transfer module of the [Ni-Fe] hydrogenases. In fact, mutagenesis of residues that are fully conserved between complex I and [Ni-Fe] hydrogenases, showed dramatic effects on complex I in terms of assembly (cysteine mutants) or catalytic activity (D99-D115). Differently, changing aspartate 174 and glutamic acid 185 (not fully conserved, Fig 4.1A) had little or no effect on the Michaelis-Menten parameters and N2 EPR signal. In recent years Y. lipolytica has been developed as a yeast genetic system to study mitochondrial complex I. The present work introduced the promoter for the isocitrate lyase (pICL1) as a useful tool for the substrate selective expression of the internal version of the alternative NADH:ubiquinone oxidoreductase (pICL1-NDH2i). This allows to rescue complex I deficiencies “in vivo” selectively by growth on acetate (or ethanol) medium. The integration of the pICL1-NDH2i construct into the genome of Y. lipolytica and subsequent deletion of nuclear-coded subunits like PSST, TYKY and 49 kDa, would contribute to further develop this organism as a useful genetic model for studying subunits of mitochondrial complex I by site directed mutagenesis.
Stability, unfolding and refolding of the outer membrane protein porin from Paracoccus denitrificans was investigated using genetic and spectroscopic methods. Structural and functional activity studies on wild type and mutant porins: The site-directed mutants were constructed based on conserved residues and evidences on the role of certain amino acids from previous studies with OmpF. Secondary structure analysis of wild type and mutants E81Q, W74C, E81Q/D148N, E81Q/D148N/W74C by FTIR and CD spectroscopy are in line with the fact that porins are predominantly ß-sheet structure. The functional activity studies by black lipid bilayer techniques showed that the wild type and mutants W74C, E81Q/D148N, E81Q/D148N/W74C have a conductance of 3.25 nS. For mutant E81Q conductance of 1.25nS was more predominant over 3.25 nS. The activity of the mutants was observed to be far less than the wild type. This indicates that structural similarities does not implies similar functional activity. Thermal stability analysis of porin in detergent micelles and reconstituted into liposomes: Thermal stability analysis of wild type and mutants in detergent micelles showed changes in secondary and quaternary structure. It was found that wild type porin unfolds into aggregated structure with a high transition temperature of 86.2 °C. For mutants E81Q, W74C, E81Q/D148N the transition temperature was found to be 84.2 °C, 80.3 °C and 80.2 °C respectively. Functional activity assays at high temperatures revealed that the protein tends to loose its activity on heating up to 50 °C. This shows that structural stability does not imply functionality in the case of porins. Thermal stability analysis of porin reconstituted into liposomes showed that there was no change in the secondary and quaternary structure of the protein up to 100 °C, revealing that the protein becomes more thermostable when it is reconstituted into liposomes. Refolding of aggregated porin: This study shows that disaggregation of ß-sheet membrane protein porin is possible by changing its chemical and thermodynamic parameters. An increase of the solution pH to 12 or above results in opening up of the aggregated protein into unordered structure, as observed by FTIR and CD spectroscopy. This unordered structure could be refolded into native-like structure forming trimers. The secondary structure of the refolded protein deviated slightly from the native one. The thermal stability analysis of the native-like refolded proteins showed that the unfolding pattern is entirely different when compared to the native porins. pH dependent unfolding of porin: Thermal stability of porin at different pH values showed that the protein is stable in a pH range of 1-11. At pH 12 and above the protein unfolds into unordered structure instead of aggregating. The high pH unfolding of porin is a reversible process. The secondary structure of the refolded protein varied slightly from the native-one. Whereas thermal stability was entirely different. This shows that even though the unfolding of porin at high pH is reversible, it results in changes in local interaction between the amino acids resulting in a difference in stability. Unfolding in presence of urea and guanidinium hydrochloride (GuHCl): Denaturation of porin in the presence of chemical denaturants like urea and GuHCl showed that porin unfold into unordered structure. The unfolding is a reversible process. Unfolded protein was refolded into detergent micelles and liposomes. Refolding into detergent micelles was faster compared to refolding into liposomes, as seen by kinetic gel shift assays. The refolding into liposomes showed the presence of intermediates similar to those reported for OmpF. This study shows the difference in thermal stability of the outer membrane protein porin from Paracoccus denitrificans in detergent micelles and native-like liposomes. It suggests various unfolding pathways, which can be further investigated for unfolding and refolding kinetics. This report also suggests that it is possible to refold a heat-aggregated protein.
Results were presented from Brownian dynamics simulations for cyt c molecules approximated as spherical particles with diameter 2R ' 3.3 nm interacting with a charged planar membrane surface. Using the well-known Ermak-McCammon algorithm of ref. [36, 37] for solving the Langevin equations (see Chapter 2), a new computer program in C++ was developed. An overview of the way it is implemented is given in Chapter 3. The program in its current state is able to compute the trajectories (translation and rotation) of hundreds of spherical particles in systems with typical dimensions of 103 − 1003 nm3 . As explained in the introductory Chapter 1 the motivation for studying the dynamics of cyt c molecules in such systems came from the progress in the research of photosynthetic bacteria, e.g. While the internal processes of energy transduction (light harvesting, channelling to RC, charge separation) are quite well understood, the dynamics of soluble cyt c as an electron transporter in this context is not yet clear. In many textbooks one can find illustrations where a single cyt c is responsible for the electron transport between two integral membrane proteins (the reaction centre RC and the bc1 complex). But as pointed out in publications like refs. [49], [59], [60], [61] or [62] biological cells are crowded with different molecules. Consequently, one can assume that the electron transport between two integral membrane proteins is not simply taken on by one single cyt c molecule. Instead it is likely that many of these particles are located in a cyt c pool above the membrane and that they perform the electron transport in turns. Thus, it is desirable to have a simulation package that is able to compute the trajectories of many proteins. Note that the detailed processes of electron transfer and binding to membrane proteins are not modelled here. The details of these processes are quite complicated so that we refrained from including them in the coarse-grained simulations. Here, the actual binding is simply defined by a particle distance zb from the membrane which marks the beginning of the attractive potential. ...
Hinreichend kalte und dichte Quarkmaterie ist ein Farbsupraleiter. Ähnlich wie Elektronen in einem gewöhnlichen Supraleiter bilden Quarks Cooper-Paare. Während bei Elektronen der Austausch von Phononen zu einer Anziehung führt, ist im Falle von Quarks der Antitriplett-Kanal der starken Wechselwirkung attraktiv. Arbeiten in den letzten Jahren haben verschiedene Phasen von farbsupraleitender Quarkmaterie untersucht und sich dabei vor allem auf Phasen konzentriert, m denen der Gesamtspin eines Cooper-Paares verschwindet. In der vorliegenden Dissertation habe ich hauptsächlich Farbsupraleiter diskutiert, deren Cooper-Paare im Spin-Triplett-Kanal kondensieren, d.h. die Cooper-Paare haben den Gesamtspin 1. Diese Art von Supraleiter ist möglicherweise relevant für Systeme in der Natur, wie z.B. das Innere von Neutronensternen. Denn bei der Spin-0-Farbsupraleitung wird vorausgesetzt, dass die Fermi-Impulse zweier Quark-Flavor gleich ist oder zumindest hinreichend klein, was für realistische Systeme, also für nicht zu große Dichten, fragwürdig ist. Diese Einschränkung gibt es im Falle von Spin-1-Farbsupraleitern nicht, da hier Quarks des gleichen Flavors Cooper-Paare bilden. Ich habe in meiner Dissertation die verschiedenen möglichen Phasen eines Spin-1-Farbsupraleiters systematisch klassifiziert. Dies wurde mit Hilfe von gruppen-theoretischen Methoden durchgeführt, basierend auf der Tatsache, dass die Farbsupraleitung durch das theoretische Konzept der spontanen Symmetriebrechung beschrieben werden kann. Ähnlich wie bei supraflüssigem Helium-3 gibt es eine Vielzahl theoretisch möglicher Phasen. Ich habe die physikalischen Eigenschaften von vier dieser Phasen untersucht, nämlich der polaren und planaren Phasen sowie der A- und CSL-(color-spin-locked)Phasen. Mit Hilfe der QCD-Lückengleichung wurde die Energielücke sowie die kritische Temperatur bestimmt. Es stellt sich heraus, dass die Energielücke eines Spin-1-Farbsupraleiters um 2-3 Größenordnungen kleiner ist als die eines Spin-0-Farbsupraleiters, d.h. sie liegt im Bereich von 10 - 100 keV. Zwei besondere Eigenschaften der Energielücke werden diskutiert, nämlich eine 2-Lücken-Struktur, die in zwei der untersuchten Fälle auftritt, sowie mögliche Anisotropien, insbesondere Nullstellen der Lückenfunktion. Die Berechnung der kritischen Temperatur zeigt, dass es durchaus farbsupraleitende Materie in einer Spin-1-Phase im Innern von Neutronensternen geben kann, da die Temperatur von alten Neutronensternen im Bereich von einigen keV oder sogar darunter liegt. Darüber hinaus wurde die Frage untersucht, ob ein Farbsupraleiter auch ein gewöhnlicher Supraleiter ist. In diesem Zusammenhang ist die Frage von Interesse, ob ein Spin-1-Farbsupraleiter gewöhnliche Magnetfelder aus seinem Innern verdrängt, was sicherlich Auswirkungen auf die Observablen eines Neutronensterns hätte. Tatsächlich stellt sich heraus, dass ein Spin-1-Farbsupraleiter, im Gegensatz zu einem Spin-0-Farbsupraleiter, einen elektronmagnetischen Meissner-Effekt aufweist. Dieses Ergebnis wurde mit Hilfe von gruppentheoretischen Überlegungen vorausgesagt und mit Hilfe einer detaillierten Berechnung der Photon-Meissner-Massen bestätigt.
A new experimental setup, for pump-probe fs DFWM measurements, which is based on a femtosecond laser system, has been constructed. It allows for the investigation of molecular species in the gas phase at different temperatures, from ~30 K in a seeded supersonic jet up to ~500 K in a heat-pipe oven. In comparison to other RCS methods the employed fs DFWM technique is less complicated and gives much higher signal-to-noise ratio [BFZ86, FeZ95a, CKS89, CCH90, HCF91, WRM02, Rie02]. A general computer code for the simulation of fs DFWM spectra of nonrigid asymmetric top molecules has been developed. This new DFWM code in combination with a non-linear fitting routine allows one to determine rotational and centrifugal distortion constants and obtain information on the polarizability tensor components from the experimental spectra. Fs DFWM spectroscopy was successfully applied to the medium-sized molecules benzene and benzene-d6 in a gas cell and in a supersonic jet. The spectrum from a seeded expansion has been measured up to delay time of 3.9 ns (restricted by the length of the delay stage) with excellent signal-to-noise ratio (102-103). In that way 87 and 72 J-type transients have been recorded for benzene and benzene-d6, correspondingly. A relative accuracy on the order of 10-5 has been achieved for the rotational constant. From the room temperature experiments, precise values of centrifugal distortion constants DJ and DJK have been extracted. The literature data for cyclohexane have been revised and a new precise rotational constant B0 has been obtained, which is (+5.5 MHz) shifted from the one reported in the former Raman investigation by Peters et al. [PWW73]. Additionally, high-level ab initio calculations of cyclohexane have been carried out using a large number of basis sets at several levels of theory. In particular, the vibrational averaging effects have been examined in order to critically compare the experimentally determined and theoretically evaluated rotational constants. The contribution of highly symmetric vibrational modes to vibrational averaging effects was clarified. More structural information could be obtained from fs DFWM measurements of asymmetric top species, since different type of rotational recurrences can appear, and all three rotational constants (A, B, C) can be extracted. On the other hand the analysis of the asymmetric top spectra is no longer trivial. In fact the simple formula for rotational recurrence periods of symmetric top species (Tab. 2.1) can not be applied to asymmetric top molecules. Thus, in order to extract high-resolution data for asymmetric species, a complete fitting of the experimental spectra is necessary. The fs DFWM and (1+2') PPI method have been applied to the asymmetric top molecules pyridine in the ground (S0) and pDFB in the S0 and electronically excited (S1) states. By fitting the measured fs DFWM spectra the rotational and centrifugal distortion constants have been extracted with good precision and the value of the parametrized polarizability angle of pDFB was obtained. In this work, the first application of fs DFWM spectroscopy to a molecular cluster has been reported. Also, the chemical equilibrium between monomeric and dimeric species was studied. In particular formic and acetic acid have been investigated in a gas cell and in a supersonic expansion. Many spectral features have been observed and analized in the fs DFWM spectrum of formic acid vapor in a gas cell at room temperature. Most of them were attributed to rotational recurrences of the formic acid monomer, but also spectral feature originating from the formic acid dimer of O-H×××O/O×××H-O type have been detected and analyzed. From the fitted simulation, the rotational and centrifugal distortion constants, and parametrized polarizability angle were extracted for the dimeric structure of O-H×××O/O×××HO type. With the assumption of unperturbed monomers a center-of-mass distance of R = 2.990 ± 0.001 Å for the monomers within the dimer has been calculated from the spectroscopic results. This distance is 0.028 Å smaller than that reported from electron diffraction [ABM69]. Thus, the centers-of-mass distance was assigned as the main point of disagreement between results of fs DFWM and electron diffraction experiments. In contrast to formic acid, acetic acid shows strong recurrences from dimeric species even in the fs DFWM spectra at room temperature. This is explained in terms of different symmetry of the moments-of-inertia tensor, which modulates the intensity of RRs (the fs DFWM signal is in general stronger from symmetric species). Due to the symmetric nature of the acetic acid dimer, only the sum (B+C) of the rotational constants has been extracted. The changes of geometrical parameters upon dimer formation have been analyzed for, both, formic and acetic acid. A heat-pipe oven has been used in order to overcome the main drawback of fs DFWM spectroscopy – the square dependence of the signal intensity on the sample number density. Two-ring molecules (cyclohexylbenzene, para-cyclohexylaniline and nicotine) with low vapor pressure (<0.1 mbar) at room temperature have been investigated. From the analysis of the experimental and ab-initio results for CHB and pCHA a nearly perpendicular conformation of the aromatic vs. cyclohexane ring for both system is inferred. The enlargement of the benzene ring of CHB in the electronically excited state (S1) has been found to cause the smaller rotational constants in S1. This conclusion has been drawn from the comparison of the ground and electronically excited state experimental rotational constants in combination with ab-initio calculations. The extraction of precise structural information for nicotine was not possible due to it weak fs DFWM signal. However, the fact that fs DFWM technique can be applied to conformational analysis of molecular species in an equilibrium mixture opens other applications for this kind of spectroscopy. In general the results obtained in this work show that the fs DFWM technique, being an experimental implementation of RCS, provides one with an important tool for structural analysis of molecular species in the gas phase in particular for the species to which microwave spectroscopy can not be applied. It gives spectra with excellent signal-to-noise ratio even at low number density samples expanded in a seeded supersonic jet. It provides an alternative and innovative approach towards rotational Raman spectroscopy of large polyatomic molecules applicable under various experimental conditions (broad temperature and pressure range). With the introduction of femtosecond (10-15s) laser pulses (usually picosecond (10-12s) laser pulses were used in RCS) an improvement in time-resolution and therefore in precision for the rotational constants by more than one order of magnitude has been achieved. Molecular systems in the ground electronic state without permanent dipole moment and chromophore can be studied with high precision, providing thereby molecular benchmark systems for the electronic structure theory. As has been shown, the study of molecular clusters by fs DFWM spectroscopy is possible, but its potential are restricted by the square dependence of the fs DFWM signal from the sample number density, which is even more important for supersonic jet expansions. Here, the application of near-resonant and resonant FWM schemes should help in order to compensate for the low sample concentration. With the introduction of the heat pipe oven for fs DFWM experiments, the investigation of large nonvolatile molecules under equilibrium conditions is possible now. In our laboratory the first results on the structural analysis of different conformers of pyrrolidine in the gas phase have been obtained [MaR04]. This method can have even more prospects for the structural investigations of large molecular species in combination with new non-thermal gas phase sources for nonvolatile molecules, like laser desorption [CTL89], laser oblation [MHL83], electrospray [FMM90], laser induced liquid beam ion desorption [KAB96, Sob00] etc. A very recent application of the fs DFWM technique is the investigation of the influence of strong laser fields on molecular gas phase sample, which could range from active alignment [PPB03] over molecular deformation to field ionization [CSD03]. In regards to future development in fs DFWM spectroscopy for more complex molecules one has to take into account, how large amplitude motions such as the van der Waals vibrations or internal rotation (see section 6.4.2) affect the rotational coherences. In any case, femtosecond Degenerate Four-Wave Mixing as experimental implementation of Rotational Coherence Spectroscopy can be considered as an innovative, developing, and powerful method for the structural investigation of the molecular species, which are hard to study by classical frequency-resolved spectroscopy [FeZ95a, Dan01, Rie02].
Nitric oxide (NO) represents a short-lived mediator that pivotally drives keratinocyte movements during cutaneous wound healing. In this study, we have identified p68 DEAD box RNA helicase (p68) from a NO-induced differential keratinocyte cDNA library. Subsequently, we have analyzed regulation of p68 by wound-associated mediators in the human keratinocyte cell line HaCaT. NO, serum, growth factors and pro-inflammatory cytokines were potent inducers of p68 expression in the cells. p68 was constitutively expressed in murine skin, but rapidly down-regulated upon injury. The down-regulation appeared to be transient, as p68 protein expression increased again after the inflammatory phase of repair. However, p68 protein expression did not completely disappear during wound inflammation, as immunohistochemistry and cell fractiona tion analysis revealed a restricted localization of p68 in keratinocyte nuclei of the developing epithelium. In line, cultured human (HaCaT) and murine (PAM 212) keratinocyte cell lines showed a nuclear localization of the helicase. Moreover, confocal microscopy revealed a strong localization of p68 protein within the nucleoli of the keratinocytes. Functional analyses demonstrated that p68 strongly participates in keratinocyte proliferation and gene expression. Keratinocytes that constitutively overexpressed p68 protein were characterized by a marked increase in serum-induced proliferation and vascular endothelial growth factor (VEGF) expression, whereas down-regulation of endogenous p68 using small interfering RNA (siRNA) markedly attenuated serum-induced proliferation and VEGF expression. Altogether, our results suggest a tightly controlled expression and nucleolar localization of p68 in keratinocytes in vitro and during skin repair in vivo that functionally contributes to keratinocyte proliferation and gene expression.
Reliable communication in the central nervous system requires the precise control of the duration and the intensity of neurotransmitter action at specific molecular targets. After their release at the synapse, neurotransmitters activate pre- and/or postsynaptic receptors. To terminate synaptic transmission, neurotransmitters are in turn inactivated by either enzymatic degradation or active uptake into neuronal and/or glial cells by neurotransmitter transporters. In the present study, two types of membrane proteins involved in transcellular signal transduction were investigated, the P2X receptors, which are ATP-gated ion channels and the glutamate transporters of the EAAT family. The first part of this study is concerned with the targeting and anchoring of P2X receptors at specific locations. P2X receptors play a role of fast excitatory neurotransmission to extracellular ATP in both the peripheral and central nervous system. For several ligand-gated ion channel, like glycine receptors or nicotinic acetylcholine receptors, it is known that specific binding proteins exist, which are involved in receptor trafficking and anchoring of the receptors at appropriate sites on the synapse. Within the P2X family, amino acid homology is scattered over the protein sequence excepted of the cytoplasmic C-terminal tails, which do not share significant sequence similarity, indicating that they might provide peculiar properties to the respective receptor isoforms. Using GST fusion proteins containing the C terminal end of the P2X2A, P2X5 and P2X7 subunits as baits, ßIII tubulin was identified by MALDI-TOF mass spectrometry as a direct interacting partner of P2X2A. ßIII tubulin did not interact with P2X5 nor with P2X7. The tubulin binding motif of P2X2A could be confined to a 42 amino acid long region ranging from amino acid 371 to 412 of the complete P2X2A subunit. This domain, which includes a total of six serine residues and twelve proline residues, interestingly overlaps to a significant extent with a 69 amino acid long sequence, which is lacking in P2X2B, a splice variant of P2X2A. P2X2B receptors are known to desensitize - significantly faster than P2X2A receptors. The interaction of the P2X2A receptor with ßIII tubulin may contribute to receptor desensitization as well as tethering of the P2X2A receptor at specialized regions of the cell. In a second part of this work, the oligomeric state of two distantly related glutamate transporters, the human glial glutamate transporter hEAAT2, and the glutamate transporter ecgltP of E.coli was determined. Excitatory amino acid transporters (EAATs) buffer and remove synaptically released L-glutamate and maintain its concentration below neurotoxic levels. Mammalian glutamate transporter subunits are known to form homomultimers, but controversial numbers of subunits per transporter complex have been reported, ranging from 2-5. Both hEAAT2 and ecgltP proteins expressed at high levels in Xenopus laevis oocytes, from which they were purified in a [35S]methionine-labeled form under nondenaturing conditions by metal affinity chromatography. Blue native PAGE analysis revealed that both the hEAAT2 and ecgltP transporters exist exclusively as homogenous populations of homotrimers in Xenopus oocytes. The trimeric structure was corroborated by chemical crosslinking. Also, ecgltP purified as a recombinant protein from its natural host E.coli migrated as a trimeric protein on blue native PAGE gels. The conservation of the quaternary structure from prokaryotes to mammals assigns an important functional role to the trimeric structure. Glutamate transporters are known to exhibit a dual mode of operation by functioning both as glutamate Na+/K+/H+ co-transporters and as anion channels. It is intriguing to speculate that the EAAT monomer is responsible for the secondary active transport of glutamate, whereas a barrel-like arrangement of the three subunits forms a central anion pore mediating anion conductivity.
The detailed mechanism of the 20 S proteasome from Thermoplasma acidophilum is unknown. Substrates are degraded processively to small fragments without the release of intermediates, but the basis for this unique degradation mode remains obscure. The proteasome is a molecular machine, but how the different nanocompartments interplay and whether more than one substrate can be treated simultaneously has not been elucidated yet. To address these questions we had to disable the functionality of one aperture in order to dissect whether the other pore can compensate for the loss. As it is challenging to introduce mutations solely around one pore aperture of the highly symmetrical construct, we chose a novel approach by unique orientation of the proteasome at interfaces. For this purpose we purified recombinant 20 S proteasomes, where hexahistidine tags were fused either around the entrances or at the sides. According to electron microscopic studies we immobilized these constructs uniformly either end-on or side-on at metal-chelating interfaces (lipid vesicles, lipid monolayers and self-assembled thiol monolayers). Degradation of small fluorogenic peptides and large proteins like casein was analyzed. Small substrates were degraded with comparable activity by free and immobilized proteasomes, irrespective of their orientation. Thus it can be assumed that peptides can pass the sealed entrance of the 'dead-end' proteasome. However, larger substrates like fluorescently labeled casein were processed near the temperature optimum by side-on immobilized and soluble proteasomes with threefold activity compared to end-on immobilized proteasomes. Hence it can be concluded that one pore is sufficient for substrate entry and product release. In other words, the pore and antechamber can fulfil a triple function in the import and unwinding of substrates and the egress of products. With means of surface plasmon resonance the exact substrate/proteasome stoichiometry could be determined to ~1 for 'dead-end' proteasomes and ~2 for side-on immobilized (active and inactive) proteasomes. Most importantly, a fit with the Hill equation revealed positive cooperativity for side-on immobilized (Hill coefficient ~2) in contrast to end-on immobilized proteasomes (Hill coefficient ~1). Thus in case of soluble proteasomes two substrates bind presumably in opposite antechambers with positive cooperativity. The off-rate of casein as substrate is twofold for the active side-on immobilized proteasome in comparison to the end-on immobilized proteasome. The exact 2:1 stoichiometry of the off-rates equals the ratio of exit pathways amenable in case of side-on orientated versus 'dead-end' immobilized proteasomes. Thus crevices along the cylindrical body of the 20 S proteasome seem not to participate in the egress of small products. An inactive proteasome mutant displays a concentration-dependent off-kinetic against casein. Accordingly, the off-rate of the bisubstrate:proteasome complex can be attributed around half the value of the monosubstrate:proteasome complex. Consequently, substrates exit the inactive proteasome via the route of access due to obstruction of the trans side with an entering substrate. Hence the active proteasomes have to chop substrates down to small fragments prior to release through both pores. Thus the processive degradation mode might result from positive binding cooperativity. The on-rate constants for casein suggested that substrate association represents a two-step process comprising a rate-limiting translocation step and a fast binding step. As fluorescence cross-correlation revealed that two substrates can be co-localized in the proteasome and bind successively with increasing affinity (KD,1 = 8 µM versus KD,2 = 700 nM), an allosteric transition in the proteasome can be assumed. Combining our results with the data from other research groups led to a mechanistic model for the 20 S proteasome. Accordingly, the first substrate undergoes a slow translocation step, binds in the antechamber and diffuses subsequently to the catalytic centers, where it is degraded. By switching on the catalytic activity, the pores at both termini are dilated via conformational changes. Hence entry of the second substrate into the proteasome is facilitated due to omission of the rate-determining translocation step. The second substrate is either accommodated in the antechamber before it is processed (alternating degradation) or, most probably, is directly threaded into the central cavity (simultaneous degradation). As effusing peptides compete with entering proteins for binding in the antechamber, the pores are kept in an open state. After finishing digestion the pores are closed and a new degradation cycle can be reinitiated. In summary, substrate association with the proteasome underlies an ordered alternating binding mechanism in contrast to the random mode of degradation. Thus the two-stroke engine offers the advantage of speeding up degradation without enhancing complexity.
Transmembrane proteins play crucial roles in biological systems as active or passive channels and receptors. Experimentally only few structures could be determined so far. Gaining structural insights enables besides a general understanding of biological mechanisms also further processing such as in drug design. Due to the lack of experimental data, reliable theoretical predictions would be of high value. However, for the same reason, missing data, the knowledge-based class of prediction methods that is well established for soluble proteins can not be applied. The goal of predicting transmembrane protein structures with ab initio methods demands locating the free energy minimum. Main difficulties here are, first, the computational costs of explicitly calculating all involved interactions and, second, providing an algorithm that is capable of finding the minimum within an extremely complex and rugged energy landscape. We have developed promising energy functions that describe the interactions of amino acids on a residue level, reducing computational costs while still containing most information on the atomistic level. We have also found a way to describe the interaction of the residues with its surrounding in a realistic manner by distinguishing residues exposed to the environment from those buried within helices using a sphere algorithm. The sphere algorithm can also be applied for a different purpose: one can measure how densely sidechains are packed for certain helical conformations, and thereby get an estimate of the sidechain entropy. In addition, overcrowding effects can be identified which are not well-described by the energy functions due to the pairwise calculation. To determine the absolute free energy minimum, we assume the helices to be located on an equidistance grid with slightly larger distances than to be expected. Optimizing the helices on the grid provides a starting point that should enable common minimizing algorithms, gradient-based or not, to find the absolute minimum beyond the grid. To simulate the dynamics of the helices on large time scales, we split them into rigid body dynamics and internal dynamics in terms of the dihedrals. The former one is well-known with its inherent problem of numerical drift and plenty of approaches to it, among which we have chosen the quaternions to represent the rotation of the rigid bodies. The latter one requires a detailed analysis of the torque size exerted on the dihedrals caused by the forces acting on the residues.
Die 5 Lipoxygenase (5 LO) ist das Schlüsselenzym in der Synthese von Leukotrienen. Sie wird auf transkriptioneller und posttranskriptioneller Ebene reguliert. Die Differenzierung myeloider Zelllinien mit 1,25-Dihydroxyvitamin D3 (1,25(OH)2D3) und transformierendem Wachstumsfaktor beta (TGFbeta) führt zu einer Erhöhung der 5 LO mRNA-, Protein-Bildung und der zellulären Enzymaktivität. Hier wurde gezeigt, dass dabei reife, nicht jedoch prä-mRNA der 5 LO im Zytosol und im Zellkern stark angereichert wird und dass beide Agentien in die mRNA-Prozessierung eigreifen. Obwohl die Bindung von VDR-Retinoid-X-Rezeptor (RXR)-Heterodimeren an Bindungsstellen im 5 LO-Promotor mittels DNAseI-Footprinting und EMSAs nachgewiesen wurde, konnten Reportergene unter der Kontrolle des 5 LO-Promotors in transienten und stabilen Transfektionen durch 1,25(OH)2D3/TGFbeta nicht stimuliert werden. Offensichtlich wird die Induktion der Expression der 5 LO durch 1,25(OH)2D3/TGFbeta durch Elemente außerhalb des Promotors vermittelt. In transienten Transfektionen führte der Einbau der kodierenden Sequenz der 5 LO in Luziferase-Plasmide bei Cotransfektion von VDR/RXR zu einer 5 fachen Induktion der Reportergen-Aktivität durch 1,25(OH)2D3/TGFbeta, was durch zusätzlichen Einbau der letzten vier Introns auf eine 13-fache Erhöhung gesteigert wurde. Der VDR zeigte einen Ligand-unabhängigen Effekt. Diese Reportergen-Effekte waren promotorunabhängig und von der kodierenden Sequenz gesteuert. RT-PCR-Analyse wies auf eine Deletion von Teilen der kodierenden Sequenz im Laufe der mRNA-Prozessierung hin, was durch 1,25(OH)2D3/TGFbeta verhindert wird. Auch Cotransfektion der TGFbeta-Effektoren Smads 3/4 führte in Abhängigkeit von der kodierenden Sequenz und in geringerem Maße von der 3'-UTR und den Introns J M, aber unabhängig vom Promotor, zu einer starken Erhöhung der Reportergenaktivität. Die 5 LO-Expression wird in den untersuchten Zellen vermutlich durch posttranskriptionelle Prozesse (Splicing, mRNA-Reifung) herunterreguliert, während 1,25(OH)2D3/TGFbeta die Expression der 5 LO durch eine Gegenregulation zu erhöhen, an der Komplexe beteiligt sind, die vermutlich Smads, VDR-RXR-Dimere, andere Transkriptionsfaktoren, Coaktivatoren, RNA-Polymerase II und Splicing-Faktoren enthalten. Hyperacetylierung des 5 LO-Promoters durch Inkubation mit mit dem Histondeacetylase-Inhibitor TsA führte zu einer transkriptionellen Aktivierung. Die kodierende Sequenz (und die Introns) wirkt diesem Effekt vermutlich durch die Rekrutierung von HDACs an VDR oder Smads, die direkt oder indirekt an die kodierende Region binden, entgegen.
The transporter associated with antigen processing (TAP) plays a pivotal role in the adaptive immune response against virus-infected or malignantly transformed cells. As member of the ABC transporter family, TAP hydrolyzes ATP to energize the transport of antigenic peptides from the cytosol into the lumen of the endoplasmic reticulum. TAP forms a heterodimeric complex composed of TAP1 and TAP2 (ABCB2/3). Both subunits contain a hydrophobic transmembrane domain and a hydrophilic nucleotide-binding domain. The aim of this work was to study the ATP hydrolysis event of the TAP complex and gain further insights into the mechanism of peptide transport process. To analyze ATP hydrolysis of each subunit I developed a method of trapping 8- azido-nucleotides to TAP in the presence of phosphate transition state analogs followed by photocross-linking, immunoprecipitation, and high-resolution SDS-PAGE. Strikingly, trapping of both TAP subunits by beryllium fluoride is peptide-specific. The peptide concentration required for half-maximal trapping is identical for TAP1 and TAP2 and directly correlates with the peptide-binding affinity. Only background levels of trapping were observed for low affinity peptides or in the presence of the herpes simplex viral protein ICP47, which specifically blocks peptide binding to TAP. Importantly, the peptideinduced trapped state is reached after ATP hydrolysis and not in a backward reaction of ADP binding and trapping. In the trapped state, TAP can neither bind nor exchange nucleotides, whereas peptide binding is not affected. In summary, these data support the model that peptide binding induces a conformation that triggers ATP hydrolysis in both subunits of the TAP complex within the catalytic cycle. The role of the ABC signature motif (C-loop) on the functional non-equivalence of the NBDs was investigated. The C-loops of TAP transporter contain a canonical C-loop (LSGGQ) for TAP1 and a degenerated ABC signature motif (LAAGQ) for TAP2. Mutation of the leucine or glycine (LSGGQ) in TAP1 fully abolished peptide transport. TAP complexes with equivalent mutations in TAP2 showed however still residual peptide transport activity. To elucidate the origin of the asymmetry of the NBDs of TAP, we further examined TAP complexes with exchanged C-loops. Strikingly, the chimera with two canonical C-loops showed the highest transport rate whereas the chimera with two degenerated C-loops had the lowest transport rate, demonstrating that the ABC signature motifs control the peptide transport efficiency. All single-site mutants and chimeras showed similar activities in peptide or ATP binding, implying that these mutations affect the ATPase activity of TAP. In addition, these results prove that the serine of the C-loop is not essential for TAP function, but rather coordinates, together with other residues of the C-loop, the ATP hydrolysis in both nucleotide-binding sites. To study the coupling between the ATP binding/hydrolysis and the peptide binding, the putative catalytic bases of the TAP complex were mutated to generate the so-called EQ mutants. The mutations did not influence the peptide-binding ability. Dimerization of the NBDs of EQ mutants upon ATP binding does not alter the peptide binding property. At 27°C, both ATP and ADP could induce the loss of peptide-binding ability (Bmax) only in the variants bearing a mutated TAP2. Further studies are required to deduce at which stage in the catalytic cycle the peptide-binding site is affected. In addition, mutation of the putative catalytic base of both subunits showed a magnesium-dependent peptide transport activity, demonstrating these mutants did not abolish the ATP hydrolysis. Thus, the function of this acidic residue as the catalytic base is not likely to be universe for all ABC transporters.
Ligands of Iron-Sulphur Cluster N2: In this work the ubiquinone reducing catalytic core of NADH:ubiquinone oxidoreductase (complex I) from Y. lipolytica was studied by a series of point mutations replacing conserved histidines or arginines in the 49-kDa subunit. Although the missing 4th ligand of cluster N2 could not be found in the 49-kDa subunit of complex I, it was clearly demonstrated that iron-sulphur cluster N2 resides directly on the interface between the PSST and 49-kDa subunits. The results presented in this work show that residues in the 49-kDa subunit have strong influence on this redox centre and also on catalytic activity. The strong influence of Arg-141 and His-226 residues in 49-kDa subunit on this cluster can be deducted from complete loss of N2 signals in EPR spectra such as in case of mutants H226A and R141A. In the case of mutant H226M the EPR signal from cluster N2 was shifted and cluster N2 even lost the pH dependence of its redox midpoint potential and became more similar to the other so called 'isopotential' clusters. Specifically in the case of mutants R141M and R141K the characteristic signature of cluster N2 became undetectable in EPR spectra. However, specific dNADH:DBQ oxidoreductase activity that could be inhibited with the specific complex I inhibitors DQA and rotenone was not absolutely abolished but rather reduced. These reductions in complex I activity did not correspond to similar reductions in the specific EPR signal of cluster N2 as it was observed in the His-226 mutant series. No indications could be found that these mutations had modified the magnetic properties of cluster N2, resulting in different EPR spectra. From these observations it could be concluded that both mutants R141K and R141M virtually or entirely lack iron-sulphur cluster N2. The rates in complex I activity could be reconciled with electron transfer theory: After removal of a single redox centre in a chain, electron transfer rates are predicted to be still much faster than steady-state turnover of complex I. These results from mutants R141K, R141M and also the result from mutant H226M that protons are being pumped even if the redox midpoint potential of cluster N2 is not pH dependent questions the prominent role in the catalytic mechanism of complex I that has been ascribed to cluster N2. Histidine 91 and 95 were found to be absolutely essential for activity of complex I since in both mutants complex I was fully assembled and artificial NADH:HAR activity was parental whereas complex I specific dNADH:DBQ activity was abolished. The signal from cluster N2 in EPR spectra was parental for all His-91 and -95 mutants. Mutations at the C-terminal arginine 466 affected ubiquinone affinity and inhibitor sensitivity but also destabilised complex I. All these results provide further support for a high degree of structural conservation between the 49-kDa subunit of complex I and the large subunit of water soluble [NiFe] hydrogenases. Remodelling of Human Pathogenic 49-kDa Mutations in Y. lipolytica: Y. lipolytica has been proven a good system for studying complex I properties and thus also for studying defects that occur in humans. In this work pathogenic mutations in the 49-kDa subunit of complex I were recreated and studied. The P232Q mutant showed non-assembly of complex I and this is probably the cause why this mutation was lethal in patients. The mutants R231Q and S416P were parental for the content, artificial and also specific complex I activity, Km for DBQ and IC50 for DQA. From these results we can conclude that these two residues Arg-228 and Ser-413 in mammalian cells have specific structural importance for the 49-kDa subunit even if they are not directly involved in catalytic process.
This dissertation study argues that 'policy advice formation', as a discourse development, is a differentiated hybrid resultant from merger between comparative education and policy studies disciplines. Through discourse analysis based on John Creswell's format, this study identifies revisions, restatements and shifts in emphasis of theories, methodological models and challenge topics of comparative education and policy studies. Findings which display the development of policy advice formation' discourse. In conclusion, this study found differential patterns seemingly formed because of collaborative affects of standardization in education science knowledge expressed within discourse.
In the present study the cryo-immunogold technique was used and optimized for investigating the ultrastructure and immunolabeling of synaptic proteins. It is evidently a suitable method for the localization of membrane proteins since the antigens are not treated with any chemical denaturation before immunolabeling except for the fixation and since the antigens are directly exposed to the surface of the cryo-ultrasections. The v-SNARE VAMP II and the vesicle-associated proteins SV2 and Rab3A were detected extensively at small vesicles in the mossy fiber terminals. The t-SNARE SNAP-25, and N-type and P/Q type Ca2+ channels were allocated to the plasma membrane both at the active zone and outside the active zone. SNAP-25 and N-type Ca2+ channels appeared also at synaptic vesicles. A significantly increased immunolabeling of VAMP II, SV2, Rab3A, SNAP-25 and N-type Ca2+ channels was found at the active zones of fast synapses, indicating a concentration of these proteins at sites of exocytosis. The widespread distribution of the t-SNARE SNAP-25 at the axonal plasma membrane reveals that membrane-targeting specificity cannot be determined solely by v/t-SNARE interactions. Additional control components are required to assure the docking and exocytosis of the synaptic vesicles at active zones. The novel protein Bassoon was only found at active zones of central synapses and showed the highest specific labeling among all proteins investigated. Its labeling pattern implies an association of Bassoon with the presynaptic dense projections, the structural guide for vesicle exocytosis. The involvement of Bassoon in the organization of the neurotransmitter release site suggests that Bassoon may play an important role in determining the specificity of vesicle docking and fusion. In the neurosecretory endings of neurohypophysis the synaptic proteins VAMP II, SNAP- 25, SV2, Rab3A, and the N-type Ca2+ channels showed a preferential labeling over microvesicles. Moreover, the immunolabeling intensity of these proteins over microvesicles corresponded closely to that over synaptic vesicles. This suggests that these synaptic proteins share an identical association with synaptic vesicle and microvesicles. A significant labeling of SNAP-25, the N-type Ca2+ channels and VAMP II was also detected at the plasma membrane near the clustered microvesicles, indicating the competence of microvesicles for docking and exocytosis along the plasma membrane in the absence of active zones. No significant labeling of VAMP II, SNAP-25, SV2 and N-type Ca2+ channel was observed at the membrane of neurosecretory granules. This is in agreement with the notion that synaptic vesicles and microvesicles possess regulatory mechanisms for exocytosis different from those of granules. In contrast, a/ß-SNAP and NSF were found on the granules, and Rab3A and the P/Q-type Ca2+ channels on granules in a subset of terminals. Rab3A is associated specifically with the oxytocin-containing granule population. Interestingly, some plasma membrane proteins, such as SNAP-25 and even N-type Ca2+ channels and P/Q-type Ca2+ channels, were observed not only at the plasma membrane but also at the vesicular organelles. This suggests that these vesicular organelles may be involved in transporting newly synthesized proteins from the soma to the plasma membrane of the terminal. Furthermore, the vesicular pool of the Ca2+ channels may serve in the stimulationinduced translocation into the plasma membrane when required. Using the conventional preembedding method with Epon and the post-embedding method with LR Gold, VAMP II was localized at vesicular organelles of varying size and on horseradish peroxidase filled endocytic organelles in cultured astrocytes, with and without stimulation in the presence of the horseradish peroxidase. This indicates that VAMP II is involved in the cycle of vesicular exocytosis and endocytosis in astrocytes. U373 cells are capable of expressing all three members of the synaptic SNARE complex (v-SNARE VAMP II, t-SNARE syntaxin I and SNAP25). This indicates the competence of U373 to carry out regulated exocytosis by means of the classical SNARE mechanism. In addition, the ubiquitous v-SNARE cellubrevin and the endosome-associated small GTPbinding protein Rab5 could be expressed in U373 cells. All recombinant synaptic proteins investigated in U373 cells revealed a punctuate cellular distribution under the fluorescence microscope, suggesting that they are mainly associated with intracellular compartments. The cryo-electron microscopy provided direct evidence for the association of all expressed proteins with electron-lucent vesicular organelles. It further supports the potential of U373 MG cells to release low molecular weight messengers by a regulated exocytosis mechanism. In addition, myc-VAMP II was found on dispersed granules. Probably, VAMP II also participates in the exocytosis event of granules in U373 cells. Gold labeling for the two presumptive t-SNAREs syntaxin I and SNAP-25 in U373 cells was confined to the vesicular organelles. At the ultrastructural level no significant labeling was identified at the plasma membrane. The high level of colocalization of the two SNARE proteins VAMP II and syntaxin I in the cell body and in cell processes suggests that the two proteins are mostly sorted into identical vesicular organelles. A partial colocalization of VAMP II and cellubrevin as well as of VAMP II and Rab5 was observed under the fluorescence microscope. At the ultrastructural level, a colocalization of VAMP II and cellubrevin as well as of VAMP II and Rab5 was found on some clustered vesicles. The partial colocalization of VAMP II and cellubrevin implies that they similarly function as v-SNAREs. The partial colocalization of Rab5 with VAMP II in U373 cells suggests that the endosomal protein Rab5 is associated with VAMP II-containing organelles during some stages of their life cycle.