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The cytochrome bc1 complex is a dimeric enzyme of the inner mitochondrial membrane that links electron transfer from ubiquinol to cytochrome c by a protonmotive Q cycle mechanism in which ubiquinol is oxidized at one center in the enzyme, referred to as center P, and ubiquinone is rereduced at a second center, referred to as center N. To better understand the mechanism of ubiquinol oxidation, we have examined catalytic activities and pre-steady-state reduction kinetics of yeast cytochrome bc1 complexes with mutations in cytochrome b that we expected would affect oxidation of ubiquinol. We mutated two residues thought to be involved in proton conduction linked to ubiquinol oxidation, Tyr132 and Glu272, and two residues proposed to be involved in docking ubiquinol into the center P pocket, Phe129 and Tyr279. Substitution of Phe129 by lysine or arginine yielded a respiration-deficient phenotype and lipid-dependent catalytic activity. Increased bypass reactions were detectable for both variants, with F129K showing the more severe effects. Substitution with lysine leads to a disturbed coordination of a b heme as deduced from changes in the midpoint potential and the EPR signature. Removal of the aromatic side chain in position Tyr279 lowers the catalytic activity accompanied by a low level of bypass reactions. Pre-steady-state kinetics of the enzymes modified at Glu272 and Tyr132 confirmed the importance of their functional groups for electron transfer. Altered center N kinetics and activation of ubiquinol oxidation by binding of cytochrome c in the Y132F and E272D enzymes indicate long range effects of these mutations.
There is a renewed interest in pseudoreceptor models which enable computational chemists to bridge the gap of ligand- and receptor-based drug design. We developed a pseudoreceptor model for the histamine H4 receptor (H4R) based on five potent antagonists representing different chemotypes. Here we present the selection of potential ligand binding pockets that occur during molecular dynamics (MD) simulations of a homology-based receptor model. We present a method for prioritizing receptor models according to their match with the consensus ligand-binding mode represented by the pseudoreceptor. In this way, ligand information can be transferred to receptor-based modelling. We use Geometric Hashing to match three-dimensional points in Cartesion space. This allows for the rapid translation- and rotation-free comparison of atom coordinates, which also permits partial matching. The only prerequisite is a hash table, which uses distance triplets as hash keys. Each time a distance triplet occurring in the candidate point set which corresponds to an existing key, the match is represented by a vote of the respective key. Finally, the global match of both point sets can be easily extracted by selection of voted distance triplets. The results revealed a preferred ligand-binding pocket in H4R, which would not have been identified using an unrefined homology model of the protein. The key idea was to rely on ligand information by pseudoreceptor modelling.
Ubiquitin fold modifier 1 (UFM1) is a member of the ubiquitin-like protein family. UFM1 undergoes a cascade of enzymatic reactions including activation by UBA5 (E1), transfer to UFC1 (E2) and selective conjugation to a number of target proteins via UFL1 (E3) enzymes. Despite the importance of ufmylation in a variety of cellular processes and its role in the pathogenicity of many human diseases, the molecular mechanisms of the ufmylation cascade remains unclear. In this study we focused on the biophysical and biochemical characterization of the interaction between UBA5 and UFC1. We explored the hypothesis that the unstructured C-terminal region of UBA5 serves as a regulatory region, controlling cellular localization of the elements of the ufmylation cascade and effective interaction between them. We found that the last 20 residues in UBA5 are pivotal for binding to UFC1 and can accelerate the transfer of UFM1 to UFC1. We solved the structure of a complex of UFC1 and a peptide spanning the last 20 residues of UBA5 by NMR spectroscopy. This structure in combination with additional NMR titration and isothermal titration calorimetry experiments revealed the mechanism of interaction and confirmed the importance of the C-terminal unstructured region in UBA5 for the ufmylation cascade.
The transcriptional regulator far upstream binding protein 1 (FUBP1) is essential for fetal and adult hematopoietic stem cell (HSC) self-renewal, and the constitutive absence of FUBP1 activity during early development leads to embryonic lethality in homozygous mutant mice. To investigate the role of FUBP1 in murine embryonic stem cells (ESCs) and in particular during differentiation into hematopoietic lineages, we generated Fubp1 knockout (KO) ESC clones using CRISPR/Cas9 technology. Although FUBP1 is expressed in undifferentiated ESCs and during spontaneous differentiation following aggregation into embryoid bodies (EBs), absence of FUBP1 did not affect ESC maintenance. Interestingly, we observed a delayed differentiation of FUBP1-deficient ESCs into the mesoderm germ layer, as indicated by impaired expression of several mesoderm markers including Brachyury at an early time point of ESC differentiation upon aggregation to EBs. Coculture experiments with OP9 cells in the presence of erythropoietin revealed a diminished differentiation capacity of Fubp1 KO ESCs into the erythroid lineage. Our data showed that FUBP1 is important for the onset of mesoderm differentiation and maturation of hematopoietic progenitor cells into the erythroid lineage, a finding that is supported by the phenotype of FUBP1-deficient mice.
Retrograde transport of NF-κB from the synapse to the nucleus in neurons is mediated by the dynein/dynactin motor complex and can be triggered by synaptic activation. The caliber of axons is highly variable ranging down to 100 nm, aggravating the investigation of transport processes in neurites of living neurons using conventional light microscopy. We quantified for the first time the transport of the NF-κB subunit p65 using high-density single-particle tracking in combination with photoactivatable fluorescent proteins in living mouse hippocampal neurons. We detected an increase of the mean diffusion coefficient (Dmean) in neurites from 0.12±0.05 to 0.61±0.03 μm2/s after stimulation with glutamate. We further observed that the relative amount of retrogradely transported p65 molecules is increased after stimulation. Glutamate treatment resulted in an increase of the mean retrograde velocity from 10.9±1.9 to 15±4.9 μm/s, whereas a velocity increase from 9±1.3 to 14±3 μm/s was observed for anterogradely transported p65. This study demonstrates for the first time that glutamate stimulation leads to an increased mobility of single NF-κB p65 molecules in neurites of living hippocampal neurons.
Das genetische Material der Zellen besteht aus Molekülketten der Desoxyribonukleinsäure (DNA), die ein Träger der Erbinformation ist. In normalen Körperzellen wird die Erbinformation der DNA in eine andere Molekülkette, die sogenannte Ribonukleinsäure (RNA), übersetzt. Die RNA reguliert die Bildung von neuem Protein in der Zelle. Dass die RNA nicht bloß ein „Stempel“ ist, der die Informationen der DNA weitervermittelt, darin sind sich die Experten heute einig. RNA-Moleküle können Informationen speichern, katalytische Aktivitäten entfalten, sich perfekt tarnen, und sie regulieren auch als Produkt ihre eigene Synthese. Manche Viren enthalten ebenfalls RNA (oder DNA) und können so den Produktionsapparat der Zelle täuschen. Erkenntnisse über die Wechselwirkung dieser RNA mit natürlichen und synthetischen Liganden können zur Suche nach potentiellen Wirkstoffen beitragen. Nukleinsäuren sind lineare Biopolymere von grundlegenden Untereinheiten, die Nukleotide genannt werden und aus Adenin (A), Cytosin (C), Guanin (G), Urazil (U), und Thymin (T) zusammengesetzt sind. Sie sind jedoch in der Lage sich zu falten und so eine Doppel-Helixstruktur auszubilden. Diese besteht größtenteils aus den bekannten "Watson-Crick-Basenpaaren" (G-C und A-U oder A-T), die zur Stabilität der Struktur beitragen, sowie aus den weniger stabilen G-U-Paaren. Durch die Wechselwirkung zwischen verschiedenen Sekundärstrukturelementen entstehen Tertiärstrukturelemente, deren Struktur und Dynamik oft nur schwer experimentell zu bestimmen sind. Fortschritte in der RNA-Strukturanalyse wurden durch Röntgenkristallographie und Kernresonanzspektroskopie (NMR) möglich. Durch die Röntgenkristallographie wurden viele RNA-Eigenschaften festgestellt. Allerdings besteht keine Kristallstruktur für alle mögliche Einzelnfaser-RNA-Haarnadeln, weil diese immer dazu neigen, in eine linearen doppelte Faserform zu kristallisieren, die geringe biologische Bedeutung hat. Außerdem wurde mit Hilfe der NMR-Spektroskopie das dynamische Verhalten von RNA, z.B. Entfaltungsprozesse bei ansteigender Temperatur, beobachtet. Jedoch erlauben diese experimentellen Daten oft keine direkte mikroskopische Beschreibung der molekularen Prozesse. Molekulardynamik (MD)-Simulationen von biologischen Systemen ermöglichen es hingegen, diese Prozesse in atomischem Detail zu untersuchen. Die MD-Simulation beschreibt ein molekulares System auf atomarer Ebene mit Hilfe der klassischen Mechanik. Kräfte werden von empirischen Potentialen abgeleitet. Sie liefern zeitabhängige Trajektorien, die sich aus den Newton'schen Bewegungsgleichungen ergeben. Durch verbesserte Computerleistung, bessere Kraftfelder, und neu entwickelte genauere Methoden stimmen heutzutage MD-Simulationen von RNA mit experimentellen Daten immer besser überein. In meiner Doktorarbeit wurden MD-Simulationen durchgeführt um die Dynamik, die Struktur und insbesondere die Stabilität von RNA-Hairpins theoretisch zu beschreiben, um so ein erweitertes Verständnis für die dynamischen Vorgänge zu erhalten. Auch der SFB 579 der Universität Frankfurt beschäftigt sich mit RNA-Systemen. Erforscht wird unter anderem der D-Loop des Coxsackievirus B3 (CVB3), der Virenmyocarditis verursacht. Die Interpretation dieser experimentellen Daten wird durch MD-Simulation möglich. In dieser Arbeit wurden das GROMACS Software-Paket und das AMBER Kraftfeld verwendet, um das strukturelle, dynamische und thermische Verhalten der RNA-Hairpins mit Hilfe von MD-Simulationen auf atomarer Ebene zu untersuchen. Betrachtet wurden die 14-mer RNA-Hairpins, uCACGg und cUUCGg. Die verfügbaren NMR-Strukturen zeigen, dass das uCACGg-Tetraloop auffallend ähnlich in der gesamten Geometrie und den Wasserstoffbindungen zu der experimentellen Struktur des cUUCGg-Tetraloop ist, obwohl die schließende Basenpaarsequenz der beiden Tetraloops unterschiedlich sind. Trotz beachtlicher struktureller Ähnlichkeit unterscheiden sich allerdings die uCACGg und cUUCGg Tetraloops in Funktionalität und Thermostabilität. Zunächst orientiert sich unser erstes Bemühen an der Frage nach einem guten Modell für RNA-Hairpins und Simulationsbedingungen, um die zu untersuchenden RNA-Hairpins in Wasser möglichst realitätsnah zu simulieren. Erstens werden drei Versionen des biomolekularen AMBER-Kraftfelds geprüft, indem man die 60 ns Simulationen des 14-mer uCACGg-Hairpins durchführt. Die simulierten strukturellen Eigenschaften und Atomfluktuationen zeigen hohe Ähnlichkeiten in den drei Kraftfeldern. Darüber hinaus stimmen die von MD-Simulationen berechneten Atomkernabstände mit den experimentellen NMR-Daten gut überein. Die gute Übereinstimmung zwischen den Simulationen und den strukturellen NMR Daten belegt die Fähigkeit des AMBER-Kraftfelds zur Beschreibung der strukturellen Eigenschaft von kleinen RNA-Hairpins. Anschließend werden die Einflüsse der Methoden, welche die langreichweitigen, elektrostatischen Wechselwirkungen beschreiben, auf die strukturellen Eigenschaften untersucht. Insbesondere werden die Ergebnisse der Reaktionfeld-Methode mit denen der Particle Mesh Ewald (PME)-Methode verglichen. Es zeigt sich, dass die PME-Methode die elektrostatischen Wechselwirkungen am besten beschreibt, auch wenn die Simulationen der beiden Methoden Ähnlichkeit in der Struktur-Stabilität und der Atomfluktuation bei niedriger Natriumkonzentration aufweisen. Drittens wird der Kationseffekt auf die RNA-Stabilität untersucht. Betrachtet wurden zwei unterschiedliche Kationen (ein- und zweiwertig) und verschiedene Konzentrationen. Die Simulationen weisen darauf hin, dass sich die Metallionen in der Affinität zum RNA-Hairpin unterscheiden, wenn Na+ und/oder Mg2+ als Gegenionen verwendet werden. Weiterhin wird gezeigt, dass sich die bevorzugten Positionen der Na+-Ionen in der großen Furche (major groove) des RNA-Hairpins befinden. Insbesondere die Anlagerungsort der Na+-Ionen liegen in der Nähe des schließenden Basenpaar U5-G10. Im Vergleich zu Na+-Ionen lagern sich Mg2+-Ionen sowohl an die RNA-Basen U3, A4-U11, und die Phosphat-Gruppe, als auch an das schließenden Basenpaar U5-G10 an. Bestätigt werden die Modelle und Simulationsbedingungen durch den Vergleich von Parametern, die sowohl experimentell als auch durch Simulationen ermittelt werden können. Ferner erlauben MD-Simulationen Einblick in das System, indem sie detallierte Konformations- und andere Verteilungen liefern. In der vorliegenden Arbeit wurden die Einflüsse der Loopsequenz und des schließenden Basenpaares auf die Verteilung der Konformationen, der internen Bewegungen, und auf die Thermostabilität von zwei RNA-Hairpins mit Hilfe dieser Modelle untersucht. Zunächst wurden die strukturellen Eigenschaften bei Raumtemperatur ausgewertet. Die starken strukturellen Ähnlichkeiten und die gute Übereinstimmung mit NMR-Daten bestätigen die Hypothese, dass die zwei Tetraloops zur gleichen “erweiterten” RNA-Familie gehören. Diese zwei Hairpins haben ähnliche Lösemittelzugängliche Oberflächen (solvent accessible surface), wobei deren Lösemittel zugänglichen funktionellen Gruppen unterschiedlich sind. Weiterhin weist das uCACGg-Hairpin eine stärkere Tendenz auf Wasserstoffe abzugeben als das cUUCGg-Hairpin, was in den unterschiedlichen Bindungsaffinitäten zwischen diesen Hairpins und der viralen Protease begründet liegt. Darüber hinaus wurde der Faltungs- und Entfaltungsprozess mit Hilfe der Replica-Exchange-Molekulardynamik-Simulationen untersucht. Diese Untersuchung zielt auf das bessere Verständnis der unterschiedlichen Thermostabilität der Hairpins, indem sie die möglichen Zwischenprodukte im atomaren Detail liefern. Sowohl experimentell als auch von den MD-Simulationen ergibt sich eine Differenz in den Schmelztemperaturen der beiden Hairpins von ungefähr 20 K. Allerdings sind die von MD beobachteten Schmelztemperaturen 20 % höher als die von Experiment zu ansehende Wert. Die Ergebnisse machen deutlich, dass die Schmelztemperaturdifferenz nicht auf die Unterschiede in der Sequenz, in der Struktur, oder in der Dynamik der Loops zurückführen sind, sondern auf die Unterschiede der Basenpaaren in den Stämmen. Weiterhin wird gezeigt, dass sich das uCACGg-Hairpin einerseits kooperativ entfaltet, und die Entfaltung des cCACGg-Hairpins anderseits weniger kooperativ stattfindet. Um die schnelle interne Dynamik der uCACGg- und cUUCGg-Hairpins zu untersuchen, erlauben die Simulationen von 50 ns eine akurate Beschreibung der schnellen internen Bewegung der RNA-Hairpin, obwohl der den Hairpins zugängliche Konformationsraum nicht vollständig abgedeckt wird. Die NMR-Relaxationsparameter, die mit Hilfe der MD-Simulationen zurückgerechnet wurden, bestätigen das Modell und die Simulationsbedingungen der MD-Simulationen. Im Hinblick auf die Übereinstimmung kann man den besten Ansatz zur Berechnung der NMR-Ordnungsparameter bestimmen. In dieser Arbeit wurden drei verschiedene Ansätze angewandt, nämlich das Fitting von 100 ps auf modellfreiem Ansatz nach Lipari-Szabo, equilibrium average, und das Gaussian Axial Fluctuation (GAF)-Modell. Die zwei letzteren können nur qualitativ mit den experimentellen Daten übereinstimmen. Die NMR-Ordnungsparameter können mit Hilfe des Modells von Lipari-Szabo richtig ermittelt werden, wenn sich die interne Bewegung in kleineren Zeitskalen als zur Gesamtbewegung vollzieht. Vorausetzung für die Berechnung dieses Modells ist aber, dass das Fitting der internen Korrelationsfunktionen nur auf den ersten Teil von 100 ps der Korrelationsfunktionen eingesetzt wird. Die berechneten Ordnungsparameter deuten auf ein unterschiedliches Verhalten der beiden Hairpins besonders im Loop-Bereich hin. Die konformationelle Umordnung, die beim UUCG-Loop beobachtet wurde, tritt beim CACG-Loop nicht ein. Zusammenfassend lässt sich sagen, dass es durch den Einsatz von MD Simulationen ermöglicht wird, die strukturellen und dynamischen Eigenschaften der RNA-Systeme auf atomarer Ebene zu untersuchen. Als Schlussfolgerung zeigt diese Doktorarbeit, dass sich die Studie der konformationell Dynamik der RNA-Systeme durch die Kombination aus MD-Simulation und NMR-Spektroskopie sowie der Leistungsfähigkeit der MD-Simulationen, die die interne Bewegungen deutlich beschreiben können, untersuchen lässt.
Molecular dynamics has been employed to study the effect of ion treatment on the stability of 14-nucleotide RNA hairpin of Coxsackievirus B3. Three AMBER force fields were used: AMBER94, AMBER98, and AMBER99, which showed no significant structural difference of the hairpin. Thereafter, we applied two different long-range electrostatic treatments that were reaction field and PME methods, and calculated the distribution of ions around the hairpin. Although the structural stabilities of the MD simulations using both methods were similar in 0.14 M Na+, ion environment around the hairpin was notably different. In particular, structural stabilition of the hairpin with increasing ion concentration and with ion Mg2+ cannot be accommodated by simulations using reaction field method. Furthermore, the MD simulations using PME method suggested the strong similarity in structural and dynamical properties of the hairpin with 0.14 M Na+, 0.50 M Na+, 1,03 M Na+, and 0.08 M Mg2+ concentrations. However, the simulations revealed different ion occupations of Na+ and Mg2+.
Movement of the Rieske domain of the iron–sulfur protein is essential for intramolecular electron transfer within complex III2 (CIII2) of the respiratory chain as it bridges a gap in the cofactor chain towards the electron acceptor cytochrome c. We present cryo-EM structures of CIII2 from Yarrowia lipolytica at resolutions up to 2.0 Å under different conditions, with different redox states of the cofactors of the high-potential chain. All possible permutations of three primary positions were observed, indicating that the two halves of the dimeric complex act independently. Addition of the substrate analogue decylubiquinone to CIII2 with a reduced high-potential chain increased the occupancy of the Qo site. The extent of Rieske domain interactions through hydrogen bonds to the cytochrome b and cytochrome c1 subunits varied depending on the redox state and substrate. In the absence of quinols, the reduced Rieske domain interacted more closely with cytochrome b and cytochrome c1 than in the oxidized state. Upon addition of the inhibitor antimycin A, the heterogeneity of the cd1-helix and ef-loop increased, which may be indicative of a long-range effect on the Rieske domain.
As cryo-EM approaches the physical resolution limits imposed by electron optics and radiation damage, it becomes increasingly urgent to address the issues that impede high-resolution structure determination of biological specimens. One of the persistent problems has been beam-induced movement, which occurs when the specimen is irradiated with high-energy electrons. Beam-induced movement results in image blurring and loss of high-resolution information. It is particularly severe for biological samples in unsupported thin films of vitreous water. By controlled devitrification of conventionally plunge-frozen samples, the suspended film of vitrified water was converted into cubic ice, a polycrystalline, mechanically stable solid. It is shown that compared with vitrified samples, devitrification reduces beam-induced movement in the first 5 e Å−2 of an exposure by a factor of ∼4, substantially enhancing the contribution of the initial, minimally damaged frames to a structure. A 3D apoferritin map reconstructed from the first frames of 20 000 particle images of devitrified samples resolved undamaged side chains. Devitrification of frozen-hydrated specimens helps to overcome beam-induced specimen motion in single-particle cryo-EM, as a further step towards realizing the full potential of cryo-EM for high-resolution structure determination.
The catalytic mechanism, electron transfer coupled to proton pumping, of heme-copper oxidases is not yet fully understood. Microsecond freeze-hyperquenching single turnover experiments were carried out with fully reduced cytochrome aa(3) reacting with O(2) between 83 micros and 6 ms. Trapped intermediates were analyzed by low temperature UV-visible, X-band, and Q-band EPR spectroscopy, enabling determination of the oxidation-reduction kinetics of Cu(A), heme a, heme a(3), and of a recently detected tryptophan radical (Wiertz, F. G. M., Richter, O. M. H., Cherepanov, A. V., MacMillan, F., Ludwig, B., and de Vries, S. (2004) FEBS Lett. 575, 127-130). Cu(B) and heme a(3) were EPR silent during all stages of the reaction. Cu(A) and heme a are in electronic equilibrium acting as a redox pair. The reduction potential of Cu(A) is 4.5 mV lower than that of heme a. Both redox groups are oxidized in two phases with apparent half-lives of 57 micros and 1.2 ms together donating a single electron to the binuclear center in each phase. The formation of the heme a(3) oxoferryl species P(R) (maxima at 430 nm and 606 nm) was completed in approximately 130 micros, similar to the first oxidation phase of Cu(A) and heme a. The intermediate F (absorbance maximum at 571 nm) is formed from P(R) and decays to a hitherto undetected intermediate named F(W)(*). F(W)(*) harbors a tryptophan radical, identified by Q-band EPR spectroscopy as the tryptophan neutral radical of the strictly conserved Trp-272 (Trp-272(*)). The Trp-272(*) populates to 4-5% due to its relatively low rate of formation (t((1/2)) = 1.2 ms) and rapid rate of breakdown (t((1/2)) = 60 micros), which represents electron transfer from Cu(A)/heme a to Trp-272(*). The formation of the Trp-272(*) constitutes the major rate-determining step of the catalytic cycle. Our findings show that Trp-272 is a redox-active residue and is in this respect on an equal par to the metallocenters of the cytochrome c oxidase. Trp-272 is the direct reductant either to the heme a(3) oxoferryl species or to Cu (2+)(B). The potential role of Trp-272 in proton pumping is discussed.
Ubiquitination relies on a subtle balance between selectivity and promiscuity achieved through specific interactions between ubiquitin-conjugating enzymes (E2s) and ubiquitin ligases (E3s). Here, we report how a single aspartic to glutamic acid substitution acts as a dynamic switch to tip the selectivity balance of human E2s for interaction toward E3 RING-finger domains. By combining molecular dynamic simulations, experimental yeast-two-hybrid screen of E2-E3 (RING) interactions and mutagenesis, we reveal how the dynamics of an internal salt-bridge network at the rim of the E2-E3 interaction surface controls the balance between an “open”, binding competent, and a “closed”, binding incompetent state. The molecular dynamic simulations shed light on the fine mechanism of this molecular switch and allowed us to identify its components, namely an aspartate/glutamate pair, a lysine acting as the central switch and a remote aspartate. Perturbations of single residues in this network, both inside and outside the interaction surface, are sufficient to switch the global E2 interaction selectivity as demonstrated experimentally. Taken together, our results indicate a new mechanism to control E2-E3 interaction selectivity at an atomic level, highlighting how minimal changes in amino acid side-chain affecting the dynamics of intramolecular salt-bridges can be crucial for protein-protein interactions. These findings indicate that the widely accepted sequence-structure-function paradigm should be extended to sequence-structure-dynamics-function relationship and open new possibilities for control and fine-tuning of protein interaction selectivity.
Plants absorb sunlight via photosynthetic pigments and convert light energy intochemical energy in the process of photosynthesis. These pigments are mainly bound to antenna protein complexes that funnel the excitation energy to the photosynthetic reaction centres. The peripheral antenna of plant photosystem II (PSII) consists of the major light-harvesting complex of PSII (LHC-II) and the minor LHCs CP29, CP26 and CP24. Light intensity can change frequently and plants need to adapt to high-light conditions in order to avoid photodamage. When more photons are absorbed than can be utilised by the photosynthetic machinery, excessive excitation energy is dissipated as heat by short-term adaptation processes collectively known as non-photochemical quenching (NPQ). A decrease in PSII antenna chlorophyll (Chl) fluorescence yield and a reduction in the average Chl fluorescence lifetime are associated with NPQ. The main component of NPQ is the so-called energy-dependent quenching (qE), and it is triggered by the rapid drop in thylakoid lumenal pH resulting from the plant’s photosynthetic activity. This process is thought to take place at the PSII antenna complexes, which therefore not only capture and transfer light energy but are also involved in balancing the energy flow. The decrease in lumenal pH acivates the enzyme violaxanthin de-epoxidase (VDE), which converts the xanthophyll violaxanthin (Vio) into zeaxanthin (Zea) in the xanthophyll cycle. In addition, the PSII subunit PsbS was discovered to be essential for qE by screening qE-deficient Arabidopsis thaliana mutants. This membrane protein is considered a member of the LHC superfamily, which also includes LHC-II and the minor LHCs. Previous studies on PsbS isolated either from native source or refolded in vitro have produced inconsistent results on its pigment binding capacity. Interestingly, a pH-dependent change in the quaternary structure of PsbS under high light conditions has been reported. This observed dimer-tomonomer transition very likely follows the protonation of lumenal glutamates upon the drop in pH and is accompanied by a change in PSII supercomplex localisation. PsbS dimers are preferentially found in association with the PSII core, whereas PsbS monomers co-localise with LHC-II.Despite the identification of !pH, Zea and PsbS as key players in qE, both the nature of the quencher(s) as well as the underlying molecular mechanism leading to excess energy dissipation still remain unknown. Several models have been put forward to explain the reversible switch in the antenna from an energy-transmitting to a quenched state. Proposals include a simple pigment exchange of Vio for Zea, and aggregation or an internal conformational change of LHC-II. Charge transfer (CT)quenching in the minor LHCs or quenching by carotenoid dark state (Car S1)-Chl interactions have also been suggested. However, none of these qE models has so far been capable of accommodating all the physiological observations and available experimental data. Most importantly, the function of PsbS remains an enigma. A recent qE model suggested that monomerisation of PsbS enables the protein to transiently bind a carotenoid and form a quenching unit with a Chl of a PSII LHC. In view of the various proposed qE mechanisms, this thesis aimed at understanding the interplay of the different qE components and the contribution of the PSII subunits LHC-II, the minor LHCs and PsbS to qE. The initial approach was to investigate the properties of the PSII subunits in the most simple in vitro model system, namely in detergent solution. For this purpose, LHC-II was isolated either from native source or refolded from recombinantly produced protein. Investigation of the minor LHCs and PsbS required heterologous expression and refolding. In addition, experiments were performed on aggregated LHC-II. Aggregates of LHC-II have been used as a popular model system for qE because they exhibit highly quenched Chl fluorescence. At the final stage of this doctoral work, a more sophisticated model system to approximate the thylakoid membrane was developed by reconstitution of the PSII subunits LHC-II and PsbS into liposomes. This system not only allowed for investigation of these membrane proteins in their native environment, but also for mimicking the xanthophyll cycle by distribution of Zea within the membrane as well as !pH by outside buffer exchange. The role of Zea in qE was first investigated with detergent solubilised antenna proteins. The requirement of this xanthophyll for qE is well-known, but the specific contribution to the molecular quenching mechansim is unclear. Previous work had shown that replacement of Vio for Zea in LHC-II was not sufficient to induce Chl fluorescence quenching in Zea-LHC-II, as suggested by the so-called molecular gearshift mechanism. However, by means of selective two-photon excitation spectroscopy, an increase in electronic interactions between Car S1 and Chls was observed for LHC-II upon lowering the pH of the detergent buffer. Electronic Car S1-Chl coupling became even stronger when Zea-LHC-II was probed. The extent of Car S1-Chl coupling correlated directly with the extent of Chl fluorescence quenching, in a similar way as observed previously in live plants under high-light conditions. However, very similar results were obtained with LHC-II aggregates. This implied that the increase in electronic interactions and fluorescence quenching was independent of Zea and low pH. Further experiments on aggregates of LHC-II Chl mutants indicated that the targeted pigments were also not essential for the observed effects. It is proposed that the same molecular mechanism causes an increase in electronic Car S1-Chl interactions and Chl fluorescence quenching in Zea-LHC-II at low pH as well as in aggregated LHC-II. Most likely, surface exposed pigments form random quenching centres in both cases. On the other hand, it was possible that Zea could act as a direct quencher of excess excitation energy in the minor LHCs. However, enrichment of refolded CP29, CP26 and CP24 with Zea did not lead to a change in the Chl excited state lifetime. Formation of a carotenoid radical cation, previously implied in CT quenching, was also not observed, although artificial generation of such a radical cation was principally possible as shown for CP29. During the course of this work, a study reporting the formation of Zea radical cations in minor LHCs was published. Therefore, Zea-enriched minor LHCs were again investigated on the experimental apparatus used in the reported study. Indeed, the presence of at least one carotenoid radical cation for each minor complex was detected. It is suggested that either the preparation method of incubating the refolded minor LHCs with Zea in contrast to refolding the complexes with only Zea and lutein causes the observed differences or that the observed spectral radical cation signatures are due to experimental artifacts. While the experiments with LHC-II and the minor LHCs gave useful insights into the putative qE mechanism, the quencher site and the mode of action of Zea could still not be unambiguously identified. Most importantly, these studies could not explain the function of the qE keyplayer PsbS. Therefore, the focus of the work was shifted to PsbS protein production, purification and characterisation. In view of inconsistent reports on the pigment binding capacity of this PSII subunit, refolding trials with and without photosynthetic pigments were conducted. The formation of a specific pigmentprotein complex typical for other LHCs was not observed and neither was the earlier reported “activation” of Zea for qE by binding to this protein. Nevertheless, PsbS refolded without pigments displayed secondary structure content in agreement with previous studies, indicating pigment-independent folding. Reconstitution of pigmentfree, refolded PsbS into liposomes confirmed that the protein is stable in the absence of pigments. Zea distributed in PsbS-containing liposomes also showed no spectral alteration that would indicate its “activation”. With the ability to reconstitute PsbS, it was then possible to proceed to modelling qE in a proteoliposome system. For this purpose, PsbS was co-reconstituted with LHC-II, which has been reported to interact with PsbS. One-photon excitation (OPE) and two-photon excitation (TPE) spectroscopy measurements were performed on LHC-II- and LHC-II/PsbS-containing liposomes. This enabled both quantification of Chl fluorescence quenching as well as determination of the extent of electronic Car S1-Chl interactions. The effect of Zea was investigated by incorporating it in the proteoliposome membrane. It was shown that Zea alone was not able to induce significant Chl fluorescence quenching when only LHC-II was present. However, when LHC-II and PsbS were co-reconstituted, pronounced Chl fluorescence quenching and an increase in electronic Car S1-Chl interactions were observed and both effects were enhanced when Zea was present. Western blot analysis indicated the presence of a LHC-II/PsbS-heterodimer in these proteoliposomes. In addition to the OPE and TPE measurements, the average Chl fluorescence lifetime was determined in detergent-free buffer at neutral pH and directly after buffer exchange to low pH. No significant changes in the average lifetime were observed for LHC-II proteoliposomes when either Zea was present or after exchange for low pH buffer. This indicated that Zea alone cannot act as a direct quencher, which concurs with the OPE measurements. Moreover, the complex was also properly reconstituted as no aggregation or significant Chl fluorescence quenching were observed. The average lifetime was not significantly affected in LHC-II/PsbS-proteoliposomes, independent of Zea or pH. However, a shortlived component in the presence of a long-lived component was not resolvable with the time resolution of the fluorescence lifetime apparatus.
Implications for qE model systems and the in vivo quenching mechanism are discussed based on the experiments in detergent solution, on LHC-II aggregates and with the proteoliposome model system.
In dieser Arbeit wurden die Strukturen von drei Membranproteinen mittels Einzelpartikel-Kryo‑Elektronenmikroskopie (Kryo‑EM) gelöst. Bei den Membranproteinen handelt es sich um den humanen TRP-Kanal Polycystin‑2, den sekundär-aktiven Transporter BetP aus Corynebacterium glutamicum und den Rotor-Ring der N‑Typ ATPase aus Burkholderia pseudomallei.
Kanäle sind Membranproteine, die Ionen durch eine Pore über die Membran diffundieren lassen. Durch einen präzisen, kanalabhängigen Regulationsmechanismus wird die Pore nur bei Bedarf geöffnet. TRP (transient receptor potential) Kanäle sind anhand von DNA-Sequenzvergleichen identifiziert worden und kommen ausschließlich in Eukaryonten vor. In dieser Arbeit lag der Fokus auf der Strukturbestimmung des humanen TRP Kanals Polycystin‑2 (PC‑2). PC‑2 wurde in einer Studie entdeckt, in der Patienten mit der autosomal dominanten Erbkrankheit „polyzystische Nierenerkrankung“ untersucht wurden. Patienten mit dieser Krankheit tragen eine Mutation in einem der beiden Gene PKD1 oder PKD2, welche für die Proteine Polycystin‑1 und ‑2 kodieren. In dieser Arbeit wurden verschiedene Deletionsmutanten von PC‑2 hergestellt und in das Genom menschlicher HEK293 GnTI‑ Zellen inseriert. Die Zellen, die PC‑2 bzw. die Deletionskonstrukte am stärksten synthetisierten, wurden isoliert und für die rekombinante Proteinherstellung verwendet. Die Expression von PC‑2 führte zu der Entstehung von kristalloidem endoplasmatischem Retikulum. Mutationsstudien in dieser Arbeit zeigen, dass diese morphologische Veränderung durch die Akkumulation von Membranproteinen, die mit sich selbst interagieren, begünstigt wird. Weiter ist es in dieser Arbeit gelungen, PC‑2 zu reinigen und die Struktur des Proteins mit Hilfe von Einzelpartikel Kryo-EM mit einer Auflösung von 4.6 Å zu bestimmen. Die Membrandomäne von PC‑2 ist sehr ähnlich zu den bekannten TRP Kanal Strukturen. Ein Vergleich der PC‑2 Struktur mit dem offenen und geschlossenen TRPV1 Kanal legt nahe, dass PC‑2 in seiner offenen Konformation gelöst wurde.
Der sekundär aktive Transporter BetP von C. glutamicum gehört zu der Familie der BCC- (betaine-carnitine-choline) Transporter und wird durch osmotischen Schock aktiviert. Nach seiner Aktivierung importiert BetP zwei Natriumionen und ein Glycinbetain Molekül. Durch die Akkumulierung von Glycinbetain in der Zelle steigt das osmotische Potential des Zytoplasmas, was den Wasserausstrom aus der Zelle stoppt. Viele Strukturen, die BetP in unterschiedlichen Stadien des Transportprozesses zeigen, konnten bereits mittels Röntgenkristallographie gelöst werden. Allerdings ist die N‑terminale Domäne für die Kristallisation entfernt worden und die C‑terminale Domäne, die komplett aufgelöst ist, ist an einem wichtigen Kristallkontakt beteiligt. Um strukturelle Informationen über die N‑ und C‑terminale Domäne ohne Kristallisationsartefakte zu erhalten, wurde in dieser Arbeit die Struktur von BetP mittels Einzelpartikel Kryo‑EM bestimmt. Die Struktur mit einer Auflösung von 6.8 Å zeigt BetP in einem zum Zytoplasma geöffneten Zustand. Der größte Unterschied zu allen Kristallstrukturen ist die Position der C‑terminalen α‑Helix, die um ~30° rotiert ist und dadurch deutlich enger am Protein zu liegen kommt. Da BetP in Abwesenheit von aktivierenden Stoffen analysiert wurde, wird vermutet, dass es sich bei der gelösten Struktur um den inaktiven Zustand von BetP handelt.
Rotierende ATPasen sind membrangebunden Enzymkomplexe, die bei der zellulären Energieumwandlung eine entscheidende Rolle einnehmen. Sie bestehen aus einem löslichen und einem membrangebundenen Teil. Während in dem löslichen Teil der zelluläre Energieträger Adenosintriphosphat (ATP) entweder synthetisiert oder hydrolysiert wird, baut der membrangebundene Teil entweder einen Ionengradienten auf oder nutzt die Energie eines existierenden Gradienten für die ATP Synthese. Ein wesentlicher Bestandteil des membrangebundenen Teils einer rotierenden ATPase ist der Rotor-Ring. Dieser transportiert Ionen über die Membran und rotiert dabei um seine eigene Achse. In dieser Arbeit wurde eine Studie fortgesetzt, die den Rotor-Ring der N‑Typ ATPase von B. pseudomallei mittels Kryo‑EM untersuchte und zeigte, dass der Rotor-Ring aus 17 identischen Untereinheiten aufgebaut ist. Damit hat die N‑Typ ATPase das größte Ionen-zu-ATP-Verhältnis aller bisher charakterisierten ATPasen. In dieser Arbeit wurde die c17 Stöchiometrie des N‑Typ ATPase Rotor-Rings bestätigt und die Struktur mittels Kryo‑EM bestimmt. Im besonderen Fokus lag dabei der Einfluss von Detergenzien auf die Strukturbestimmung. Es konnte gezeigt werden, dass die beiden Parameter Dichte und Mizellengröße der verwendeten Detergenzien ausschlaggebend für den Erfolg der Strukturbestimmung dieses sehr kleinen Membranproteins sind.
Hydride transfers play a crucial role in a multitude of biological redox reactions and are mediated by flavin, deazaflavin or nicotinamide adenine dinucleotide cofactors at standard redox potentials ranging from 0 to –340 mV. 2-Naphthoyl-CoA reductase, a key enzyme of oxygen-independent bacterial naphthalene degradation, uses a low-potential one-electron donor for the two-electron dearomatization of its substrate below the redox limit of known biological hydride transfer processes at E°’ = −493 mV. Here we demonstrate by X-ray structural analyses, QM/MM computational studies, and multiple spectroscopy/activity based titrations that highly cooperative electron transfer (n = 3) from a low-potential one-electron (FAD) to a two-electron (FMN) transferring flavin cofactor is the key to overcome the resonance stabilized aromatic system by hydride transfer in a highly hydrophobic pocket. The results evidence how the protein environment inversely functionalizes two flavins to switch from low-potential one-electron to hydride transfer at the thermodynamic limit of flavin redox chemistry.
Telomeric G-quadruplexes have recently emerged as drug targets in cancer research. Herein, we present the first NMR structure of a telomeric DNA G-quadruplex that adopts the biologically relevant hybrid-2 conformation in a ligand-bound state. We solved the complex with a metalorganic gold(III) ligand that stabilizes G-quadruplexes. Analysis of the free and bound structures reveals structural changes in the capping region of the G-quadruplex. The ligand is sandwiched between one terminal G-tetrad and a flanking nucleotide. This complex structure involves a major structural rearrangement compared to the free G-quadruplex structure as observed for other G-quadruplexes in different conformations, invalidating simple docking approaches to ligand-G-quadruplex structure determination
Experimental results are presented for 180 in silico designed octapeptide sequences and their stabilizing effects on the major histocompatibility class I molecule H-2Kb. Peptide sequence design was accomplished by a combination of an ant colony optimization algorithm with artificial neural network classifiers. Experimental tests yielded nine H-2Kb stabilizing and 171 nonstabilizing peptides. 28 among the nonstabilizing octapeptides contain canonical motif residues known to be favorable for MHC I stabilization. For characterization of the area covered by stabilizing and non-stabilizing octapeptides in sequence space, we visualized the distribution of 100,603 octapeptides using a self-organizing map. The experimental results present evidence that the canonical sequence motives of the SYFPEITHI database on their own are insufficient for predicting MHC I protein stabilization.
To investigate the contribution of hydrophobic residues to the molecular recognition of cytochrome c with cytochrome oxidase, we mutated several hydrophobic amino acids exposed on subunit II of the Paracoccus denitrificans oxidase. KM and kcat values and the bimolecular rate constant were determined under steady- or presteady-state conditions, respectively. We present evidence that Trp-121 which is surrounded by a hydrophobic patch is the electron entry site to oxidase. Mutations in this cluster do not affect the binding of cytochrome c as the KM remains largely unchanged. Rather, the kcat is reduced, proposing that these hydrophobic residues are required for a fine tuning of the redox partners in the initial collisional complex to obtain a configuration optimal for electron transfer.
Photoelectron (PE) spectra of ethylene and vinylene carbonates and thiocarbonates as well as of methylene trithiocarbonate and some open-chain derivatives are reported.
The low energy bands, well separated in the unsaturated compounds, are assigned to lone pair and π type ionizations. The assignment is based on comparison of PE spectra, modified CNDO calculations, and sulfur Κβ emission spectra. The pronounced substituent effects due to which the first ionization potential varies from 8.4 eV to 11.1 eV are discussed.
Sulfhydryl Groups, Methylmercury Containing Inactivator, Coenzyme Analogue Nicotinamide-(S-methylmercury-thioinosine) dinucleotide was formed by reaction of nicotin amide-(6-thiopurine) dinucleotide with methylmercury chloride. The compound exhibits coenzyme properties in the test with LDH (Km=1.5 × 10-4 м , Vmax=12500) and LADH (Km=1.7 × 10-4 м, Vmax=27) and inactivates YADH and GAPDH. From incubations with LDH and LADH the mercury containing coenzyme could be regained by column chromatography. The compound seems to be qualified for the X-ray structure analysis of the coenzyme-enzyme complex for some dehyrogenases based on the proportion of the heavy metal.