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Massive global spread of multidrug-resistant (MDR) Salmonella spp. expressing extended-spectrum beta-lactamase (ESBL) and additional resistance to fluoroquinolones has often been attributed to high international mobility as well as excessive use of oral antibiotics in livestock farming. However, MDR Salmonella spp. have not been mentioned as a widespread pathogen in clinical settings so far. We demonstrate the case of a 25-year-old male with primary sclerosing cholangitis who tested positive for MDR Salmonella enterica serotype Choleraesuis expressing ESBL and fluoroquinolone resistance. The pathogen was supposedly acquired during a trip to Thailand, causing severe fever, cholangitis and pancreatitis. To our knowledge, this is the first report of Salmonella enterica serotype Choleraesuis in Europe expressing such a multidrug resistance pattern. ESBL resistance of Salmonella enterica spp. should be considered in patients with obstructive biliary tract pathology and travel history in endemic countries.
The CDK inhibitor SNS-032 had previously exerted promising anti-neuroblastoma activity via CDK7 and 9 inhibition. ABCB1 expression was identified as major determinant of SNS-032 resistance. Here, we investigated the role of ABCB1 in acquired SNS-032 resistance. In contrast to ABCB1-expressing UKF-NB-3 sub-lines resistant to other ABCB1 substrates, SNS-032-adapted UKF-NB-3 (UKF-NB-3rSNS- 032300nM) cells remained sensitive to the non-ABCB1 substrate cisplatin and were completely re-sensitized to cytotoxic ABCB1 substrates by ABCB1 inhibition. Moreover, UKF-NB-3rSNS-032300nM cells remained similarly sensitive to CDK7 and 9 inhibition as UKF-NB-3 cells. In contrast, SHEPrSNS-0322000nM, the SNS-032-resistant sub-line of the neuroblastoma cell line SHEP, displayed low level SNS-032 resistance also when ABCB1 was inhibited. This discrepancy may be explained by the higher SNS-032 concentrations that were used to establish SHEPrSNS-0322000nM cells, since SHEP cells intrinsically express ABCB1 and are less sensitive to SNS-032 (IC50 912 nM) than UKF-NB-3 cells (IC50 153 nM). In conclusion, we show that ABCB1 expression represents the primary (sometimes exclusive) resistance mechanism in neuroblastoma cells with acquired resistance to SNS-032. Thus, ABCB1 inhibitors may increase the SNS-032 efficacy in ABCB1-expressing cells and prolong or avoid resistance formation.
The Hepatitis C virus (HCV) infects more than 170 million individuals worldwide and causes challenging HCV-related diseases. Unfortunately, there is no vaccine available. Therefore, a better understanding of the HCV life cycle is urgently needed to develop more effective and better tolerated therapies.
It has been reported that the secretory pathway plays an essential role for the release of HCV, and the SNARE complexes are a central factor controlling intracellular vesicular trafficking. Recently, our group observed that α-taxilin that binds to free syntaxin 4 prevents the SNARE complex formation and exerts an inhibitory effect on the release of HCV particles. Therefore, it was analyzed whether the t-SNARE protein syntaxin 4 is involved in the HCV life cycle.
An increased intracellular amount of syntaxin 4 was found in HCV-positive cells, while the level of syntaxin 4-specific transcripts was decreased as observed in HCV-positive Huh7.5 cells and in HCV-infected primary human hepatocytes (PHH). Since in HCV-positive cells a significant longer half-life of syntaxin 4 was found, the decreased expression is overcompensated, leading to the elevated amount of syntaxin 4. Overexpression of syntaxin 4 increases the amount of secreted infectious viral particles, while silencing of syntaxin 4 expression decreases the number of released viral particles, which indicates that HCV could use the SNARE-dependent secretory pathway for viral release. Confocal immunofluorescence microscopy and co-immunoprecipitation experiments revealed that syntaxin 4 interacts with HCV core and NS5A. To identify the binding domain, various mutants of syntaxin 4 were generated. Based on these mutants, it was found that the H3 domain of syntaxin 4 interacts with core. These data show that the t-SNARE protein syntaxin 4 is an essential cellular factor for HCV morphogenesis and secretion.
HCV induces autophagy, and in HCV-infected cells a major fraction of the de novo synthesized viral particles is not released but intracellularly degraded. Syntaxin 17 is an autophagosomal SNARE required for the fusion of autophagosomes with lysosomes to form autolysosomes and thereby to deliver the enclosed contents for degradation. Therefore, we aim to investigate whether syntaxin 17 is a relevant factor for the HCV life cycle by regulating the fusion between autophagosomes and lysosomes. It was found that HCV-positive cells possess a decreased amount of syntaxin 17, and HCV reduces the intracellular level of syntaxin 17 by NS5A-mediated interruption of c-Raf signaling, which triggers the syntaxin 17 transcription, and by HCV-dependently induced autophagy. Overexpression of syntaxin 17 decreases the intracellular amount of viral particles and reduces the number of released infectious viral particles by favoring the formation of autolysosomes, in which HCV particles can be degraded. Vice versa, inhibition of syntaxin 17 expression by specific siRNAs results in an elevated amount of intracellular viral particles and increases the number of released viral particles by impaired autophagosome-lysosome fusion. Confocal immunofluorescence microscopy analyses show a fraction of core protein in autophagosomes as stained by lysotracker and the autophagy maker p62. These data identify syntaxin 17 as a novel factor controlling the release of HCV and reveal the autophagosome-autolysosome fusion as an essential step affecting the equilibrium between the release of infectious viral particles and lysosomal degradation of intracellular viral particles.
Taken together, these data identify the t-SNARE proteins syntaxin 4 and syntaxin 17 as essential cellular factors for HCV morphogenesis and secretion.
Der Sufi-Meister und Dichter Ken’ân Rifâî gilt als eine der bedeutendsten und einflussreichsten Persönlichkeiten der osmanisch-türkischen Sufi-Tradition im 20. Jahrhundert. Sein Leben zwischen den Jahren 1867-1950, welches die vier Phasen, die Monarchie, die erste und zweite Verfassungsperiode (1876 und 1908), die Republik (1923) und auch die Anfangsphase der Demokratie (1950) umfasst, und seine Lehre reflektieren die Entwicklung, die Umwälzung und den letzten Zustand, die das sufische Leben im letzten Zeitabschnitt des Osmanischen Reiches und nach der Ṭarīqa-Phase in der Periode der Republik erlebt und erreicht hat. Ken’ân Rifâî fungierte zwischen den Jahren 1908-1925 als Tekke-Scheich, und zwar bis 1925, wo alle vorhandenen Tekkes in der Türkei gesetzlich verboten und dementsprechend geschlossen wurden...
Bartonella Adhäsin A (BadA), das zur Gruppe der TAAs gehört, ist ein essentieller Pathogenitätsfaktor von B. henselae und übernimmt während des Infektionsverlaufs wichtige Funktion wie Autoagglutination, Adhärenz an ECM-Proteine und Endothelzellen. BadA weist die für die für die Proteinklasse der TAAs charakteristische modulare Architektur bestehend aus N-terminaler Kopf-Domäne, Stiel-Domäne, Hals-Domäne und C-terminaler Membrananker-Domäne auf. Der modulare Aufbau des Proteins deutet daraufhin, dass bestimmte Domänen mit bestimmten biologischen Funktionen des Proteins verknüpft sind. Zur Untersuchung dieser Hypothese wurden Deletionsmutanten des BadA generiert.
Die Generierung weiterer BadA-Deletionsmutanten wird durch das langsame Wachstum des Erregers und die geringe Auswahl an molekularbiologischen Werkzeugen zur genetischen Manipulation von B. henselae erschwert. Daher sollte in ersten Teil dieser Arbeit ein Expressionsmodell für Deletionsmutanten des BadA etabliert und charakterisiert werden. Dies sollte am Beispiel des trunkierten BadA, BadA HN23, durchgeführt werden. Hierzu sollten drei Hybrid-Varianten des BadA HN23 erstellt werden: (i) Austausch der BadA-Signalsequenz gegen die E. coli OmpA-Signalsequenz, (ii) Austausch der BadA-Membrananker-Domäne gegen die YadA-Membrananker-Domäne sowie (iii) Austausch von sowohl der BadA-Signalsequenz als auch der BadA-Membrananker-Domäne gegen die bereits genannten Elemente. Danach sollten die konstruierten BadA HN23 Hybride und das BadA HN23 in induzierbare Expressionsvektoren kloniert und spezielle E. coli-Expressionsstämme mit diesen Plasmiden transformiert werden. Bei erfolgreicher Expression sollten die optimalen Bedingungen für die Expression (Temperatur, Induktorkonzentration) ermittelt werden und an-schließend die biologische Funktion der heterolog exprimierten BadA HN23 Hybride überprüft werden.
Der erste Abschnitt der hier vorliegenden Arbeit zeigte folgende Ergebnisse:
1) Die beschrieben BadA HN23 Hybrid Konstrukte wurden durch Austausch von: (i) BadA-Signalsequenz gegen E. coli OmpA-Signalsequenz im BadA HN23,
(ii) BadA-Membrananker-Domäne gegen YadA-Membrananker-Domäne im BadA HN23 und
(iii) Austausch von BadA-Signalsequenz und BadA-Membrananker-Domäne gegen E. coli OmpA-Signalsequenz und YadA-Membrananker-Domäne im BadA HN23 generiert.
Die BadA HN23 Hybride und BadA HN23 wurden in Expressionsvektoren kloniert und E. coli Omp2, E. coli Omp8 und E. coli Omp8ΔdegP transformiert.
2) Alle BadA HN23 Hybrid-Konstrukte und BadA HN23 lagen in einer monomeren und trimeren Form vor.
3) Durch IFT und - Durchflusszytometrie-Untersuchungen wurde die Oberflächenexpression der einzelnen Konstrukte quantifiziert. Es zeigte sich, dass es deutliche Unterschiede in der Menge des auf der Zelloberfläche befindlichen jeweiligen BadA HN23 Proteins gab. Dabei wiesen die Konstrukte, die die YadA-Membrananker-Domäne besaßen (BadA HN23 Hybrid 2 und 3), die stärkste Oberflächenexpression auf.
4) Die biologische Funktion des BadA HN23 wurde mittels des E. coli Omp2 BadA HN23 Hybrid 3 charakterisiert. Heterolog exprimiertes BadA HN23 vermittelt Autoagglutination, die Adhärenz des Expressionsstammes an Kollagen G und Endothelzellen.
5) Die Expression des BadA HN23 führt zur signifikant verstärkten in-vivo-Pathogenität im Galleria mellonella-Infektionsmodell.
6) Das E. coli-Expressionsmodell lieferte keine Aussage über eventuelle immunodominate Funktionen des heterolog exprimierten BadA HN23, da auch mit im IFT als anti- B. henselae negativ eingestuften Patientenseren im WB ein BadA HN23 spezifisches Bandensignal detektiert wurde. Dot Blot-Experimente ermöglichten ebenfalls keine Aussage über eventuelle immunodominate Funktion des nativen BadA HN23, da das verwendete anti-B. henselae-positive Patientenserum unspezifische Reaktion gegenüber dem Kontrollstamm zeigte.
Für verschiedene TAAs ist beschrieben worden, dass sie die Serumresistenz der exprimierenden Spezies vermitteln. Daher sollte im zweiten Teil dieser Arbeit der Einfluss von BadA auf eventuelle Serumresistenz zweier B. henselae-Isolate untersucht werden. Dieser Teil lieferte folgende Ergebnisse:
1) B. henselae zeigte Sensitivität gegenüber normalem humanem Serum.
2) Sowohl BadA-positive als auch BadA-negative B. henselae-Isolate können Komplementinhibitoren wie Faktor H binden. Die dabei gebundene Menge ist relativ klein.
Die Expression von Deletionsmutanten des BadA in E. coli ist ein vielversprechendes Modell zur Analyse der Domänen-Funktionsbeziehung des BadA, da die meisten biologischen Funktionen einer homolog exprimierten BadA-Deletionsmutante reproduziert werden konnten und es sich bei E. coli um ein schnell wachsendes Bakterium, das sich leicht genetisch manipulieren lässt, handelt. Allerdings stellt das zytotoxische LPS des E. coli sowie das schnelle Wachstums der Bakterien eine Limitation des Expressionssystems dar, indem es Untersuchungen zum Einfluss der jeweiligen BadA-Deletionsmutante auf die Induktion der proangiogenetischen Wirtszellantwort verhindert oder Untersuchungen zum Einfluss der jeweiligen BadA-Deletionsmutante auf die Adhärenz an Endothelzellen deutlich erschwert. Außerdem kann eine mögliche Interaktion zwischen BadA bzw. BadA-Deletionsmutanten und dem TIVSS und zwischen BadA bzw. BadA-Deletionsmutanten und weiteren Adhäsinen (wie z.B. dem FHA) mit Hilfe dieses Expressionssystems nicht untersucht werden. Dies wäre nur im B. henselae Wildtyp-Stamm möglich.
Weltweit sind ca. 130–180 Millionen Menschen mit HCV infiziert und jährlich sterben etwa 500.000 Menschen an dessen Folgen. Die neuartigen Therapien versprechen zwar eine sehr hohe Heilungsrate, sind aber aufgrund ihrer enorm hohen Kosten nur in Industrieländern verfügbar. Noch immer gibt es keine prophylaktische Vakzinierung gegen HCV. Deshalb ist es wichtig, den HCV-Lebenszyklus und die Interaktion zwischen Wirtszelle und Virus detailliert zu verstehen, um die Entwicklung von Therapien und Impfungen zu ermöglichen. Außerdem kann ein fundiertes Wissen von HCV translatiert werden und auf neuartige Erreger der Familie der Flaviviridae, wie Denguevirus und Zikavirus, angewendet werden. Während der Zelleintritt und die Replikation von HCV relativ gut charakterisiert sind, bleiben die Assemblierung und Freisetzung der viralen Partikel schlecht verstandene Schritte des HCV-Lebenszyklus. In dieser Arbeit sollte die Rolle des zellulären Proteins α-Taxilin im Lebenszyklus von HCV untersucht werden. In einer späteren Phase der Arbeit wurde der endosomale Freisetzungsweg von HCV untersucht. Dazu wurden HCV Varianten generiert und charakterisiert, die Fluoreszenz-Proteine im NS5A- und E1-Protein enthalten, durch die es möglich ist, den Replikationskomplex und die Viruspartikel zu visualisieren und zu quantifizieren und den viralen Lebenszyklus dadurch besser untersuchen zu können...
FUSE Binding Protein 1 (FUBP1) is a transcriptional regulator, which is overexpressed in various cancer entities, including hepatocellular carcinoma (HCC) and colorectal cancer (CRC). It fulfills pro-proliferative and anti-apoptotic functions in cancer cells, resulting in increased proliferation and reduced sensitivity towards apoptotic stimuli.
Previously, camptothecin (CPT) and its clinically used analog 7-ethyl 10hydroxycamptothecin (SN-38) were shown to inhibit FUBP1 in biophysical interaction displacement assays (AlphaScreen; surface plasmon resonance, SPR), and first insights into the cellular effects of FUBP1 inhibition were obtained. CPT and SN-38 are known to potently inhibit topoisomerase 1 (TOP 1), and until today, these inhibitors were thought to be specific for this target. This could be disproved by our FUBP1 binding studies. An open issue, which is addressed in this thesis, was the contribution of FUBP1 inhibition to SN-38-mediated apoptosis apoptosis.
During this thesis, a low micromolar efficacy of CPT/SN-38-induced inhibition of FUBP1 binding to the Far Upstream Sequence Element (FUSE) oligonucleotide of p21 was determined. Furthermore, FUBP1 was for the first time shown to directly interact with a potential FUSE sequence upstream of the transcription start in pro-apoptotic gene BIK. In proof of-principle experiments, an effective inhibition of the binding of FUBP1 to the FUSE BIK DNA by CPT/SN-38 was verified.
One of the main goals of this thesis was to further elucidate the contribution of cellular FUBP1-inhibition by CPT/SN-38 to the anti-cancer potential of these substances. For this purpose, the TOP 1 mutant and TOP 1 wild type colorectal cancer sub-cell lines HCT116 G7 and HCT116 S were used. CPT/SN-38 was shown to induce apoptosis in single and combinatorial treatments with mitomycin c (MMC), independently of the TOP 1 mutation status of the cells. Furthermore, a prominent induction of a FUBP1 target gene signature was observed upon treatment of both cell lines with CPT/SN-38. Consequently, CPT/SN-38 was able to fulfill its anticancer effects in these cells, although TOP 1 could not be the main target in the mutant cell line.
In a second approach to gain indirect evidence for FUBP1 dependent effects of CPT/SN-38, the TOP 1-specific inhibitors topotecan (TTN) and β lapachone (BL) were used for the treatment of HCC and CRC cell lines. Interestingly, the TOP 1 inhibitors TTN and BL exhibited a reduced potency in apoptosis induction compared to the dual (FUBP1 and TOP 1) inhibitor SN-38.
Finally, two independent screens for a specific FUBP1 inhibitor were performed. In the first approach, a small number of structural and functional CPT-derivatives that exhibited a reduced inhibitory potential against TOP 1, were tested for their ability to interfere with the FUBP1/FUSE binding. Two particular indenoisoquinoline derivatives revealed potent in vitro inhibition of FUBP1 with low micromolar IC50 values.
In a second approach, previously identified candidate FUBP1 inhibitors that had been isolated from the Maybridge Hit Finder library served as lead structures for a structure activity relationship (SAR) study of the inhibition of FUBP1 binding to the FUSE oligonucleotide. After two cycles of optimization, a medium-potent FUBP1 inhibitor was obtained that induced effective deregulation of FUBP1 target genes in cell culture experiments.
This thesis describes the adaptation of Acinetobacter species to dry environments with the soil bacterium A. baylyi and the opportunistic hospital pathogen A. baumanii in its focus. The adaptation of A. baylyi and A. baumannii to osmotic stress was investigated. Compatible solutes that were uptaken from the environment or synthesized de novo to cope with the loss of water at high salinity were identified. The corresponding transporters and enzymes involved were characzerized. In addition, the desiccation resistance of A. baumannii was analyzed to elucidate its survival in hospital environments. The usage of compatible solutes during desiccation stress was analyzed and proteins that were produced were identified.
The availability of water is essential for bacterial life and if environmental conditions are awkward, bacteria have to cope with high salinitiy to prevent loss of water. In this thesis it was shown that A. baylyi synthesizes glutamate and mannitol de novo as compatible solutes in response to osmotic stress to balance the osmotic potential. The pathway for mannitol biosynthesis from Fructose-6-Phosphate (F-6-P) via Mannitol-1-Phosphate (Mtl-1-P) was elucidated and the isolation and characterization of a novel type of biofunctional enzyme was described. Interestingly, the unique bifunctional enzyme MtlD, acting as dehydrogenase and phosphatase, mediates both steps of the mannitol biosynthesis pathway. This enzyme catalyzes the reduction of F-6-P to Mtl-1-P with NADPH as reducing equivalent. The dehydrogenase activity of MtlD was salt dependent and the phosphatase activity was dependent on Mg2+ as cofactor. Phylogenetic analyses revealed that MtlD is broadly distributed among other Acinetobacter strains but not in other phylogenetic tribes.
In this thesis it is also described that, besides de novo synthesis of compatible solutes, A. baylyi takes up glycine betaine (GB) or its precursor choline by different transport systems and uses this solutes as osmoprotectants. The uptake of GB occurs via a secondary transporter (ACIAD3460) of the BCCT family. Choline is taken up as precursor and oxidized to GB by two dehydrogenases. The uptake and use of choline as GB precursor involves two transporters, whose genes are encoded in the bet cluster (BetT1, BetT2), two dehydrogenases (BetA, BetB) and a regulatory protein (BetI). Both transporters differ from each other in structure and function: BetT1 is osmo-independent and active independently of osmotic stress. BetT2 contains - in contrast to BetT1 - a long C-terminal domain for osmo-sensing and its activity highly increases in the presence of high osmolarity. The oxidation of choline occurs independently of the osmolarity of the medium but in the absence of salt stress, GB is exported. In contrast, in the presence of high salinity, GB is accumulated in the cytoplasm to balance the osmotic potential in order to prevent loss of water. The regulation of both transporters, the uptake of choline independently of the osmolarity and the export of GB under isoosmotic conditions are regulated by the transcriptional regulator BetI.
A. baumannii ATCC 19606 was also shown to cope with high salinity. Analogously to A. baylyi, A. baumannii ATCC19606 synthesizes glutamate and mannitol de novo in response to osmotic stress. The genes for the synthesis of these compatible solutes are identical to those found in A. baylyi. This suggests that the solute biosynthesis pathways of A. baumannii and A. baylyi are identical. A. baumannii was also able to take up GB and choline in response to osmotic stress and growth at high salinity was restored upon addition of GB and its precursor choline. The bet cluster was also present in the genome A. baumannii and also contains the two different choline transporters BetT1 and BetT2.
Our suggestion that choline or GB or the utilization of phosphatidylcholine as carbon source led to an increase in the survival under desiccation stress was not confirmed. However, 2D analysis of proteins produced during desiccation stress in A. baumannii led to elevated amounts of proteins implicated in biofilm formation, regulation, cell morphology and general stress response, such as Hsp60 or superoxide dismutase, both might play a role in general stress protection.
Protein synthesis is a central process within every living cell, where information embodied in the nucleotide sequence of the mRNA is translated into the primary sequence of proteins. The translation procedure comprises four steps: initiation, elongation, termination, and recycling. Ribosome recycling orchestrated by the ATP‐binding cassette (ABC) protein ABCE1, renders mRNA translation into a cyclic process, connecting termination with re initiation. In Archaea and Eukarya, the ABC protein ABCE1 catalyzes ribosome recycling by splitting the ribosome (80S/70S) into the small 40S/30S and large 60S/50S subunits, providing them for the next translation round.
The ABC‐type ATPase one of the most conserved proteins, present in all Archaea and Eukarya, but not in Bacteria, is essential for life in all organisms examined so far. ABCE1 was initially identified as RNase L inhibitor (Rli1), involved in the antiviral RNA immunity, and as host protein 68 (HP68) playing a role in HIV capsid assembly. However, the strong sequence conservation of ABCE1 points towards a more fundamental function within cell homeostasis, which was found by its involvement in various translation processes. ABCE1 turned out to be the major ribosome recycling factor indispensable for life in Eukarya and Archaea, being involved in canonical translation, mRNA surveillance, ribosome biogenesis, and translation initiation.
Recent functional and structural data provided first insights into the mechanism of ABCE1 in ribosome recycling. The nucleotide‐binding domains (NBDs) sandwich two ATP molecules in the NBD1‐NBD2 interface causing an NBD engagement, which is released upon ATP hydrolysis. In case of ABCE1, this ATP‐dependent tweezer‐like motion of the NBDs transfers mechanical energy to the ribosome and tears the subunits apart. The FeS‐cluster domain may swing out of the NBD cleft into the inter‐subunit space of the ribosome, which drives the subunits apart either directly or via the bound a/eRF1. Hence, the subunits are released and the post‐splitting complex (PSC, 40S/30S∙ABCE1∙ATP) is available for re‐initiation events, presumably occurring via the known interactions of ABCE1with initiation factors.
One of the most crucial aspects of this model is the nucleotide‐dependent conformational switch of ABCE1, which drives ribosomal subunit splitting. However, the conformational states, which ABCE1 undergoes during ribosome recycling, including their mechanistic importance for its diverse functions, remain unknown. Further, the exact role and movement of the essential FeScluster domain during ribosome recycling are not yet understood. Additional, it remains elusive where ABCE1 is bound in the post‐splitting complex and how the splitting mechanism is regulated concerning the asymmetric NBDs and the coupling of nucleotide binding with NBD closing and ATP hydrolysis.
Thus, in order to monitor the conformational dynamics of the ribosome recycling factor ABCE1 two complementing methods in structural biology, namely single‐molecule based Förster resonance energy transfer (smFRET) and pulsed electron‐electron double resonance (PELDOR) spectroscopy were applied.
Single‐molecule FRET as an integrated biophysical approach based on Förster resonance energy transfer and single‐molecule detection was used to understand the fundamental molecular principles of ABCE1. Contrary to the anticipated two‐state model of ABC proteins, it was shown in this thesis that both nucleotide‐binding sites of ABCE1 are always in a dynamic equilibrium between conformational states with distinct properties: open, intermediate, and closed. The equilibrium in the two nucleotide‐binding sites is distinctly affected when ABCE1 interacts with ribosomal subunits and nucleotides. While ABCE1 can adopt all three conformational states in its free or 30S bound situation, the closed state has the highest affinity for 30S subunit. Further, dissociation of ABCE1 from the small ribosomal subunit, a step that completes the recycling process, is followed by the opening of the NBSs. Hence, the current findings have important implications not only for ribosome recycling but represent a new paradigm for the molecular mechanisms of twin‐ATPases.
The complementing PELDOR measurements provide the advantage of high distance precision and reliability studying macromolecular complexes. Distance distributions of a number of ABCE1 variants even bound to the 1‐MDa post‐splitting complex (30S∙ABCE1∙AMP‐PNP), composed of the 16S rRNA, 28 ribosomal proteins, and ABCE1, was analyzed. Thus, the available crystal structures of ABCE1 in the open state were validated, since all distances of ABCE1 measured in this study perfectly correspond to this crystallized state. Unfortunately, ABCE1 could not be trapped in the closed state under the experimental conditions applied, although plenty different approaches to stabilize this state were performed.
In the second part of this study the architecture yet unknown of the 1‐MDa post splitting complex (40S/30S∙ABCE1∙ATP), concerning especially the ABCE1 binding site and its interactions with translational proteins, was probed by a method, which combines chemical cross linking with mass‐spectrometry (XL‐MS). Following this approach, it was demonstrated that ABCE1 remains bound at the translational GTPase‐binding site after ribosome splitting, contacting the S24e protein of the small subunit. The platform for the intensive contacts to the small ribosomal subunit is thereby provided by the unique helix‐loop‐helix motif of ABCE1. Notably, the FeScluster domain of ABCE1 undergoes a large rotational and translational rearrangement towards the small ribosomal subunit S12 upon nucleotide‐dependent closure of the NBDs. Thus, a key complex in the translational cycle, resembling the link between translation initiation and ribosome recycling processes, was reconstituted and structurally analyzed.
In view of the diverse functionalities of RNA, the search for tools suitable for regulating and understanding RNA grows continuously. Dysfunction of RNA controlled processes can lead to diseases, calling for external regulation mechanisms – a difficult task in view of the complexity of biological systems. One of the recently developed methods that aim to systematically control RNA relates to photoregulation. Here, the RNA functions are triggered by photochromic molecules – for example, azobenzene or spiropyran – which are bound either covalently or non-covalently to the target RNA. This is a flexible approach, which can be improved by using suitably substituted chromophores. However, many issues regarding the details of photocontrol are still open. A detailed understanding of the mechanism of photocontrol is therefore of crucial importance.
The present thesis explores theoretical approaches to the photocontrol of RNA, focussing upon azobenzene chromophores covalently bound to RNA. The aim of the thesis is to characterize, at a molecular level, the effect of trans-to-cis isomerization of the azobenzene chromophore on RNA, and thus understand the mechanism of RNA unfolding triggered by azobenzene isomerization. In particular, we attempt to answer the following questions:
How does azobenzene isomerization happen in an RNA environment, i.e., how is
the isomerization influenced by the local RNA environment?
Conversely, how is RNA dynamics, on a longer time scale, affected by azobenzene attachment and photoisomerization?
Further, can regulation be enhanced by substituted azobenzenes? And, does simulation yield a picture that is consistent with experiment?
Due to the very different times scales of azobenzene isomerization (femtoseconds to picoseconds) and the much slower RNA response (nanoseconds to milliseconds), complementary techniques have been chosen: (i) hybrid quantum-classical approaches, i.e., on-the-fly Quantum Mechanics/Molecular Mechanics (QM/MM), to characterize the isomerization and RNA response on an ultrafast time scale, and (ii) molecular dynamics with enhanced sampling techniques, in particular, Replica Exchange MD (REMD), to explore longer time scales where the effect of RNA unfolding becomes manifest. Furthermore, substituent effects on azobenzene were separately investigated, in collaboration with two experimental groups.
The first part of this thesis is focused on the conformational influence of azobenzene on a small RNA hairpin on longer time scales using REMD simulations. In accordance with experiment, it is found that both the trans and cis form of azobenzene destabilize the RNA system. Trans azobenzene stays stacked in the double strand, whereas the cis form flips out of the RNA. These stacking interactions are the main reason why a trans azobenzene-RNA-complex is more stable than a cis-azobenzene-RNA-complex. Furthermore, the loop region of the RNA hairpin is highly destabilized by the intercalation of azobenzene.
In the second part, on-the-fly QM/MM simulations of the same azobenzene substituted hairpin are undertaken. These simulations use a surface hopping (SH) algorithm in conjunction with hybrid QM/MM electronic structure calculations to give a complete picture of the isomerization process on a picosecond time scale. It is shown that, due to the constraints of the RNA environment, the isomerization time of the azobenzene chromophore is significantly increased (from 300 femtoseconds in the gas phase to around 20 picoseconds in the RNA environment), and the isomerization yield is low. To the best of our knowledge, these are the first QM/MM simulations reported for azobenzene in a nucleic acid environment.
In the third and final part of this thesis, the properties of substituted azobenzenes have been explored, in collaboration with two experimental groups at the department. In particular, para- and meta-hydroxy substituted azobenzenes were suggested as improved photoswitches for the photoregulation of RNA, but spectroscopic investigations showed that isomerization was inefficient in some of the investigated species. Therefore, we investigated the photoisomerisation pathway of the keto/enol-form of para- and meta-hydroxy-azobenzenes by Time-Dependent Density Functional Theory (TDDFT) calculations. These calculations show that the competing keto/enol-tautomerism can result in an unstable cis form, making these substituted chromophores unsuitable as photoswitches.
Overall, the present thesis has contributed to obtaining a molecular-level understanding of photocontrol in azobenzene substituted RNAs, showing that theory and simulations can provide useful guidance for new experiments.