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If the biotechnological production of chemicals can further replace or support regular synthetic chemistry, industry will be able to move away from fossil oils towards renewable sources. However, in many cases the much needed adaptation of biotechnological production systems is not yet developed to the necessary level.
For processes where short fatty acids (FA) are needed, as for example in the microbial production of biofuels in the gasoline range, protein engineering had not yet delivered feasible solutions. In this thesis, several approaches to introduce chain length control on type I fatty acid synthases (FAS) were established and made available in a publication and two patents. Therein, engineering was focused on rational design based on available structural information.
First, the type I FAS from C. ammoniagenes was used as a model enzyme to probe modifications on FAS in a low complex in vitro environment in order to gain information about structure-function relationships. At this stage, engineering was conducted in several rounds, first addressing possible ways to alter product distributions by changing substrate affinities through concise mutations in binding channels. Several FAS constructs were generated ranging from first successes, where short FA were produced as side products, to FAS where native chain length programming was overwritten and only short FA were produced.
Furthermore, another engineering target was addressed with the modification of domain-domain interactions on FAS. For its exploitation to direct synthesis, contact surfaces on catalytic domains were changed to interfere with acyl carrier protein binding. This channeling of the kinetic process on the enzyme led to similar successes and short FA became the primary product.
The two approaches have proven to be potent tools to introduce systems of chain length control in FAS. This rational engineering has the big advantage that it is mostly minimally invasive and due to the high conservation of de novo FA synthesis, individual mutations could easily be used in other FAS (and their organisms) as well. Even heterologous expression of modified FAS genes is feasible.
Engineering was not only tested in a defined in vitro environment and but also in S. cerevisiae as an exemplary in vivo system. The results eventually confirmed the in vitro findings and proved that the chosen engineering could be transferred to more complex systems. Even before any optimization for highest output, the titers of short FA from S. cerevisiae fermentation matched previous reports with 118 mg/L.
In sum, this work covers several layers from basic research to preliminary applications. The presented modifications to create short FA producing FAS can be a key step in synthesis pathways and will likely enable a whole range of new succeeding research. It can be seen as a valuable contribution towards establishing novel ways for the production of chemicals from renewable sources.
The soluble loop BC region guides, but not dictates, the assembly of the transmembrane cytochrome b6
(2017)
Studying folding and assembly of naturally occurring α-helical transmembrane proteins can inspire the design of membrane proteins with defined functions. Thus far, most studies have focused on the role of membrane-integrated protein regions. However, to fully understand folding pathways and stabilization of α–helical membrane proteins, it is vital to also include the role of soluble loops. We have analyzed the impact of interhelical loops on folding, assembly and stability of the heme-containing four-helix bundle transmembrane protein cytochrome b6 that is involved in charge transfer across biomembranes. Cytochrome b6 consists of two transmembrane helical hairpins that sandwich two heme molecules. Our analyses strongly suggest that the loop connecting the helical hairpins is not crucial for positioning the two protein “halves” for proper folding and assembly of the holo-protein. Furthermore, proteolytic removal of any of the remaining two loops, which connect the two transmembrane helices of a hairpin structure, appears to also not crucially effect folding and assembly. Overall, the transmembrane four-helix bundle appears to be mainly stabilized via interhelical interactions in the transmembrane regions, while the soluble loop regions guide assembly and stabilize the holo-protein. The results of this study might steer future strategies aiming at designing heme-binding four-helix bundle structures, involved in transmembrane charge transfer reactions.
Die Paarverteilungsfunktion (PDF) beschreibt die Wahrscheinlichkeit, zwei Atome eines Materials in einem Abstand r voneinander zu finden. Diese Methode bewährt sich seit längerer Zeit zur Untersuchung von Gläsern, Flüssigkeiten, amorphen, stark fehlgeordneten und nanokristallinen anorganischen Substanzen. Die Anwendung für organische Substanzen ist jedoch relativ neu, mit etwa 20 Veröffentlichungen und Patenten insgesamt.
Im Rahmen dieser Dissertation wurden zwei Methoden zur Strukturverfeinerung und Strukturlösung organischer Substanzen anhand von PDF-Daten erfolgreich entwickelt und an diversen Beispielen validiert. Als erster Schritt hierzu wurde eine Methodenverbesserung vorgenommen. Hierbei handelte es sich um eine Verbesserung der Simulation der PDF-Kurven organischer Verbindungen anhand eines gegebenen Strukturmodells. Mit Hilfe der bisherigen Methoden können die PDF-Kurven anorganischer Substanzen erfolgreich simuliert werden. Für organische Substanzen werden bei Anwendung der bisherigen Methode die Signalbreiten der intramolekularen und intermolekularen Beiträge zu der PDF-Kurve falsch wiedergegeben, dies führt zu einer schlechten Anpassung der simulierten PDF-Daten and die experimentellen PDF-Daten. Deshalb wurde ein neuer Ansatz entwickelt, in welchem für die Berechnung der intramolekularen Beiträge zum PDF-Signal ein anderer isotroper Auslenkungsparameter verwendet wurde, als bei der Berechnung der intermolekularen Beiträge zum PDF-Signal. Mit diesem Ansatz konnte eine sehr gute Simulation der PDF-Kurve für alle Testbeispiele erzielt werden. Zur Strukturverfeinerung organischer Substanzen anhand von PDF-Daten wurden zwei Ansätze entwickelt: der Rigid-Body-Ansatz zur Behandlung starrer organischer Moleküle und der Restraint-Ansatz zur Behandlung flexibler organischer Moleküle.
Neben methodischen Entwicklungen wurden in dieser Arbeit zwei weitere Untersuchungen organischer Verbindungen mittels PDF-Analyse durchgeführt.
Es wurden drei, auf unterschiedliche Weise hergestellte, amorphe Proben des Wirkstoffes Telmisartan untersucht. Des Weiteren wurde mittels PDF-Analyse eine pharmazeutische Nanosuspension untersucht.
Der gezielte, effiziente Aufbau komplexer Struktureinheiten, die mehrere Stereozentren besitzen, ist bis heute eine der größten Herausforderungen in der organischen Synthese. Gerade hinsichtlich der Wirkstoffentwicklung ist es von großer Bedeutung alle möglichen Stereoisomere einer Verbindung zugänglich zu machen. Die 1,3-Diamin-Struktureinheit ist Bestandteil interessanter Naturstoffe, biologisch aktiver Substanzen oder chiraler Liganden. Zusammenfassend konnte erfolgreich eine neue hoch modulare, stereokonvergente, Enamid/Acylimin-basierte Methode zur Synthese von 1,3-Diaminen mit drei fortlaufenden Stereozentren entwickelt werden. Diese Route bietet Zugang zur kompletten Tetrade möglicher Diastereomere, ausgehend von einfach zugänglichen Startmaterialien. Die Konfiguration der beiden zuerst gebildeten Stereozentren kann durch die Enamid-Geometrie kontrolliert werden ((E) -> 1,2 anti, (Z) -> 1,2-syn-Konfiguration). Die 2,3 Konfiguration kann hingegen über die geschickte Wahl der Reagenzien und den damit assoziierten Reaktionsbedingungen gesteuert werden. Weiterhin konnte eine Bi(OTf)3-katalysierte Ein-Topf-Sequenz zur diastereoselektiven Synthese von 1,2-anti-2,3-anti-1,3-Diaminen 6 etabliert werden. Darüber hinaus konnte die Synthese der N,O-Acetale, als auch die der Enamide optimiert und bzgl. der Synthesen im Multigrammmaßstab verbessert werden. Die N,O-Acetale konnten erfolgreich aus Amiden, Aldehyden und Alkoholen dargestellt werden. Die Enamide wurden unter Zuhilfenahme luftunempfindlicher Ni-Katalystoren aus Allylamiden mittels Isomerisierung zugänglich gemacht.
Rhabdomyosarcoma is the most common paediatric soft-tissue sarcoma, and for tumour recurrence, the prognosis is still unfavourable. The current standard therapy consisting of surgery, radiation and combined chemotherapy does not consider the specific biology of this tumour.
Histone deacetylases (HDACs) and the Lysine-specific demethylase-1 (LSD1) are two epigenetic modifiers which are both part of repressor complexes leading to transcriptional silencing of target genes. Whereas HDACs lead to deacetylation of several lysine-residues within the histone tail, LSD1 is specific for demethylation of H3K4me2 and H3K4me1, as well as in a different context for H3K9me2. Rhabdomyosarcoma is reported to harbour high levels of LSD1, but the functional relevance is yet unclear. HDAC inhibition proved to be effective as single agent treatment, however, the proximity of HDAC1/2 and LSD1 in repressor complexes at the DNA implies a suitable rationale for a combination therapy potentially leading to cooperative effects on target gene transcription. In this study, we aimed to evaluate the potential of a combined LSD1 and HDAC inhibition for cell death induction in rhabdomyosarcoma cell lines. Whereas LSD1 inhibitors failed to induce cell death on their own, the combined inhibition of HDACs and LSD1 resulted in highly synergistic cell death induction. This effect extended to several combinations of LSD1 and HDAC inhibitors as well as to four different rhabdomyosarcoma cell lines, two of embryonal and two of alveolar histology.
With the use of the HDAC inhibitor JNJ-26481585 and the reversible LSD1 inhibitor GSK690, we demonstrated that the cell death induced by the combination matches with the details of intrinsic mitochondrial apoptosis. JNJ-26481585/GSK690-induced cell death is partially caspase-dependent and leads to caspase cleavage, followed by substrate cleavage as shown for PARP, as well as loss of the mitochondrial membrane potential.
Furthermore, JNJ-26481585 and GSK690 acted together to transcriptionally upregulate the proapoptotic proteins NOXA, BIM and BMF, which resulted in respective changes on protein level for both cell lines. However, the antiapoptotic BCL-2 family proteins BCL-2, MCL-1 and BCL-xL displayed only minor changes in protein levels upon treatment with GSK690 and JNJ-26481585, which did not rely on transcriptional activity. Therefore, the increase in proapoptotic proteins induces a shift towards proapoptotic signalling at the mitochondrial membrane. This shift is functionally relevant since knockdown of a proapoptotic protein or overexpression of one of the antiapoptotic proteins BCL-2 and MCL-1, as well as a stabilized mutant MCL-1, can significantly protect from GSK690/JNJ-26481585-induced cell death.
Knockdown of the mitochondrial membrane protein BAK, which is directly guarding the mitochondrial membrane integrity, potently protected from GSK690/JNJ-26481585- induced cell death, directly linking the shift in the BCL-2 family proteins to the observed loss of mitochondrial membrane potential and the further downstream activation of caspases. Furthermore, treatment with JNJ-26481585 and GSK690 resulted in a cell cycle arrest in G2/M phase, indicating additional effects on the tumour cells beside apoptosis induction. Taken together, the combined inhibition of LSD1 and HDACs is a promising strategy for rhabdomyosarcoma treatment.
Der Name Histamin hat seinen Ursprung aus dem griechischen Wort "histos" (Gewebe) und spielt auf sein breites Spektrum an Aktivitäten, sowohl unter physiologischen als auch unter pathophysiologischen Bedingungen an. Histamin ist eines der Moleküle mit welchem man sich im letzten Jahrhundert am intensivsten beschäftigt hat.
Im Jahr 1907 wurde das Histamin erstmals synthetisiert. Drei Jahre später gelang es, dieses Monoamin erstmals aus dem Mutterkornpilz Claviceps purpurea zu isolieren. Weitere 17 Jahre vergingen, ehe Best et al. Histamin aus der humanen Leber und der humanen Lunge isolieren konnten. Best konnte somit beweisen, dass dieses biogene Amin einen natürlichen Bestandteil des menschlichen Körpers darstellt. Nach der Entdeckung wurden dem Histamin mehrere Effekte zugeschrieben. Dale et al. beobachteten, dass Histamin einen stimulierenden Effekt auf die glatte Muskulatur des Darms und des Respirationstraktes hat, stimulierend auf die Herzkontraktion wirkt, Vasodepression und ein schockähnliches Syndrom verursacht.
Popielski demonstrierte, dass Histamin dosisabhängig einen stimulierenden Effekt auf die Magensäuresekretion von Hunden hat. Lewis wiederum beschrieb erstmals, dass Histamin einen Effekt auf der Haut hervorruft. Dies zeigte sich durch verschiedene Merkmale, wie geröteter Bereich aufgrund der Vasodilatation und Quaddeln aufgrund der erhöhten Gefäßpermeabilität. Des Weiteren wurde Histamin eine mediatorische Eigenschaft bei anaphylaktischen und allergischen Reaktionen zugeschrieben. Zusätzlich spielt das biogene Amin eine entscheidende Rolle im zentralen Nervensystem (ZNS), unter anderem beim Lernen, bei der Erinnerung, beim Appetit und beim Schlaf-Wach-Rhythmus. Von den zahlreichen physiologischen Effekten des Histamins ist seine Rolle bei Entzündungsprozessen, der Magensäuresekretion und als Neurotransmitter am besten verstanden.
Pulsed electron-electron double resonance (PELDOR), also called Double Electron-Electron Resonance, (DEER) is a pulsed EPR technique that can provide structural information of biomolecules, such as proteins or nucleic acids, complementary to other structure determination methods by measuring long distances (from 1.5 up to 10 nm) between two paramagnetic labels. Incorporation of the rigid Ç-label pairwise into DNA or RNA molecules enables the determination not only of the distance but also of the mutual orientation between the two Ç-labels by multi-frequency orientation-selective PELDOR data (X-, Q- and G-band frequencies). Thus, information about the orientation of secondary structure elements of nucleic acids can be revealed and used as additional angular information for structure determination. Since Ç does not have motion independent from the helix where it resides, the conformational flexibility of the nucleic acid molecule can be directly determined. This thesis demonstrates the advancement of PELDOR spectroscopy, beyond its original scope of distance measurements, to determine the mutual orientation between two rigid spin labels towards the characterization of the conformational space sampled by highly flexible nucleic acid molecules. Applications of the methodology are shown on two systems: a three-way junction, namely a cocaine aptamer in its bound-state, and a two-way junction, namely a bent DNA.
More in detail, the conformational changes of the cocaine aptamer upon cocaine binding were investigated by analysis of the distance distributions. The cocaine-bound and the unbound states could be differentiated by their conformational flexibility, which decreases in the presence of the ligand. Moreover, the obtained distance distributions revealed a small change in the mean distance between the two spin labels upon cocaine binding. This indicates a ligand-induced conformational change, which presumably originates at the junction where cocaine is known to bind. The investigation of the relative orientation between the two spin-labeled helices of the aptamer revealed further structural insights into the conformational dynamics of the cocaine-bound state. The angular information from the orientation-selective PELDOR data and the a priori knowledge about the secondary structure of the aptamer were helpful in obtaining a molecular model describing its global folding and flexibility. In spite of a large flexible aptamer, the kink angle between the Ç-labeled helices was found to be rather well-defined.
As for the bent DNA molecule, a two-step protocol was proposed to investigate the conformational flexibility. In the first step, a database with all the possible conformers was created, using available restraints from NMR and distance restraints derived from PELDOR. In a second step, a weighted ensemble of these conformers fitting the multi-frequency PELDOR data was built. The uniqueness of the obtained structural ensemble was checked by validation against an independent PELDOR data set recorded at a higher magnetic field strength. In addition, the kink and twist angle pairs were determined and the resulting structural ensemble was compared with the conformational space deduced both from FRET experiments and from the structure determined by the NMR restraints alone.
Overall, this thesis underlines the potential of using PELDOR spectroscopy combined with rigid spin labels in the context of structure determination of nucleic acids in order to determine the relative orientation between two helices, the conformational flexibility and the conformational changes of nucleic acid molecules upon ligand binding.
Structural and functional dissection of the DH and PH domains of oncogenic Bcr-Abl tyrosine kinase
(2017)
The two isoforms of the Bcr-Abl tyrosine kinase, p210 and p190, are associated with different leukemias and have a dramatically different signaling network, despite similar kinase activity. To provide a molecular rationale for these observations, we study the Dbl-homology (DH) and Pleckstrin-homology (PH) domains of Bcr-Abl p210, which constitute the only structural differences to p190. Here we report high-resolution structures of the DH and PH domains and characterize conformations of the DH–PH unit in solution. Our structural and functional analyses show no evidence that the DH domain acts as a guanine nucleotide exchange factor, whereas the PH domain binds to various phosphatidylinositol-phosphates. PH-domain mutants alter subcellular localization and result in decreased interactions with p210-selective interaction partners. Hence, the PH domain, but not the DH domain, plays an important role in the formation of the differential p210 and p190 Bcr-Abl signaling networks.
In dieser Dissertation wurde die Rolle des Proteins Carboxypeptidase E (CPE) im Glioblastom (GBM) untersucht. Ursprünglich wurde CPE in der neuroendokrinen Regulation beschrieben, wo es die Reifung der meisten Neuropeptide und Hormone reguliert und somit Einfluss auf Stoffwechsel und humorale Effekte hat (Fricker et al., 1982; Fricker & Snyder, 1982 and 1983; Davidson & Hutton, 1987; Shen & Loh, 1997; Lou et al., 2005). Ab 1989 wurde CPE in unterschiedlichen Tumorentitäten nachgewiesen (Grimwood et al., 1989; Manser et al., 1991), jedoch ohne Hinweise, welche Bedeutung das Protein dort haben könnte. Erst im letzten Jahrzehnt konnten sowohl pro- als auch anti-tumorigene Wirkungen von CPE gezeigt werden. Die beschriebenen Wirkungen von CPE sind jedoch von dessen Isoform abhängig. Das ∂(delta)N-trunkierte CPE zeigte sich mit erhöhtem Tumorwachstum und schlechter Überlebensprognose in verschiedenen Krebsentitäten assoziiert (Murthy et al., 2010; Lee et al., 2011; Zhou et al., 2013). Im Gegensatz dazu verringerte sezerniertes CPE (sCPE) im Fibrosarkom und Glioblastom die Zellmigration, was einen anti-tumorigenen Effekt suggeriert (Höring et al., 2012; Murthy et al., 2013a). Die Molekularmechanismen, die für die Regulation der Migration zuständig sind, sind jedoch kaum untersucht. Die meisten Untersuchungen von sCPE in Normal- und Tumorgewebe beschränken sich hauptsächlich auf Apoptose und Zellüberleben (Skalka et al., 2013; Murthy et al., 2013b; Cheng et al., 2013; Selvaraj et al., 2015; Cheng et al., 2015). Die vorliegende Arbeit ist demzufolge die erste Studie, die sich dem Mechanismus der Migrationsregulation durch sCPE im Glioblastom widmet.
Humane Gliome stellen die größte und bösartigste Gruppe hirneigener Tumore dar. Bösartige Gliome sind höchst resistent gegen alle zurzeit verfügbaren Behandlungsmethoden. Einer der Hauptgründe dafür ist, dass die Tumorzellen durch diffuse Infiltration in das Gehirn einwandern können. Ferner sind Gliomzellen metabolisch sehr aktiv und können sich dadurch an schnell verändertes Milieu anpassen (Fack et al., 2015; Demeure et al., 2016). Über die grundlegenden Mechanismen für diese Art des infiltrierenden Tumorwachstums ist bisher noch nicht viel bekannt. Zurzeit sind nur wenige Schlüsselfaktoren beschrieben, die den sogenannten Mechanismus der Migration oder Proliferation ("go or grow") in bösartigen Tumoren beeinflussen: wenige Transkriptionsfaktoren, miRNAs sowie metabolische Faktoren. Interessanterweise, sind miRNAs zum Teil mit der Regulation des Metabolismus in Tumorzellen assoziiert. Eine vorangehende Studie aus unserem Labor hat sCPE aufgrund seines Potentials, Zellwanderung zu verringern, als einen weiteren Schlüsselfaktor identifiziert. Wir konnten zeigen, dass sCPE in der Gliomzelllinie LNT-229 zur einer differentiellen Regulation von Migration und Proliferation führt (Höring et al., 2012). Die vorliegende Arbeit widmet sich nun der Frage nach den genauen zugrundeliegenden Mechanismen, wie sCPE seine Effekte auf molekularer Ebene vermittelt. Darüber hinaus soll geklärt werden, ob sCPE auch in der metabolischen Adaptation eine Rolle spielt und dadurch ebenfalls die Gliomzellmigration beeinflußen kann.
The turnover of endoplasmic reticulum (ER) ensures the correct biological activity of its distinct domains. In mammalian cells, the ER is degraded via a selective autophagy pathway (ER-phagy), mediated by two specific receptors: FAM134B, responsible for the turnover of ER sheets and SEC62 that regulates ER recovery following stress. Here, we identified reticulon 3 (RTN3) as a specific receptor for the degradation of ER tubules. Oligomerization of the long isoform of RTN3 is sufficient to trigger fragmentation of ER tubules. The long N-terminal region of RTN3 contains several newly identified LC3-interacting regions (LIR). Binding to LC3s/GABARAPs is essential for the fragmentation of ER tubules and their delivery to lysosomes. RTN3-mediated ER-phagy requires conventional autophagy components, but is independent of FAM134B. None of the other reticulon family members have the ability to induce fragmentation of ER tubules during starvation. Therefore, we assign a unique function to RTN3 during autophagy.
Denisovite is a rare mineral occurring as aggregates of fibres typically 200–500 nm diameter. It was confirmed as a new mineral in 1984, but important facts about its chemical formula, lattice parameters, symmetry and structure have remained incompletely known since then. Recently obtained results from studies using microprobe analysis, X-ray powder diffraction (XRPD), electron crystallography, modelling and Rietveld refinement will be reported. The electron crystallography methods include transmission electron microscopy (TEM), selected-area electron diffraction (SAED), high-angle annular dark-field imaging (HAADF), high-resolution transmission electron microscopy (HRTEM), precession electron diffraction (PED) and electron diffraction tomography (EDT). A structural model of denisovite was developed from HAADF images and later completed on the basis of quasi-kinematic EDT data by ab initio structure solution using direct methods and least-squares refinement. The model was confirmed by Rietveld refinement. The lattice parameters are a = 31.024 (1), b = 19.554 (1) and c = 7.1441 (5) Å, β = 95.99 (3)°, V = 4310.1 (5) Å3 and space group P12/a1. The structure consists of three topologically distinct dreier silicate chains, viz. two xonotlite-like dreier double chains, [Si6O17]10−, and a tubular loop-branched dreier triple chain, [Si12O30]12−. The silicate chains occur between three walls of edge-sharing (Ca,Na) octahedra. The chains of silicate tetrahedra and the octahedra walls extend parallel to the z axis and form a layer parallel to (100). Water molecules and K+ cations are located at the centre of the tubular silicate chain. The latter also occupy positions close to the centres of eight-membered rings in the silicate chains. The silicate chains are geometrically constrained by neighbouring octahedra walls and present an ambiguity with respect to their z position along these walls, with displacements between neighbouring layers being either Δz = c/4 or −c/4. Such behaviour is typical for polytypic sequences and leads to disorder along [100]. In fact, the diffraction pattern does not show any sharp reflections with l odd, but continuous diffuse streaks parallel to a* instead. Only reflections with l even are sharp. The diffuse scattering is caused by (100) nanolamellae separated by stacking faults and twin boundaries. The structure can be described according to the order–disorder (OD) theory as a stacking of layers parallel to (100).
In the title compound, C17H18N2O, the central carbon atom with the OH substituent and one of the (E)-benzylideneamino substituents are disordered over two sets of sites with occupancies of 0.851 (4) and 0.149 (4). The relative positions of the two disorder components is equivalent to a rotation of approximately 60° about the C—N single bond. In the crystal, the molecules are held together by O—H...N hydrogen bonds, forming simple C(5) chains along the b-axis direction. In addition, pairs of the chains are further aggregated by weak C—H...π interactions.
The asymmetric unit of the title compound, C21H28N4O, consists of two unique molecules linked by an O—H⋯N hydrogen bond. The conformation of both C=N bonds is E and the azomethine functional groups lie close to the plane of their associated benzene rings in each of the independent molecules. The dihedral angles between the two benzene rings are 83.14 (4) and 75.45 (4)°. The plane of the one of the N(CH3)2 units is twisted away from the benzene ring by 18.8 (2)°, indicating loss of conjugation between the lone electron pair and the benzene ring. In the crystal structure, O—H⋯N hydrogen bonds together with C—H⋯O hydrogen bonds link neighbouring supramolecular dimers into a three-dimensional network.
The asymmetric unit of the title co-crystalline adduct, 1,3,6,8-tetraazatricyclo[4.4.1.13,8]dodecane (TATD)–4-iodophenol (1/2), C8H16N4·2C6H5IO, comprises a half molecule of the aminal cage polyamine plus a 4-iodophenol molecule. A twofold rotation axis generates the other half of the adduct. The components are linked by two intermolecular O—H⋯N hydrogen bonds. The adducts are further linked into a three-dimensional framework structure by a combination of N⋯I halogen bonds and weak non-conventional C—H⋯O and C—H⋯I hydrogen bonds.
In the title compound, C26H24N2O2, the oxazine moiety is fused to a naphthalene ring system. The asymmetric unit consists of one half of the molecule, which lies about an inversion centre. The C atoms of the ethylene spacer group adopt an antiperiplanar arrangement. The oxazine ring adopts a half-chair conformation. In the crystal, supramolecular chains running along the b axis are formed via short C—H⋯π contacts. The crystal studied was a non-merohedral twin with a fractional contribution of 0.168 (2) of the minor twin component.
The asymmetric unit of the title compound, C18H18I2N2O2, consists of one half-molecule, completed by the application of inversion symmetry. The molecule adopts the typical structure for this class of bis-benxozazines, characterized by an anti orientation of the two benzoxazine rings around the central C—C bond. The oxazinic ring adopts a half-chair conformation. In the crystal, molecules are linked by C—I⋯N short contacts [I⋯N = 3.378 (2) Å], generating layers lying parallel to the bc plane.
Infections with multidrug resistant bacterial strains like Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa or Acinetobacter baumanii that can accumulate resistance mechanisms against different groups of drugs cause increasing problems for the health care system. Multidrug efflux pumps are able to transport different classes of substances, providing a basic resistance to different antibiotics. Especially when they are overexpressed they can keep bacterial cells alive under antibiotic pressure unless other high level resistance mechanisms like expression of β-lactamases are established. One example for a clinically relevant multidrug efflux pump is the AcrAB/TolC tripartite system of E. coli, that transports a variety of different substrates, including besides antibiotics dyes, detergents, bile salts and organic compounds from the periplasm or the inner membrane out of the cell. AcrB is the inner membrane component of the protein complex that determines not only the substrate specificity of the tripartite system but energises the transport through the whole system process via proton transduction as well. TolC is the outer membrane spanning protein that forms a pore in the outer membrane enabling the system to transport drugs over the latter out of the cell. The periplasmic membrane fusion protein AcrA connects AcrB and TolC in the periplasm completing the channel from the periplasm, respective the inner membrane to the extracellular space. AcrB assembles as trimers, in asymmetric crystal structures each of the protomers adapts a different conformation designated L(oose), T(ight) and O(pen). In the protomers tunnels open up and collaps in different conformations. In the L protomer a periplasmic cleft opens up that can initially bind substrates to the periplasmic part of AcrB. In the T conformation the deep binding pocket opens that is assumed to bind substrates tightly that were bound to the access pocket before. As well in the T conformation a second pathway leading to the deep binding pocket opens that can guide substrates from a groove between transmembrane helices TM7, TM8 and TM9, the TM8 groove, that is connected with socalled tunnel 1 that ends in the deep binding pocket. In the O conformation a new tunnel opens that connects the collapsing deep binding pocket with the periplasmic space, respective the channel through the periplasmic space formed from AcrA and TolC. Substrates were cocrystallised in access and deep binding pocket verifying their role in substrate transport. In the TM8 groove in high resolution crystal structures DDM molecules were cocrystallised in L and T conformation, indicating that the AcrB substrate DDM may utilise this entrance to the deep binding pocket. The asymmetry observed in the AcrB trimers trongly suggests a peristaltic pump mechanism. The functional rotation cycle demands communication between the subunits and tight control of substrate load of protomers during the transport to optimise the ration between protons that are transduced and substrates transported. Indeed it was shown that AcrB transport mechanism is positively cooperative for some β-lactam substrates. For the communication between the subunits it was assumed that ionic interaction between ion pairs established between charged amino acids at the interfaces of protomers in different conformations are of special importance. Thus the amino acids engaged in ionic interactions, respective ion pairs D73-K131, E130-K110, D174-K110, R168, R259-E734 were substituted with non-charged amino acids pairwise and phenotypes were determined in plate dilution assays and MIC experiments. No evidence for a general, substrate independent, reduction of AcrB activity, that would be expected when the ionic residues are of special importance for AcrB function, could be found with the methods applied. Substitutions were not only combined pairwise according to the putative ion pairs but as well in combinations of R168A with D174N, E130Q and K131M. AcrB activity is reduced for the variant R168A_D174N significantly, activity decreases further for quadruple variant E130Q_K131M_ R168A_D174N. Because the reduced activity is only observed in this combination of substitutions the phenotype must result from accumulation of small effects of the single substitutions. R168A may destabilise the protomer interfaces, as its side chain is oriented in direction to the neighbouring protomer at all interfaces, enhancing substratespecific effects of substitutions E130Q, K131M, D174N that are not in all conformations oriented towards the neighbouring protomer but as well along the substrate transport pathway. Further investigations to figure out the details of the effects observed were not conducted because fluctuating expression of the variants hindered experimental procedures.
In another approach TM8 was in focus of the interest. As mentioned above it is a possible substrate entrance in the inner membrane. The linker between TM8 and the periplasmic PC2 subdomain undergoes a coil-to-helix transition when AcrB cycles through L, T and O conformations. Linking the transmembrane part of AcrB that provides the energy for the transport process via proton transduction with the periplasmic part harbouring the major part of the substrate pathway assignes TM8 and the periplasmic linker (859-876) an important role in the function of AcrB. Thus it was investigated with an alanine-scan of residues 859 to 884 and G/P respective P/G exchange followed by phenotype characterisation in growth curve and plate dilution assays of selected variants. In the phenotype determinations none of the variants, except G861P that seems to cause massive sterical restriction in an α-helical region, displayed a general, substrate independent decrease of AcrB activity. Thus it is concluded that the individual properties of amino acids in TM8 and the periplasmic linker are not of general importance for the mechanism of AcrB. The substitution of individual amino acids had impact on uptake of different substrates in plate dilution assays in a substrate dependent manner. The uptake of some substrates, like erythromycin or chloramphenicol is more affected than that of others with rhodamine 6G resistance being only reduced for the G861P variant. A relation between the PSA of substrates and reduced activity of AcrB was observed. in Substrates with higher PSA values are more affected by substitutions in TM8 or periplasmic linker, resulting in the conclusion that substrates with higher PSA are more likely to be taken up via the TM8 groove/tunnel 1 pathway than those with lower PSA values.
Ion channel gating is essential for cellular homeostasis and is tightly controlled. In some eukaryotic and most bacterial ligand-gated K+ channels, RCK domains regulate ion fluxes. Until now, a single regulatory mechanism has been proposed for all RCK-regulated channels, involving signal transduction from the RCK domain to the gating area. Here, we present an inactive ADP-bound structure of KtrAB from Vibrio alginolyticus, determined by cryo-electron microscopy, which, combined with EPR spectroscopy and molecular dynamics simulations, uncovers a novel regulatory mechanism for ligand-induced action at a distance. Exchange of activating ATP to inactivating ADP triggers short helical segments in the K+-translocating KtrB dimer to organize into two long helices that penetrate deeply into the regulatory RCK domains, thus connecting nucleotide-binding sites and ion gates. As KtrAB and its homolog TrkAH have been implicated as bacterial pathogenicity factors, the discovery of this functionally relevant inactive conformation may advance structure-guided drug development.
β-barrel proteins mediate nutrient uptake in bacteria and serve vital functions in cell signaling and adhesion. For the 14-strand outer membrane protein G of Escherichia coli, opening and closing is pH-dependent. Different roles of the extracellular loops in this process were proposed, and X-ray and solution NMR studies were divergent. Here, we report the structure of outer membrane protein G investigated in bilayers of E. coli lipid extracts by magic-angle-spinning NMR. In total, 1847 inter-residue 1H–1H and 13C–13C distance restraints, 256 torsion angles, but no hydrogen bond restraints are used to calculate the structure. The length of β-strands is found to vary beyond the membrane boundary, with strands 6–8 being the longest and the extracellular loops 3 and 4 well ordered. The site of barrel closure at strands 1 and 14 is more disordered than most remaining strands, with the flexibility decreasing toward loops 3 and 4. Loop 4 presents a well-defined helix.
The human MET receptor tyrosine kinase contributes to vertebrate development and cell proliferation. As a proto‐oncogene, it is a target in cancer therapies. MET is also relevant for bacterial infection by Listeria monocytogenes and is activated by the bacterial protein internalin B. The processes of ligand binding, receptor activation, and the diffusion behavior of MET within the plasma membrane as well as its interconnections with various cell components are not fully understood. We investigated the receptor diffusion dynamics using single‐particle tracking and imaging fluorescence correlation spectroscopy and elucidated mobility states of resting and internalin B‐bound MET. We show that internalin B‐bound MET exhibits lower diffusion coefficients and diffuses in a more confined area in the membrane. We report that the fraction of immobile receptors is larger for internalin B‐bound receptors than for resting MET. Results of single‐particle tracking in cells treated with various cytotoxins depleting cholesterol from the membrane and disrupting the actin cytoskeleton and microtubules suggest that cholesterol and actin influence MET diffusion dynamics, while microtubules do not have any effect.
In bacteria, the regulation of gene expression by cis-acting transcriptional riboswitches located in the 5'-untranslated regions of messenger RNA requires the temporal synchronization of RNA synthesis and ligand binding-dependent conformational refolding. Ligand binding to the aptamer domain of the riboswitch induces premature termination of the mRNA synthesis of ligand-associated genes due to the coupled formation of 3'-structural elements acting as terminators. To date, there has been no high resolution structural description of the concerted process of synthesis and ligand-induced restructuring of the regulatory RNA element. Here, we show that for the guanine-sensing xpt-pbuX riboswitch from Bacillus subtilis, the conformation of the full-length transcripts is static: it exclusively populates the functional off-state but cannot switch to the on-state, regardless of the presence or absence of ligand. We show that only the combined matching of transcription rates and ligand binding enables transcription intermediates to undergo ligand-dependent conformational refolding.
The synergetic effects of combining structural biology and epr spectroscopy on membrane proteins
(2017)
Protein structures as provided by structural biology such as X-ray crystallography, cryo-electron microscopy and NMR spectroscopy are key elements to understand the function of a protein on the molecular level. Nonetheless, they might be error-prone due to crystallization artifacts or, in particular in case of membrane-imbedded proteins, a mostly artificial environment. In this review, we will introduce different EPR spectroscopy methods as powerful tools to complement and validate structural data gaining insights in the dynamics of proteins and protein complexes such that functional cycles can be derived. We will highlight the use of EPR spectroscopy on membrane-embedded proteins and protein complexes ranging from receptors to secondary active transporters as structural information is still limited in this field and the lipid environment is a particular challenge.