Oligomerization and protein-protein interactions of the sensory histidine kinase DcuS in Escherichia coli

DcuS is a membrane-integral sensory histidine kinase involved in the DcuSR two-component regulatory system in Escherichia coli by regulating the gene expression of C4-dicarboxylate metabolism in response to external stimuli. How DcuS mediates the signal transduction across the membrane remains little understood. This study focused on the oligomerization and protein-protein interactions of DcuS by using quantitative Fluorescence Resonance Energy Transfer (FRET) spectroscopy. A quantitative FRET analysis for fluorescence spectroscopy has been developed in this study, consisting of three steps: (1) flexible background subtraction to yield background-free spectra, (2) a FRET quantification method to determine FRET efficiency (E) and donor fraction (fD = [donor] / ([donor]+[acceptor])) from the spectra, and (3) a model to determine the degree of oligomerization (interaction stoichiometry) in the protein complexes based on E vs. fD. The accuracy and applicability of this analysis was validated by theoretical simulations and experimental systems. These three steps were integrated into a computer procedure as an automatic quantitative FRET analysis which is easy, fast, and allows high-throughout to quantify FRET accurately and robustly, even in living cells. This method was subsequently applied to investigate oligomerization and protein-protein interactions, in particular in living cells. Cyan (CFP) and yellow fluorescent protein (YFP), two spectral variants of green fluorescent protein, were used as a donor-acceptor pair for in vivo measurements. Based on CFP- and YFP-fusions of non-interacting membrane proteins in the cell membrane, a minor FRET signal (E = 0.06 ± 0.01) can be regarded as an estimate of direct interaction between CFP and YFP moieties of fusion proteins co-localized in the cell membrane (false-positive). To confirm if the FRET occurrence is specific to the interaction of the investigated proteins, their FRET efficiency should be clearly above E = 0.06. The oligomeric state of DcuS was examined both in vivo (CFP/YFP) and in vitro (two different donor-acceptor pairs of organic dyes) by three independent experimental systems. The consistent occurrence of FRET in vitro and in vivo provides the evidence for the homo-dimerization of DcuS as full-length protein for the first time. Moreover, novel interactions (hetero-complexes) between DcuS and its functionally related proteins, citrate-specific sensor kinase CitA and aerobic dicarboxylate transporter DctA respectively, have been identified for the first time by intermolecular FRET in vivo. This analysis can be widely applied as a robust method to determine the interaction stoichiometry of protein complexes for other proteins of interest labeled with adequate fluorophores in vitro or in vivo.

Expanding the scope of poly(ethylene glycol)s for bioconjugation to squaric acid-mediated PEGylation and pH-sensitivity

Poly(ethylene glycol) (PEG) is used in a broad range of applications due to its unique combination of properties and is approved use in formulations for body-care products, edibles and medicine. This thesis aims at the synthesis and characterization of novel heterofunctional PEG structures and the establishment of diethyl squarate as a suitable linker for the covalent attachment to proteins. Chapter 1 is an introduction on the properties and applications of PEG as well as the fascinating chemistry of squaric acid derivatives. In Chapter 1.1, the synthesis and properties of PEG are described, and the versatile applications of PEG derivatives in everyday products are emphasized with a focus on PEG-based pharmaceuticals and nonionic surfactants. This chapter is written in German, as it was published in the German Journal Chemie in unserer Zeit. Chapter 1.2 deals with PEGs major drawbacks, its non-biodegradability, which impedes parenteral administration of PEG conjugates with polyethers exceeding the renal excretion limit, although these would improve blood circulation times and passive tumor targeting. This section gives a comprehensive overview of the cleavable groups that have been implemented in the polyether backbone to tackle this issue as well as the synthetic strategies employed to accomplish this task. Chapter 1.3 briefly summarizes the chemical properties of alkyl squarates and the advantages in protein conjugation chemistry that can be taken from its use as a coupling agent. In Chapter 2, the application of diethyl squarate as a coupling agent in the PEGylation of proteins is illustrated. Chapter 2.1 describes the straightforward synthesis and characterization of squaric acid ethyl ester amido PEGs with terminal hydroxyl functions or methoxy groups. The reactivity and selectivity of theses activated PEGs are explored in kinetic studies on the reactions with different lysine and other amino acid derivatives, followed by 1H NMR spectroscopy. Further, the efficient attachment of the novel PEGs to a model protein, i.e., bovine serum albumin (BSA), demonstrates the usefulness of the new linker for the PEGylation with heterofunctional PEGs. In Chapter 2.3 initial studies on the biocompatibility of polyether/BSA conjugates synthesized by the squaric acid mediated PEGylation are presented. No cytotoxic effects on human umbilical vein endothelial cells exposed to various concentrations of the conjugates were observed in a WST-1 assay. A cell adhesion molecule - enzyme immunosorbent assay did not reveal the expression of E-selectin or ICAM-1, cell adhesion molecules involved in inflammation processes. The focus of Chapter 3 lies on the syntheses of novel heterofunctional PEG structures which are suitable candidates for the squaric acid mediated PEGylation and exhibit superior features compared to established PEGs applied in bioconjugation. Chapter 3.1 describes the synthetic route to well-defined, linear heterobifunctional PEGs carrying a single acid-sensitive moiety either at the initiation site or at a tunable position in the polyether backbone. A universal concept for the implementation of acetal moieties into initiators for the anionic ring-opening polymerization (AROP) of epoxides is presented and proven to grant access to the degradable PEG structures aimed at. The hydrolysis of the heterofunctional PEG with the acetal moiety at the initiating site is followed by 1H NMR spectroscopy in deuterium oxide at different pH. In an exploratory study, the same polymer is attached to BSA via the squarate acid coupling and subsequently cleaved from the conjugate under acidic conditions. Furthermore, the concept for the generation of acetal-modified AROP initiators is demonstrated to be suitable for cholesterol, and the respective amphiphilic cholesteryl-PEG is cleaved at lowered pH. In Chapter 3.2, the straightforward synthesis of α-amino ω2-dihydroxyl star-shaped three-arm PEGs is described. To assure a symmetric length of the hydroxyl-terminated PEG arms, a novel AROP initiator is presented, who’s primary and secondary hydroxyl groups are separated by an acetal moiety. Upon polymerization of ethylene oxide for these functionalities and subsequent cleavage of the acid-labile unit no difference in the degree of polymerization is seen for both polyether fragments.

Tailored epoxide monomers as building units for multifunctional poly(ethylene glycol)

Poly(ethylenglykol) (PEG) ist eines der wichtigsten Polymere für pharmazeutische und biomedizinische Zwecke. Dies lässt sich vor allen Dingen auf seine ausgezeichnete Biokompatibilität, seine hohe chemische Stabilität sowie seine sehr gute Wasserlöslichkeit zurückführen. Neben seiner Anwendung in Produkten wie Lebensmitteln und Kosmetika ist PEG vor allem im pharmazeutischen Bereich unersetzlich geworden. Hier dient PEG als Grundlage für Salben, es kommt aber auch in der sogenannten „PEGylierung“ zum Einsatz. Unter PEGylierung versteht man die kovalente Verknüpfung von PEG mit Wirkstoffmolekülen, beispielsweise Proteinen oder niedermolekularen Medikamenten. In der akademischen Forschung sind aber auch PEGylierte Nanopartikel oder durch PEG stablisierte Liposomen für die Applikation im Bereich der Medizin von hohem Interesse. Trotz seiner breiten Verwendung hat PEG zwei entscheidende Nachteile: Zum einen benötigt man gerade im Hinblick auf PEGylierungen viele funktionelle Gruppe, jedoch trägt PEG maximal zwei Hydroxyl-Gruppen (die Endgruppen), die für kovalente Verknüpfungen genutzt werden können. Zum anderen ist PEG nicht in physiologischer Umgebung abbaubar und kann daher in vivo oberhalb eines Molekulargewichts von 40 000 g/mol nicht eingesetzt werden, da sonst eine Ausscheidung über die Niere nicht möglich ist und eine ungewollte Anreicherung im Körper stattfindet.rnDie durch die geringe Anzahl an Endgruppen limitierte Beladungsdichte kann durch das Design neuer Epoxid-Derivate und deren statistischen Einbau in das PEG Rückgrat deutlich verbessert werden. Im ersten Teil dieser Arbeit werden drei neuartige funktionelle Oxirane vorgestellt, die systematisch mit Ethylenoxid copolymerisiert wurden, was die selektive Einführung verschiedener funktioneller Gruppen am Polymerrückgrat ermöglicht. Im Vordergrund der Betrachtungen standen die Eigenschaften der neuartigen multifunktionellen (mf)-PEG Copolymere im Hinblick auf ihr thermisches Verhalten sowie die Verteilung der funktionellen Gruppen (Mikrostruktur) innerhalb des PEG-Rückgrats. Die gezielte Adressierbarkeit der funktionellen Gruppen konnte durch verschiedene Modellreaktionen bestätigt werden. Darüber hinaus konnte gezeigt werden, dass sich mit der vorgestellten Synthesestrategie komplexe Hybridmaterialien, beispielsweise metallhaltige Polyether, darstellen lassen. Mit Hinblick auf die biomedizinischen Anwendungen und die Konkurrenz zu etablierten PEG-Hompolymeren, standen die Wasserlöslichkeit und die Toxizität der synthetisierten Materialien im Zentrum weiterer Untersuchungen. Alle dargestellten Polymere zeigten einen Trübungspunkt in Wasser, der sich in Abhängigkeit der Zusammensetzung und Hydrophobizität der Comonomere über ein weites Temperaturspektrum variieren und somit systematisch einstellen ließ. Die Toxizität der statistischen mf-PEGs lag im Bereich von PEG, was die mf-PEGs interessant für biomedizinische Anwendung macht.rnIm zweiten Teil der Arbeit wurden Copolymerisationen verwendet, um über erstmals hergestellte Epoxid-Inimere sauer spaltbare Einheiten in das Polyetherrückgrat einzuführen. Die neuen, verzweigten Strukturen wurden auf die Zersetzung in physiologisch relevantem Milieu untersucht. Die erzielte pH-abhängige Spaltbarkeit, kann für potenzielle Anwendungen beispielsweise in der Krebstherapie, von Vorteil sein.rn