540 Chemie und zugeordnete Wissenschaften
Refine
Year of publication
Document Type
- Article (998)
- Doctoral Thesis (607)
- Book (22)
- Contribution to a Periodical (17)
- Preprint (14)
- Conference Proceeding (11)
- Report (9)
- Review (5)
- diplomthesis (3)
- Diploma Thesis (2)
Has Fulltext
- yes (1692)
Is part of the Bibliography
- no (1692)
Keywords
- crystal structure (39)
- Crystal Structure (24)
- Synthesis (15)
- ESR Spectra (14)
- NMR spectroscopy (14)
- RNA (14)
- NMR (12)
- hydrogen bonding (11)
- IR Spectra (10)
- photochemistry (10)
Institute
- Biochemie und Chemie (1128)
- Biochemie, Chemie und Pharmazie (260)
- Pharmazie (151)
- Zentrum für Biomolekulare Magnetische Resonanz (BMRZ) (49)
- Biowissenschaften (40)
- Medizin (37)
- Physik (34)
- Präsidium (28)
- MPI für Biophysik (19)
- Exzellenzcluster Makromolekulare Komplexe (18)
Die Oberflächenchemie ist mittlerweile in vielen chemischen, biochemischen und anderen Forschungsbereichen präsent und stellt eine interdisziplinäre Forschungsdisziplin dar. Diese Arbeit fokussierte sich auf die Interaktionen von biochemischen Systemen mit Oberflächen, insbesondere auf die Entwicklung von biochemischen Sensoren. Die Optimierung der Sensoroberfläche, insbesondere die Erhöhung der Selektivität durch die Verwendung von Polyglycerol (PG), wurde untersucht. Insgesamt wurden vier Teilprojekte durchgeführt, die sich auf die Unterdrückung unerwünschter Interaktionen, die Einführung von Bioerkennungsstellen, die Stabilisierung von PG-Filmen und die Entwicklung eines leitfähigen Hybridmaterials konzentrierten.
Teilprojekt 1: Stabilisierung von PG-Filmen durch Quervernetzung
Im ersten Abschnitt wurde die Stabilisierung von PG-Filmen durch eine oberflächeninitiierte ringöffnende Polymerisationsreaktion auf SiOx-Substrate realisiert. Dabei wurde die Dicke der Filme (10, 50 und 100 nm) über die Reaktionszeit kontrolliert. Die Quervernetzung erfolgte mit Ethylenglycoldiglycidylether (EGDGE), Divinylsulfon (DVS), Glutaraldehyd (GA), 1,11-Di(mesyl-oxy)-3,6,9-trioxaundecan (TEG-Ms2) und 1,11-Dibrom-3,6,9-trioxaundecan (TEG-Br2). Die Wahl des Quervernetzungsmittels zeigte signifikante Auswirkungen auf die Dicke der Filme und deren Biorepulsivität. Insbesondere die Untersuchungen an PG-EGDGE-Filmen waren vielversprechend, da sie nicht nur Biorepulsivität zeigten, sondern auch eine hohe mechanische Stabilität aufwiesen. Die Erkenntnis, dass dünnere Filme mit einem höheren Elastizitätsmodul gewünscht waren, erforderte eine gezielte Auswahl des Quervernetzungsmittels.
Teilprojekt 2: Einführung einer Bioerkennungsstelle auf einem EGDGE-quervernetzten PG-Film
Im nächsten Abschnitt wurde die Einführung einer Bioerkennungsstelle auf einem EGDGE-quervernetzten PG-Film erforscht. Hierbei kam ein Nitrilotriessigsäure (NTA)-Derivat (NTA4-Cyclen) zum Einsatz, um Histidin (His)-Tag-markierte Proteine selektiv zu binden. Die Modifikation erfolgte durch die Polymerisation von Glycidol auf ein amino-terminiertes Disulfid, gefolgt von einer Quervernetzung mit EGDGE. Die optimierte Synthese des NTA-Derivats ermöglichte nicht nur die erfolgreiche Anbindung von His-markierten Proteinen, sondern auch eine quasi-reversible Anbindung. Diese Erkenntnisse eröffnen neue Möglichkeiten für die Regenerierbarkeit von biochemischen Oberflächen.
Teilprojekt 3: Entwicklung eines leitfähigen und biorepulsiven Hybridmaterials
Das dritte Teilprojekt konzentrierte sich auf die Entwicklung eines leitfähigen und biorepulsiven Hybridmaterials. Ein PG-funktionalisiertes Pyrrol-Derivat (PyPG) wurde elektrochemisch polymerisiert, wodurch Netzwerke aus PG-funktionalisierten Polypyrrol-Strängen (PPG) auf Goldoberflächen entstanden. Die Elektropolymerisation wurde detailliert durch Cyclovoltammetrie (CV) und einer Quarzkristall-Mikrowaage (QCM) charakterisiert. Dabei konnte ein selbstterminierender Mechanismus identifiziert werden, der von der Anwesenheit der verzweigten PG-Gruppen dominiert wird. Mit Hilfe der elektrochemischen Impedanzspektroskopie (EIS) wurde gezeigt, dass dünnere Schichten mit geringerer Schichtdicke hoch leitfähig sind und dass die Veränderungen der Leitfähigkeit tatsächlich nur durch die äußere Oberflächenschicht bestimmt wird. Die Biorepulsivität des Materials wurde durch Proteinadsorptions- und Bakterienadhäsions-Assays nachgewiesen. Der zweite Abschnitt dieses Projekts konzentrierte sich auf die Einführung einer Erkennungsstelle basierend auf Glycosiden, um nicht nur eine Oberflächenbindung, sondern auch eine Quantifizierung von Biomolekülen zu ermöglichen. Die elektrochemische Charakterisierung der Nanoschichtsysteme zeigte eine sehr gute Linearität der Ladungsübertragungsadmittanz (Sct) in Abhängigkeit von der Anbindung der Bakterienstämme. Dies eröffnet Perspektiven für die selektive Quantifizierung von biologischen Analyten mittels elektrochemischer Methoden.
Die Wunder-Moleküle
(2024)
Wie speichern wir in Zukunft Sonnenenergie? An der Goethe-Universität wird eine ganz neue Technologie erforscht. Am Projekt FORMOST sind neben der Universität Frankfurt noch die Universitäten in Tübingen, Gießen, Heidelberg und Erlangen-Nürnberg beteiligt. Wachtveitls Gruppe erforscht die molekularen Mechanismen der Energiespeicherung und -freisetzung bei MOST-Molekülen. Andere Gruppen kümmern sich um die Synthese der Moleküle oder die Modellierung. Das Projekt läuft von 2023 bis 2027 und wird von der Deutschen Forschungsgemeinschaft (DFG) mit insgesamt rund 4,8 Millionen Euro gefördert.
The β-barrel assembly machinery (BAM) mediates the folding and insertion of the majority of outer membrane proteins (OMPs) in gram-negative bacteria. BAM is a penta-heterooligomeric complex consisting of the central β-barrel BamA and four interacting lipoproteins BamB, C, D, and E. The conformational switching of BamA between inward-open (IO) and lateral-open (LO) conformations is required for substrate recognition and folding. However, the mechanism for the lateral gating or how the structural details observed in vitro correspond with the cellular environment remains elusive. In this study, we addressed these questions by characterizing the conformational heterogeneity of BamAB, BamACDE, and BamABCDE complexes in detergent micelles and/or Escherichia coli using pulsed dipolar electron spin resonance spectroscopy (PDS). We show that the binding of BamB does not induce any visible changes in BamA, and the BamAB complex exists in the IO conformation. The BamCDE complex induces an IO to LO transition through a coordinated movement along the BamA barrel. However, the extracellular loop 6 (L6) is unaffected by the presence of lipoproteins and exhibits large segmental dynamics extending to the exit pore. PDS experiments with the BamABCDE complex in intact E. coli confirmed the dynamic behavior of both the lateral gate and the L6 in the native environment. Our results demonstrate that the BamCDE complex plays a key role in the function by regulating lateral gating in BamA.
Lipopolysaccharides (LPS) confer resistance against harsh conditions, including antibiotics, in Gram-negative bacteria. The lipopolysaccharide transport (Lpt) complex, consisting of seven proteins (A-G), exports LPS across the cellular envelope. LptB2FG forms an ATP-binding cassette transporter that transfers LPS to LptC. How LptB2FG couples ATP binding and hydrolysis with LPS transport to LptC remains unclear. We observed the conformational heterogeneity of LptB2FG and LptB2FGC in micelles and/or proteoliposomes using pulsed dipolar electron spin resonance spectroscopy. Additionally, we monitored LPS binding and release using laser-induced liquid bead ion desorption mass spectrometry. The β-jellyroll domain of LptF stably interacts with the LptG and LptC β-jellyrolls in both the apo and vanadate-trapped states. ATP binding at the cytoplasmic side is allosterically coupled to the selective opening of the periplasmic LptF β-jellyroll domain. In LptB2FG, ATP binding closes the nucleotide binding domains, causing a collapse of the first lateral gate as observed in structures. However, the second lateral gate, which forms the putative entry site for LPS, exhibits a heterogeneous conformation. LptC binding limits the flexibility of this gate to two conformations, likely representing the helix of LptC as either released from or inserted into the transmembrane domains. Our results reveal the regulation of the LPS entry gate through the dynamic behavior of the LptC transmembrane helix, while its β-jellyroll domain is anchored in the periplasm. This, combined with long-range ATP-dependent allosteric gating of the LptF β-jellyroll domain, may ensure efficient and unidirectional transport of LPS across the periplasm.
In spite of the increasing number of biologics license applications, the development of covalent inhibitors is still a growing field within drug discovery. The successful approval of some covalent protein kinase inhibitors, such as ibrutinib (BTK covalent inhibitor) and dacomitinib (EGFR covalent inhibitor), and the very recent discovery of covalent inhibitors for viral proteases, such as boceprevir, narlaprevir, and nirmatrelvir, represent a new milestone in covalent drug development. Generally, the formation of covalent bonds that target proteins can offer drugs diverse advantages in terms of target selectivity, drug resistance, and administration concentration. The most important factor for covalent inhibitors is the electrophile (warhead), which dictates selectivity, reactivity, and the type of protein binding (i.e., reversible or irreversible) and can be modified/optimized through rational designs. Furthermore, covalent inhibitors are becoming more and more common in proteolysis, targeting chimeras (PROTACs) for degrading proteins, including those that are currently considered to be ‘undruggable’. The aim of this review is to highlight the current state of covalent inhibitor development, including a short historical overview and some examples of applications of PROTAC technologies and treatment of the SARS-CoV-2 virus.
The impact of 2-desaza-annomontine on processes of inflammation and its resolution in leukocytes
(2024)
This present study investigated the effects of the b-carboline derivative C81, also called 2-desaza-annomontine, on the inflammatory response and resolution processes in vivo and in vitro. The study focused on leukocytes and on the elucidation of the underlying pharmacological mode of action. C81 potently reduced the inflammatory response in an imiquimod-induced psoriasis mouse model and additionally resolved the inflammation more quickly. In a CNV model, C81 significantly decreased the microglial infiltration in the inflamed laser lesion in vivo. In vitro experiments revealed that C81 inhibits the migration of macrophages and leukocyte-endothelial cell interaction by reducing the activation of integrins on leukocytes, in particular LFA-1, without affecting the total protein level on the cell surface.
Further experiments revealed that C81 inhibited the expression of EPAC-1, required for Rap1 activation. Consequently, C81 reduced the LPS/PMA-induced Rap1 activity, which is responsible for integrin activation. Moreover, C81 potently reduced the LPS-induced formation of pro-inflammatory mediators, including cytokines and eicosanoids, in macrophages. The C81-derived inhibition of eicosanoid release was surprisingly potent, probably due to the C81-evoked inhibition of cPLA2 expression, resulting in less liberated arachidonic acid, the precursor for eicosanoids. At the same time, C81 only delayed COX-2 expression, but completely diminished LPS-induced mPGES-1 expression. In addition to the potent anti-inflammatory effects in vitro, C81-derived impact was complemented with promising pro-resolving effects. Hence, C81 significantly induced neutrophil apoptosis without affecting the cell viability of other leukocytes, such as macrophages. Accordingly, the caspase 3 activity in neutrophils increased upon C81 treatment. The underlying mechanism altered by C81 was the expression of the anti-apoptotic mediator Mcl-1, which is required for the survival of neutrophils, but not macrophages. Furthermore, neutrophils treated with C81 were significantly better efferocytosed by macrophages. Analyzes of the pharmacological mode of action of C81 revealed DYRK1B as the key target kinase in inflammatory processes in leukocytes. Of note, experiments with pharmacological inhibition of DYRK1B by C81 or the ‘selective’ DYRK1B inhibitor AZ-DYRK1B-33, could not completely exclude the involvement of the CLKs and other DYRKs. Therefore, DYRK1B knockdown and overexpression experiments were conducted to elucidate the impact of DYRK1B alone. Pharmacological inhibition of DYRK1B and DYRK1B knockdown phenocopied the inhibitory effect of C81 on leukocyte adhesion. In parallel, DYRK1B overexpression mitigated the C81-evoked effect, supporting the hypothesis that C81 inhibits DYRK1B to mediate its effects on leukocytes. Furthermore, DYRK1B inhibition and DYRK1B knockdown resulted in depletion of STAT3 phosphorylation. In addition, C81-evoked STAT3 inhibition was again mitigated by DYRK1B overexpression, suggesting a link or even an interaction between DYRK1B and STAT3. Indeed, direct interaction between DYRK1B and STAT3 was confirmed by a NanoBRET assay. Importantly, in vitro experiments demonstrated, that C81 did not affect LPS recognition mechanisms, investigated by TLR-4 and CD14 expression, and other important inflammatory signaling pathways. Although C81 inhibited the regeneration of IkBa, this had no effect on the translocation of the NFkB subunit p65. Furthermore, C81 did not alter the activation of MAPK pathways, including p38, JNK and ERK. As a result, the focus was on the potent inhibition of LPS-nduced STAT3 activation mediated by DYRK1B, which was shown to be IL-6 independent. Indeed, direct STAT3 inhibition by Stattic phenocopied all tested C81-derived effects on leukocytes, including migration, adhesion, pro-inflammatory cytokine expression, eicosanoid formation and cell type specific induction of neutrophil apoptosis. The underlying mechanisms altered by Stattic in terms of migration/adhesion and lipid mediator formation were the same as for C81. STAT3 inhibition led to decreased EPAC1 expression and accordingly to reduced Rap1 activation. In addition, inhibited STAT3 phosphorylation resulted in reduced cPLA2 expression and also in attenuated mPGES-1 expression.
Finally, the C81-derived depleted Mcl-1 expression was linked to reduced STAT3 inhibition. As C81 abolished STAT3 phosphorylation, less STAT3 was translocated into the nucleus upon LPS stimulation and less STAT3 enrichment at the MCL1 promoter was observed, leading to reduced gene expression and consequently protein levels.
In summary, using the natural product-derived compound C81, the DYRK1B/STAT3 axis was identified as a novel key regulator of inflammatory processes in human leukocytes. This present study revealed that interfering with the DYRK1B-STAT3 signaling can address essential cell functions including leukocyte extravasation, pro-inflammatory mediator release, neutrophil apoptosis and efferocytosis (Figure 1). Furthermore, two different mouse models demonstrated the in vivo relevance of this signaling axis and highlight DYRK1B as an important kinase modulating inflammation and resolution.
In integrative structural biology/hybrid modeling approaches, we integrate structural models of macromolecules and experimental data to obtain faithful representations of the structures underlying the data. For example, in ensemble refinement by reweighting we first generate structural ensembles of flexible and dynamic biological macromolecules in molecular simulations. In a subsequent reweighting step, we refine the statistical weights of the structures to strike a balance between the information provided by simulations and by experimental data. For the "Bayesian inference of ensembles" approach (BioEn), we present two complementary methods to solve the underlying challenging high-dimensional optimization problem. We systematically investigate reliability, accuracy, and efficiency of these methods and integrate molecular dynamics simulations of the disordered peptide Ala-5 and NMR J-couplings. We provide an open-source library free of charge at https://github.com/bio-phys/BioEn.
In integrative structural biology/hybrid modeling approaches, we integrate structural models of macromolecules and experimental data to obtain faithful representations of the structures underlying the data. For example, in ensemble refinement by reweighting we first generate structural ensembles of flexible and dynamic biological macromolecules in molecular simulations. In a subsequent reweighting step, we refine the statistical weights of the structures to strike a balance between the information provided by simulations and by experimental data. For the "Bayesian inference of ensembles" approach (BioEn), we present two complementary methods to solve the underlying challenging high-dimensional optimization problem. We systematically investigate reliability, accuracy, and efficiency of these methods and integrate molecular dynamics simulations of the disordered peptide Ala-5 and NMR J-couplings. We provide an open-source library free of charge at https://github.com/bio-phys/BioEn.
Ensemble refinement produces structural ensembles of flexible and dynamic biomolecules by integrating experimental data and molecular simulations. Here we present two efficient numerical methods to solve the computationally challenging maximum-entropy problem arising from a Bayesian formulation of ensemble refinement. Recasting the resulting constrained weight optimization problem into an unconstrained form enables the use of gradient-based algorithms. In two complementary formulations that differ in their dimensionality, we optimize either the log-weights directly or the generalized forces appearing in the explicit analytical form of the solution. We first demonstrate the robustness, accuracy, and efficiency of the two methods using synthetic data. We then use NMR J-couplings to reweight an all-atom molecular dynamics simulation ensemble of the disordered peptide Ala-5 simulated with the AMBER99SB*-ildn-q force field. After reweighting, we find a consistent increase in the population of the polyproline-II conformations and a decrease of α-helical-like conformations. Ensemble refinement makes it possible to infer detailed structural models for biomolecules exhibiting significant dynamics, such as intrinsically disordered proteins, by combining input from experiment and simulation in a balanced manner.