TY - JOUR A1 - Wehner, Marius A1 - Röhr, Merle Insa Silja A1 - Stepanenko, Vladimir A1 - Würthner, Frank T1 - Control of self-assembly pathways toward conglomerate and racemic supramolecular polymers JF - Nature Communications N2 - Homo- and heterochiral aggregation during crystallization of organic molecules has significance both for fundamental questions related to the origin of life as well as for the separation of homochiral compounds from their racemates in industrial processes. Herein, we analyse these phenomena at the lowest level of hierarchy - that is the self-assembly of a racemic mixture of (R,R)- and (S,S)-PBI into 1D supramolecular polymers. By a combination of UV/vis and NMR spectroscopy as well as atomic force microscopy, we demonstrate that homochiral aggregation of the racemic mixture leads to the formation of two types of supramolecular conglomerates under kinetic control, while under thermodynamic control heterochiral aggregation is preferred, affording a racemic supramolecular polymer. FT-IR spectroscopy and quantum-chemical calculations reveal unique packing arrangements and hydrogen-bonding patterns within these supramolecular polymers. Time-, concentration- and temperature-dependent UV/vis experiments provide further insights into the kinetic and thermodynamic control of the conglomerate and racemic supramolecular polymer formation. Homo- and heterochiral aggregation is a process of interest to prebiotic and chiral separation chemistry. Here, the authors analyze the self-assembly of a racemic mixture into 1D supramolecular polymers and find homochiral aggregation into conglomerates under kinetic control, while under thermodynamic control a racemic polymer is formed. KW - perylene bismide dye KW - nucleation-elongation KW - PI stacking KW - polymerization KW - complexity KW - mechanism KW - crystals KW - kinetics KW - growth Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-230580 VL - 11 ER - TY - THES A1 - Stock, Patrick Maria T1 - Binding site contribution in high resolution records of nicotinic receptor channel currents T1 - Beitrag der Bindungsstellen zum Öffnungsverhalten des nAChRs N2 - The nicotinic acetylcholine receptor of skeletal muscle is one of the best-investigated synaptic proteins and often serves as model for the entire family of pentameric ligand gated ion channels (pLGICs). Receptors of this superfamily share a common architecture. After binding the agonist the characteristic C-loop structure closes around the ligand-binding site and triggers a wave of conformational changes that spread through the protein and finally result in the opening of the channel gate. As shown before, high-resolution single channel data can hardly be described by simple kinetic mechanisms (Parzefall et al., 1998, Hallermann et al., 2005). Recent advances in the field of kinetic modelling on receptor currents demonstrate that the introduction of additional short lived shut states in kinetic schemes enhances the quality of estimates of reaction rates. The additional shut states that immediately follow ligand bound states in the mechanism are suggested to resemble the closing movement of the C-loop (Lape et al., 2008; Mukhtasimova et al., 2009). It has not been described yet whether and how the structural differences of the 2 binding sites of the receptor influence the opening behaviour. To address this question, high-resolution single channel recordings, in combination with agonists that are known to exhibit different binding site selectivity, were performed. Thereby, a detailed description of the binding site dependent generation of channel currents is possible. At the embryonic mouse-muscle receptor used in this study the ligand binding sites are located at the α-γ and α-δ subunit interfaces. By allocation of opening characteristics to the α-δ and α-γ sites it is possible to show the binding site dependent activation of distinct kinetic states. Furthermore, it will be shown that the recently introduced short-lived shut states are sufficient to describe high-resolution single channel data. Finally an enhanced kinetic mechanism based on the ‘primed states’ model, published in 2009 by Mukhtasimova et al., will be presented. In this model the structurally diverse α-δ and α-γ binding sites elicit different kinetic channel characteristics. Thus the complex high-resolution kinetic characteristics of the embryonic receptor can be described coherently. N2 - Der nicotinische Acetylcholin-Rezeptorkanal des Skelettmuskels zählt zu den bestuntersuchten synaptischen Proteinen und gilt als Modell für die Familie der Liganden gesteuerten pentameren Ionenkanäle. Rezeptoren dieser Großfamilie besitzen als charakteristisches strukturelles Merkmal ein Cystein-Schleifen-Motiv (C-loop), welches sich nach Bindung eines Agonisten um die Bindungstasche herum schließt und eine Kette weiterer Konformationsänderungen nach sich zieht. Wie in früheren Publikationen festgestellt wurde, ist es nur schwer möglich hochaufgelöste Messdaten mit konservativen kinetischen Modellen ausreichend zu beschreiben (Parzefall et al., 1998; Hallermann et al., 2005). Aktuelle Fortschritte auf dem Gebiet der kinetischen Modellierung von mechanistischen Rezeptormodellen auf Rezeptorströme, zeigen, dass die Einführung zusätzlicher kurzlebiger Geschlossenzustände in den kinetischen Mechanismen die Qualität der Voraussagen der Modelle verbessert. Diese zusätzlichen Geschlossenzustände, welche Zuständen mit gebundenen Agonisten des Rezeptormodells folgen, spiegeln höchstwahrscheinlich die Schließung des Cystein-Schleifen-Motivs wider (Lape et al., 2008; Mukhtasimova et al., 2009). Trotz der jüngsten Fortschritte wurde bisher nicht beschrieben, wie und ob die strukturellen Unterschiede der 2 vorhandenen Bindungsstellen sich auf die Charakteristika des Öffnungsverhaltens auswirken. Die Bindungsstellen für Agonisten befinden sich am embryonalen nicotinischen Acetylcholinrezeptor des Muskels der Maus an den Schnittstellen der α-δ und der α-γ Untereinheiten. Um der Frage des Einflusses der Bindungsstellendiversität auf den Grund zu gehen, wurden hochaufgelöste Einzelkanalmessungen unter der Verwendung von unterschiedlichen Agonisten, für die bekannt ist, dass sie unterschiedliche Selektivitäten zu den Bindungsstellen besitzen, durchgeführt. Hierdurch ist es möglich ein detailliertes Bild der bindungsstellenbedingten Auslösung definierter Öffnungscharakteristika zu beschreiben. Durch die Zuweisung der Öffnungscharakteristika zu den α-δ und α-γ Bindungsstellen gelingt es die bindungsstellenabhängige Aktivierung von einzelnen kinetischen Zuständen zu zeigen. Darüber hinaus werden direkte Anhaltspunkte dafür gezeigt, dass es möglich ist mit den angeführten kurzlebigen Geschlossenzuständen hochaufgelöste Einzelkanaldaten kinetisch hinreichend zu beschreiben. Schließlich wird ein erweiterter kinetischer Mechanismus vorgestellt, welcher auf dem ‚primed-states’ Modell, das 2009 von Mukhtasimova veröffentlicht wurde, basiert. Zusätzlich ist dieser in der Lage die komplexen kinetischen Charakteristika des embryonalen nicotinischen Rezeptorkanals, unter hoher zeitlicher Auflösung der Messdaten, zu beschreiben. KW - Nicotinischer Acetylcholinrezeptor KW - Bindestelle KW - Ionenkanal KW - Kinetik KW - Neurobiologie KW - nAChR KW - Kanalkinetik KW - Bindungsstellen KW - Rezeptor KW - neurobiology KW - nAChR KW - receptor channel KW - binding sites KW - kinetics Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-71769 ER - TY - JOUR A1 - Schulte, Clemens A1 - Soldà, Alice A1 - Spänig, Sebastian A1 - Adams, Nathan A1 - Bekić, Ivana A1 - Streicher, Werner A1 - Heider, Dominik A1 - Strasser, Ralf A1 - Maric, Hans Michael T1 - Multivalent binding kinetics resolved by fluorescence proximity sensing JF - Communications Biology N2 - Multivalent protein interactors are an attractive modality for probing protein function and exploring novel pharmaceutical strategies. The throughput and precision of state-of-the-art methodologies and workflows for the effective development of multivalent binders is currently limited by surface immobilization, fluorescent labelling and sample consumption. Using the gephyrin protein, the master regulator of the inhibitory synapse, as benchmark, we exemplify the application of Fluorescence proximity sensing (FPS) for the systematic kinetic and thermodynamic optimization of multivalent peptide architectures. High throughput synthesis of +100 peptides with varying combinatorial dimeric, tetrameric, and octameric architectures combined with direct FPS measurements resolved on-rates, off-rates, and dissociation constants with high accuracy and low sample consumption compared to three complementary technologies. The dataset and its machine learning-based analysis deciphered the relationship of specific architectural features and binding kinetics and thereby identified binders with unprecedented protein inhibition capacity; thus, highlighting the value of FPS for the rational engineering of multivalent inhibitors. KW - combinatorial libraries KW - kinetics KW - peptides KW - screening KW - thermodynamics Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-301157 VL - 5 ER - TY - JOUR A1 - Scheiner, Matthias A1 - Sink, Alexandra A1 - Spatz, Philipp A1 - Endres, Erik A1 - Decker, Michael T1 - Photopharmacology on Acetylcholinesterase: Novel Photoswitchable Inhibitors with Improved Pharmacological Profiles JF - ChemPhotoChem N2 - Considerable effort has previously been invested in a light‐controlled inhibition of the enzyme acetylcholinesterase (AChE). We found that a novel azobenzene‐based bistacrine AChE inhibitor switched faster than the known dithienylethene based bistacrine and inverted the photo‐controlled interactions of the photoisomers compared to its dithienylethene congener. Furthermore, we have optimized a previously described light‐controlled tacrine‐based AChE inhibitor. Isomerization upon irradiation with UV light of the novel inhibitor was observed in aqueous medium and showed no fatigue over several cycles. The cis‐enriched form showed an 8.4‐fold higher inhibition of hAChE compared with its trans‐enriched form and was about 30‐fold more active than the reference compound tacrine with a single‐digit nanomolar inhibition. We went beyond proof‐of‐concept to discover photoswitchable AChE inhibitors with pharmacologically desirable nanomolar inhibition, “cis‐on” effect, and pronounces differences between the photoisomers. KW - azobenzenes KW - enzymes KW - kinetics KW - photopharmacology KW - tacrine Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-218445 VL - 5 IS - 2 SP - 149 EP - 159 ER - TY - JOUR A1 - Sawatzky, Edgar A1 - Drakopoulos, Antonios A1 - Rölz, Martin A1 - Sotriffer, Christoph A1 - Engels, Bernd A1 - Decker, Michael T1 - Experimental and theoretical investigations into the stability of cyclic aminals JF - Beilstein Journal of Organic Chemistry N2 - Background: Cyclic aminals are core features of natural products, drug molecules and important synthetic intermediates. Despite their relevance, systematic investigations into their stability towards hydrolysis depending on the pH value are lacking. Results: A set of cyclic aminals was synthesized and their stability quantified by kinetic measurements. Steric and electronic effects were investigated by choosing appropriate groups. Both molecular mechanics (MM) and density functional theory (DFT) based studies were applied to support and explain the results obtained. Rapid decomposition is observed in acidic aqueous media for all cyclic aminals which occurs as a reversible reaction. Electronic effects do not seem relevant with regard to stability, but the magnitude of the conformational energy of the ring system and pK a values of the N-3 nitrogen atom. Conclusion: Cyclic aminals are stable compounds when not exposed to acidic media and their stability is mainly dependent on the conformational energy of the ring system. Therefore, for the preparation and work-up of these valuable synthetic intermediates and natural products, appropriate conditions have to be chosen and for application as drug molecules their sensitivity towards hydrolysis has to be taken into account. KW - quantum mechanics KW - hydrolysis KW - kinetics KW - molecular mechanics KW - natural products Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-160976 VL - 12 ER - TY - JOUR A1 - Rajab, Suhaila A1 - Bismin, Leah A1 - Schwarze, Simone A1 - Pinggera, Alexandra A1 - Greger, Ingo H. A1 - Neuweiler, Hannes T1 - Allosteric coupling of sub-millisecond clamshell motions in ionotropic glutamate receptor ligand-binding domains JF - Communications Biology N2 - Ionotropic glutamate receptors (iGluRs) mediate signal transmission in the brain and are important drug targets. Structural studies show snapshots of iGluRs, which provide a mechanistic understanding of gating, yet the rapid motions driving the receptor machinery are largely elusive. Here we detect kinetics of conformational change of isolated clamshell-shaped ligand-binding domains (LBDs) from the three major iGluR sub-types, which initiate gating upon binding of agonists. We design fluorescence probes to measure domain motions through nanosecond fluorescence correlation spectroscopy. We observe a broad kinetic spectrum of LBD dynamics that underlie activation of iGluRs. Microsecond clamshell motions slow upon dimerization and freeze upon binding of full and partial agonists. We uncover allosteric coupling within NMDA LBD hetero-dimers, where binding of L-glutamate to the GluN2A LBD stalls clamshell motions of the glycine-binding GluN1 LBD. Our results reveal rapid LBD dynamics across iGluRs and suggest a mechanism of negative allosteric cooperativity in NMDA receptors. KW - fluorescence spectroscopy KW - kinetics KW - ligand-gated ion channels KW - molecular neuroscience Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-261678 VL - 4 IS - 1 ER - TY - JOUR A1 - Quast, Helmut A1 - Gescheidt, Georg A1 - Spichty, Martin T1 - Topological dynamics of a radical ion pair: Experimental and computational assessment at the relevant nanosecond timescale JF - Chemistry N2 - Chemical processes mostly happen in fluid environments where reaction partners encounter via diffusion. The bimolecular encounters take place at a nanosecond time scale. The chemical environment (e.g., solvent molecules, (counter)ions) has a decisive influence on the reactivity as it determines the contact time between two molecules and affects the energetics. For understanding reactivity at an atomic level and at the appropriate dynamic time scale, it is crucial to combine matching experimental and theoretical data. Here, we have utilized all-atom molecular-dynamics simulations for accessing the key time scale (nanoseconds) using a QM/MM-Hamiltonian. Ion pairs consisting of a radical ion and its counterion are ideal systems to assess the theoretical predictions because they reflect dynamics at an appropriate time scale when studied by temperature-dependent EPR spectroscopy. We have investigated a diketone radical anion with its tetra-ethylammonium counterion. We have established a funnel-like transition path connecting two (equivalent) complexation sites. The agreement between the molecular-dynamics simulation and the experimental data presents a new paradigm for ion–ion interactions. This study exemplarily demonstrates the impact of the molecular environment on the topological states of reaction intermediates and how these states can be consistently elucidated through the combination of theory and experiment. We anticipate that our findings will contribute to the prediction of bimolecular transformations in the condensed phase with relevance to chemical synthesis, polymers, and biological activity. KW - ion pairing KW - radical anion KW - kinetics KW - thermodynamics KW - molecular dynamics KW - QM/MM KW - EPR Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-285195 SN - 2624-8549 VL - 2 IS - 2 SP - 219 EP - 230 ER - TY - THES A1 - Peng, Kun T1 - iClick reactions as a modular access to palladium(II) and platinum(II) triazolato complexes: Trends in kinetics and biological activity T1 - iClick-Reaktionen als modularer Zugang zu Palladium (II)- und Platin (II)-Triazolato-Komplexen: Trends in der Kinetik und biologischen Aktivität N2 - In the context of this work, important trends in the influence of the metal center, coligand, and alkyne reaction partner on the iClick reaction of square-planar palladium(II) and platinum(II) complexes with a N^N^N, C^N^N, or S^N^N coordination sphere and a number of internal as well as terminal alkynes were elaborated. Preliminary bioactivity studies on a human cancer cell line gave low micromolar EC50 values, for the most promising compound comparable to cisplatin serving as a reference drug. The further application of the iClick reaction to bioconjugation will be explored in future work. N2 - Insgesamt konnten im Rahmen dieser Arbeit systematische Einflüsse des Metallzentrums, des Coliganden und des Alkins auf die Geschwindigkeit der iClick-Reaktion von quadratisch-planaren Palladium(II)- und Platin(II)-Azid-Komplexen mit internen und terminalen Alkinen identifiziert werden. So reagiert auch in dieser Serie das 4d-Element schneller als das entsprechend 5d-Metall, interne Alkinen mit elektronenarmen Substituenten führen zu einer höheren Reaktionsgeschwindigkeit als terminale Alkine und Geschwindigkeitskonstante steigt für tridentate Chelatliganden in der Reihenfolge N^N^N < S^N^N < C^N^N an. Erste orientierende biologische Studien an menschlichen Tumorzellen ergaben vielversprechende EC50-Werte im unteren mikromolaren Bereich. Das Potential dieser Verbindungen und der iClick-Reaktion allgemein für die Biokonjugation und tiefgehende Untersuchungen des Mechanismus der Antitumor-Wirkung sollte in zukünftigen Studien noch weiter ausgedehnt werden. KW - iClick reactions KW - palladium(II) and platinum(II) triazolato complexes KW - kinetics KW - biological activity KW - Click-Chemie KW - Palladiumkomplexe KW - Platinkomplexe Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-211613 ER - TY - JOUR A1 - Müller, Diana A1 - Bessi, Irene A1 - Richter, Christian A1 - Schwalbe, Harald T1 - The Folding Landscapes of Human Telomeric RNA and DNA G‐Quadruplexes are Markedly Different JF - Angewandte Chemie International Edition N2 - We investigated the folding kinetics of G‐quadruplex (G4) structures by comparing the K\(^{+}\)‐induced folding of an RNA G4 derived from the human telomeric repeat‐containing RNA (TERRA25) with a sequence homologous DNA G4 (wtTel25) using CD spectroscopy and real‐time NMR spectroscopy. While DNA G4 folding is biphasic, reveals kinetic partitioning and involves kinetically favoured off‐pathway intermediates, RNA G4 folding is faster and monophasic. The differences in kinetics are correlated to the differences in the folded conformations of RNA vs. DNA G4s, in particular with regard to the conformation around the glycosidic torsion angle χ that uniformly adopts anti conformations for RNA G4s and both, syn and anti conformation for DNA G4s. Modified DNA G4s with \(^{19}\)F bound to C2′ in arabino configuration adopt exclusively anti conformations for χ. These fluoro‐modified DNA (antiTel25) reveal faster folding kinetics and monomorphic conformations similar to RNA G4s, suggesting the correlation between folding kinetics and pathways with differences in χ angle preferences in DNA and RNA, respectively. KW - folding landscapes KW - G-quadruplexes KW - kinetics KW - real-time NMR spectroscopy KW - TERRA RNA Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-238917 VL - 60 IS - 19 SP - 10895 EP - 10901 ER - TY - JOUR A1 - Bing-Shi Tan, Ariel A1 - Kress, Sebastian A1 - Castro, Leticia A1 - Sheppard, Allan A1 - Raghunath, Michael T1 - Cellular re- and de-programming by microenvironmental memory: why short TGF-β1 pulses can have long effects JF - Fibrogenesis Tissue Repair N2 - Background Fibrosis poses a substantial setback in regenerative medicine. Histopathologically, fibrosis is an excessive accumulation of collagen affected by myofibroblasts and this can occur in any tissue that is exposed to chronic injury or insult. Transforming growth factor (TGF)-β1, a crucial mediator of fibrosis, drives differentiation of fibroblasts into myofibroblasts. These cells exhibit α-smooth muscle actin (α-SMA) and synthesize high amounts of collagen I, the major extracellular matrix (ECM) component of fibrosis. While hormones stimulate cells in a pulsatile manner, little is known about cellular response kinetics upon growth factor impact. We therefore studied the effects of short TGF-β1 pulses in terms of the induction and maintenance of the myofibroblast phenotype. Results Twenty-four hours after a single 30 min TGF-β1 pulse, transcription of fibrogenic genes was upregulated, but subsided 7 days later. In parallel, collagen I secretion rate and α-SMA presence were elevated for 7 days. A second pulse 24 h later extended the duration of effects to 14 days. We could not establish epigenetic changes on fibrogenic target genes to explain the long-lasting effects. However, ECM deposited under singly pulsed TGF-β1 was able to induce myofibroblast features in previously untreated fibroblasts. Dependent on the age of the ECM (1 day versus 7 days’ formation time), this property was diminished. Vice versa, myofibroblasts were cultured on fibroblast ECM and cells observed to express reduced (in comparison with myofibroblasts) levels of collagen I. Conclusions We demonstrated that short TGF-β1 pulses can exert long-lasting effects on fibroblasts by changing their microenvironment, thus leaving an imprint and creating a reciprocal feed-back loop. Therefore, the ECM might act as mid-term memory for pathobiochemical events. We would expect this microenvironmental memory to be dependent on matrix turnover and, as such, to be erasable. Our findings contribute to the current understanding of fibroblast induction and maintenance, and have bearing on the development of antifibrotic drugs. KW - cytokine KW - fibrosis KW - transforming growth factor-beta 1 KW - extracellular matrix KW - memory KW - pulses KW - phenotype KW - kinetics Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-131898 VL - 6 IS - 12 ER -