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Software updates are a critical success factor in mobile app ecosystems. Through publishing regular updates, platform providers enhance their operating systems for the benefit of both end users and third-party developers. It is also a way of attracting new customers. However, this platform evolution poses the risk of inadvertently introducing software problems, which can severely disturb the ecosystem’s balance by compromising its foundational technologies. So far, little to no research has addressed this issue from a user-centered perspective. The thesis at hand draws on IS post-adoption literature to investigate the potential negative influences of operating system updates on mobile app users. The release of Apple’s iOS 13 update serves as research object. Based on over half a million user reviews from the AppStore, data mining techniques are applied to study the impact of the new platform version. The results show that iOS 13 caused complications with a large number of popular apps, leading to a significant decline in user ratings and an uptrend in negative sentiment. Feature requests, functional complaints, and device compatibility are identified as the three major issue categories. These issue types are compared in terms of their quantifiable negative effect on users’ continuance intention. In essence, the findings contribute to IS research on post-adoption behavior and provide guidance to ecosystem participants in dealing with update-induced platform issues.
Accumulating evidence suggests that iron homeostasis is disturbed in tumors. We aimed at clarifying the distribution of iron in renal cell carcinoma (RCC). Considering the pivotal role of macrophages for iron homeostasis and their association with poor clinical outcome, we investigated the role of macrophage-secreted iron for tumor progression by applying a novel chelation approach. We applied flow cytometry and multiplex-immunohistochemistry to detect iron-dependent markers and analyzed iron distribution with atomic absorption spectrometry in patients diagnosed with RCC. We further analyzed the functional significance of iron by applying a novel extracellular chelator using RCC cell lines as well as patient-derived primary cells. The expression of iron-regulated genes was significantly elevated in tumors compared to adjacent healthy tissue. Iron retention was detected in tumor cells, whereas tumor-associated macrophages showed an iron-release phenotype accompanied by enhanced expression of ferroportin. We found increased iron amounts in extracellular fluids, which in turn stimulated tumor cell proliferation and migration. In vitro, macrophage-derived iron showed pro-tumor functions, whereas application of an extracellular chelator blocked these effects. Our study provides new insights in iron distribution and iron-handling in RCC. Chelators that specifically scavenge iron in the extracellular space confirmed the importance of macrophage-secreted iron in promoting tumor growth
This PhD thesis is dedicated to the extension of the portfolio of nuclear magnetic resonance (NMR) methods to characterize ribonucleic acids (RNAs). Only within the last few decades it has been realized that the cellular role of RNA goes well beyond the central dogma of molecular biology. In fact, RNA takes part in numerous cellular processes, executes numerous functions and acts either as a single player or in larger complexes, mostly RNA-protein complexes (RNPs) such as the ribosome or the spliceosome. This versatility in RNA function is coupled to a structural variety and the ability to adopt multiple long-lived and intricate conformations. Due to this high molecular complexity special demands are placed on the methods that are required for RNA structural characterization. With the ability to capture dynamics at atomic resolution and to measure under close to native conditions, NMR spectroscopy is undoubtedly a prime method for this purpose.
A general introduction to the current state of research, selected achievements as well as challenges in the field of NMR spectroscopy on RNA is given in Chapter I. This thesis is further composed of three independent chapters covering the three separate projects, which form the main body of work within the course of this thesis.
The imino group found in two of the four RNA nucleobases is generally considered to be the most powerful reporter group in the process of the NMR spectroscopic characterization of RNA. Its resonance assignment provides key information for a rapid determination of the RNA’s secondary structure. This is possible, since the imino proton can only be detected, if it is protected from rapid solvent exchange through hydrogen bonding interactions or, in rare cases, steric shielding. Consequently, information on flexible regions of RNA that are not protected against solvent exchange cannot be derived using this NMR spy. It is a key finding of the thesis that nucleobase interactions can also be mapped through the amino groups, as they similarly take part in base pairing or RNA-ligand interactions. Notably, solvent exchange of the amino protons is always slower compared to the imino proton. Thus, 1H,15N resonances of the amino group can be detected even for dynamic regions of RNA. Moreover, focusing on characterizing amino groups of RNA nucleobases increases the number of available reporters as amino groups are present in three out of four RNA nucleobases.
However, there is a reason that up to work conducted in this thesis, amino groups have not been used for monitoring RNA nucleobases: the rate of the C-NH2 bond rotation is most often close to the chemical shift differences of the two non-identical amino proton resonances, in particular for guanosines and adenosines, amino resonances regularly remain elusive in NMR spectra. Therefore, we developed experiments that excite double quantum (DQ) coherences of the two amino group protons and that further utilize 13C-detection. Results on these experiments are discussed in Chapter II and show that the rotational exchange can be avoided by evolving double quantum instead of single quantum (SQ) coherence in the indirect dimension of a 13C-detected C(N)H-HDQC experiment. The new experiment enables the detection of a full set of sharp amino resonances. The advantages of this experiment are immediately apparent when comparing the number of observable imino resonances in a classic 1H,15N-HSQC spectrum with the number of amino resonances obtained in the 13C-detected C(N)H-HDQC spectrum of the same RNA.
Furthermore, based on the newly available resonance assignment of amino groups, we developed a 13C-detected “amino”-NOESY experiment to obtain precious additional structural restraints. The 13C-detected “amino”-NOESY experiment enables the observation of NOE contacts that are not accessible using other 1H-detected NOESY experiment. Among these new NOE contacts are valuable, inter-residual correlations, which are otherwise scarce in RNA due to the proton deficiency of its nucleobases. We showed that the newly obtained NOE contacts are especially important in the structure determination of RNAs with only few NOE restraints. Under such circumstances, the inclusion of the newly obtained amino NOE contacts lead to a significant improvement in the root-mean-square deviation (RMSD) of the three-dimensional structure of the 34 nts GTP class II aptamer. Together the novel 13C-detected NMR experiments developed within this PhD project provide a valuable alternative for the imino-based characterization of nucleobase interactions.
...
NMR spectroscopy is a potent method for the structural and biophysical characterization of RNAs. The application of NMR spectroscopy is restricted in RNA size and most often requires isotope‐labeled or even selectively labeled RNAs. Additionally, new NMR pulse sequences, such as the heteronuclear‐detected NMR experiments, are introduced. We herein provide detailed protocols for the preparation of isotope‐labeled RNA for NMR spectroscopy via in vitro transcription. This protocol covers all steps, from the preparation of DNA template to the transcription of milligram RNA quantities. Moreover, we present a protocol for a chemo‐enzymatic approach to introduce a single modified nucleotide at any position of any RNA. Regarding NMR methodology, we share protocols for the implementation of a suite of heteronuclear‐detected NMR experiments including 13C‐detected experiments for ribose assignment and amino groups, the CN‐spin filter heteronuclear single quantum coherence (HSQC) for imino groups and the 15N‐detected band‐selective excitation short transient transverse‐relaxation‐optimized spectroscopy (BEST‐TROSY) experiment.
Basic Protocol 1: Preparation of isotope‐labeled RNA samples with in vitro transcription using T7 RNAP, DEAE chromatography, and RP‐HPLC purification
Alternate Protocol 1: Purification of isotope‐labeled RNA from in vitro transcription with preparative PAGE
Alternate Protocol 2: Purification of isotope‐labeled RNA samples from in vitro transcription via centrifugal concentration
Support Protocol 1: Preparation of DNA template from plasmid
Support Protocol 2: Preparation of PCR DNA as template
Support Protocol 3: Preparation of T7 RNA Polymerase (T7 RNAP)
Support Protocol 4: Preparation of yeast inorganic pyrophosphatase (YIPP)
Basic Protocol 2: Preparation of site‐specific labeled RNAs using a chemo‐enzymatic synthesis
Support Protocol 5: Synthesis of modified nucleoside 3′,5′‐bisphosphates
Support Protocol 6: Preparation of T4 RNA Ligase 2
Support Protocol 7: Setup of NMR spectrometer for heteronuclear‐detected NMR experiments
Support Protocol 8: IPAP and DIPAP for homonuclear decoupling
Basic Protocol 3: 13C‐detected 3D (H)CC‐TOCSY, (H)CPC, and (H)CPC‐CCH‐TOCSY experiments for ribose assignment
Basic Protocol 4: 13C‐detected 2D CN‐spin filter HSQC experiment
Basic Protocol 5: 13C‐detected C(N)H‐HDQC experiment for the detection of amino groups
Support Protocol 9: 13C‐detected CN‐HSQC experiment for amino groups
Basic Protocol 6: 13C‐detected “amino”‐NOESY experiment
Basic Protocol 7: 15N‐detected BEST‐TROSY experiment
Background: Lipodystrophy syndromes comprise a group of extremely rare and heterogeneous diseases characterized by a selective loss of adipose tissue in the absence of nutritional deprivation or catabolic state. Because of the rarity of each lipodystrophy subform, research in this area is difficult and international co-operation mandatory. Therefore, in 2016, the European Consortium of Lipodystrophies (ECLip) decided to create a registry for patients with lipodystrophy.
Results: The registry was build using the information technology Open Source Registry System for Rare Diseases in the EU (OSSE), an open-source software and toolbox. Lipodystrophy specific data forms were developed based on current knowledge of typical signs and symptoms of lipodystrophy. The platform complies with the new General Data Protection Regulation (EU) 2016/679 by ensuring patient pseudonymization, informational separation of powers, secure data storage and security of communication, user authentication, person specific access to data, and recording of access granted to any data. Inclusion criteria are all patients with any form of lipodystrophy (with the exception of HIV-associated lipodystrophy). So far 246 patients from nine centres (Amsterdam, Bologna, Izmir, Leipzig, Münster, Moscow, Pisa, Santiago de Compostela, Ulm) have been recruited. With the help from the six centres on the brink of recruitment (Cambridge, Lille, Nicosia, Paris, Porto, Rome) this number is expected to double within the next one or 2 years.
Conclusions: A European registry for all patients with lipodystrophy will provide a platform for improved research in the area of lipodystrophy. All physicians from Europe and neighbouring countries caring for patients with lipodystrophy are invited to participate in the ECLip Registry.
Study registration: ClinicalTrials.gov (NCT03553420). Registered 14 March 2018, retrospectively registered.
Broadly neutralizing antibodies (bNAbs) represent a promising approach to prevent and treat HIV-1 infection. However, viral escape through mutation of the HIV-1 envelope glycoprotein (Env) limits clinical applications. Here we describe 1-18, a new VH1-46-encoded CD4 binding site (CD4bs) bNAb with outstanding breadth (97%) and potency (GeoMean IC50 = 0.048 μg/mL). Notably, 1-18 is not susceptible to typical CD4bs escape mutations and effectively overcomes HIV-1 resistance to other CD4bs bNAbs. Moreover, mutational antigenic profiling uncovered restricted pathways of HIV-1 escape. Of most promise for therapeutic use, even 1-18 alone fully suppressed viremia in HIV-1-infected humanized mice without selecting for resistant viral variants. A 2.5-Å cryo-EM structure of a 1-18-BG505SOSIP.664 Env complex revealed that these characteristics are likely facilitated by a heavy-chain insertion and increased inter-protomer contacts. The ability of 1-18 to effectively restrict HIV-1 escape pathways provides a new option to successfully prevent and treat HIV-1 infection.
Seit der Entdeckung des HI-Virus in 1983, wurden diverse Beobachtungen zu neurologischen Komplikationen bei infizierten Patienten publiziert. Dabei standen initial lebensbedrohliche Komplikationen wie opportunistische Infektionen oder cerebrale Lymphome im Vordergrund. In Zeiten der antiretroviralen Therapie rücken jedoch vermehrt andere, chronisch verlaufende Folgen der Erkrankung in den Fokus. Neurokognitive Störungen bei HIV-infizierten wurden bereits erstmals im Jahre 1986 beschrieben. Seitdem wurden neben der manifesten HIV-assoziierten Demenz auch mildere Einbußen im kongitiven Bereich - sogenannte HIV-assoziierte neurokognitive Störungen (HAND) - klassifiziert, deren Diagnostik mittels diverser neuropsychologischer Testungen erfolgen kann. Hierfür sind geeignete Screening-Tools notwendig, die entsprechenden Anforderungen entsprechen sollten. Einheitliche Empfehlungen für einen bestimmten Test finden sich jedoch in aktuellen Leitlinien und Publikationen nicht. Die vorliegende Arbeit wurde zur Evaluation des MoCA-Tests (Montreal Cognitive Assessment) zur Detektion HIV-1-assoziierter neurokognitiver Störungen angefertigt.
Hierfür wurde der MoCA-Test an 89 HIV-infizierten Männern und Frauen zwischen 21 und 64 Jahren des HIV-Centers Frankfurt am Main durchgeführt und die Ergebnisse mit der gut validierten HIV-Demenz-Skala verglichen. Zudem wurde der Einfluss verschiedener Faktoren wie Geschlecht, Alter, CDC-Stadium, antiretrovirale Therapie, Dauer der HIV-Infektion, CD4-Zellzahl, Viruslast, HCV-Koinfektion, Bildung, Risikogruppenzugehörigkeit, Alkoholkonsum und CPE-Score untersucht.
Der Vergleich zwischen den absoluten Ergebnissen der HDS und des MoCA ergab einen hochsignifikanten statistischen Zusammenhang. Ein statistischer Zusammenhang konnte auch für die Parameter Alter, medikamentöse HIV-Therapie, Dauer der HIV-Infektion zum Untersuchungszeitpunkt sowie Bildung errechnet werden. Die relativen MoCA-Testergebnisse wurden sowohl mit einem Cut-off-Wert von 10 als auch einem Cut-off-Wert von 14 der HDS verglichen.
In Zusammenschau der Ergebnisse korreliert der MoCA-Test auf Grundlage der erhobenen Daten mit der HDS, wobei die Sensitivität in Bezug auf mildere kognitive Störungen niedriger als wünschenswert ist. Eine manifeste HIV-Demenz kann zuverlässig diagnostiziert werden, bei der Diagnostik von milderen Funktionseinschränkungen bestehen jedoch Limitationen. Auf Grund der einfachen Durchführung stellt er ein akzeptables alternatives Screening-Tool dar, wobei Personen mit auffälligen Testergebnissen einer weiteren neuropsychologischen Testung zugeführt werden sollten.
Dieser Band versammelt die Vorträge einer Tagung der Johannes- Althusius-Gesellschaft e. V., die vom 26.–29.5.2016 in Wittenberg stattfand.
Die umfassende Thematik wurde auf vier Aspekte konzentriert: 1) Religion und Konstitutionalisierung 2) die Bedeutung der Reformation für Rechts- und Staatslehren der frühen Neuzeit, 3) Völkerrecht, 4) Recht, Gehorsam und Religion. Dem folgt auch die Gliederung des Buches. Leider ist die Einleitung des Herausgebers sehr formal. Angesichts einiger sehr anregender neuer Forschungsthesen bzw. -ergebnisse wäre der inhaltliche Schwung der Tagung gleich als Eröffnung gut vermittelbar gewesen. ...
La creación de audio-podcasts ofrece una excelente oportunidad para representar de forma oral los contenidos de matemáticas usando medios digitales tanto en la formación docente, como en la educación primaria. Sin embargo, en el proceso de creación de los audio- -podcasts hay fases gráficas-escritas y otras orales que están estrechamente vinculadas entre sí. Este artículo trata sobre la creación y utilización de podcast en la educación primaria (PriMaPodcast) y en la formación docente (MathePodcast) tanto para la enseñanza como para la investigación.Mathematics audio-podcasts: communication and representation with ICTLa creación de audio-podcasts ofrece una excelente oportunidad para representar de forma oral los contenidos de matemáticas usando medios digitales tanto en la formación docente, como en la educación primaria. Sin embargo, en el proceso de creación de los audio- -podcasts hay fases gráficas-escritas y otras orales que están estrechamente vinculadas entre sí. Este artículo trata sobre la creación y utilización de podcast en la educación primaria (PriMaPodcast) y en la formación docente (MathePodcast) tanto para la enseñanza como para la investigación.
Abstract
Divergence is mostly viewed as a progressive process often initiated by selection targeting individual loci, ultimately resulting in ever increasing genomic isolation due to linkage. However, recent studies show that this process may stall at intermediate stable equilibrium states without achieving complete genomic isolation. We tested the extent of genomic isolation between two recurrently hybridizing nonbiting midge sister taxa, Chironomus riparius and Chironomus piger, by analyzing the divergence landscape. Using a principal component‐based method, we estimated that only about 28.44% of the genomes were mutually isolated, whereas the rest was still exchanged. The divergence landscape was fragmented into isolated regions of on average 30 kb, distributed throughout the genome. Selection and divergence time strongly influenced lengths of isolated regions, whereas local recombination rate only had minor impact. Comparison of divergence time distributions obtained from several coalescence‐simulated divergence scenarios with the observed divergence time estimates in an approximate Bayesian computation framework favored a short and concluded divergence event in the past. Most divergence happened during a short time span about 4.5 million generations ago, followed by a stable equilibrium between mutual gene flow through ongoing hybridization for the larger part of the genome and isolation in some regions due to rapid purifying selection of introgression, supported by high effective population sizes and recombination rates.
Impact Summary
The process of speciation has fascinated biologists from early on. Prevailing theory suggested that gene flow among populations is the main obstacle for their divergence. Recently, it became clear that speciation with gene flow is possible under certain circumstances. However, it remains unclear how the divergence process proceeds in time, how widespread the phenomenon is, and whether it always and inevitably leads to complete isolation. Comparing the genomes of individuals of two regularly hybridizing sister taxa of nonbiting midges, we could show that they diverged during a short period millions of generations ago. Their divergence process apparently ceased before the entire genome was mutually isolated. The taxa remain distinct since, even though they share most of their genome. Our findings thus extend our view of the nature of species and the temporal dynamics of their divergence and describe novel approaches to analyze both current and past divergence processes.
Ice-nucleating particle concentrations of the past: insights from a 600-year-old Greenland ice core
(2020)
Ice-nucleating particles (INPs) affect the microphysics in cloud and precipitation processes. Hence, they modulate the radiative properties of clouds. However, atmospheric INP concentrations of the past are basically unknown. Here, we present INP measurements from an ice core in Greenland, which dates back to the year 1370. In total 135 samples were analyzed with the FRIDGE droplet freezing assay in the temperature range from −14 to −35 ∘C. The sampling frequency was set to 1 in 10 years from 1370 to 1960. From 1960 to 1990 the frequency was increased to one sample per year. Additionally, a few special events were probed, including volcanic episodes. The typical time coverage of a sample was on the order of a few months. Historical atmospheric INP concentrations were estimated with a conversion factor, which depends on the snow accumulation rate of the ice core, particle dry deposition velocity, and wet scavenging ratio. Typical atmospheric INP concentrations were on the order of 0.1 L−1 at −25 ∘C. The INP variability was found to be about 1–2 orders of magnitude. Yet, the short-term variability from samples over a seasonal cycle was considerably lower. INP concentrations were significantly correlated to some chemical tracers derived from continuous-flow analysis (CFA) and ion chromatography (IC) over a broad range of nucleation temperatures. The highest correlation coefficients were found for the particle concentration (spherical diameter dp > 1.2 µm). The correlation is higher for a time period of seasonal samples, where INP concentrations follow a clear annual pattern, highlighting the importance of the annual dust input in Greenland from East Asian deserts during spring. Scanning electron microscopy (SEM) analysis of selected samples found mineral dust to be the dominant particle fraction, verifying their significance as INPs. Overall, the concentrations compare reasonably well to present-day INP concentrations, albeit they are on the lower side. However, we found that the INP concentration at medium supercooled temperatures differed before and after 1960. Average INP concentrations at −23, −24, −25, −26, and −28 ∘C were significantly higher (and more variable) in the modern-day period, which could indicate a potential anthropogenic impact, e.g., from land-use change.
Ice nucleating particle concentrations of the past: insights from a
600 year old Greenland ice core
(2020)
Ice nucleating particles (INPs) affect the microphysics in cloud and precipitation processes. Hence, they modulate the radiative properties of clouds. However, atmospheric INP concentrations of the past are basically unknown. Here, we present INP measurements from an ice core in Greenland, which dates back to the year 1370. In total 135 samples were analyzed with the FRIDGE droplet freezing assay in the temperature range from −14 ◦C to −35 ◦C. The sampling frequency was set to 1 in 10 years from 1370 to 1960. From 1960 to 1990 the frequency was increased to 1 sample per year. Additionally, a number of special events were probed, including volcanic episodes. The typical time coverage of a sample was on the order of a few months. Historical atmospheric INP concentrations were estimated with a conversion factor, which depends on the snow accumulation rate of the ice core, particle dry deposition velocity and the wet scavenging ratio. Typical atmospheric INP concentrations were on the order of 0.1 L -1 at −25 ◦C. The INP variability was found to be about 1 – 2 orders of magnitude. Yet, the short-term variability from samples over a seasonal cycle was considerably lower. INP concentrations were significantly correlated to chemical tracers derived from continuous flow analysis (CFA) and ion chromatography (IC) over a broad range of nucleation temperatures. The highest correlation coefficients were found for the particle concentration (dp > 1.2 µm). The correlation is higher for the seasonal samples, where INP concentrations follow a clear annual pattern, highlighting the importance of the annual dust input in Greenland from East Asian deserts during spring. Scanning electron microscopy (SEM) of single particles retrieved from selected samples found particles of soil origin to be the dominant fraction, verifying the significance of mineral dust particles as INPs. Overall, the concentrations compare reasonably well to present day INP concentrations, albeit they are on the lower side. However, we found that the INP concentration at medium supercooled temperatures differed before and after 1960. Average INP concentrations at −23 ◦C, −24 ◦C, −25 ◦C, −26 ◦C and −28 ◦C were significantly higher (and more variable) in the modern day period, which could indicate a potential anthropogenic impact or some post-coring contamination of the topmost, very porous firn.
Ice particle activation and evolution have important atmospheric implications for cloud formation, initiation of precipitation and radiative interactions. The initial formation of atmospheric ice by heterogeneous ice nucleation requires the presence of a nucleating seed, an ice-nucleating particle (INP), to facilitate its first emergence. Unfortunately, only a few long-term measurements of INPs exist, and as a result, knowledge about geographic and seasonal variations of INP concentrations is sparse. Here we present data from nearly 2 years of INP measurements from four stations in different regions of the world: the Amazon (Brazil), the Caribbean (Martinique), central Europe (Germany) and the Arctic (Svalbard). The sites feature diverse geographical climates and ecosystems that are associated with dissimilar transport patterns, aerosol characteristics and levels of anthropogenic impact (ranging from near pristine to mostly rural). Interestingly, observed INP concentrations, which represent measurements in the deposition and condensation freezing modes, do not differ greatly from site to site but usually fall well within the same order of magnitude. Moreover, short-term variability overwhelms all long-term trends and/or seasonality in the INP concentration at all locations. An analysis of the frequency distributions of INP concentrations suggests that INPs tend to be well mixed and reflective of large-scale air mass movements. No universal physical or chemical parameter could be identified to be a causal link driving INP climatology, highlighting the complex nature of the ice nucleation process. Amazonian INP concentrations were mostly unaffected by the biomass burning season, even though aerosol concentrations increase by a factor of 10 from the wet to dry season. Caribbean INPs were positively correlated to parameters related to transported mineral dust, which is known to increase during the Northern Hemisphere summer. A wind sector analysis revealed the absence of an anthropogenic impact on average INP concentrations at the site in central Europe. Likewise, no Arctic haze influence was observed on INPs at the Arctic site, where low concentrations were generally measured. We consider the collected data to be a unique resource for the community that illustrates some of the challenges and knowledge gaps of the field in general, while specifically highlighting the need for more long-term observations of INPs worldwide.
Reactive oxygen species (ROS) have been shown or at least suggested to play an essential role for cellular signaling as second messengers. NADPH oxidases represent a source of controlled ROS formation. Accordingly, understanding the role of individual NADPH oxidases bears potential to interfere with intracellular signaling cascades without disturbing the signaling itself. Many tools have been developed to study or inhibit the functions and roles of the NADPH oxidases. This short review summarizes diseases, potentially associated with NADPH oxidases, genetically modified animals, and inhibitors.
Selectivity remains a challenge for ATP-mimetic kinase inhibitors, an issue that may be overcome by targeting unique residues or binding pockets. However, to date only few strategies have been developed. Here we identify that bulky residues located N-terminal to the DFG motif (DFG-1) represent an opportunity for designing highly selective inhibitors with unexpected binding modes. We demonstrate that several diverse inhibitors exerted selective, non-canonical binding modes that exclusively target large hydrophobic DFG-1 residues present in many kinases including PIM, CK1, DAPK and CLK. Using the CLK family as a model, structural and biochemical data revealed that the DFG-1 valine controlled a non-canonical binding mode in CLK1, providing a rational for selectivity over the closely-related CLK3 which harbors a smaller DFG-1 alanine. Our data suggests that targeting the restricted back pocket in the small fraction of kinases that harbor bulky DFG-1 residues offers a versatile selectivity filter for inhibitor design.
Selectivity remains a challenge for ATP-mimetic kinase inhibitors, an issue that may be overcome by targeting unique residues or binding pockets. However, to date only few strategies have been developed. Here we identify that bulky residues located N-terminal to the DFG motif (DFG-1) represent an opportunity for designing highly selective inhibitors with unexpected binding modes. We demonstrate that several diverse inhibitors exerted selective, noncanonical binding modes that exclusively target large hydrophobic DFG-1 residues present in many kinases including PIM, CK1, DAPK, and CLK. By use of the CLK family as a model, structural and biochemical data revealed that the DFG-1 valine controlled a noncanonical binding mode in CLK1, providing a rationale for selectivity over the closely related CLK3 which harbors a smaller DFG-1 alanine. Our data suggest that targeting the restricted back pocket in the small fraction of kinases that harbor bulky DFG-1 residues offers a versatile selectivity filter for inhibitor design.
Extracellular signal-regulated kinase 3 (ERK3), known also as mitogen-activated protein kinase 6 (MAPK6), is an atypical member of MAPK kinase family, which has been poorly studied. Little is known regarding its function in biological processes, yet this atypical kinase has been suggested to play important roles in the migration and invasiveness of certain cancers. The lack of tools, such as a selective inhibitor, hampers the study of ERK3 biology. Here, we report the crystal structure of the kinase domain of this atypical MAPK kinase, providing molecular insights into its distinct ATP binding pocket compared to the classical MAPK ERK2, explaining differences in their inhibitor binding properties. Medium-scale small molecule screening identified a number of inhibitors, several of which unexpectedly exhibited remarkably high inhibitory potencies. The crystal structure of CLK1 in complex with CAF052, one of the most potent inhibitors identified for ERK3, revealed typical type-I binding mode of the inhibitor, which by structural comparison could likely be maintained in ERK3. Together with the presented structural insights, these diverse chemical scaffolds displaying both reversible and irreversible modes of action, will serve as a starting point for the development of selective inhibitors for ERK3, which will be beneficial for elucidating the important functions of this understudied kinase.
MKK7 (MEK7) is a key regulator of the JNK stress signaling pathway and targeting MKK7 has been proposed as a chemotherapeutic strategy. Detailed understanding of the MKK7 structure and factors that impact its activity is therefore of critical importance. Here, we present a comprehensive set of MKK7 crystal structures revealing insights into catalytic domain plasticity and the role of the N-terminal regulatory helix, conserved in all MAP2Ks, mediating kinase activation. Crystal structures harboring this regulatory helix revealed typical structural features of active kinase, providing exclusively a first model of the MAP2K active state. A small molecule screening campaign yielded multiple scaffolds, including type-II irreversible inhibitors a binding mode that has not been reported previously. We also observed an unprecedented allosteric pocket located in the N-terminal lobe for the approved drug ibrutinib. Collectively, our structural and functional data expand and provide alternative targeting strategies for this important MAP2K kinase.
Mit dem Klimawandel könnte das Grundwasser künftig weltweit in vielen Regionen knapp werden. Das zeigt eine große internationale Studie, die vom Doktoranden Robert Reinecke und der Geographin Prof. Petra Döll initiiert wurde. Vielerorts könnte das zu Wassermangel führen oder einen bestehenden Wassermangel verschärfen. Gleichzeitig werden andere Regionen unter steigenden Grundwasserständen zu leiden haben. Ackerflächen könnten durch Vernässung verloren gehen.