Observation of conformational changes that underlie the catalytic cycle of Xrn2

Nuclear magnetic resonance (NMR) methods that quantitatively probe motions on molecular and atomic levels have propelled the understanding of biomolecular processes for which static structures cannot provide a satisfactory description. In this work, we studied the structure and dynamics of the essential 100-kDa eukaryotic 5′→3′ exoribonuclease Xrn2. A combination of complementary fluorine and methyl-TROSY NMR spectroscopy reveals that the apo enzyme is highly dynamic around the catalytic center. These observed dynamics are in agreement with a transition of the enzyme from the ground state into a catalytically competent state. We show that the conformational equilibrium in Xrn2 shifts substantially toward the active state in the presence of substrate and magnesium. Finally, our data reveal that the dynamics in Xrn2 correlate with the RNA degradation rate, as a mutation that attenuates motions also affects catalytic activity. In that light, our results stress the importance of studies that go beyond static structural information

Multi‐Site Conformational Exchange in the Synthetic Neomycin‐Sensing Riboswitch Studied by 19 F NMR

The synthetic neomycin-sensing riboswitch interacts with its cognate ligand neomycin as well as with the related antibiotics ribostamycin and paromomycin. Binding of these aminoglycosides induces a very similar ground state structure in the RNA, however, only neomycin can efficiently repress translation initiation. The molecular origin of these differences has been traced back to differences in the dynamics of the ligand:riboswitch complexes. Here, we combine five complementary fluorine based NMR methods to accurately quantify seconds to microseconds dynamics in the three riboswitch complexes. Our data reveal complex exchange processes with up to four structurally different states. We interpret our findings in a model that shows an interplay between different chemical groups in the antibiotics and specific bases in the riboswitch. More generally, our data underscore the potential of 19F NMR methods to characterize complex exchange processes with multiple excited states

Tunable quantum dots from atomically precise graphene nanoribbons using a multi-gate architecture

Atomically precise graphene nanoribbons (GNRs) are increasingly attracting interest due to their largely modifiable electronic properties, which can be tailored by controlling their width and edge structure during chemical synthesis. In recent years, the exploitation of GNR properties for electronic devices has focused on GNR integration into field-effect-transistor (FET) geometries. However, such FET devices have limited electrostatic tunability due to the presence of a single gate. Here, we report on the device integration of 9-atom wide armchair graphene nanoribbons (9-AGNRs) into a multi-gate FET geometry, consisting of an ultra-narrow finger gate and two side gates. We use high-resolution electron-beam lithography (EBL) for defining finger gates as narrow as 12 nm and combine them with graphene electrodes for contacting the GNRs. Low-temperature transport spectroscopy measurements reveal quantum dot (QD) behavior with rich Coulomb diamond patterns, suggesting that the GNRs form QDs that are connected both in series and in parallel. Moreover, we show that the additional gates enable differential tuning of the QDs in the nanojunction, providing the first step towards multi-gate control of GNR-based multi-dot systems

Tunable Quantum Dots from Atomically Precise Graphene Nanoribbons Using a Multi‐Gate Architecture

Atomically precise graphene nanoribbons (GNRs) are increasingly attracting interest due to their largely modifiable electronic properties, which can be tailored by controlling their width and edge structure during chemical synthesis. In recent years, the exploitation of GNR properties for electronic devices has focused on GNR integration into field-effect-transistor (FET) geometries. However, such FET devices have limited electrostatic tunability due to the presence of a single gate. Here, on the device integration of 9-atom wide armchair graphene nanoribbons (9-AGNRs) into a multi-gate FET geometry, consisting of an ultra-narrow finger gate and two side gates is reported. High-resolution electron-beam lithography (EBL) is used for defining finger gates as narrow as 12 nm and combine them with graphene electrodes for contacting the GNRs. Low-temperature transport spectroscopy measurements reveal quantum dot (QD) behavior with rich Coulomb diamond patterns, suggesting that the GNRs form QDs that are connected both in series and in parallel. Moreover, it is shown that the additional gates enable differential tuning of the QDs in the nanojunction, providing the first step toward multi-gate control of GNR-based multi-dot systems

TRY plant trait database – enhanced coverage and open access

Plant traits - the morphological, anatomical, physiological, biochemical and phenological characteristics of plants - determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits - almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

A suite of 19F based relaxation dispersion experiments to assess biomolecular motions

Proteins and nucleic acids are highly dynamic bio-molecules that can populate a variety of conformational states. NMR relaxation dispersion (RD) methods are uniquely suited to quantify the associated kinetic and thermodynamic parameters. Here, we present a consistent suite of F-19-based CPMG, on-resonance R-1 rho and off-resonance R-1 rho RD experiments. We validate these experiments by studying the unfolding transition of a 7.5 kDa cold shock protein. Furthermore we show that the F-19 RD experiments are applicable to very large molecular machines by quantifying dynamics in the 360 kDa half-proteasome. Our approach significantly extends the timescale of chemical exchange that can be studied with F-19 RD, adds robustness to the extraction of exchange parameters and can determine the absolute chemical shifts of excited states. Importantly, due to the simplicity of F-19 NMR spectra, it is possible to record complete datasets within hours on samples that are of very low costs. This makes the presented experiments ideally suited to complement static structural information from cryo-EM and X-ray crystallography with insights into functionally relevant motions

LEGO-NMR Spectroscopy: A Method to Visualize Individual Subunits in Large Heteromeric Complexes

Seeing the big picture: Asymmetric macromolecular complexes that are NMR active in only a subset of their subunits can be prepared, thus decreasing NMR spectral complexity. For the hetero heptameric LSm1-7 and LSm2-8 rings NMR spectra of the individual subunits of the complete complex are obtained, showing a conserved RNA binding site. This LEGO-NMR technique makes large asymmetric complexes accessible to detailed NMR spectroscopic studies

Changes in conformational equilibria regulate the activity of the Dcp2 decapping enzyme

Crystal structures of enzymes are indispensable to understanding their mechanisms on a molecular level. It, however, remains challenging to determine which structures are adopted in solution, especially for dynamic complexes. Here, we study the bilobed decapping enzyme Dcp2 that removes the 5' cap structure from eukaryotic mRNA and thereby efficiently terminates gene expression. The numerous Dcp2 structures can be grouped into six states where the domain orientation between the catalytic and regulatory domains significantly differs. Despite this wealth of structural information it is not possible to correlate these states with the catalytic cycle or the activity of the enzyme. Using methyl transverse relaxation-optimized NMR spectroscopy, we demonstrate that only three of the six domain orientations are present in solution, where Dcp2 adopts an open, a closed, or a catalytically active state. We show how mRNA substrate and the activator proteins Dcp1 and Edc1 influence the dynamic equilibria between these states and how this modulates catalytic activity. Importantly, the active state of the complex is only stably formed in the presence of both activators and the mRNA substrate or the m7GDP decapping product, which we rationalize based on a crystal structure of the Dcp1: Dcp2: Edc1: m7GDP complex. Interestingly, we find that the activating mechanisms in Dcp2 also result in a shift of the substrate specificity from bacterial to eukaryotic mRNA

Changes in conformational equilibria regulate the activity of the Dcp2 decapping enzyme

Crystal structures of enzymes are indispensable to understanding their mechanisms on a molecular level. It, however, remains challenging to determine which structures are adopted in solution, especially for dynamic complexes. Here, we study the bilobed decapping enzyme Dcp2 that removes the 5' cap structure from eukaryotic mRNA and thereby efficiently terminates gene expression. The numerous Dcp2 structures can be grouped into six states where the domain orientation between the catalytic and regulatory domains significantly differs. Despite this wealth of structural information it is not possible to correlate these states with the catalytic cycle or the activity of the enzyme. Using methyl transverse relaxation-optimized NMR spectroscopy, we demonstrate that only three of the six domain orientations are present in solution, where Dcp2 adopts an open, a closed, or a catalytically active state. We show how mRNA substrate and the activator proteins Dcp1 and Edc1 influence the dynamic equilibria between these states and how this modulates catalytic activity. Importantly, the active state of the complex is only stably formed in the presence of both activators and the mRNA substrate or the m7GDP decapping product, which we rationalize based on a crystal structure of the Dcp1: Dcp2: Edc1: m7GDP complex. Interestingly, we find that the activating mechanisms in Dcp2 also result in a shift of the substrate specificity from bacterial to eukaryotic mRNA

Blocking Lithium Dendrite Growth in Solid-State Batteries with an Ultrathin Amorphous Li-La-Zr-O Solid Electrolyte

Lithium metal dendrites have become a roadblock in the realization of next-generation solid-state batteries with lithium metal as high-capacity anode. The presence of surface and bulk inhomogeneities with non-negligible electronic conductivity in crystalline electrolytes such as the lithium garnet Li7La3Zr2O12 (LLZO) facilitates the growth of lithium filaments, posing a critical safety risk. Here we explore the amorphous phase of LLZO (aLLZO) as a lithium dendrite shield owing to its grain-boundary-free microstructure, stability against metallic lithium, and high electronic insulation. We demonstrate that by tuning the lithium stoichiometry in sputtered aLLZO films, the ionic conductivity can be increased up to 10-7 S cm-1 while retaining an ultralow electronic conductivity of 10-14 S cm-1. In Li/aLLZO/Li symmetric cells, plating-stripping results in no degradation of the films and current densities up to 3.2 mA cm-2 can be applied with no signs of lithium penetration. The defect-free and conformal nature of the films enables microbatteries with an electrolyte thickness as low as 70 nm, which withstand charge-discharge at 0.2 mA cm-2 for over 500 cycles. Finally, we demonstrate that the application of aLLZO as a coating on crystalline LLZO lowers the interface resistance and significantly impedes the formation of lithium dendrites, increasing the critical current density of a symmetric cell up to 1.3 mA cm-2 at room temperature and without external pressure. The effectiveness of the amorphous Li-La-Zr-O as lithium dendrite blocking layer can accelerate the development of more powerful and safer solid-state batteries.</div