@article{13353, abstract = {We show that the optical properties of indigo carmine can be modulated by encapsulation within a coordination cage. Depending on the host/guest molar ratio, the cage can predominantly encapsulate either one or two dye molecules. The 1 : 1 complex is fluorescent, unique for an indigo dye in an aqueous solution. We have also found that binding two dye molecules stabilizes a previously unknown conformation of the cage.}, author = {Yanshyna, Oksana and Avram, Liat and Shimon, Linda J. W. and Klajn, Rafal}, issn = {1364-548X}, journal = {Chemical Communications}, keywords = {Materials Chemistry, Metals and Alloys, Surfaces, Coatings and Films, General Chemistry, Ceramics and Composites, Electronic, Optical and Magnetic Materials, Catalysis}, number = {21}, pages = {3461--3464}, publisher = {Royal Society of Chemistry}, title = {{Coexistence of 1:1 and 2:1 inclusion complexes of indigo carmine}}, doi = {10.1039/d1cc07081a}, volume = {58}, year = {2022}, } @article{13993, abstract = {Photoionization is a process taking place on attosecond time scales. How its properties evolve from isolated particles to the condensed phase is an open question of both fundamental and practical relevance. Here, we review recent work that has advanced the study of photoionization dynamics from atoms to molecules, clusters and the liquid phase. The first measurements of molecular photoionization delays have revealed the attosecond dynamics of electron emission from a molecular shape resonance and their sensitivity to the molecular potential. Using electron-ion coincidence spectroscopy these measurements have been extended from isolated molecules to clusters. A continuous increase of the delays with the water-cluster size has been observed up to a size of 4-5 molecules, followed by a saturation towards larger clusters. Comparison with calculations has revealed a correlation of the time delay with the spatial extension of the created electron hole. Using cylindrical liquid-microjet techniques, these measurements have also been extended to liquid water, revealing a delay relative to isolated water molecules that was very similar to the largest water clusters studied. Detailed modeling based on Monte-Carlo simulations confirmed that these delays are dominated by the contributions of the first two solvation shells, which agrees with the results of the cluster measurements. These combined results open the perspective of experimentally characterizing the delocalization of electronic wave functions in complex systems and studying their evolution on attosecond time scales.}, author = {Gong, Xiaochun and Jordan, Inga and Huppert, Martin and Heck, Saijoscha and Baykusheva, Denitsa Rangelova and Jelovina, Denis and Schild, Axel and Wörner, Hans Jakob}, issn = {2673-2424}, journal = {Chimia}, keywords = {General Medicine, General Chemistry}, number = {6}, pages = {520--528}, publisher = {Swiss Chemical Society}, title = {{Attosecond photoionization dynamics: from molecules over clusters to the liquid phase}}, doi = {10.2533/chimia.2022.520}, volume = {76}, year = {2022}, } @article{15133, abstract = {In the evolutionary arms race against phage, bacteria have assembled a diverse arsenal of antiviral immune strategies. While the recently discovered DISARM (Defense Island System Associated with Restriction-Modification) systems can provide protection against a wide range of phage, the molecular mechanisms that underpin broad antiviral targeting but avoiding autoimmunity remain enigmatic. Here, we report cryo-EM structures of the core DISARM complex, DrmAB, both alone and in complex with an unmethylated phage DNA mimetic. These structures reveal that DrmAB core complex is autoinhibited by a trigger loop (TL) within DrmA and binding to DNA substrates containing a 5′ overhang dislodges the TL, initiating a long-range structural rearrangement for DrmAB activation. Together with structure-guided in vivo studies, our work provides insights into the mechanism of phage DNA recognition and specific activation of this widespread antiviral defense system.}, author = {Bravo, Jack Peter Kelly and Aparicio-Maldonado, Cristian and Nobrega, Franklin L. and Brouns, Stan J. J. and Taylor, David W.}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{Structural basis for broad anti-phage immunity by DISARM}}, doi = {10.1038/s41467-022-30673-1}, volume = {13}, year = {2022}, } @article{15134, abstract = {CRISPR-Cas systems are adaptive immune systems that protect prokaryotes from foreign nucleic acids, such as bacteriophages. Two of the most prevalent CRISPR-Cas systems include type I and type III. Interestingly, the type I-D interference proteins contain characteristic features of both type I and type III systems. Here, we present the structures of type I-D Cascade bound to both a double-stranded (ds)DNA and a single-stranded (ss)RNA target at 2.9 and 3.1 Å, respectively. We show that type I-D Cascade is capable of specifically binding ssRNA and reveal how PAM recognition of dsDNA targets initiates long-range structural rearrangements that likely primes Cas10d for Cas3′ binding and subsequent non-target strand DNA cleavage. These structures allow us to model how binding of the anti-CRISPR protein AcrID1 likely blocks target dsDNA binding via competitive inhibition of the DNA substrate engagement with the Cas10d active site. This work elucidates the unique mechanisms used by type I-D Cascade for discrimination of single-stranded and double stranded targets. Thus, our data supports a model for the hybrid nature of this complex with features of type III and type I systems.}, author = {Schwartz, Evan A. and McBride, Tess M. and Bravo, Jack Peter Kelly and Wrapp, Daniel and Fineran, Peter C. and Fagerlund, Robert D. and Taylor, David W.}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{Structural rearrangements allow nucleic acid discrimination by type I-D Cascade}}, doi = {10.1038/s41467-022-30402-8}, volume = {13}, year = {2022}, } @article{12237, abstract = {Thermoelectric technology requires synthesizing complex materials where not only the crystal structure but also other structural features such as defects, grain size and orientation, and interfaces must be controlled. To date, conventional solid-state techniques are unable to provide this level of control. Herein, we present a synthetic approach in which dense inorganic thermoelectric materials are produced by the consolidation of well-defined nanoparticle powders. The idea is that controlling the characteristics of the powder allows the chemical transformations that take place during consolidation to be guided, ultimately yielding inorganic solids with targeted features. Different from conventional methods, syntheses in solution can produce particles with unprecedented control over their size, shape, crystal structure, composition, and surface chemistry. However, to date, most works have focused only on the low-cost benefits of this strategy. In this perspective, we first cover the opportunities that solution processing of the powder offers, emphasizing the potential structural features that can be controlled by precisely engineering the inorganic core of the particle, the surface, and the organization of the particles before consolidation. We then discuss the challenges of this synthetic approach and more practical matters related to solution processing. Finally, we suggest some good practices for adequate knowledge transfer and improving reproducibility among different laboratories.}, author = {Fiedler, Christine and Kleinhanns, Tobias and Garcia, Maria and Lee, Seungho and Calcabrini, Mariano and Ibáñez, Maria}, issn = {1520-5002}, journal = {Chemistry of Materials}, keywords = {Materials Chemistry, General Chemical Engineering, General Chemistry}, number = {19}, pages = {8471--8489}, publisher = {American Chemical Society}, title = {{Solution-processed inorganic thermoelectric materials: Opportunities and challenges ∇}}, doi = {10.1021/acs.chemmater.2c01967}, volume = {34}, year = {2022}, } @article{11373, abstract = {The actin-homologue FtsA is essential for E. coli cell division, as it links FtsZ filaments in the Z-ring to transmembrane proteins. FtsA is thought to initiate cell constriction by switching from an inactive polymeric to an active monomeric conformation, which recruits downstream proteins and stabilizes the Z-ring. However, direct biochemical evidence for this mechanism is missing. Here, we use reconstitution experiments and quantitative fluorescence microscopy to study divisome activation in vitro. By comparing wild-type FtsA with FtsA R286W, we find that this hyperactive mutant outperforms FtsA WT in replicating FtsZ treadmilling dynamics, FtsZ filament stabilization and recruitment of FtsN. We could attribute these differences to a faster exchange and denser packing of FtsA R286W below FtsZ filaments. Using FRET microscopy, we also find that FtsN binding promotes FtsA self-interaction. We propose that in the active divisome FtsA and FtsN exist as a dynamic copolymer that follows treadmilling filaments of FtsZ.}, author = {Radler, Philipp and Baranova, Natalia S. and Dos Santos Caldas, Paulo R and Sommer, Christoph M and Lopez Pelegrin, Maria D and Michalik, David and Loose, Martin}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry}, publisher = {Springer Nature}, title = {{In vitro reconstitution of Escherichia coli divisome activation}}, doi = {10.1038/s41467-022-30301-y}, volume = {13}, year = {2022}, } @article{12585, abstract = {Glaciers in High Mountain Asia generate meltwater that supports the water needs of 250 million people, but current knowledge of annual accumulation and ablation is limited to sparse field measurements biased in location and glacier size. Here, we present altitudinally-resolved specific mass balances (surface, internal, and basal combined) for 5527 glaciers in High Mountain Asia for 2000–2016, derived by correcting observed glacier thinning patterns for mass redistribution due to ice flow. We find that 41% of glaciers accumulated mass over less than 20% of their area, and only 60% ± 10% of regional annual ablation was compensated by accumulation. Even without 21st century warming, 21% ± 1% of ice volume will be lost by 2100 due to current climatic-geometric imbalance, representing a reduction in glacier ablation into rivers of 28% ± 1%. The ablation of glaciers in the Himalayas and Tien Shan was mostly unsustainable and ice volume in these regions will reduce by at least 30% by 2100. The most important and vulnerable glacier-fed river basins (Amu Darya, Indus, Syr Darya, Tarim Interior) were supplied with >50% sustainable glacier ablation but will see long-term reductions in ice mass and glacier meltwater supply regardless of the Karakoram Anomaly.}, author = {Miles, Evan and McCarthy, Michael and Dehecq, Amaury and Kneib, Marin and Fugger, Stefan and Pellicciotti, Francesca}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{Health and sustainability of glaciers in High Mountain Asia}}, doi = {10.1038/s41467-021-23073-4}, volume = {12}, year = {2021}, } @article{13357, abstract = {Coulombic interactions can be used to assemble charged nanoparticles into higher-order structures, but the process requires oppositely charged partners that are similarly sized. The ability to mediate the assembly of such charged nanoparticles using structurally simple small molecules would greatly facilitate the fabrication of nanostructured materials and harnessing their applications in catalysis, sensing and photonics. Here we show that small molecules with as few as three electric charges can effectively induce attractive interactions between oppositely charged nanoparticles in water. These interactions can guide the assembly of charged nanoparticles into colloidal crystals of a quality previously only thought to result from their co-crystallization with oppositely charged nanoparticles of a similar size. Transient nanoparticle assemblies can be generated using positively charged nanoparticles and multiply charged anions that are enzymatically hydrolysed into mono- and/or dianions. Our findings demonstrate an approach for the facile fabrication, manipulation and further investigation of static and dynamic nanostructured materials in aqueous environments.}, author = {Bian, Tong and Gardin, Andrea and Gemen, Julius and Houben, Lothar and Perego, Claudio and Lee, Byeongdu and Elad, Nadav and Chu, Zonglin and Pavan, Giovanni M. and Klajn, Rafal}, issn = {1755-4349}, journal = {Nature Chemistry}, keywords = {General Chemical Engineering, General Chemistry}, number = {10}, pages = {940--949}, publisher = {Springer Nature}, title = {{Electrostatic co-assembly of nanoparticles with oppositely charged small molecules into static and dynamic superstructures}}, doi = {10.1038/s41557-021-00752-9}, volume = {13}, year = {2021}, } @article{13358, abstract = {DNA nanotechnology offers a versatile toolbox for precise spatial and temporal manipulation of matter on the nanoscale. However, rendering DNA-based systems responsive to light has remained challenging. Herein, we describe the remote manipulation of native (non-photoresponsive) chiral plasmonic molecules (CPMs) using light. Our strategy is based on the use of a photoresponsive medium comprising a merocyanine-based photoacid. Upon exposure to visible light, the medium decreases its pH, inducing the formation of DNA triplex links, leading to a spatial reconfiguration of the CPMs. The process can be reversed simply by turning the light off and it can be repeated for multiple cycles. The degree of the overall chirality change in an ensemble of CPMs depends on the CPM fraction undergoing reconfiguration, which, remarkably, depends on and can be tuned by the intensity of incident light. Such a dynamic, remotely controlled system could aid in further advancing DNA-based devices and nanomaterials.}, author = {Ryssy, Joonas and Natarajan, Ashwin K. and Wang, Jinhua and Lehtonen, Arttu J. and Nguyen, Minh‐Kha and Klajn, Rafal and Kuzyk, Anton}, issn = {1521-3773}, journal = {Angewandte Chemie International Edition}, keywords = {General Chemistry, Catalysis}, number = {11}, pages = {5859--5863}, publisher = {Wiley}, title = {{Light‐responsive dynamic DNA‐origami‐based plasmonic assemblies}}, doi = {10.1002/anie.202014963}, volume = {60}, year = {2021}, } @article{13359, abstract = {Dissipative self-assembly is ubiquitous in nature, where it gives rise to complex structures and functions such as self-healing, homeostasis, and camouflage. These phenomena are enabled by the continuous conversion of energy stored in chemical fuels, such as ATP. Over the past decade, an increasing number of synthetic chemically driven systems have been reported that mimic the features of their natural counterparts. At the same time, it has been shown that dissipative self-assembly can also be fueled by light; these optically fueled systems have been developed in parallel to the chemically fueled ones. In this perspective, we critically compare these two classes of systems. Despite the complementarity and fundamental differences between these two modes of dissipative self-assembly, our analysis reveals that multiple analogies exist between chemically and light-fueled systems. We hope that these considerations will facilitate further development of the field of dissipative self-assembly.}, author = {Weißenfels, Maren and Gemen, Julius and Klajn, Rafal}, issn = {2451-9294}, journal = {Chem}, keywords = {Materials Chemistry, Biochemistry (medical), General Chemical Engineering, Environmental Chemistry, Biochemistry, General Chemistry}, number = {1}, pages = {23--37}, publisher = {Elsevier}, title = {{Dissipative self-assembly: Fueling with chemicals versus light}}, doi = {10.1016/j.chempr.2020.11.025}, volume = {7}, year = {2021}, } @article{13996, abstract = {We report the observation of an anomalous nonlinear optical response of the prototypical three-dimensional topological insulator bismuth selenide through the process of high-order harmonic generation. We find that the generation efficiency increases as the laser polarization is changed from linear to elliptical, and it becomes maximum for circular polarization. With the aid of a microscopic theory and a detailed analysis of the measured spectra, we reveal that such anomalous enhancement encodes the characteristic topology of the band structure that originates from the interplay of strong spin–orbit coupling and time-reversal symmetry protection. The implications are in ultrafast probing of topological phase transitions, light-field driven dissipationless electronics, and quantum computation.}, author = {Baykusheva, Denitsa Rangelova and Chacón, Alexis and Lu, Jian and Bailey, Trevor P. and Sobota, Jonathan A. and Soifer, Hadas and Kirchmann, Patrick S. and Rotundu, Costel and Uher, Ctirad and Heinz, Tony F. and Reis, David A. and Ghimire, Shambhu}, issn = {1530-6992}, journal = {Nano Letters}, keywords = {Mechanical Engineering, Condensed Matter Physics, General Materials Science, General Chemistry, Bioengineering}, number = {21}, pages = {8970--8978}, publisher = {American Chemical Society}, title = {{All-optical probe of three-dimensional topological insulators based on high-harmonic generation by circularly polarized laser fields}}, doi = {10.1021/acs.nanolett.1c02145}, volume = {21}, year = {2021}, } @article{15137, abstract = {Characteristic properties of type III CRISPR-Cas systems include recognition of target RNA and the subsequent induction of a multifaceted immune response. This involves sequence-specific cleavage of the target RNA and production of cyclic oligoadenylate (cOA) molecules. Here we report that an exposed seed region at the 3′ end of the crRNA is essential for target RNA binding and cleavage, whereas cOA production requires base pairing at the 5′ end of the crRNA. Moreover, we uncover that the variation in the size and composition of type III complexes within a single host results in variable seed regions. This may prevent escape by invading genetic elements, while controlling cOA production tightly to prevent unnecessary damage to the host. Lastly, we use these findings to develop a new diagnostic tool, SCOPE, for the specific detection of SARS-CoV-2 from human nasal swab samples, revealing sensitivities in the atto-molar range.}, author = {Steens, Jurre A. and Zhu, Yifan and Taylor, David W. and Bravo, Jack Peter Kelly and Prinsen, Stijn H. P. and Schoen, Cor D. and Keijser, Bart J. F. and Ossendrijver, Michel and Hofstra, L. Marije and Brouns, Stan J. J. and Shinkai, Akeo and van der Oost, John and Staals, Raymond H. J.}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation}}, doi = {10.1038/s41467-021-25337-5}, volume = {12}, year = {2021}, } @article{15260, abstract = {Significant advances in the synthesis and processing of colloidal nanocrystals have given scientists and engineers access to a vast library of building blocks with precisely defined size, shape, and composition. These materials have inspired exciting prospects to enable bottom-up fabrication of programmable materials with properties by design. Successfully assembling and connecting the building blocks into superstructures in which constituent nanocrystals can purposefully interact requires robust understanding of and control over a complex interplay of dynamic physicochemical processes. Fluid interfaces provide an advantageous experimental workbench to both probe and control these processes. Despite the ostensible simplicity of fabricating nanocrystal assemblies at a fluid interface, sensitivity to processing conditions and limited reproducibility have underscored the complexity of this process. In situ studies have provided mechanistic insights into the competing dynamics of key subprocesses including solvent spreading and evaporation, superlattice formation, ligand detachment kinetics, and nanocrystal attachment. Understanding how these subprocesses influence the complex choreography of self-assembly, structure transformation, and oriented attachment processes presents a rich research challenge. In this context, we present a detailed methodology for self-assembly and attachment of lead chalcogenide nanocrystals at a liquid–gas interface as a model system for the fabrication of mono- and multilayer cubic connected superlattices. We discuss key experimental parameters such as the characteristics of the building blocks and processing conditions and detailed steps from colloidal nanocrystal injection to superlattice transfer. We hope that this Methods/Protocols paper will provide guidance for future advances in the exciting path toward bringing the prospect of nanocrystal-based programmable materials to fruition.}, author = {Cimada daSilva, Jessica and Balazs, Daniel and Dunbar, Tyler A. and Hanrath, Tobias}, issn = {1520-5002}, journal = {Chemistry of Materials}, keywords = {Materials Chemistry, General Chemical Engineering, General Chemistry}, number = {24}, pages = {9457--9472}, publisher = {American Chemical Society}, title = {{Fundamental processes and practical considerations of lead chalcogenide mesocrystals formed via self-assembly and directed attachment of nanocrystals at a fluid interface}}, doi = {10.1021/acs.chemmater.1c02910}, volume = {33}, year = {2021}, } @article{10163, abstract = {The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay.}, author = {Appel, Lisa-Marie and Franke, Vedran and Bruno, Melania and Grishkovskaya, Irina and Kasiliauskaite, Aiste and Kaufmann, Tanja and Schoeberl, Ursula E. and Puchinger, Martin G. and Kostrhon, Sebastian and Ebenwaldner, Carmen and Sebesta, Marek and Beltzung, Etienne and Mechtler, Karl and Lin, Gen and Vlasova, Anna and Leeb, Martin and Pavri, Rushad and Stark, Alexander and Akalin, Altuna and Stefl, Richard and Bernecky, Carrie A and Djinovic-Carugo, Kristina and Slade, Dea}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {general physics and astronomy, general biochemistry, genetics and molecular biology, general chemistry}, number = {1}, publisher = {Springer Nature}, title = {{PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC}}, doi = {10.1038/s41467-021-26360-2}, volume = {12}, year = {2021}, } @article{10339, abstract = {We study the effects of osmotic shocks on lipid vesicles via coarse-grained molecular dynamics simulations by explicitly considering the solute in the system. We find that depending on their nature (hypo- or hypertonic) such shocks can lead to bursting events or engulfing of external material into inner compartments, among other morphology transformations. We characterize the dynamics of these processes and observe a separation of time scales between the osmotic shock absorption and the shape relaxation. Our work consequently provides an insight into the dynamics of compartmentalization in vesicular systems as a result of osmotic shocks, which can be of interest in the context of early proto-cell development and proto-cell compartmentalisation.}, author = {Vanhille-Campos, Christian and Šarić, Anđela}, issn = {1744-6848}, journal = {Soft Matter}, keywords = {condensed matter physics, general chemistry}, number = {14}, pages = {3798--3806}, publisher = {Royal Society of Chemistry}, title = {{Modelling the dynamics of vesicle reshaping and scission under osmotic shocks}}, doi = {10.1039/d0sm02012e}, volume = {17}, year = {2021}, } @article{9282, abstract = {Several Ising-type magnetic van der Waals (vdW) materials exhibit stable magnetic ground states. Despite these clear experimental demonstrations, a complete theoretical and microscopic understanding of their magnetic anisotropy is still lacking. In particular, the validity limit of identifying their one-dimensional (1-D) Ising nature has remained uninvestigated in a quantitative way. Here we performed the complete mapping of magnetic anisotropy for a prototypical Ising vdW magnet FePS3 for the first time. Combining torque magnetometry measurements with their magnetostatic model analysis and the relativistic density functional total energy calculations, we successfully constructed the three-dimensional (3-D) mappings of the magnetic anisotropy in terms of magnetic torque and energy. The results not only quantitatively confirm that the easy axis is perpendicular to the ab plane, but also reveal the anisotropies within the ab, ac, and bc planes. Our approach can be applied to the detailed quantitative study of magnetism in vdW materials.}, author = {Nauman, Muhammad and Kiem, Do Hoon and Lee, Sungmin and Son, Suhan and Park, J-G and Kang, Woun and Han, Myung Joon and Jo, Youn Jung}, issn = {2053-1583}, journal = {2D Materials}, keywords = {Mechanical Engineering, General Materials Science, Mechanics of Materials, General Chemistry, Condensed Matter Physics}, number = {3}, publisher = {IOP Publishing}, title = {{Complete mapping of magnetic anisotropy for prototype Ising van der Waals FePS3}}, doi = {10.1088/2053-1583/abeed3}, volume = {8}, year = {2021}, } @article{9431, abstract = {Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles.}, author = {Obr, Martin and Ricana, Clifton L. and Nikulin, Nadia and Feathers, Jon-Philip R. and Klanschnig, Marco and Thader, Andreas and Johnson, Marc C. and Vogt, Volker M. and Schur, Florian KM and Dick, Robert A.}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry}, number = {1}, publisher = {Nature Research}, title = {{Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer}}, doi = {10.1038/s41467-021-23506-0}, volume = {12}, year = {2021}, } @article{9540, abstract = {The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases.}, author = {Prattes, Michael and Grishkovskaya, Irina and Hodirnau, Victor-Valentin and Rössler, Ingrid and Klein, Isabella and Hetzmannseder, Christina and Zisser, Gertrude and Gruber, Christian C. and Gruber, Karl and Haselbach, David and Bergler, Helmut}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry}, number = {1}, publisher = {Springer Nature}, title = {{Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine}}, doi = {10.1038/s41467-021-23854-x}, volume = {12}, year = {2021}, } @article{9778, abstract = {The hippocampal mossy fiber synapse is a key synapse of the trisynaptic circuit. Post-tetanic potentiation (PTP) is the most powerful form of plasticity at this synaptic connection. It is widely believed that mossy fiber PTP is an entirely presynaptic phenomenon, implying that PTP induction is input-specific, and requires neither activity of multiple inputs nor stimulation of postsynaptic neurons. To directly test cooperativity and associativity, we made paired recordings between single mossy fiber terminals and postsynaptic CA3 pyramidal neurons in rat brain slices. By stimulating non-overlapping mossy fiber inputs converging onto single CA3 neurons, we confirm that PTP is input-specific and non-cooperative. Unexpectedly, mossy fiber PTP exhibits anti-associative induction properties. EPSCs show only minimal PTP after combined pre- and postsynaptic high-frequency stimulation with intact postsynaptic Ca2+ signaling, but marked PTP in the absence of postsynaptic spiking and after suppression of postsynaptic Ca2+ signaling (10 mM EGTA). PTP is largely recovered by inhibitors of voltage-gated R- and L-type Ca2+ channels, group II mGluRs, and vacuolar-type H+-ATPase, suggesting the involvement of retrograde vesicular glutamate signaling. Transsynaptic regulation of PTP extends the repertoire of synaptic computations, implementing a brake on mossy fiber detonation and a “smart teacher” function of hippocampal mossy fiber synapses.}, author = {Vandael, David H and Okamoto, Yuji and Jonas, Peter M}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {general physics and astronomy, general biochemistry, genetics and molecular biology, general chemistry}, number = {1}, publisher = {Springer}, title = {{Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses}}, doi = {10.1038/s41467-021-23153-5}, volume = {12}, year = {2021}, } @article{9250, abstract = {Aprotic alkali metal–O2 batteries face two major obstacles to their chemistry occurring efficiently, the insulating nature of the formed alkali superoxides/peroxides and parasitic reactions that are caused by the highly reactive singlet oxygen (1O2). Redox mediators are recognized to be key for improving rechargeability. However, it is unclear how they affect 1O2 formation, which hinders strategies for their improvement. Here we clarify the mechanism of mediated peroxide and superoxide oxidation and thus explain how redox mediators either enhance or suppress 1O2 formation. We show that charging commences with peroxide oxidation to a superoxide intermediate and that redox potentials above ~3.5 V versus Li/Li+ drive 1O2 evolution from superoxide oxidation, while disproportionation always generates some 1O2. We find that 1O2 suppression requires oxidation to be faster than the generation of 1O2 from disproportionation. Oxidation rates decrease with growing driving force following Marcus inverted-region behaviour, establishing a region of maximum rate.}, author = {Petit, Yann K. and Mourad, Eléonore and Prehal, Christian and Leypold, Christian and Windischbacher, Andreas and Mijailovic, Daniel and Slugovc, Christian and Borisov, Sergey M. and Zojer, Egbert and Brutti, Sergio and Fontaine, Olivier and Freunberger, Stefan Alexander}, issn = {1755-4349}, journal = {Nature Chemistry}, keywords = {General Chemistry, General Chemical Engineering}, number = {5}, pages = {465--471}, publisher = {Springer Nature}, title = {{Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation}}, doi = {10.1038/s41557-021-00643-z}, volume = {13}, year = {2021}, }