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Influence of Elastic Scattering on Electron Swarm Distribution in Electrified Gases 期刊论文
JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES, 2020, 125 (10)
作者:  Schmalzried, A.;  Luque, A.
收藏  |  浏览/下载:19/0  |  提交时间:2020/07/02
thermal runaway  electron elastic scattering  differential cross section  screened Rutherford  electron swarm dynamics  Monte Carlo electron simulation  
Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping 期刊论文
NATURE, 2020, 583 (7817) : 638-+
作者:  Lin, Yiheng;  Leibrandt, David R.;  Leibfriedz, Dietrich;  Chou, Chin-wen
收藏  |  浏览/下载:41/0  |  提交时间:2020/07/03

A method termed ac(4)C-seq is introduced for the transcriptome-wide mapping of the RNA modificationN(4)-acetylcytidine, revealing widespread temperature-dependent acetylation that facilitates thermoadaptation in hyperthermophilic archaea.


N-4-acetylcytidine (ac(4)C) is an ancient and highly conserved RNA modification that is present on tRNA and rRNA and has recently been investigated in eukaryotic mRNA(1-3). However, the distribution, dynamics and functions of cytidine acetylation have yet to be fully elucidated. Here we report ac(4)C-seq, a chemical genomic method for the transcriptome-wide quantitative mapping of ac(4)C at single-nucleotide resolution. In human and yeast mRNAs, ac(4)C sites are not detected but can be induced-at a conserved sequence motif-via the ectopic overexpression of eukaryotic acetyltransferase complexes. By contrast, cross-evolutionary profiling revealed unprecedented levels of ac(4)C across hundreds of residues in rRNA, tRNA, non-coding RNA and mRNA from hyperthermophilic archaea. (AcC)-C-4 is markedly induced in response to increases in temperature, and acetyltransferase-deficient archaeal strains exhibit temperature-dependent growth defects. Visualization of wild-type and acetyltransferase-deficient archaeal ribosomes by cryo-electron microscopy provided structural insights into the temperature-dependent distribution of ac(4)C and its potential thermoadaptive role. Our studies quantitatively define the ac(4)C landscape, providing a technical and conceptual foundation for elucidating the role of this modification in biology and disease(4-6).


  
Femtosecond-to-millisecond structural changes in a light-driven sodium pump 期刊论文
NATURE, 2020, 583 (7815) : 314-+
作者:  Moore, Luiza;  Leongamornlert, Daniel;  Coorens, Tim H. H.;  Sanders, Mathijs A.;  Ellis, Peter;  Dentro, Stefan C.;  Dawson, Kevin J.;  Butler, Tim;  Rahbari, Raheleh;  Mitchell, Thomas J.;  Maura, Francesco;  Nangalia, Jyoti;  Tarpey, Patrick S.;  Brunner, Simon F.;  Lee-Six, Henry;  Hooks, Yvette;  Moody, Sarah;  Mahbubani, Krishnaa T.;  Jimenez-Linan, Mercedes;  Brosens, Jan J.;  Iacobuzio-Donahue, Christine A.;  Martincorena, Inigo;  Saeb-Parsy, Kourosh;  Campbell, Peter J.;  Stratton, Michael R.
收藏  |  浏览/下载:54/0  |  提交时间:2020/07/03

Light-driven sodium pumps actively transport small cations across cellular membranes(1). These pumps are used by microorganisms to convert light into membrane potential and have become useful optogenetic tools with applications in neuroscience. Although the resting state structures of the prototypical sodium pump Krokinobacter eikastus rhodopsin 2 (KR2) have been solved(2,3), it is unclear how structural alterations overtime allow sodium to be translocated against a concentration gradient. Here, using the Swiss X-ray Free Electron Laser(4), we have collected serial crystallographic data at ten pump-probe delays from femtoseconds to milliseconds. High-resolution structural snapshots throughout the KR2 photocycle show how retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds. Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds. Structural and spectroscopic data, in combination with quantum chemical calculations, indicate that a sodium ion bind stransiently close to the retinal within one millisecond. In the last structural intermediate, at 20 milliseconds after activation, we identified a potential second sodium-binding site close to the extracellular exit. These results provide direct molecular insight into the dynamics of active cation transport across biological membranes.


  
Two-dimensional halide perovskite lateral epitaxial heterostructures 期刊论文
NATURE, 2020, 580 (7805) : 614-+
作者:  Cabrita, Rita;  Lauss, Martin;  Sanna, Adriana;  Donia, Marco;  Larsen, Mathilde;  Mitra, Shamik;  Johansson, Iva;  Phung, Bengt;  Harbst, Katja;  Vallon-Christersson, Johan;  van Schoiack, Alison;  Lovgren, Kristina;  Warren, Sarah;  Jirstrom, Karin;  Olsson, Hakan;  Pietras, Kristian;  Ingvar, Christian;  Isaksson, Karolin
收藏  |  浏览/下载:45/0  |  提交时间:2020/07/03

Epitaxial heterostructures based on oxide perovskites and III-V, II-VI and transition metal dichalcogenide semiconductors form the foundation of modern electronics and optoelectronics(1-7). Halide perovskites-an emerging family of tunable semiconductors with desirable properties-are attractive for applications such as solution-processed solar cells, light-emitting diodes, detectors and lasers(8-15). Their inherently soft crystal lattice allows greater tolerance to lattice mismatch, making them promising for heterostructure formation and semiconductor integration(16,17). Atomically sharp epitaxial interfaces are necessary to improve performance and for device miniaturization. However, epitaxial growth of atomically sharp heterostructures of halide perovskites has not yet been achieved, owing to their high intrinsic ion mobility, which leads to interdiffusion and large junction widths(18-21), and owing to their poor chemical stability, which leads to decomposition of prior layers during the fabrication of subsequent layers. Therefore, understanding the origins of this instability and identifying effective approaches to suppress ion diffusion are of great importance(22-26). Here we report an effective strategy to substantially inhibit in-plane ion diffusion in two-dimensional halide perovskites by incorporating rigid pi-conjugated organic ligands. We demonstrate highly stable and tunable lateral epitaxial heterostructures, multiheterostructures and superlattices. Near-atomically sharp interfaces and epitaxial growth are revealed by low-dose aberration-corrected high-resolution transmission electron microscopy. Molecular dynamics simulations confirm the reduced heterostructure disorder and larger vacancy formation energies of the two-dimensional perovskites in the presence of conjugated ligands. These findings provide insights into the immobilization and stabilization of halide perovskite semiconductors and demonstrate a materials platform for complex and molecularly thin superlattices, devices and integrated circuits.


An epitaxial growth strategy that improves the stability of two-dimensional halide perovskites by inhibiting ion diffusion in their heterostructures using rigid pi-conjugated ligands is demonstrated, and shows near-atomically sharp interfaces.


  
Ball-and-chain inactivation in a calcium-gated potassium channel 期刊论文
NATURE, 2020, 580 (7802) : 288-+
作者:  Peron, Simon;  Pancholi, Ravi;  Voelcker, Bettina;  Wittenbach, Jason D.;  olafsdottir, H. Freyja;  Freeman, Jeremy;  Svoboda, Karel
收藏  |  浏览/下载:32/0  |  提交时间:2020/07/03

Cryo-electron microscopy structures and molecular dynamics simulations of the calcium-activated potassium channel MthK from Methanobacterium thermoautotrophicum are used to show that gating of this channel involves a ball-and-chain inactivation mechanism mediated by a previously unresolved N-terminal peptide.


Inactivation is the process by which ion channels terminate ion flux through their pores while the opening stimulus is still present(1). In neurons, inactivation of both sodium and potassium channels is crucial for the generation of action potentials and regulation of firing frequency(1,2). A cytoplasmic domain of either the channel or an accessory subunit is thought to plug the open pore to inactivate the channel via a '  ball-and-chain'  mechanism(3-7). Here we use cryo-electron microscopy to identify the molecular gating mechanism in calcium-activated potassium channels by obtaining structures of the MthK channel from Methanobacterium thermoautotrophicum-a purely calcium-gated and inactivating channel-in a lipid environment. In the absence of Ca2+, we obtained a single structure in a closed state, which was shown by atomistic simulations to be highly flexible in lipid bilayers at ambient temperature, with large rocking motions of the gating ring and bending of pore-lining helices. In Ca2+-bound conditions, we obtained several structures, including multiple open-inactivated conformations, further indication of a highly dynamic protein. These different channel conformations are distinguished by rocking of the gating rings with respect to the transmembrane region, indicating symmetry breakage across the channel. Furthermore, in all conformations displaying open channel pores, the N terminus of one subunit of the channel tetramer sticks into the pore and plugs it, with free energy simulations showing that this is a strong interaction. Deletion of this N terminus leads to functionally non-inactivating channels and structures of open states without a pore plug, indicating that this previously unresolved N-terminal peptide is responsible for a ball-and-chain inactivation mechanism.


  
Attosecond pulse shaping using a seeded free-electron laser 期刊论文
NATURE, 2020
作者:  Achar, Yathish Jagadheesh;  Adhil, Mohamood;  Choudhary, Ramveer;  Gilbert, Nick;  Foiani, Marco
收藏  |  浏览/下载:14/0  |  提交时间:2020/07/03

Generation of intense attosecond waveforms with independently controllable amplitude and phase is performed by using a seeded free-electron laser.


Attosecond pulses are central to the investigation of valence- and core-electron dynamics on their natural timescales(1-3). The reproducible generation and characterization of attosecond waveforms has been demonstrated so far only through the process of high-order harmonic generation(4-7). Several methods for shaping attosecond waveforms have been proposed, including the use of metallic filters(8,9), multilayer mirrors(10) and manipulation of the driving field(11). However, none of these approaches allows the flexible manipulation of the temporal characteristics of the attosecond waveforms, and they suffer from the low conversion efficiency of the high-order harmonic generation process. Free-electron lasers, by contrast, deliver femtosecond, extreme-ultraviolet and X-ray pulses with energies ranging from tens of microjoules to a few millijoules(12,13). Recent experiments have shown that they can generate subfemtosecond spikes, but with temporal characteristics that change shot-to-shot(14-16). Here we report reproducible generation of high-energy (microjoule level) attosecond waveforms using a seeded free-electron laser(17). We demonstrate amplitude and phase manipulation of the harmonic components of an attosecond pulse train in combination with an approach for its temporal reconstruction. The results presented here open the way to performing attosecond time-resolved experiments with free-electron lasers.


  
Processive extrusion of polypeptide loops by a Hsp100 disaggregase 期刊论文
NATURE, 2020, 578 (7794) : 317-+
作者:  Zhao, Peishen;  Liang, Yi-Lynn;  Belousoff, Matthew J.;  Deganutti, Giuseppe;  Fletcher, Madeleine M.;  Willard, Francis S.;  Bell, Michael G.;  Christe, Michael E.;  Sloop, Kyle W.;  Inoue, Asuka;  Truong, Tin T.;  Clydesdale, Lachlan;  Furness, Sebastian G. B.;  Christopoulos, Arthur;  Wang, Ming-Wei;  Miller, Laurence J.;  Reynolds, Christopher A.;  Danev, Radostin;  Sexton, Patrick M.;  Wootten, Denise
收藏  |  浏览/下载:41/0  |  提交时间:2020/07/03

The ability to reverse protein aggregation is vital to cells(1,2). Hsp100 disaggregases such as ClpB and Hsp104 are proposed to catalyse this reaction by translocating polypeptide loops through their central pore(3,4). This model of disaggregation is appealing, as it could explain how polypeptides entangled within aggregates can be extracted and subsequently refolded with the assistance of Hsp70(4,5). However, the model is also controversial, as the necessary motor activity has not been identified(6-8) and recent findings indicate non-processive mechanisms such as entropic pulling or Brownian ratcheting(9,10). How loop formation would be accomplished is also obscure. Indeed, cryo-electron microscopy studies consistently show single polypeptide strands in the Hsp100 pore(11,12). Here, by following individual ClpB-substrate complexes in real time, we unambiguously demonstrate processive translocation of looped polypeptides. We integrate optical tweezers with fluorescent-particle tracking to show that ClpB translocates both arms of the loop simultaneously and switches to single-arm translocation when encountering obstacles. ClpB is notably powerful and rapid  it exerts forces of more than 50 pN at speeds of more than 500 residues per second in bursts of up to 28 residues. Remarkably, substrates refold while exiting the pore, analogous to co-translational folding. Our findings have implications for protein-processing phenomena including ubiquitin-mediated remodelling by Cdc48 (or its mammalian orthologue p97)(13) and degradation by the 26S proteasome(14).


A combination of optical tweezers and fluorescent-particle tracking is used to dissect the dynamics of the Hsp100 disaggregase ClpB, and show that the processive extrusion of polypeptide loops is the mechanistic basis of its activity.


  
Energy Range of Electron Rolling Pin Distribution Behind Dipolarization Front 期刊论文
GEOPHYSICAL RESEARCH LETTERS, 2019, 46 (5) : 2390-2398
作者:  Zhao, M. J.;  Fu, H. S.;  Liu, C. M.;  Chen, Z. Z.;  Xu, Y.;  Giles, B. L.;  Burch, J. L.
收藏  |  浏览/下载:21/0  |  提交时间:2019/11/26
dipolarization front  rolling pin distribution  energy range  gyrotropic distribution  electron dynamics