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523 items found (0 items not approved), displaying 1 to 10.[First/Prev] 1, 2, 3, 4, 5, 6, 7, 8 [Next/Last]

Instruments / Technical Area	Publication Details	Published
B21-High Throughput SAXS	Autophagy receptor NDP52 alters DNA conformation to modulate RNA polymerase II transcription Ália Dos Santos , Daniel E. Rollins , Yukti Hari-Gupta , Hannah Mcarthur , Mingxue Du , Sabrina Yong Zi Ru , Kseniia Pidlisna , Ane Stranger , Faeeza Lorgat , Danielle Lambert , Ian Brown , Kevin Howland , Jesse Aaron , Lin Wang , Peter J. I. Ellis , Teng-Leong Chew , Marisa Martin-Fernandez , Alice L. B. Pyne , Christopher P. Toseland Nature Communications 14 DOI: 10.1038/s41467-023-38572-9 Diamond Proposal Number(s): [16207] Open Access Show Abstract ▼ Abstract: NDP52 is an autophagy receptor involved in the recognition and degradation of invading pathogens and damaged organelles. Although NDP52 was first identified in the nucleus and is expressed throughout the cell, to date, there is no clear nuclear functions for NDP52. Here, we use a multidisciplinary approach to characterise the biochemical properties and nuclear roles of NDP52. We find that NDP52 clusters with RNA Polymerase II (RNAPII) at transcription initiation sites and that its overexpression promotes the formation of additional transcriptional clusters. We also show that depletion of NDP52 impacts overall gene expression levels in two model mammalian cells, and that transcription inhibition affects the spatial organisation and molecular dynamics of NDP52 in the nucleus. This directly links NDP52 to a role in RNAPII-dependent transcription. Furthermore, we also show that NDP52 binds specifically and with high affinity to double-stranded DNA (dsDNA) and that this interaction leads to changes in DNA structure in vitro. This, together with our proteomics data indicating enrichment for interactions with nucleosome remodelling proteins and DNA structure regulators, suggests a possible function for NDP52 in chromatin regulation. Overall, here we uncover nuclear roles for NDP52 in gene expression and DNA structure regulation.	May 2023
B18-Core EXAFS I11-High Resolution Powder Diffraction	Anion redox as a means to derive layered manganese oxychalcogenides with exotic intergrowth structures Shunsuke Sasaki , Souvik Giri , Simon J. Cassidy , Sunita Dey , Maria Batuk , Daphne Vandemeulebroucke , Giannantonio Cibin , Ronald I. Smith , Philip Holdship , Clare P. Grey , Joke Hadermann , Simon J. Clarke Nature Communications 14 DOI: 10.1038/s41467-023-38489-3 Diamond Proposal Number(s): [25166, 14239] Open Access Show Abstract ▼ Abstract: Topochemistry enables step-by-step conversions of solid-state materials often leading to metastable structures that retain initial structural motifs. Recent advances in this field revealed many examples where relatively bulky anionic constituents were actively involved in redox reactions during (de)intercalation processes. Such reactions are often accompanied by anion-anion bond formation, which heralds possibilities to design novel structure types disparate from known precursors, in a controlled manner. Here we present the multistep conversion of layered oxychalcogenides Sr2MnO2Cu1.5Ch2 (Ch = S, Se) into Cu-deintercalated phases where antifluorite type [Cu1.5Ch2]2.5- slabs collapsed into two-dimensional arrays of chalcogen dimers. The collapse of the chalcogenide layers on deintercalation led to various stacking types of Sr2MnO2Ch2 slabs, which formed polychalcogenide structures unattainable by conventional high-temperature syntheses. Anion-redox topochemistry is demonstrated to be of interest not only for electrochemical applications but also as a means to design complex layered architectures.	May 2023
Krios IV-Titan Krios IV at Diamond	Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex Mandy S. M. Wan , Reyhan Muhammad , Marios G. Koliopoulos , Theodoros I. Roumeliotis , Jyoti S. Choudhary , Claudio Alfieri Nature Communications 14 DOI: 10.1038/s41467-023-38276-0 Diamond Proposal Number(s): [21809] Open Access Show Abstract ▼ Abstract: Lysine acetylation in histone tails is a key post-translational modification that controls transcription activation. Histone deacetylase complexes remove histone acetylation, thereby repressing transcription and regulating the transcriptional output of each gene. Although these complexes are drug targets and crucial regulators of organismal physiology, their structure and mechanisms of action are largely unclear. Here, we present the structure of a complete human SIN3B histone deacetylase holo-complex with and without a substrate mimic. Remarkably, SIN3B encircles the deacetylase and contacts its allosteric basic patch thereby stimulating catalysis. A SIN3B loop inserts into the catalytic tunnel, rearranges to accommodate the acetyl-lysine moiety, and stabilises the substrate for specific deacetylation, which is guided by a substrate receptor subunit. Our findings provide a model of specificity for a main transcriptional regulator conserved from yeast to human and a resource of protein-protein interactions for future drug designs.	May 2023
	Rehybridization dynamics into the pericyclic minimum of an electrocyclic reaction imaged in real-time Y. Liu , D. M. Sanchez , M. R. Ware , E. G. Champenois , J. Yang , J. P. F. Nunes , A. Attar , M. Centurion , J. P. Cryan , R. Forbes , K. Hegazy , M. C. Hoffmann , F. Ji , M.-F. Lin , D. Luo , S. K. Saha , X. Shen , X. J. Wang , T. J. Martínez , T. J. A. Wolf Nature Communications 14 DOI: 10.1038/s41467-023-38513-6 Open Access Show Abstract ▼ Abstract: Electrocyclic reactions are characterized by the concerted formation and cleavage of both σ and π bonds through a cyclic structure. This structure is known as a pericyclic transition state for thermal reactions and a pericyclic minimum in the excited state for photochemical reactions. However, the structure of the pericyclic geometry has yet to be observed experimentally. We use a combination of ultrafast electron diffraction and excited state wavepacket simulations to image structural dynamics through the pericyclic minimum of a photochemical electrocyclic ring-opening reaction in the molecule α-terpinene. The structural motion into the pericyclic minimum is dominated by rehybridization of two carbon atoms, which is required for the transformation from two to three conjugated π bonds. The σ bond dissociation largely happens after internal conversion from the pericyclic minimum to the electronic ground state. These findings may be transferrable to electrocyclic reactions in general.	May 2023
E02-JEM ARM 300CF	Cryogenic electron ptychographic single particle analysis with wide bandwidth information transfer Xudong Pei , Liqi Zhou , Chen Huang , Mark Boyce , Judy S. Kim , Emanuela Liberti , Yiming Hu , Takeo Sasaki , Peter D. Nellist , Peijun Zhang , David I. Stuart , Angus I. Kirkland , Peng Wang Nature Communications 14 DOI: 10.1038/s41467-023-38268-0 Diamond Proposal Number(s): [17918] Open Access Show Abstract ▼ Abstract: Advances in cryogenic transmission electron microscopy have revolutionised the determination of many macromolecular structures at atomic or near-atomic resolution. This method is based on conventional defocused phase contrast imaging. However, it has limitations of weaker contrast for small biological molecules embedded in vitreous ice, in comparison with cryo-ptychography, which shows increased contrast. Here we report a single-particle analysis based on the use of ptychographic reconstruction data, demonstrating that three dimensional reconstructions with a wide information transfer bandwidth can be recovered by Fourier domain synthesis. Our work suggests future applications in otherwise challenging single particle analyses, including small macromolecules and heterogeneous or flexible particles. In addition structure determination in situ within cells without the requirement for protein purification and expression may be possible.	May 2023
I21-Resonant Inelastic X-ray Scattering (RIXS)	Magnetic excitations beyond the single- and double-magnons Hebatalla Elnaggar , Abhishek Nag , Maurits W. Haverkort , Mirian Garcia-Fernandez , Andrew Walters , Ru-Pan Wang , Ke-Jin Zhou , Frank De Groot Nature Communications 14 DOI: 10.1038/s41467-023-38341-8 Open Access Show Abstract ▼ Abstract: A photon carrying one unit of angular momentum can change the spin angular momentum of a magnetic system with one unit (ΔMs = ±1) at most. This implies that a two-photon scattering process can manipulate the spin angular momentum of the magnetic system with a maximum of two units. Herein we describe a triple-magnon excitation in α-Fe2O3, which contradicts this conventional wisdom that only 1- and 2-magnon excitations are possible in a resonant inelastic X-ray scattering experiment. We observe an excitation at exactly three times the magnon energy, along with additional excitations at four and five times the magnon energy, suggesting quadruple and quintuple-magnons as well. Guided by theoretical calculations, we reveal how a two-photon scattering process can create exotic higher-rank magnons and the relevance of these quasiparticles for magnon-based applications.	May 2023
Krios II-Titan Krios II at Diamond	Cryo-electron microscopy of the f1 filamentous phage reveals insights into viral infection and assembly Rebecca Conners , Rayén Ignacia León-Quezada , Mathew Mclaren , Nicholas J. Bennett , Bertram Daum , Jasna Rakonjac , Vicki Gold Nature Communications 14 DOI: 10.1038/s41467-023-37915-w Diamond Proposal Number(s): [25452] Open Access Show Abstract ▼ Abstract: Phages are viruses that infect bacteria and dominate every ecosystem on our planet. As well as impacting microbial ecology, physiology and evolution, phages are exploited as tools in molecular biology and biotechnology. This is particularly true for the Ff (f1, fd or M13) phages, which represent a widely distributed group of filamentous viruses. Over nearly five decades, Ffs have seen an extraordinary range of applications, yet the complete structure of the phage capsid and consequently the mechanisms of infection and assembly remain largely mysterious. In this work, we use cryo-electron microscopy and a highly efficient system for production of short Ff-derived nanorods to determine a structure of a filamentous virus including the tips. We show that structure combined with mutagenesis can identify phage domains that are important in bacterial attack and for release of new progeny, allowing new models to be proposed for the phage lifecycle.	May 2023
Krios IV-Titan Krios IV at Diamond	IS21 family transposase cleaved donor complex traps two right-handed superhelical crossings Mercedes Spínola-Amilibia , Lidia Araujo-Bazan , Alvaro De La Gandara , James M. Berger , Ernesto Arias-Palomo Nature Communications 14 DOI: 10.1038/s41467-023-38071-x Diamond Proposal Number(s): [26399] Open Access Show Abstract ▼ Abstract: Transposases are ubiquitous enzymes that catalyze DNA rearrangement events with broad impacts on gene expression, genome evolution, and the spread of drug-resistance in bacteria. Here, we use biochemical and structural approaches to define the molecular determinants by which IstA, a transposase present in the widespread IS21 family of mobile elements, catalyzes efficient DNA transposition. Solution studies show that IstA engages the transposon terminal sequences to form a high-molecular weight complex and promote DNA integration. A 3.4 Å resolution structure of the transposase bound to transposon ends corroborates our biochemical findings and reveals that IstA self-assembles into a highly intertwined tetramer that synapses two supercoiled terminal inverted repeats. The three-dimensional organization of the IstA•DNA cleaved donor complex reveals remarkable similarities with retroviral integrases and classic transposase systems, such as Tn7 and bacteriophage Mu, and provides insights into IS21 transposition.	Apr 2023
I06-Nanoscience	Current-driven writing process in antiferromagnetic Mn2Au for memory applications S. Reimers , Y. Lytvynenko , Y. R. Niu , E. Golias , B. Sarpi , L. S. I. Veiga , T. Denneulin , A. Kovács , R. E. Dunin-Borkowski , J. Bläßer , M. Klaui , M. Jourdan Nature Communications 14 DOI: 10.1038/s41467-023-37569-8 Diamond Proposal Number(s): [30141] Open Access Show Abstract ▼ Abstract: Current pulse driven Néel vector rotation in metallic antiferromagnets is one of the most promising concepts in antiferromagnetic spintronics. We show microscopically that the Néel vector of epitaxial thin films of the prototypical compound Mn2Au can be reoriented reversibly in the complete area of cross shaped device structures using single current pulses. The resulting domain pattern with aligned staggered magnetization is long term stable enabling memory applications. We achieve this switching with low heating of ≈20 K, which is promising regarding fast and efficient devices without the need for thermal activation. Current polarity dependent reversible domain wall motion demonstrates a Néel spin-orbit torque acting on the domain walls.	Apr 2023
I04-Macromolecular Crystallography	Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs Filip Mihalič , Leandro Simonetti , Girolamo Giudice , Marie Rubin Sander , Richard Lindqvist , Marie Berit Akpiroro Peters , Caroline Benz , Eszter Kassa , Dilip Badgujar , Raviteja Inturi , Muhammad Ali , Izabella Krystkowiak , Ahmed Sayadi , Eva Andersson , Hanna Aronsson , Ola Söderberg , Doreen Dobritzsch , Evangelia Petsalaki , Anna K. Överby , Per Jemth , Norman E. Davey , Ylva Ivarsson Nature Communications 14 DOI: 10.1038/s41467-023-38015-5 Diamond Proposal Number(s): [23773] Open Access Show Abstract ▼ Abstract: Viruses mimic host short linear motifs (SLiMs) to hijack and deregulate cellular functions. Studies of motif-mediated interactions therefore provide insight into virus-host dependencies, and reveal targets for therapeutic intervention. Here, we describe the pan-viral discovery of 1712 SLiM-based virus-host interactions using a phage peptidome tiling the intrinsically disordered protein regions of 229 RNA viruses. We find mimicry of host SLiMs to be a ubiquitous viral strategy, reveal novel host proteins hijacked by viruses, and identify cellular pathways frequently deregulated by viral motif mimicry. Using structural and biophysical analyses, we show that viral mimicry-based interactions have similar binding strength and bound conformations as endogenous interactions. Finally, we establish polyadenylate-binding protein 1 as a potential target for broad-spectrum antiviral agent development. Our platform enables rapid discovery of mechanisms of viral interference and the identification of potential therapeutic targets which can aid in combating future epidemics and pandemics.	Apr 2023

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