I19-Small Molecule Single Crystal Diffraction
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Open Access
Abstract: The guest-dependent flexibility of the pillared-layered metal-organic framework (MOF), Zn2bdc2dabco·X(guest), where guest = EtOH, DMF or benzene, has been examined by high-pressure single crystal X-ray diffraction. A pressure-induced structural phase transition is found for the EtOH- and DMF-included frameworks during compression in a hydrostatic medium of the guest species, which is dependent upon the nature and quantity of the guest in the channels. The EtOH-included material undergoes a phase transition from P4/mmm to C2/m at 0.69 GPa, which is accompanied by a change in the pore shape from square to rhombus via super-filling of the pores. The DMF-included material undergoes a guest-medaited phase transition from I4/mcm to P4/mmm at 0.32 GPa via disordering of the DMF guest. In contrast, the benzene-included framework features a structure with rhombus-shaped channels at ambient pressure and shows direct compression as well as negative linear compressibility parallel to the long diagonal of the channels under hydrostatic pressure. These results demonstrate the large influence of guest molecules on the phase behavior of flexible MOFs. Thus, guest-mediated framework flexibility is useful to engineering MOFs with bespoke pore shapes and compressibility.
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Sep 2021
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Diamond Proposal Number(s):
[15292]
Abstract: We report the crystal structure of the copper-containing nitrite reductase (NirK) from the Gram-negative bacterium Sinorhizobium meliloti 2011 (Sm), together with complex structural alignment and docking studies with both non-cognate and the physiologically-related pseudoazurins, SmPaz1 and SmPaz2, respectively. S. meliloti is a rhizobacterium used for the formulation of Medicago sativa bionoculants, and SmNirK plays a key role in this symbiosis through the denitrification pathway. The structure of SmNirK, solved at a resolution of 2.5 å, showed a striking resemblance with the overall structure of the well-known class I NirKs composed of two Greek key β-barrel domains. The activity of SmNirK is ~12% of the activity reported for classical NirKs, which could be attributed to several factors such as subtle structural differences in the secondary proton channel, solvent accessibility of the substrate channel, and that the denitrifying activity has to be finely regulated within the endosymbiont. In vitro kinetics performed in homogenous and heterogeneous media showed that both SmPaz1 and SmPaz2, which are coded in different regions of the genome, donate electrons to SmNirK with similar performance. Even though the energetics of the interprotein electron transfer (ET) process is not favorable with either electron donors, adduct formation mediated by conserved residues allows minimizing the distance between the copper centers involved in the interprotein ET process.
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Sep 2021
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I09-Surface and Interface Structural Analysis
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Diamond Proposal Number(s):
[18787]
Abstract: One of the most important functionalities of the atomically thin insulator hexagonal boron nitride (hBN) is its ability to chemically and electronically decouple functional materials from highly reactive surfaces. It is therefore of utmost importance to uncover its structural properties on surfaces on an atomic and mesoscopic length scale. In this paper, we quantify the relative coverages of structurally different domains of a hBN layer on the Ni(111) surface using low-energy electron microscopy and the normal incidence x-ray standing wave technique. We find that hBN nucleates on defect sites of the Ni(111) surface and predominantly grows in two epitaxial domains that are rotated by
60
∘
with respect to each other. The two domains reveal identical adsorption heights, indicating a similar chemical interaction strength with the Ni(111) surface. The different azimuthal orientations of these domains originate from different adsorption sites of N and B. We demonstrate that the majority (
≈
70
%
) of hBN domains exhibit a
(
N
,
B
)
=
(
top
,
fcc
)
adsorption site configuration while the minority (
≈
30
%
) show a
(
N
,
B
)
=
(
top
,
hcp
)
configuration. Our study hence underlines the crucial role of the atomic adsorption configuration in the mesoscopic domain structures of in situ fabricated two-dimensional materials on highly reactive surfaces.
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Sep 2021
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[1580]
Open Access
Abstract: Latent TGFβ binding protein-4 (LTBP4) is a multi-domain glycoprotein, essential for regulating the extracellular bioavailability of TGFβ and assembly of elastic fibre proteins, fibrillin-1 and tropoelastin. LTBP4 mutations are linked to autosomal recessive cutis laxa type 1C (ARCL1C), a rare congenital disease characterised by high mortality and severely disrupted connective tissues. Despite the importance of LTBP4, the structure and molecular consequences of disease mutations are unknown. Therefore, we analysed the structural and functional consequences of three ARCL1C causing point mutations which effect highly conserved cysteine residues. Our structural and biophysical data show that the LTBP4 N- and C-terminal regions are monomeric in solution and adopt extended conformations with the mutations resulting in subtle changes to their conformation. Similar to LTBP1, the N-terminal region is relatively inflexible, whereas the C-terminal region is flexible. Interaction studies show that one C-terminal mutation slightly decreases binding to fibrillin-1. We also found that the LTBP4 C-terminal region directly interacts with tropoelastin which is perturbed by both C-terminal ARCL1C mutations, whereas an N-terminal mutation increased binding to fibulin-4 but did not affect the interaction with heparan sulphate. Our results suggest that LTBP4 mutations contribute to ARCL1C by disrupting the structure and interactions of LTBP4 which are essential for elastogenesis in a range of mammalian connective tissues.
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Sep 2021
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Krios I-Titan Krios I at Diamond
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Dmitry
Ghilarov
,
Satomi
Inaba-Inoue
,
Piotr
Stepien
,
Feng
Qu
,
Elizabeth
Michalczyk
,
Zuzanna
Pakosz
,
Norimichi
Nomura
,
Satoshi
Ogasawara
,
Graham Charles
Walker
,
Sylvie
Rebuffat
,
So
Iwata
,
Jonathan
Gardiner Heddle
,
Konstantinos
Beis
Diamond Proposal Number(s):
[18659]
Open Access
Abstract: Antibiotic metabolites and antimicrobial peptides mediate competition between bacterial species. Many of them hijack inner and outer membrane proteins to enter cells. Sensitivity of enteric bacteria to multiple peptide antibiotics is controlled by the single inner membrane protein SbmA. To establish the molecular mechanism of peptide transport by SbmA and related BacA, we determined their cryo–electron microscopy structures at 3.2 and 6 Å local resolution, respectively. The structures show a previously unknown fold, defining a new class of secondary transporters named SbmA-like peptide transporters. The core domain includes conserved glutamates, which provide a pathway for proton translocation, powering transport. The structures show an outward-open conformation with a large cavity that can accommodate diverse substrates. We propose a molecular mechanism for antibacterial peptide uptake paving the way for creation of narrow-targeted therapeutics.
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Sep 2021
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I07-Surface & interface diffraction
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Shuai
Yuan
,
Lin-Song
Cui
,
Linjie
Dai
,
Yun
Liu
,
Qing-Weii
Liu
,
Yu-Qi
Sun
,
Florian
Auras
,
Miguel
Anaya
,
Xiaopeng
Zheng
,
Edoardo
Ruggeri
,
You-Jun
Yu
,
Yang-Kun
Qu
,
Mojtaba
Abdi-Jalebi
,
Osman M.
Bakr
,
Zhao-Kui
Wang
,
Samuel D.
Stranks
,
Neil C.
Greenham
,
Liang-Sheng
Liao
,
Richard H.
Friend
Diamond Proposal Number(s):
[17223]
Open Access
Abstract: Metal halide perovskite semiconductors have demonstrated remarkable potentials in solution-processed blue light-emitting diodes (LEDs). However, the unsatisfied efficiency and spectral stability responsible for trap-mediated non-radiative losses and halide phase segregation remain the primary unsolved challenges for blue perovskite LEDs. In this study, it is reported that a fluorene-based π-conjugated cationic polymer can be blended with the perovskite semiconductor to control film formation and optoelectronic properties. As a result, sky-blue and true-blue perovskite LEDs with Commission Internationale de l'Eclairage coordinates of (0.08, 0.22) and (0.12, 0.13) at the record external quantum efficiencies of 11.2% and 8.0% were achieved. In addition, the mixed halide perovskites with the conjugated cationic polymer exhibit excellent spectral stability under external bias. This result illustrates that π-conjugated cationic polymers have a great potential to realize efficient blue mixed-halide perovskite LEDs with stable electroluminescence.
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Sep 2021
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Krios III-Titan Krios III at Diamond
Krios IV-Titan Krios IV at Diamond
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Diamond Proposal Number(s):
[20287]
Open Access
Abstract: RNA polymerase inhibition plays an important role in the regulation of transcription in response to environmental changes and in the virus-host relationship. Here we present the high-resolution structures of two such RNAP-inhibitor complexes that provide the structural bases underlying RNAP inhibition in archaea. The Acidianus two-tailed virus encodes the RIP factor that binds inside the DNA-binding channel of RNAP, inhibiting transcription by occlusion of binding sites for nucleic acid and the transcription initiation factor TFB. Infection with the Sulfolobus Turreted Icosahedral Virus induces the expression of the host factor TFS4, which binds in the RNAP funnel similarly to eukaryotic transcript cleavage factors. However, TFS4 allosterically induces a widening of the DNA-binding channel which disrupts trigger loop and bridge helix motifs. Importantly, the conformational changes induced by TFS4 are closely related to inactivated states of RNAP in other domains of life indicating a deep evolutionary conservation of allosteric RNAP inhibition.
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Sep 2021
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B21-High Throughput SAXS
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Open Access
Abstract: In organisms from all domains of life, multi-enzyme assemblies play central roles in defining transcript lifetimes and facilitating RNA-mediated regulation of gene expression. An assembly dedicated to such roles, known as the RNA degradosome, is found amongst bacteria from highly diverse lineages. About a fifth of the assembly mass of the degradosome of Escherichia coli and related species is predicted to be intrinsically disordered – a property that has been sustained for over a billion years of bacterial molecular history and stands in marked contrast to the high degree of sequence variation of that same region. Here, we characterize the conformational dynamics of the degradosome using a hybrid structural biology approach that combines solution scattering with ad hoc ensemble modelling, cryo-electron microscopy, and other biophysical methods. The E. coli degradosome can form punctate bodies in vivo that may facilitate its functional activities, and based on our results, we propose an electrostatic switch model to account for the propensity of the degradosome to undergo programmable puncta formation.
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Sep 2021
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I13-2-Diamond Manchester Imaging
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Clara
Anduix-Canto
,
Mark A.
Levenstein
,
Yi-Yeoun
Kim
,
Jose R. A.
Godinho
,
Alexander N.
Kulak
,
Carlos
Gonzalez Nino
,
Philip J.
Withers
,
Jonathan P.
Wright
,
Nikil
Kapur
,
Hugo K.
Christenson
,
Fiona C.
Meldrum
Diamond Proposal Number(s):
[13578, 17314]
Open Access
Abstract: Characterizing the pathways by which crystals form remains a significant challenge, particularly when multiple pathways operate simultaneously. Here, an imaging-based strategy is introduced that exploits confinement effects to track the evolution of a population of crystals in 3D and to characterize crystallization pathways. Focusing on calcium sulfate formation in aqueous solution at room temperature, precipitation is carried out within nanoporous media, which ensures that the crystals are fixed in position and develop slowly. The evolution of their size, shape, and polymorph can then be tracked in situ using synchrotron X-ray computed tomography and diffraction computed tomography without isolating and potentially altering the crystals. The study shows that bassanite (CaSO4 0.5H2O) forms via an amorphous precursor phase and that it exhibits long-term stability in these nanoscale pores. Further, the thermodynamically stable phase gypsum (CaSO4 2H2O) can precipitate by different pathways according to the local physical environment. Insight into crystallization in nanoconfinement is also gained, and the crystals are seen to grow throughout the nanoporous network without causing structural damage. This work therefore offers a novel strategy for studying crystallization pathways and demonstrates the significant impact of confinement on calcium sulfate precipitation, which is relevant to its formation in many real-world environments.
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Sep 2021
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Jonathan
Youngs
,
Nicholas M.
Provine
,
Nicholas
Lim
,
Hannah R.
Sharpe
,
Ali
Amini
,
Yi-Ling
Chen
,
Jian
Luo
,
Matthew D.
Edmans
,
Panagiota
Zacharopoulou
,
Wentao
Chen
,
Oliver
Sampson
,
Robert
Paton
,
William J.
Hurt
,
David A.
Duncan
,
Anna L.
Mcnaughton
,
Vincent N.
Miao
,
Susannah
Leaver
,
Duncan L. A.
Wyncoll
,
Jonathan
Ball
,
Philip
Hopkins
,
Donal T.
Skelly
,
Eleanor
Barnes
,
Susanna
Dunachie
,
Graham
Ogg
,
Teresa
Lambe
,
Ian
Pavord
,
Alex K.
Shalek
,
Craig P.
Thompson
,
Luzheng
Xue
,
Derek C.
Macallan
,
Philip
Goulder
,
Paul
Klenerman
,
Tihana
Bicanic
Open Access
Abstract: Prior studies have demonstrated that immunologic dysfunction underpins severe illness in COVID-19 patients, but have lacked an in-depth analysis of the immunologic drivers of death in the most critically ill patients. We performed immunophenotyping of viral antigen-specific and unconventional T cell responses, neutralizing antibodies, and serum proteins in critically ill patients with SARS-CoV-2 infection, using influenza infection, SARS-CoV-2-convalescent health care workers, and healthy adults as controls. We identify mucosal-associated invariant T (MAIT) cell activation as an independent and significant predictor of death in COVID-19 (HR = 5.92, 95% CI = 2.49–14.1). MAIT cell activation correlates with several other mortality-associated immunologic measures including broad activation of CD8+ T cells and non-Vδ2 γδT cells, and elevated levels of cytokines and chemokines, including GM-CSF, CXCL10, CCL2, and IL-6. MAIT cell activation is also a predictor of disease severity in influenza (ECMO/death HR = 4.43, 95% CI = 1.08–18.2). Single-cell RNA-sequencing reveals a shift from focused IFNα-driven signals in COVID-19 ICU patients who survive to broad pro-inflammatory responses in fatal COVID-19 –a feature not observed in severe influenza. We conclude that fatal COVID-19 infection is driven by uncoordinated inflammatory responses that drive a hierarchy of T cell activation, elements of which can serve as prognostic indicators and potential targets for immune intervention.
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Sep 2021
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