I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[13467]
Open Access
Abstract: Arms race co-evolution drives rapid adaptive changes in pathogens and in the immune systems of their hosts. Plant intracellular NLR immune receptors detect effectors delivered by pathogens to promote susceptibility, activating an immune response that halts colonization. As a consequence, pathogen effectors evolve to escape immune recognition and are highly variable. In turn, NLR receptors are one of the most diverse protein families in plants, and this variability underpins differential recognition of effector variants. The molecular mechanisms underlying natural variation in effector recognition by NLRs are starting to be elucidated. The rice NLR pair Pik-1/Pik-2 recognizes AVR-Pik effectors from the blast fungus Magnaporthe oryzae, triggering immune responses that limit rice blast infection. Allelic variation in a heavy metal associated (HMA) domain integrated in the receptor Pik-1 confers differential binding to AVR-Pik variants, determining resistance specificity. Previous mechanistic studies uncovered how a Pik allele, Pikm, has extended recognition to effector variants through a specialized HMA/AVR-Pik binding interface. Here, we reveal the mechanistic basis of extended recognition specificity conferred by another Pik allele, Pikh. A single residue in Pikh-HMA increases binding to AVR-Pik variants, leading to an extended effector response in planta. The crystal structure of Pikh-HMA in complex with an AVR-Pik variant confirmed that Pikh and Pikm use a similar molecular mechanism to extend their pathogen recognition profile. This study shows how different NLR receptor alleles functionally converge to extend recognition specificity to pathogen effectors.
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Mar 2021
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Open Access
Abstract: In situ synchrotron X-ray tomography has been used to observe the initiation and propagation of pits during atmospheric corrosion of aluminium alloy AA2024 under droplets of NaCl and simulated seawater at 21 ± 2 °C and a relative humidity of 85% over a period of 120 minutes. Each complete tomogram took 300 s to collect (pixel size 0.74 µm). Two metastable pits initiated at intermetallic particles, forming a crevice around the edge of the particles. Three other metastable pits formed at sites with no obvious micron-sized features. Only one pit, which had initiated under a fragment of debris, continued to stable growth. Metastable pits initiated sequentially, and all initiation events were accompanied by the formation of one or more bubbles, presumed to be hydrogen. Pit propagation was spatially non-uniform, with rapid growth in local regions while the remainder of the pit remained passive. The growth rate was highest parallel to the rolling direction of the plate. The highest local current density was estimated from the loss of metal between successive measurements to be ~0.5 A/cm2. This is the first time that the transition from initiation to propagation of individual localised pits in an aluminium alloy has been characterised in situ.
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Mar 2021
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Open Access
Abstract: Batteries are the most abundant form of electrochemical energy storage. Lithium and sodium ion batteries account for a significant portion of the battery market, but high-performance electrochemically active materials still need to be discovered and optimized for these technologies. Recently, tin(II) oxide (SnO) has emerged as a highly promising battery electrode. In this work, we present a facile synthesis method to produce SnO microparticles whose size and shape can be tailored by changing the solvent nature. We study the complex relationship between wet-chemistry synthesis conditions and resulting layered nanoparticle morphology. Furthermore, high-level electronic structure theory, including dispersion corrections to account for van der Waals forces, is employed to enhance our understanding of the underlying chemical mechanisms. The electronic vacuum alignment and surface energies are determined, allowing the prediction of the thermodynamically favoured crystal shape (Wulff construction) and surface-weighted work function. Finally, the synthesized nanomaterials were tested as Li-ion battery anodes, demonstrating significantly enhanced electrochemical performance for morphologies obtained from specific synthesis conditions.
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Mar 2021
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I05-ARPES
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Paulina
Majchrzak
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Ryan
Muzzio
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Alfred J. H.
Jones
,
Davide
Curcio
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Klara
Volckaert
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Deepnarayan
Biswas
,
Jacob
Gobbo
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Simranjeet
Singh
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Jeremy T.
Robinson
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Kenji
Watanabe
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Takashi
Taniguchi
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Timur K.
Kim
,
Cephise
Cacho
,
Jill A.
Miwa
,
Philip
Hofmann
,
Jyoti
Katoch
,
Soeren
Ulstrup
Diamond Proposal Number(s):
[24072]
Open Access
Abstract: To pinpoint the electronic and structural mechanisms that affect intrinsic and extrinsic performance limits of two‐dimensional material devices, it is of critical importance to resolve the electronic properties on the mesoscopic length scale of such devices under operating conditions. The present work utilizes angle‐resolved photoemission spectroscopy with nanoscale spatial resolution (nanoARPES) to map the quasiparticle electronic structure of a twisted bilayer graphene device. The dispersion and linewidth of the Dirac cones associated with top and bottom graphene layers are determined as a function of spatial position on the device under both static and operating conditions. The analysis reveals that microscopic rotational domains in the two graphene layers establish a range of twist angles from 9.8∘ to 12.7∘. Application of current and electrostatic gating lead to strong electric fields with peak strengths of 0.75 V/μm at the rotational domain boundaries in the device. These proof‐of‐principle results demonstrate the potential of nanoARPES to link mesoscale structural variations with electronic states in operating device conditions and to disentangle such extrinsic factors from the intrinsic quasiparticle dispersion.
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Mar 2021
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[18022]
Abstract: The human immunoglobulin G (IgG) class is the most prevalent antibody in serum, with the IgG1 subclass being the most abundant. IgG1 is comprised of two Fab regions connected to a Fc region through a 15-residue hinge peptide. Two glycan chains are conserved in the Fc region in IgG, however their importance for the structure of intact IgG1 has remained unclear. Here, we subjected glycosylated and deglycosylated monoclonal human IgG1 (designated as A33) to a comparative multidisciplinary structural study of both forms. Following deglycosylation using PNGase F, analytical ultracentrifugation showed that IgG1 remained monomeric and the sedimentation coefficients s020,w of IgG1 decreased from 6.45 S by 0.16-0.27 S. This change was attributed to the reduction in mass following glycan removal. X-ray and neutron scattering revealed changes in the Guinier structural parameters after deglycosylation. While the radius of gyration RG was unchanged, the cross-sectional radius of gyration, RXS-1, increased by 0.1 nm and the commonly occurring distance peak M2 of the distance distribution curve P(r) increased by 0.4 nm. These changes revealed that the Fab-Fc separation in IgG1 was perturbed following deglycosylation. To explain these changes, atomistic scattering modelling based on Monte Carlo simulations resulted in 123,284 and 119,191 trial structures for glycosylated and deglycosylated IgG1 respectively. From these, 100 X-ray and neutron best-fit models were determined. For these, principal component analyses identified five groups of structural conformations that were different for glycosylated and deglycosylated IgG1. The Fc region in glycosylated IgG1 showed a restricted range of conformations relative to the Fab regions, while the Fc region in deglycosylated IgG1 showed a broader conformational spectrum. These more variable Fc conformations account for the loss of binding to the FcγR receptor in deglycosylated IgG1.
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Mar 2021
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Derun
Li
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Yongqi
Deng
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Abdelghani
Achab
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Indu
Bharathan
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Brett Andrew
Hopkins
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Wensheng
Yu
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Hongjun
Zhang
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Sulagna
Sanyal
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Qinglin
Pu
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Hua
Zhou
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Kun
Liu
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Jongwon
Lim
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Xavier
Fradera
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Charles A.
Lesburg
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Alfred
Lammens
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Theodore A.
Martinot
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Ryan D.
Cohen
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Amy C.
Doty
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Heidi
Ferguson
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Elliott B.
Nickbarg
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Mangeng
Cheng
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Peter
Spacciapoli
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Prasanthi
Geda
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Xuelei
Song
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Nadya
Smotrov
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Pravien
Abeywickrema
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Christine
Andrews
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Chad
Chamberlin
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Omar
Mabrouk
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Patrick
Curran
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Matthew
Richards
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Peter
Saradjian
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J. Richard
Miller
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Ian
Knemeyer
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Karin M.
Otte
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Stella
Vincent
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Nunzio
Sciammetta
,
Alexander
Pasternak
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David Jonathan
Bennett
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Yongxin
Han
Abstract: Indoleamine-2,3-dioxygenase-1 (IDO1) has emerged as an attractive target for cancer immunotherapy. An automated ligand identification system screen afforded the tetrahydroquinoline class of novel IDO1 inhibitors. Potency and pharmacokinetic (PK) were key issues with this class of compounds. Structure-based drug design and strategic incorporation of polarity enabled the rapid improvement on potency, solubility, and oxidative metabolic stability. Metabolite identification studies revealed that amide hydrolysis in the D-pocket was the key clearance mechanism for this class. Strategic survey of amide isosteres revealed that carbamates and N-pyrimidines, which maintained exquisite potencies, mitigated the amide hydrolysis issue and led to an improved rat PK profile. The lead compound 28 is a potent IDO1 inhibitor, with clean off-target profiles and the potential for quaque die dosing in humans.
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Mar 2021
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I05-ARPES
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Christopher W.
Nicholson
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Maxime
Rumo
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Aki
Pulkkinen
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Geoffroy
Kremer
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Björn
Salzmann
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Marie-Laure
Mottas
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Baptiste
Hildebrand
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Thomas
Jaouen
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Timur K.
Kim
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Saumya
Mukherjee
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Keyuan
Ma
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Matthias
Muntwiler
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Fabian O.
Von Rohr
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Cephise
Cacho
,
Claude
Monney
Diamond Proposal Number(s):
[24880]
Open Access
Abstract: Strain is ubiquitous in solid-state materials, but despite its fundamental importance and technological relevance, leveraging externally applied strain to gain control over material properties is still in its infancy. In particular, strain control over the diverse phase transitions and topological states in two-dimensional transition metal dichalcogenides remains an open challenge. Here, we exploit uniaxial strain to stabilize the long-debated structural ground state of the 2D topological semimetal IrTe2, which is hidden in unstrained samples. Combined angle-resolved photoemission spectroscopy and scanning tunneling microscopy data reveal the strain-stabilized phase has a 6 × 1 periodicity and undergoes a Lifshitz transition, granting unprecedented spectroscopic access to previously inaccessible type-II topological Dirac states that dominate the modified inter-layer hopping. Supported by density functional theory calculations, we show that strain induces an Ir to Te charge transfer resulting in strongly weakened inter-layer Te bonds and a reshaped energetic landscape favoring the 6×1 phase. Our results highlight the potential to exploit strain-engineered properties in layered materials, particularly in the context of tuning inter-layer behavior.
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Mar 2021
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Theoretical Physics
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Abstract: Nonlinear optics, and particularly second harmonic generation (SHG), is increasingly used in many modern
disciplines from material characterization in physical sciences to bioimaging in medicine and optical signal processing in information technology. We present a theoretical analysis yielding a strong estimate of the energy integrated SHG response. Compact spherical multipoles are provided for the corresponding natural and magnetic circular dichroic signals. Like symmetry requirements in time and space are traced in the amplitude for magnetic neutron scattering, which includes all axial and polar (Dirac) contributions. Our method of working in terms of,now standard, electronic multipoles and Racah algebra, with full implementation of discrete symmetries, could be of use in a variety of other probes of matter.
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Mar 2021
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I07-Surface & interface diffraction
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Diamond Proposal Number(s):
[21899]
Abstract: Organic charge transfer complexes (CTCs) with near-infrared absorption received growing interest in the past years, but the details of their photophysics, especially in thin films, remain largely unknown. We combined experimental and computational methods to thoroughly investigate and compare CTCs formed by tetracene with 2,2′-(perfluoronaphthalene-2,6-diylidene)dimalononitrile and 2,3,5,6-tetrafluoro-7,7,8,8,-tetracyanoquinodimethane, respectively. Using ultrafast transient absorption spectroscopy, the photophysics of these small bandgap CTCs was revealed, which is dominated by a sub-picosecond relaxation of the excitons back to the ground state. In equimolar blends, tetracene singlet fission is suppressed while in blends with excess of tetracene reduced lifetimes of tetracene, singlet and triplet excitons were found.
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Mar 2021
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Theoretical Physics
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Abstract: A recent polarized neutron diffraction experiment on the 5d2 rhenium double perovskite Ba2YReO6 held at a low temperature uncovered weak magnetic diffraction peaks. Data analysis inferred a significantly reduced Re dipole moment, and long-range order compatible with an antiferromagnetic, noncollinear motif. To interpret the experimental findings, we present a model wave function for Re ions derived from the crystal field potential, Coulomb interaction, and spin-orbit coupling that fully respects the symmetry of the low temperature ordered state. It is used to calculate in analytic form all multipole moments visible in neutron and resonance enhanced x-ray diffraction. A minimal model consistent with available neutron diffraction data predicts significant multipolar moments up to the hexadecapole and, in particular, a dominant charge like quadrupole moment. Calculated diffraction patterns embrace single crystal x-ray diffraction at the Re L edge, and renewed neutron diffraction, to probe the presumed underlying multipolar order.
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Mar 2021
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