I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Marcin J.
Suskiewicz
,
Florian
Zobel
,
Tom E. H.
Ogden
,
Pietro
Fontana
,
Antonio
Ariza
,
Ji-chun
Yang
,
Kang
Zhu
,
Lily
Bracken
,
William J.
Hawthorne
,
Dragana
Ahel
,
David
Neuhaus
,
Ivan
Ahel
Diamond Proposal Number(s):
[9306, 18069]
Abstract: The anti-cancer drug target poly(ADP-ribose) polymerase 1 (PARP1) and its close homologue, PARP2, are early responders to DNA damage in human cells1,2. Upon binding to genomic lesions, these enzymes utilise NAD+ to modify a plethora of proteins with mono- and poly(ADP-ribose) signals that are important for subsequent chromatin decompaction and repair factor recruitment3,4. These post-translational modification events are predominantly serine-linked and require HPF1, an accessory factor that is specific for the DNA damage response and switches the amino-acid specificity of PARP1/2 from aspartate/glutamate to serine residues5–10. Here, we report a co-structure of HPF1 bound to the catalytic domain of PARP2 that, in combination with NMR and biochemical data, reveals a composite active site formed by residues from both PARP1/2 and HPF1. We further show that the assembly of this new catalytic centre is essential for DNA damage-induced protein ADP-ribosylation in human cells. In response to DNA damage and NAD+ binding site occupancy, the HPF1–PARP1/2 interaction is enhanced via allosteric networks operating within PARP1/2, providing an additional level of regulation in DNA repair induction. As HPF1 forms a joint active site with PARP1/2, our data implicate HPF1 as an important determinant of the response to clinical PARP inhibitors.
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Feb 2020
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I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[14891]
Abstract: Serine racemase (SR) is a pyridoxal 5′-phosphate (PLP)-containing enzyme that converts L-serine to D-serine, an endogenous co-agonist for the N-methyl-D-aspartate receptor (NMDAR) subtype of glutamate ion channels. SR regulates D-serine levels by the reversible racemization of L-serine to D-serine, as well as the catabolism of serine by α,β-elimination to produce pyruvate. The modulation of SR activity is therefore an attractive therapeutic approach to disorders associated with abnormal glutamatergic signalling since it allows an indirect modulation of NMDAR function. In the present study, a 1.89 Å resolution crystal structure of the human SR holoenzyme (including the PLP cofactor) with four subunits in the asymmetric unit is described. Comparison of this new structure with the crystal structure of human SR with malonate (PDB entry 3l6b) shows an interdomain cleft that is open in the holo structure but which disappears when the inhibitor malonate binds and is enclosed. This is owing to a shift of the small domain (residues 78–155) in human SR similar to that previously described for the rat enzyme. This domain movement is accompanied by changes within the twist of the central four-stranded β-sheet of the small domain, including changes in the φ–ψ angles of all three residues in the C-terminal β-strand (residues 149–151). In the malonate-bound structure, Ser84 (a catalytic residue) points its side chain at the malonate and is preceded by a six-residue β-strand (residues 78–83), but in the holoenzyme the β-strand is only four residues (78–81) and His82 has φ–ψ values in the α-helical region of the Ramachandran plot. These data therefore represent a crystallographic platform that enables the structure-guided design of small-molecule modulators for this important but to date undrugged target.
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Feb 2020
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I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[19844]
Open Access
Abstract: Cytisine, a natural product with high affinity for clinically relevant nicotinic acetylcholine receptors (nAChRs), is used as a smoking-cessation agent. The compound displays an excellent clinical profile and hence there is an interest in derivatives that may be further improved or find use in the treatment of other conditions. Here, the binding of a cytisine derivative modified by the addition of a 3-(hydroxypropyl) moiety (ligand 4) to Aplysia californica acetylcholine-binding protein (AcAChBP), a surrogate for nAChR orthosteric binding sites, was investigated. Isothermal titration calorimetry revealed that the favorable binding of cytisine and its derivative to AcAChBP is driven by the enthalpic contribution, which dominates an unfavorable entropic component. Although ligand 4 had a less unfavorable entropic contribution compared with cytisine, the affinity for AcAChBP was significantly diminished owing to the magnitude of the reduction in the enthalpic component. The high-resolution crystal structure of the AcAChBP–4 complex indicated close similarities in the protein–ligand interactions involving the parts of 4 common to cytisine. The point of difference, the 3-(hydroxypropyl) substituent, appears to influence the conformation of the Met133 side chain and helps to form an ordered solvent structure at the edge of the orthosteric binding site.
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Feb 2020
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I03-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[20113]
Open Access
Abstract: The human gut microbiota plays a central role not only in regulating the metabolism of nutrients but also promoting immune homeostasis, immune responses and protection against pathogen colonization. The genome of the Gram-negative symbiont Bacteroides thetaiotaomicron, a dominant member of the human intestinal microbiota, encodes polysaccharide utilization loci PULs, the apparatus required to orchestrate the degradation of a specific glycan. EndoBT-3987 is a key endo-β-N-acetylglucosaminidase (ENGase) that initiates the degradation/processing of mammalian high-mannose-type (HM-type) N-glycans in the intestine. Here, we provide structural snapshots of EndoBT-3987, including the unliganded form, the EndoBT-3987-Man9GlcNAc2Asn substrate complex, and two EndoBT-3987-Man9GlcNAc and EndoBT-3987-Man5GlcNAc product complexes. In combination with alanine scanning mutagenesis and activity measurements we unveil the molecular mechanism of HM-type recognition and specificity for EndoBT-3987 and an important group of the GH18 ENGases, including EndoH, an enzyme extensively used in biotechnology, and for which the mechanism of substrate recognition was largely unknown.
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Feb 2020
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B18-Core EXAFS
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Diamond Proposal Number(s):
[14239]
Open Access
Abstract: A synthesis method for the preparation of mixed manganese–ruthenium oxides is presented along with a detailed characterisation of the solids produced. The use of 1 M aqueous sulfuric acid mediates the redox reaction between KRuO4, KMnO4 and Mn2+ to form ternary oxides. At reaction temperature of 100 °C the products are mixtures of α-MnO2 (hollandite-type) and β-MnO2 (rutile-type), with some evidence of Ru incorporation in each from their expanded unit cell volumes. At reaction temperature of 200 °C solid-solutions β-Mn1−xRuxO2 are formed and materials with x ≤ 0.6 have been studied. The amount of Ru included in the oxide is greater than expected from the ratio of metals used in the synthesis, as determined by elemental analysis, implying that some Mn remains unreacted in solution. Powder X-ray diffraction (XRD) shows that while the unit cell volume expands in a linear manner, following Vegard's law, the tetragonal lattice parameters, and the a/c ratio, do not follow the extrapolated trends: this anisotropic behaviour is consistent with the different local coordination of the metals in the end members. Powder XRD patterns show increased peak broadening with increasing ruthenium content, which is corroborated by electron microscopy that shows nanocrystalline material. X-ray absorption near-edge spectra show that the average oxidation state of Mn in the solid solutions is reduced below +4 while that of Ru is increased above +4, suggesting some redistribution of charge. Analysis of the extended X-ray absorption fine structure provides complementary local structural information, confirming the formation of a solid solution, while X-ray photoelectron spectroscopy shows that the surface oxidation states of both Ru and Mn are on average lower than +4, suggesting a disordered surface layer may be present in the materials.
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Feb 2020
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Krios II-Titan Krios II at Diamond
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Diamond Proposal Number(s):
[16410]
Open Access
Abstract: Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP:Met-tRNAiMet. Here, we determine the cryo-EM structure of a 30S:mRNA:aIF1A:aIF2:GTP:Met-tRNAiMet complex from Pyrococcus abyssi at 3.2 Å resolution. It highlights archaeal features in ribosomal proteins and rRNA modifications. We find an aS21 protein, at the location of eS21 in eukaryotic ribosomes. Moreover, we identify an N-terminal extension of archaeal eL41 contacting the P site. We characterize 34 N4-acetylcytidines distributed throughout 16S rRNA, likely contributing to hyperthermostability. Without aIF1, the 30S head is stabilized and initiator tRNA is tightly bound to the P site. A network of interactions involving tRNA, mRNA, rRNA modified nucleotides and C-terminal tails of uS9, uS13 and uS19 is observed. Universal features and domain-specific idiosyncrasies of translation initiation are discussed in light of ribosomal structures from representatives of each domain of life.
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Feb 2020
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I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[20141]
Abstract: Tetrahedrite, Cu12Sb4S13, is an abundant mineral with excellent thermoelectric properties owing to its low thermal conductivity. The electronic and structural origin of the intriguing physical properties of tetrahedrite, including its metal‐to‐semiconductor transition (MST), remains largely unknown. This work presents the first determination of the low‐temperature structure of tetrahedrite that accounts for its unique properties. Contrary to prior conjectures, the results show that the trigonal–planar copper cations remain in planar coordination below the MST. The atomic displacement parameters of the trigonal–planar copper cations, which have been linked to low thermal conductivity, increase by 200% above the MST. The phase transition is a consequence of the orbital degeneracy of the highest occupied 3d cluster orbitals of the copper clusters found in the cubic phase. This study reveals that a Jahn–Teller electronic instability leads to the formation of “molecular‐like” Cu57+ clusters and suppresses copper rattling vibrations due to the strengthening of direct copper–copper interactions. First principles calculations demonstrate that the structural phase transition opens a small band gap in the electronic density of states and eliminates the unstable phonon modes. These results provide insights on the interplay between phonon transport, electronic properties, and crystal structure in mixed‐valence compounds.
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Feb 2020
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Krios IV-Titan Krios IV at Diamond
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Alister
Burt
,
C. Keith
Cassidy
,
Peter
Ames
,
Maria
Bacia-verloop
,
Megghane
Baulard
,
Karine
Huard
,
Zaida
Luthey-schulten
,
Ambroise
Desfosses
,
Phillip J.
Stansfeld
,
William
Margolin
,
John S.
Parkinson
,
Irina
Gutsche
Diamond Proposal Number(s):
[18112]
Open Access
Abstract: Motile bacteria sense chemical gradients with transmembrane receptors organised in supramolecular signalling arrays. Understanding stimulus detection and transmission at the molecular level requires precise structural characterisation of the array building block known as a core signalling unit. Here we introduce an Escherichia coli strain that forms small minicells possessing extended and highly ordered chemosensory arrays. We use cryo-electron tomography and subtomogram averaging to provide a three-dimensional map of a complete core signalling unit, with visible densities corresponding to the HAMP and periplasmic domains. This map, combined with previously determined high resolution structures and molecular dynamics simulations, yields a molecular model of the transmembrane core signalling unit and enables spatial localisation of its individual domains. Our work thus offers a solid structural basis for the interpretation of a wide range of existing data and the design of further experiments to elucidate signalling mechanisms within the core signalling unit and larger array.
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Feb 2020
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I11-High Resolution Powder Diffraction
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Abstract: A series of Mn5Co1Ox catalysts calcined at different temperatures in the range of 400–800 °C were synthesized by coprecipitation of manganese and cobalt nitrates and tested in the oxidation of CO. The specific surface area, structure, and chemistry of the catalysts were studied. In addition, the reduction of the catalysts by hydrogen was studied using in situ X-ray diffraction and temperature-programmed reduction techniques. It was found that the low-temperature catalyst calcined at 400 °C displays the best catalytic activity, which is attributed to its high surface area, low-temperature reducibility, and a high surface content of Mn4+. The formation of highly disperse and active CoMnO3 species and excess oxygen in a Mn3−xCoxO4+δ spinel leads to excellent low-temperature redox properties. The elevated temperature calcination results in a decline in the catalytic activity in CO oxidation due to formation of a well crystalline Mn3−xCoxO4 spinel, a decrease in the surface area and reducibility.
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Feb 2020
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B21-High Throughput SAXS
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Abstract: Polymerisation-induced self-assembly (PISA) has become widely recognised as a versatile and efficient strategy to prepare well-defined diblock copolymer nanoparticles in a range of solvents. In this article, we report the synthesis of anionic, sterically-stabilised, sulfonate-functional diblock copolymer nanoparticles via PISA using a reversible addition–fragmentation chain-transfer (RAFT) polymerisation formulation. Anionic poly(potassium 3-sulfopropyl methacrylate) (PKSPMA) macromolecular chain-transfer agents (macro-CTAs) were synthesised via RAFT solution polymerisation followed by chain-extension with benzyl methacrylate (BzMA) in alcohol/water mixtures to form PKSPMA–PBzMA nanoparticles. The influence of solvent quality on the formation of these nanoparticles was investigated by judiciously changing the alcohol/water ratio, the alcohol co-solvent (ethanol or methanol) and relative copolymer composition. The resulting diblock copolymer nanoparticles were analysed by dynamic light scattering (DLS), transmission electron microscopy (TEM), small-angle X-ray scattering (SAXS), and aqueous electrophoresis. The results demonstrated that nanoparticles with controllable diameters for a fixed copolymer composition can be prepared by altering the co-solvent composition. More specifically, when using different ratios of ethanol/water or methanol/water, the nanoparticle diameter can be tuned from approximately 20 to 200 nm with fixed copolymer composition. This indicates that the solvency of both the stabiliser and core-forming block has a marked impact on both the aggregation of polymer chains during self-assembly and the resulting nanoparticles. Additionally, these nanoparticles remain colloidally stable and highly anionic over a wide pH range from 4 to 10, as judged by aqueous electrophoresis.
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Feb 2020
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