DL-SAXS-Offline SAXS and Sample Environment Development
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Diamond Proposal Number(s):
[29797]
Open Access
Abstract: In the present study, gels based on xanthan gum and poloxamer 407 have been developed and characterized in order to convey natural antioxidant molecules included in niosomes. Specifically, the studies were conducted to evaluate how the vesicular systems affect the release of the active ingredient and which formulation is most suitable for cutaneous application. Niosomes, composed of Span 20 or Tween 20, were produced through the direct hydration method, and therefore, borate buffer or a micellar solution of poloxamer 188 was used as the aqueous phase. The niosomes were firstly characterized in terms of morphology, dimensional and encapsulation stability. Afterwards, gels based on poloxamer 407 or xanthan gum were compared in terms of spreadability and adhesiveness. It was found to have greater spreadability for gels based on poloxamer 407 and 100% adhesiveness for those based on xanthan gum. The in vitro diffusion of drugs studied using Franz cells associated with membranes of mixed cellulose esters showed that the use of a poloxamer micellar hydration phase determined a lower release as well as the use of Span 20. The thickened niosomes ensured controlled diffusion of the antioxidant molecules. Lastly, the in vivo irritation test confirmed the safeness of niosomal gels after cutaneous application.
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Jan 2023
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I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[24447]
Open Access
Abstract: Adenosine tripolyphosphate (ATP) is a small polyvalent anion that has recently been shown to interact with proteins and have a major impact on assembly processes involved in biomolecular condensate formation and protein aggregation. However, the nature of non-specific protein–ATP interactions and their effects on protein solubility are largely unknown. Here, the binding of ATP to the globular model protein is characterized in detail using X-ray crystallography and nuclear magnetic resonance (NMR). Using NMR, we identified six ATP binding sites on the lysozyme surface, with one known high-affinity nucleic acid binding site and five non-specific previously unknown sites with millimolar affinities that also bind tripolyphosphate (TPP). ATP binding occurs primarily through the polyphosphate moiety, which was confirmed by the X-ray structure of the lysozyme–ATP complex. Importantly, ATP binds preferentially to arginine over lysine in non-specific binding sites. ATP and TPP have similar effects on solution-phase protein–protein interactions. At low salt concentrations, ion binding to lysozyme causes precipitation, while at higher salt concentrations, redissolution occurs. The addition of an equimolar concentration of magnesium to ATP does not alter ATP binding affinities but prevents lysozyme precipitation. These findings have important implications for both protein crystallization and cell biology. Crystallization occurs readily in ATP solutions outside the well-established crystallization window. In the context of cell biology, the findings suggest that ATP binds non-specifically to folded proteins in physiological conditions. Based on the nature of the binding sites identified by NMR, we propose several mechanisms for how ATP binding can prevent the aggregation of natively folded proteins.
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Jan 2023
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B21-High Throughput SAXS
I03-Macromolecular Crystallography
I23-Long wavelength MX
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Eugene
Kuatsjah
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Michael
Zahn
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Xiangyang
Chen
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Ryo
Kato
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Daniel J.
Hinchen
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Mikhail O.
Konev
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Rui
Katahira
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Christian
Orr
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Armin
Wagner
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Yike
Zou
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Stefan J.
Haugen
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Kelsey J.
Ramirez
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Joshua K.
Michener
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Andrew R.
Pickford
,
Naofumi
Kamimura
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Eiji
Masai
,
Kendall N.
Houk
,
John
Mcgeehan
,
Gregg T.
Beckham
Diamond Proposal Number(s):
[23269]
Open Access
Abstract: Lignin valorization is being intensely pursued via tandem catalytic depolymerization and biological funneling to produce single products. In many lignin depolymerization processes, aromatic dimers and oligomers linked by carbon–carbon bonds remain intact, necessitating the development of enzymes capable of cleaving these compounds to monomers. Recently, the catabolism of erythro-1,2-diguaiacylpropane-1,3-diol (erythro-DGPD), a ring-opened lignin-derived β-1 dimer, was reported in Novosphingobium aromaticivorans. The first enzyme in this pathway, LdpA (formerly LsdE), is a member of the nuclear transport factor 2 (NTF-2)-like structural superfamily that converts erythro-DGPD to lignostilbene through a heretofore unknown mechanism. In this study, we performed biochemical, structural, and mechanistic characterization of the N. aromaticivorans LdpA and another homolog identified in Sphingobium sp. SYK-6, for which activity was confirmed in vivo. For both enzymes, we first demonstrated that formaldehyde is the C1 reaction product, and we further demonstrated that both enantiomers of erythro-DGPD were transformed simultaneously, suggesting that LdpA, while diastereomerically specific, lacks enantioselectivity. We also show that LdpA is subject to a severe competitive product inhibition by lignostilbene. Three-dimensional structures of LdpA were determined using X-ray crystallography, including substrate-bound complexes, revealing several residues that were shown to be catalytically essential. We used density functional theory to validate a proposed mechanism that proceeds via dehydroxylation and formation of a quinone methide intermediate that serves as an electron sink for the ensuing deformylation. Overall, this study expands the range of chemistry catalyzed by the NTF-2-like protein family to a prevalent lignin dimer through a cofactorless deformylation reaction.
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Jan 2023
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I19-Small Molecule Single Crystal Diffraction
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Abstract: The reactions of a terminal aluminium imide with a range of oxygen-containing substrates have been probed with a view to developing its use as a novel main group transfer agent for the [NR]2- fragment. We demonstrate transfer of the imide moiety to [N2], [CO] and [Ph(H)C] units driven thermodynamically by Al-O bond formation. N2O reacts rapidly to generate the organoazide DippN3 (Dipp = 2,6- iPr2C6H3), while CO2 (under dilute reaction conditions) yields the corresponding isocyanate, DippNCO. Mechanistic studies, using both experimental and quantum chemical techniques, identify a carbamate complex K2[(NON)Al{κ2-(N,O)-N(Dipp)CO2}]2 (formed via [2+2] cycloaddition) as an intermediate in the formation of DippNCO, and also in an alternative reaction leading to the generation of the amino-dicarboxylate complex K2[(NON)Al{κ2(O,O')-(O2C)2N(Dipp)}] (via the take-up of a second equivalent of CO2). In the case of benzaldehyde, a similar [2+2] cycloaddition process generates the metallacyclic hemi-aminal complex, Kn[(NON)Al{κ2-(N,O)-(N(Dipp)C(Ph)(H)O}]n. Extrusion of the imine, PhC(H)NDipp, via cyclo-reversion is disfavoured thermally, due to the high energy of the putative aluminium oxide co-product, K2[(NON)Al(O)]2. However, addition of CO2 allows the imine to be released, driven by the formation of the thermodynamically more stable aluminium carbonate co-product, K2[(NON)Al(κ2-(O,O')-CO3)]2.
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Jan 2023
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I22-Small angle scattering & Diffraction
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Miguel
Paez-Perez
,
Aurimas
Vyšniauskas
,
Ismael
López-Duarte
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Eulalie J.
Lafarge
,
Raquel
López-Ríos De Castro
,
Carlos M.
Marques
,
André P.
Schroder
,
Pierre
Muller
,
Christian D.
Lorenz
,
Nicholas J.
Brooks
,
Marina K.
Kuimova
Open Access
Abstract: Lipid peroxidation is a process which is key in cell signaling and disease, it is exploited in cancer therapy in the form of photodynamic therapy. The appearance of hydrophilic moieties within the bilayer’s hydrocarbon core will dramatically alter the structure and mechanical behavior of membranes. Here, we combine viscosity sensitive fluorophores, advanced microscopy, and X-ray diffraction and molecular simulations to directly and quantitatively measure the bilayer’s structural and viscoelastic properties, and correlate these with atomistic molecular modelling. Our results indicate an increase in microviscosity and a decrease in the bending rigidity upon peroxidation of the membranes, contrary to the trend observed with non-oxidized lipids. Fluorescence lifetime imaging microscopy and MD simulations give evidence for the presence of membrane regions of different local order in the oxidized membranes. We hypothesize that oxidation promotes stronger lipid-lipid interactions, which lead to an increase in the lateral heterogeneity within the bilayer and the creation of lipid clusters of higher order.
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Jan 2023
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Abstract: Crystal engineering has, so far, exclusively focused on the development of advanced materials based on small organic molecules. We demonstrate how the cocrystallization of a polymer significantly enhances its thermal stability without compromising its mechanical flexibility, while isomorphous replacement of one of the cocrystal components enables the formation of solid solutions with melting points that can be readily fine-tuned over a practically wide temperature range. The results of this study credibly extend the scope of crystal engineering and cocrystallization from small molecules to polymers.
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Jan 2023
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I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[28394]
Open Access
Abstract: Stl, the master repressor of the Staphylococcus aureus pathogenicity islands (SaPIs), targets phage-encoded proteins to derepress and synchronize the SaPI and the helper phage life cycles. To activate their cycle, some SaPI Stls target both phage dimeric and phage trimeric dUTPases (Duts) as antirepressors, which are structurally unrelated proteins that perform identical functions for the phage. This intimate link between the SaPI’s repressor and the phage inducer has imposed an evolutionary optimization of Stl that allows the interaction with Duts from unrelated organisms. In this work, we structurally characterize this sophisticated mechanism of specialization by solving the structure of the prototypical SaPIbov1 Stl in complex with a prokaryotic and a eukaryotic trimeric Dut. The heterocomplexes with Mycobacterium tuberculosis and Homo sapiens Duts show the molecular strategy of Stl to target trimeric Duts from different kingdoms. Our structural results confirm the participation of the five catalytic motifs of trimeric Duts in Stl binding, including the C-terminal flexible motif V that increases the affinity by embracing Stl. In silico and in vitro analyses with a monomeric Dut support the capacity of Stl to recognize this third family of Duts, confirming this protein as a universal Dut inhibitor in the different kingdoms of life.
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Jan 2023
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[19880]
Abstract: Rieske monooxygenases undertake complex catalysis integral to marine, terrestrial and human gut-ecosystems. Group-I to IV Rieske monooxygenases accept aromatic substrates and have well characterised catalytic mechanisms. Nascent to our understanding are Group-V members catalysing the oxidation/breakdown of quaternary ammonium substrates. Phylogenetic analysis of Group V highlights a cysteine residue-pair adjacent to the mononuclear Fe active site with no established role. Following our elucidation of the carnitine monooxygenase CntA structure, we probed the function of the cysteine pair Cys206/Cys209. Utilising biochemical and biophysical techniques, we found the cysteine residues do not play a structural role nor influence the electron transfer pathway, but rather are used in a non-stoichiometric role to ensure the catalytic iron centre remains in an Fe(II) state.
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Jan 2023
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Open Access
Abstract: Type 4 filaments (T4F)—of which type 4 pili (T4P) are the archetype—are a superfamily of nanomachines nearly ubiquitous in prokaryotes. T4F are polymers of one major pilin, which also contain minor pilins whose roles are often poorly understood. Here, we complete the structure/function analysis of the full set of T4P pilins in the opportunistic bacterial pathogen Streptococcus sanguinis. We determined the structure of the minor pilin PilA, which is unexpectedly similar to one of the subunits of a tip-located complex of four minor pilins, widely conserved in T4F. We found that PilA interacts and dramatically stabilizes the minor pilin PilC. We determined the structure of PilC, showing that it is a modular pilin with a lectin module binding a subset of glycans prevalent in the human glycome, the host of S. sanguinis. Altogether, our findings support a model whereby the minor pilins in S. sanguinis T4P form a tip-located complex promoting adhesion to various host receptors. This has general implications for T4F.
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Jan 2023
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B07-B-Versatile Soft X-ray beamline: High Throughput
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Diamond Proposal Number(s):
[31119]
Open Access
Abstract: Tin-containing layers with different degrees of oxidation are uniformly distributed along the length of silicon nanowires formed by a top-down method by applying metalorganic chemical vapor deposition. The electronic and atomic structure of the obtained layers is investigated by applying nondestructive surface-sensitive X-ray absorption near edge spectroscopy using synchrotron radiation. The results demonstrated, for the first time, a distribution effect of the tin-containing phases in the nanostructured silicon matrix compared to the results obtained for planar structures at the same deposition temperatures. The amount and distribution of tin-containing phases can be effectively varied and controlled by adjusting the geometric parameters (pore diameter and length) of the initial matrix of nanostructured silicon. Due to the occurrence of intense interactions between precursor molecules and decomposition by-products in the nanocapillary, as a consequence of random thermal motion of molecules in the nanocapillary, which leads to additional kinetic energy and formation of reducing agents, resulting in effective reduction of tin-based compounds to a metallic tin state for molecules with the highest penetration depth in the nanostructured silicon matrix. This effect will enable clear control of the phase distributions of functional materials in 3D matrices for a wide range of applications.
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Jan 2023
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