I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Andrej Emanuel
Cotman
,
Martina
Durcik
,
Davide
Benedetto Tiz
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Federica
Fulgheri
,
Daniela
Secci
,
Maša
Sterle
,
Štefan
Možina
,
Žiga
Skok
,
Nace
Zidar
,
Anamarija
Zega
,
Janez
Ilaš
,
Lucija
Peterlin Mašič
,
Tihomir
Tomašič
,
Diarmaid
Hughes
,
Douglas L.
Huseby
,
Sha
Cao
,
Linnéa
Garoff
,
Talía
Berruga Fernández
,
Paraskevi
Giachou
,
Lisa
Crone
,
Ivailo
Simoff
,
Richard
Svensson
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Bryndis
Birnir
,
Sergiy V.
Korol
,
Zhe
Jin
,
Francisca
Vicente
,
Maria C.
Ramos
,
Mercedes
De La Cruz
,
Björn
Glinghammar
,
Lena
Lenhammar
,
Sara R.
Henderson
,
Julia E. A.
Mundy
,
Anthony
Maxwell
,
Claren E. M.
Stevenson
,
David M.
Lawson
,
Guido V.
Janssen
,
Geert Jan
Sterk
,
Danijel
Kikelj
Diamond Proposal Number(s):
[18565, 25108]
Open Access
Abstract: We have developed compounds with a promising activity against Acinetobacter baumannii and Pseudomonas aeruginosa, which are both on the WHO priority list of antibiotic-resistant bacteria. Starting from DNA gyrase inhibitor 1, we identified compound 27, featuring a 10-fold improved aqueous solubility, a 10-fold improved inhibition of topoisomerase IV from A. baumannii and P. aeruginosa, a 10-fold decreased inhibition of human topoisomerase IIα, and no cross-resistance to novobiocin. Cocrystal structures of 1 in complex with Escherichia coli GyrB24 and (S)-27 in complex with A. baumannii GyrB23 and P. aeruginosa GyrB24 revealed their binding to the ATP-binding pocket of the GyrB subunit. In further optimization steps, solubility, plasma free fraction, and other ADME properties of 27 were improved by fine-tuning of lipophilicity. In particular, analogs of 27 with retained anti-Gram-negative activity and improved plasma free fraction were identified. The series was found to be nongenotoxic, nonmutagenic, devoid of mitochondrial toxicity, and possessed no ion channel liabilities.
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Jan 2023
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Open Access
Abstract: Newcastle disease virus (NDV) is an oncolytic agent against various types of mammalian cancers. As with all cancer therapies, the development of cancer resistance, both innate and acquired, is becoming a challenge. In this study, we investigated persistently NDV-infected Caco-2 colon cancer cells, designated as virus-resistant (VR) Caco-2 cells, which were then able to resist NDV-mediated oncolysis. We applied single-cell Raman spectroscopy, combined with deuterium isotope probing (Raman-DIP) techniques, to investigate the metabolic adaptations and dynamics in VR Caco-2 cells. A linear discriminant analysis (LDA) model demonstrated excellent performance in differentiating VR Caco-2 from Caco-2 cells at single-cell level. By comparing the metabolic profiles in a time-resolved manner, the de novo synthesis of proteins and lipids was found upregulated, along with decreased DNA synthesis in VR Caco-2. The results suggest that VR Caco-2 cells might reprogram their metabolism and divert energy from proliferation to protein synthesis and lipidic modulation. The ability to identify and characterise single resistant cells among a population of cancer cells would help develop a deeper understanding of the resistance mechanisms and better tactics for developing effective cancer treatment.
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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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I04-Macromolecular Crystallography
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Amelia K.
Gilio
,
Thomas W.
Thorpe
,
Alex
Heyam
,
Mark R.
Petchey
,
Balázs
Pogrányi
,
Scott P.
France
,
Roger M.
Howard
,
Michael J.
Karmilowicz
,
Russell
Lewis
,
Nicholas
Turner
,
Gideon
Grogan
Diamond Proposal Number(s):
[18598]
Open Access
Abstract: Imine reductases (IREDs) catalyze the asymmetric reduction of cyclic imines, but also in some cases the coupling of ketones and amines to form secondary amine products in an enzyme-catalyzed reductive amination (RedAm) reaction. Enzymatic RedAm reactions have typically used small hydrophobic amines, but many interesting pharmaceutical targets require that larger amines be used in these coupling reactions. Following the identification of IR77 from Ensifer adhaerens as a promising biocatalyst for the reductive amination of cyclohexanone with pyrrolidine, we have characterized the ability of this enzyme to catalyze couplings with larger bicyclic amines such as isoindoline and octahydrocyclopenta(c)pyrrole. By comparing the activity of IR77 with reductions using sodium cyanoborohydride in water, it was shown that, while the coupling of cyclohexanone and pyrrolidine involved at least some element of reductive amination, the amination with the larger amines likely occurred ex situ, with the imine recruited from solution for enzyme reduction. The structure of IR77 was determined, and using this as a basis, structure-guided mutagenesis, coupled with point mutations selecting improving amino acid sites suggested by other groups, permitted the identification of a mutant A208N with improved activity for amine product formation. Improvements in conversion were attributed to greater enzyme stability as revealed by X-ray crystallography and nano differential scanning fluorimetry. The mutant IR77-A208N was applied to the preparative scale amination of cyclohexanone at 50 mM concentration, with 1.2 equiv of three larger amines, in isolated yields of up to 93%.
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Jan 2023
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I22-Small angle scattering & Diffraction
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Miguel
Paez-Perez
,
Aurimas
Vyšniauskas
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Ismael
López-Duarte
,
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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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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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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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[21497]
Abstract: We derive design principles for the assembly of rectangular tetramines into Zn8L6 pseudo-cubic coordination cages. Because of the rectangular, as opposed to square, geometry of the ligand panels, and the possibility of either Δ or Λ handedness of each metal center at the eight corners of the pseudo-cube, many different cage diastereomers are possible. Each of the six tetra-aniline subcomponents investigated in this work assembled with zinc(II) and 2-formylpyridine in acetonitrile into a single Zn8L6 pseudo-cube diastereomer, however. Each product corresponded to one of four diastereomeric configurations, with T, Th, S6 or D3 symmetry. The preferred diastereomer for a given tetra-aniline subcomponent was shown to be dependent on its aspect ratio and conformational flexibility. Analysis of computationally modeled individual faces or whole pseudo-cubes provided insight as to why the observed diastereomers were favored.
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Jan 2023
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I11-High Resolution Powder Diffraction
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Bixian
Ying
,
Jack R.
Fitzpatrick
,
Zhenjie
Teng
,
Tianxiang
Chen
,
Tsz Woon Benedict
Lo
,
Vassilios
Siozios
,
Claire A.
Murray
,
Helen E. A.
Brand
,
Sarah
Day
,
Chiu C.
Tang
,
Robert S.
Weatherup
,
Peter
Nagel
,
Stefan
Schuppler
,
Martin
Winter
,
Karin
Kleiner
,
Michael
Merz
Diamond Proposal Number(s):
[19772]
Open Access
Abstract: The syntheses of Ni-poor (NCM111, LiNi1/3Co1/3Mn1/3O2) and Ni-rich (NCM811 LiNi0.8Co0.1Mn0.1O2) lithium transition-metal oxides (space group R3̅m) from hydroxide precursors (Ni1/3Co1/3Mn1/3(OH)2, Ni0.8Co0.1Mn0.1(OH)2) are investigated using in situ synchrotron powder diffraction and near-edge X-ray absorption fine structure spectroscopy. The development of the layered structure of these two cathode materials proceeds via two utterly different reaction mechanisms. While the synthesis of NCM811 involves a rock salt-type intermediate phase, NCM111 reveals a layered structure throughout the entire synthesis. Moreover, the necessity and the impact of a preannealing step and a high-temperature holding step are discussed.
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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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Diamond Proposal Number(s):
[17221, 23620]
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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