I03-Macromolecular Crystallography
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Open Access
Abstract: The biosynthetic enzyme, ForT, catalyses the formation of a C-C bond between 4-amino-1H-pyrazoledicarboxylic acid and MgPRPP to produce a C-nucleoside precursor of formycin A. The transformation catalysed by ForT is of chemical interest because it is one of only a few examples in which C-C bond formation takes place via an electrophilic substitution of a small, aromatic heterocycle. In addition, ForT is capable of discriminating between the aminopyrazoledicarboxylic acid and an analogue in which the amine is replaced by a hydroxyl group; a remarkable feat given the steric and electronic similarities of the two molecules. Here we report biophysical measurements, structural biology and quantum chemical calculations that provide a detailed molecular picture of ForT-catalysed C-C bond formation and the conformational changes that are coupled to catalysis. Our findings set the scene for employing engineered ForT variants in the biocatalytic production of novel, anti-viral C-nucleoside and C-nucleotide analogues.
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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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B18-Core EXAFS
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Diamond Proposal Number(s):
[30958]
Open Access
Abstract: The heterogeneous solid–gas reactions of crystals of [Rh(L2)(propene)][BArF4] (1, L2 = tBu2PCH2CH2PtBu2) with H2 and propene, 1-butene, propyne, or 1-butyne are explored by gas-phase nuclear magnetic resonance (NMR) spectroscopy under batch conditions at 25 °C. The temporal evolution of the resulting parahydrogen-induced polarization (PHIP) effects measures catalytic flux and thus interrogates the efficiency of catalytic pairwise para-H2 transfer, speciation changes in the crystalline catalyst at the molecular level, and allows for high-quality single-scan 1H, 13C NMR gas-phase spectra for the products to be obtained, as well as 2D-measurements. Complex 1 reacts with H2 to form dimeric [Rh(L2)(H)(μ-H)]2[BArF4]2 (4), as probed using EXAFS; meanwhile, a single-crystal of 1 equilibrates NMR silent para-H2 with its NMR active ortho isomer, contemporaneously converting into 4, and 1 and 4 each convert para-H2 into ortho-H2 at different rates. Hydrogenation of propene using 1 and para-H2 results in very high initial polarization levels in propane (>85%). Strong PHIP was also detected in the hydrogenation products of 1-butene, propyne, and 1-butyne. With propyne, a competing cyclotrimerization deactivation process occurs to afford [Rh(tBu2PCH2CH2PtBu2)(1,3,4-Me3C6H3)][BArF4], while with 1-butyne, rapid isomerization of 1-butyne occurs to give a butadiene complex, which then reacts with H2 more slowly to form catalytically active 4. Surprisingly, the high PHIP hydrogenation efficiencies allow hyperpolarization effects to be seen when H2 is taken directly from a regular cylinder at 25 °C. Finally, changing the chelating phosphine to Cy2PCH2CH2PCy2 results in initial high polarization efficiencies for propene hydrogenation, but rapid quenching of the catalyst competes to form the zwitterion [Rh(Cy2PCH2CH2PCy2){η6-(CF3)2(C6H3)}BArF3].
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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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B21-High Throughput SAXS
I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Laura C.
Clark
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Kate E.
Atkin
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Fiona
Whelan
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Andrew S.
Brentnall
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Gemma
Harris
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Aisling M.
Towell
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Johan P.
Turkenburg
,
Yan
Liu
,
Ten
Feizi
,
Samuel C.
Griffiths
,
Joan A.
Geoghegan
,
Jennifer R.
Potts
Diamond Proposal Number(s):
[7864, 18598]
Open Access
Abstract: Staphylococcus aureus and Staphylococcus epidermidis are frequently associated with medical device infections that involve establishment of a bacterial biofilm on the device surface. Staphylococcal surface proteins Aap, SasG and Pls are members of the Periscope Protein class and have been implicated in biofilm formation and host colonisation; they comprise a repetitive region (“B region”) and an N-terminal host colonisation domain within the “A region”, predicted to be a lectin domain. Repetitive E-G5 domains (as found in Aap, SasG and Pls) form elongated ‘stalks’ that would vary in length with repeat number, resulting in projection of the N-terminal A domain variable distances from the bacterial cell surface. Here, we present the structures of the lectin domains within A regions of SasG, Aap and Pls and a structure of the Aap lectin domain attached to contiguous E-G5 repeats, suggesting the lectin domains will sit at the tip of the variable length rod. We demonstrate that these isolated domains (Aap, SasG) are sufficient to bind to human host desquamated nasal epithelial cells. Previously, proteolytic cleavage or a deletion within the A domain have been reported to induce biofilm formation; the structures suggest a potential link between these observations. Intriguingly, whilst the Aap, SasG and Pls lectin domains bind a metal ion, they lack the non-proline cis peptide bond thought to be key for carbohydrate binding by the lectin fold. This suggestion of non-canonical ligand binding should be a key consideration when investigating the host cell interactions of these bacterial surface proteins.
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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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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Sudarshan
Murthy
,
Maria Giulia
Nizi
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Mirko M.
Maksimainen
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Serena
Massari
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Juho
Alaviuhkola
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Barbara E.
Lippok
,
Chiara
Vagaggini
,
Sven T.
Sowa
,
Albert
Galera-Prat
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Yashwanth
Ashok
,
Harikanth
Venkannagari
,
Renata
Prunskaite-Hyyryläinen
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Elena
Dreassi
,
Bernhard
Lüscher
,
Patricia
Korn
,
Oriana
Tabarrini
,
Lari
Lehtio
Diamond Proposal Number(s):
[23346, 26794, 19951]
Open Access
Abstract: We report [1,2,4]triazolo[3,4-b]benzothiazole (TBT) as a new inhibitor scaffold, which competes with nicotinamide in the binding pocket of human poly- and mono-ADP-ribosylating enzymes. The binding mode was studied through analogues and cocrystal structures with TNKS2, PARP2, PARP14, and PARP15. Based on the substitution pattern, we were able to identify 3-amino derivatives 21 (OUL243) and 27 (OUL232) as inhibitors of mono-ARTs PARP7, PARP10, PARP11, PARP12, PARP14, and PARP15 at nM potencies, with 27 being the most potent PARP10 inhibitor described to date (IC50 of 7.8 nM) and the first PARP12 inhibitor ever reported. On the contrary, hydroxy derivative 16 (OUL245) inhibits poly-ARTs with a selectivity toward PARP2. The scaffold does not possess inherent cell toxicity, and the inhibitors can enter cells and engage with the target protein. This, together with favorable ADME properties, demonstrates the potential of TBT scaffold for future drug development efforts toward selective inhibitors against specific enzymes.
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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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I04-Macromolecular Crystallography
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Michelle H.
Nelson
,
Sara
Fritzell
,
Robert
Miller
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Doreen
Werchau
,
Danielle
Van Citters
,
Anneli
Nilsson
,
Lynda
Misher
,
Lill
Ljung
,
Robert
Bader
,
Adnan
Deronic
,
Allison G.
Chunyk
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Lena
Schultz
,
Laura A.
Varas
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Nadia
Rose
,
Maria
Håkansson
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Jane
Gross
,
Christina
Furebring
,
Peter
Pavlik
,
Anette
Sundstedt
,
Niina
Veitonmäki
,
Hilario J.
Ramos
,
Anna
Säll
,
Anna
Dahlman
,
David
Bienvenue
,
Laura
Von Schantz
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Catherine J.
Mcmahan
,
Maria
Askmyr
,
Gabriela
Hernandez-Hoyos
,
Peter
Ellmark
Diamond Proposal Number(s):
[23282]
Open Access
Abstract: 4–1BB (CD137) is an activation-induced costimulatory receptor that regulates immune responses of activated CD8 T and natural killer cells, by enhancing proliferation, survival, cytolytic activity, and IFNγ production. The ability to induce potent antitumor activity by stimulating 4–1BB on tumor-specific cytotoxic T cells makes 4–1BB an attractive target for designing novel immuno-oncology therapeutics. To minimize systemic immune toxicities and enhance activity at the tumor site, we have developed a novel bispecific antibody that stimulates 4–1BB function when co-engaged with the tumor-associated antigen 5T4. ALG.APV-527 was built on the basis of the ADAPTIR bispecific platform with optimized binding domains to 4–1BB and 5T4 originating from the ALLIGATOR-GOLD human single-chain variable fragment library. The epitope of ALG.APV-527 was determined to be located at domain 1 and 2 on 4–1BB using X-ray crystallography. As shown in reporter and primary cell assays in vitro, ALG.APV-527 triggers dose-dependent 4–1BB activity mediated only by 5T4 crosslinking. In vivo, ALG.APV-527 demonstrates robust antitumor responses, by inhibiting growth of established tumors expressing human 5T4 followed by a long-lasting memory immune response. ALG.APV-527 has an antibody-like half-life in cynomolgus macaques and was well tolerated at 50.5 mg/kg. ALG.APV-527 is uniquely designed for 5T4-conditional 4–1BB–mediated antitumor activity with potential to minimize systemic immune activation and hepatotoxicity while providing efficacious tumor-specific responses in a range of 5T4-expressing tumor indications as shown by robust activity in preclinical in vitro and in vivo models. On the basis of the combined preclinical dataset, ALG.APV-527 has potential as a promising anticancer therapeutic for the treatment of 5T4-expressing tumors.
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Jan 2023
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Krios I-Titan Krios I at Diamond
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Friederike
Leesch
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Laura
Lorenzo-Orts
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Carina
Pribitzer
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Irina
Grishkovskaya
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Josef
Roehsner
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Anastasia
Chugunova
,
Manuel
Matzinger
,
Elisabeth
Roitinger
,
Katarina
Belačić
,
Susanne
Kandolf
,
Tzi-Yang
Lin
,
Karl
Mechtler
,
Anton
Meinhart
,
David
Haselbach
,
Andrea
Pauli
Diamond Proposal Number(s):
[2018127]
Abstract: Ribosomes are produced in large quantities during oogenesis and are stored in the egg. However, the egg and early embryo are translationally repressed1,2,3,4. Here, using mass spectrometry and cryo-electron microscopy analyses of ribosomes isolated from zebrafish (Danio rerio) and Xenopus laevis eggs and embryos, we provide molecular evidence that ribosomes transition from a dormant state to an active state during the first hours of embryogenesis. Dormant ribosomes are associated with four conserved factors that form two modules, consisting of Habp4–eEF2 and death associated protein 1b (Dap1b) or Dap in complex with eIF5a. Both modules occupy functionally important sites and act together to stabilize ribosomes and repress translation. Dap1b (also known as Dapl1 in mammals) is a newly discovered translational inhibitor that stably inserts into the polypeptide exit tunnel. Addition of recombinant zebrafish Dap1b protein is sufficient to block translation and reconstitute the dormant egg ribosome state in a mammalian translation extract in vitro. Thus, a developmentally programmed, conserved ribosome state has a key role in ribosome storage and translational repression in the egg.
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Jan 2023
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