I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Tzu-lan
Yeh
,
Thomas m.
Leissing
,
Martine I.
Abboud
,
Cyrille C.
Thinnes
,
Onur
Atasoylu
,
James P.
Holt-martyn
,
Dong
Zhang
,
Anthony
Tumber
,
Kerstin
Lippl
,
Christopher T.
Lohans
,
Ivanhoe K. H.
Leung
,
Helen
Morcrette
,
Ian J.
Clifton
,
Timothy D. W.
Claridge
,
Akane
Kawamura
,
Emily
Flashman
,
Xin
Lu
,
Peter J.
Ratcliffe
,
Rasheduzzaman
Chowdhury
,
Christopher W.
Pugh
,
Christopher J.
Schofield
Diamond Proposal Number(s):
[12346, 9306]
Open Access
Abstract: Inhibition of the human 2-oxoglutarate (2OG) dependent hypoxia inducible factor (HIF) prolyl hydroxylases (human PHD1–3) causes upregulation of HIF, thus promoting erythropoiesis and is therefore of therapeutic interest. We describe cellular, biophysical, and biochemical studies comparing four PHD inhibitors currently in clinical trials for anaemia treatment, that describe their mechanisms of action, potency against isolated enzymes and in cells, and selectivities versus representatives of other human 2OG oxygenase subfamilies. The ‘clinical’ PHD inhibitors are potent inhibitors of PHD catalyzed hydroxylation of the HIF-α oxygen dependent degradation domains (ODDs), and selective against most, but not all, representatives of other human 2OG dependent dioxygenase subfamilies. Crystallographic and NMR studies provide insights into the different active site binding modes of the inhibitors. Cell-based results reveal the inhibitors have similar effects on the upregulation of HIF target genes, but differ in the kinetics of their effects and in extent of inhibition of hydroxylation of the N- and C-terminal ODDs; the latter differences correlate with the biophysical observations.
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Sep 2017
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
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Open Access
Abstract: Modulation of enzyme activity is a powerful means of probing cellular function and can be exploited for diverse applications. Here, we explore a method of enzyme activation where covalent tethering of a small molecule to an enzyme can increase catalytic activity (kcat/KM) up to 35-fold. Using a bacterial glycoside hydrolase, BtGH84, we demonstrate how small molecule “fragments”, identified as activators in free solution, can be covalently tethered to the protein using Michael-addition chemistry. We show how tethering generates a constitutively-activated enzyme-fragment conjugate, which displays both improved catalytic efficiency and increased susceptibility to certain inhibitor classes. Structure guided modifications of the tethered fragment demonstrate how specific interactions between the fragment and the enzyme influence the extent of activation. This work suggests that a similar approach may be used to modulate the activity of enzymes such as to improve catalytic efficiency or increase inhibitor susceptibility.
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Sep 2017
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I11-High Resolution Powder Diffraction
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Open Access
Abstract: Control of intermolecular interactions is integral to harnessing self-assembly in nature. Here we demonstrate that control of the competition between hydrogen bonds and halogen bonds, the two most highly studied directional intermolecular interactions, can be exerted by choice of solvent (polarity) to direct the self-assembly of co-crystals. Competitive co-crystal formation has been investigated for three pairs of hydrogen bond and halogen bond donors, which can compete for a common acceptor group. These competitions have been examined in seven different solvents. Product formation has been determined and phase purity has been examined by analysis of powder X-ray diffraction patterns. Formation of hydrogen-bonded co-crystals is favoured from less polar solvents and halogen-bonded co-crystals from more polar solvents. The solvent polarity at which the crystal formation switches from hydrogen-bond to halogen-bond dominance depends on the relative strengths of the interactions, but is not a function of the solution-phase interactions alone. The results clearly establish that an appreciation of solvent effects is critical to obtain control of the intermolecular interactions.
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Jun 2017
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[11968]
Abstract: A carbon dioxide and nitrous oxide solid solution has been captured in a diamond anvil cell following the thermal decomposition of 1,3,5-trinitroperhydro-1,3,5-triazine (RDX) at high temperatures and pressures. This is the first time a carbon dioxide binary solid has been observed at high pressure. This observation has stimulated low temperature crystallographic studies of this binary system using recently developed gas absorption apparatus and computational modelling.
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May 2017
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I11-High Resolution Powder Diffraction
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Christopher G.
Morris
,
Nicholas M.
Jacques
,
Harry G. W.
Godfrey
,
Tamoghna
Mitra
,
Detlev
Fritsch
,
Zhenzhong
Lu
,
Claire
Murray
,
Jonathan
Potter
,
Tom M.
Cobb
,
Fajin
Yuan
,
Chiu C.
Tang
,
Sihai
Yang
,
Martin
Schröder
Open Access
Abstract: The identification of preferred binding domains within a host structure provides important insights into the function of materials. State-of-the-art reports mostly focus on crystallographic studies of empty and single component guest-loaded host structures to determine the location of guests. However, measurements of material properties (e.g., adsorption and breakthrough of substrates) are usually performed for a wide range of pressure (guest coverage) and/or using multi-component gas mixtures. Here we report the development of a multifunctional gas dosing system for use in X-ray powder diffraction studies on Beamline I11 at Diamond Light Source. This facility is fully automated and enables in situ crystallographic studies of host structures under (i) unlimited target gas loadings and (ii) loading of multi-component gas mixtures. A proof-of-concept study was conducted on a hydroxyl-decorated porous material MFM-300(VIII) under (i) five different CO2 pressures covering the isotherm range and (ii) the loading of equimolar mixtures of CO2/N2. The study has successfully captured the structural dynamics underpinning CO2 uptake as a function of surface coverage. Moreover, MFM-300(VIII) was incorporated in a mixed matrix membrane (MMM) with PIM-1 in order to evaluate the CO2/N2 separation potential of this material. Gas permeation measurements on the MMM show a great improvement over the bare PIM-1 polymer for CO2/N2 separation based on the ideal selectivity.
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Feb 2017
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I15-Extreme Conditions
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Paul J.
Smith
,
Simon A.
Kondrat
,
Philip A.
Chater
,
Benjamin R.
Yeo
,
Greg M.
Shaw
,
Li
Lu
,
Jonathan K.
Bartley
,
Stuart H.
Taylor
,
Michael S.
Spencer
,
Christopher J.
Kiely
,
Gordon
Kelly
,
Colin W.
Park
,
Graham J.
Hutchings
Open Access
Abstract: Zincian georgeite, an amorphous copper–zinc hydroxycarbonate, has been prepared by co-precipitation using acetate salts and ammonium carbonate. Incorporation of zinc into the georgeite phase and mild ageing conditions inhibits crystallisation into zincian malachite or aurichalcite. This zincian georgeite precursor was used to prepare a Cu/ZnO catalyst, which exhibits a superior performance to a zincian malachite derived catalyst for methanol synthesis and the low temperature water–gas shift (LTS) reaction. Furthermore, the enhanced LTS activity and stability in comparison to that of a commercial Cu/ZnO/Al2O3 catalyst, indicates that the addition of alumina as a stabiliser may not be required for the zincian georgeite derived Cu/ZnO catalyst. The enhanced performance is partly attributed to the exclusion of alkali metals from the synthesis procedure, which are known to act as catalyst poisons. The effect of residual sodium on the microstructural properties of the catalyst precursor was investigated further from preparations using sodium carbonate.
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Jan 2017
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Open Access
Abstract: Water splitting performed in acidic media relies on the exceptional performance of iridium-based materials to catalyze the oxygen evolution reaction (OER). In the present work, we use in situ X-ray photoemission and absorption spectroscopy to resolve the long-standing debate about surface species present in iridium-based catalysts during the OER. We find that the surface of an initially metallic iridium model electrode converts into a mixed-valent, conductive iridium oxide matrix during the OER, which contains OII− and electrophilic OI− species. We observe a positive correlation between the OI− concentration and the evolved oxygen, suggesting that these electrophilic oxygen sites may be involved in catalyzing the OER. We can understand this observation by analogy with photosystem II; their electrophilicity renders the OI− species active in O–O bond formation, i.e. the likely potential- and rate-determining step of the OER. The ability of amorphous iridium oxyhydroxides to easily host such reactive, electrophilic species can explain their superior performance when compared to plain iridium metal or crystalline rutile-type IrO2.
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Dec 2016
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I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[9007, 9537, 14043]
Open Access
Abstract: The development of selective inhibitors of protein kinases is challenging because of the significant conservation of the ATP binding site. Here, we describe a new mechanism by which the protein kinase CK2α can be selectively inhibited using features outside the ATP site. We have identified a new binding site for small molecules on CK2α adjacent to the ATP site and behind the αD loop, termed the αD pocket. An elaborated fragment anchored in this site has been linked with a low affinity fragment binding in the ATP site, creating a novel and selective inhibitor (CAM4066) that binds CK2α with a Kd of 320 nM and shows significantly improved selectivity compared to other CK2α inhibitors. CAM4066 shows target engagement in several cell lines and similar potency to clinical trial candidate CX4945. Our data demonstrate that targeting a poorly conserved, cryptic pocket allows inhibition of CK2α via a novel mechanism, enabling the development of a new generation of selective CK2α inhibitors.
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Jul 2016
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Verena
Pfeifer
,
Travis E.
Jones
,
Sabine
Wrabetz
,
Cyriac
Massué
,
Juan J.
Velasco Vélez
,
Rosa
Arrigo
,
Michael
Scherzer
,
Simone
Piccinin
,
Michael
Hävecker
,
Axel
Knop-gericke
,
Robert
Schlögl
Open Access
Abstract: Tremendous effort has been devoted towards elucidating the fundamental reasons for the higher activity of hydrated amorphous IrIII/IV oxyhydroxides (IrOx) in the oxygen evolution reaction (OER) in comparison with their crystalline counterpart, rutile-type IrO2, by focusing on the metal oxidation state. Here we demonstrate that, through an analogy to photosystem II, the nature of this reactive species is not solely a property of the metal but is intimately tied to the electronic structure of oxygen. We use a combination of synchrotron-based X-ray photoemission and absorption spectroscopies, ab initio calculations, and microcalorimetry to show that holes in the O 2p states in amorphous IrOx give rise to a weakly bound oxygen that is extremely susceptible to nucleophilic attack, reacting stoichiometrically with CO already at room temperature. As such, we expect this species to play the critical role of the electrophilic oxygen involved in O–O bond formation in the electrocatalytic OER on IrOx. We propose that the dynamic nature of the Ir framework in amorphous IrOx imparts the flexibility in Ir oxidation state required for the formation of this active electrophilic oxygen.
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Jul 2016
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I09-Surface and Interface Structural Analysis
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Peter
Deimel
,
Reda M.
Bababrik
,
Bin
Wang
,
Philip
Blowey
,
Luke
Rochford
,
Pardeep K.
Thakur
,
Tien-lin
Lee
,
Marie-laure
Bocquet
,
Johannes V.
Barth
,
Phil
Woodruff
,
David
Duncan
,
Francesco
Allegretti
Diamond Proposal Number(s):
[8940]
Open Access
Abstract: The strong parallels between coordination chemistry and adsorption on metal surfaces, with molecules and ligands forming local bonds to individual atoms within a metal surface, have been established over many years of study. The recently proposed “surface trans-effect” (STE) appears to be a further manifestation of this analogous behaviour, but so far the true nature of the modified molecule–metal surface bonding has been unclear. The STE could play an important role in determining the reactivities of surface-supported metal–organic complexes, influencing the design of systems for future applications. However, the current understanding of this effect is incomplete and lacks reliable structural parameters with which to benchmark theoretical calculations. Using X-ray standing waves, we demonstrate that ligation of ammonia and water to iron phthalocyanine (FePc) on Ag(111) increases the adsorption height of the central Fe atom; dispersion corrected density functional theory calculations accurately model this structural effect. The calculated charge redistribution in the FePc/H2O electronic structure induced by adsorption shows an accumulation of charge along the σ-bonding direction between the surface, the Fe atom and the water molecule, similar to the redistribution caused by ammonia. This apparent σ-donor nature of the observed STE on Ag(111) is shown to involve bonding to the delocalised metal surface electrons rather than local bonding to one or more surface atoms, thus indicating that this is a true surface trans-effect.
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Jun 2016
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