B22-Multimode InfraRed imaging And Microspectroscopy
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Philip A.
Ash
,
Sophie E. T.
Kendall-Price
,
Rhiannon M.
Evans
,
Stephen
Carr
,
Amelia
Brasnett
,
Simone
Morra
,
Ricardo
Hidalgo
,
Adam J.
Healy
,
Gianfelice
Cinque
,
Mark D.
Frogley
,
Fraser A
Armstrong
,
Kylie A.
Vincent
Diamond Proposal Number(s):
[17753, 19269, 21651]
Open Access
Abstract: Controlled formation of catalytically-relevant states within crystals of complex metalloenzymes represents a significant challenge to structure-function studies. Here we show how electrochemical control over single crystals of [NiFe] hydrogenase 1 (Hyd1) from Escherichia coli makes it possible to navigate through the full array of active site states previously observed in solution. Electrochemical control is combined with synchrotron infrared microspectroscopy, which enables us to measure high signal-to-noise IR spectra in situ from a small area of crystal. The output reports on active site speciation via the vibrational stretching band positions of the endogenous CO and CN- ligands at the hydrogenase active site. Variation of pH further demonstrates how equilibria between catalytically-relevant protonation states can be deliberately perturbed in the crystals, generating a map of electrochemical potential and pH conditions which lead to enrichment of specific states. Comparison of in crystallo redox titrations with measurements in solution or of electrode-immobilised Hyd1 confirms the integrity of the proton transfer and redox environment around the active site of the enzyme in crystals. Slowed proton-transfer equilibria in the hydrogenase in crystallo reveals transitions which are only usually observable by ultrafast methods in solution. This study therefore demonstrates the possibilities of electrochemical control over single metalloenzyme crystals in stabilising specific states for further study, and extends mechanistic understanding of proton transfer during the [NiFe] hydrogenase catalytic cycle.
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Jun 2021
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B18-Core EXAFS
E01-JEM ARM 200CF
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Diamond Proposal Number(s):
[20856]
Open Access
Abstract: Coinage metal nanoparticles with high dispersion can serve as highly efficient heterogeneous catalysts. However, owing to their low melting point, poor thermal stability remains a major obstacle towards their application under reaction conditions. It is a common practice to use porous inorganic templates such as mesoporous silica SBA-15 to disperse Ag nanoparticles (NPs) against aggregation but their stability is far from satisfactory. Here, we show that the catalytic activity for hydrogenation of dimethyl oxalate (DMO) to methyl glycolate (MG) over Ag NPs dispersed on SBA-15 silica can be further promoted by incorporation of alkali metal ions at small loading, which follows the inverse order of their cationic size: Li+ > Na+ > K+ > Rb+. Among these, 5Ag1–Li0.05/SBA-15 can double the MG yield compared to pristine 5Ag/SBA-15 under identical conditions with superior thermal stability. Akin to the effect of an ionic surfactant on stabilization of a micro-emulsion, the cationic charge of an alkali metal ion can maintain dispersion and modulate the surface valence of Ag NPs. Interstitial Li in the octahedral holes of the face center packed Ag lattice is for the first time confirmed by X-ray pair distribution function and electron ptychography. It is believed that this interstitial-stabilization of coinage metal nanoparticles could be broadly applicable to multi-metallic nanomaterials for a broad range of C–O bond activating catalytic reactions of esters.
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May 2021
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[12342, 23269]
Open Access
Abstract: The rational design of linear peptides that assemble controllably and predictably in water is challenging. Short sequences must encode unique target structures and avoid alternative states. However, the non-covalent forces that stabilize and discriminate between states are weak. Nonetheless, for α-helical coiled-coil assemblies considerable progress has been made in rational de novo design. In these, sequence repeats of nominally hydrophobic (h) and polar (p) residues, hpphppp, direct the assembly of amphipathic helices into dimeric to tetrameric bundles. Expanding this pattern to hpphhph can produce larger α-helical barrels. Here, we show that pentameric to nonameric barrels are accessed by varying the residue at one of the h sites. In peptides with four L/I–K–E–I–A–x–Z repeats, decreasing the size of Z from threonine to serine to alanine to glycine gives progressively larger oligomers. X-ray crystal structures of the resulting α-helical barrels rationalize this: side chains at Z point directly into the helical interfaces, and smaller residues allow closer helix contacts and larger assemblies.
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Apr 2021
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E02-JEM ARM 300CF
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Diamond Proposal Number(s):
[23260]
Open Access
Abstract: We induce and study reactions of polyoxometalate (POM) molecules, [PW12O40]3− (Keggin) and [P2W18O62]6− (Wells–Dawson), at the single-molecule level. Several identical carbon nanotubes aligned side by side within a bundle provided a platform for spatiotemporally resolved imaging of ca. 100 molecules encapsulated within the nanotubes by transmission electron microscopy (TEM). Due to the entrapment of POM molecules their proximity to one another is effectively controlled, limiting molecular motion in two dimensions but leaving the third dimension available for intermolecular reactions between pairs of neighbouring molecules. By coupling the information gained from high resolution structural and kinetics experiments via the variation of key imaging parameters in the TEM, we shed light on the reaction mechanism. The dissociation of W–O bonds, a key initial step of POM reactions, is revealed to be reversible by the kinetic analysis, followed by an irreversible bonding of POM molecules to their nearest neighbours, leading to a continuous tungsten oxide nanowire, which subsequently transforms into amorphous tungsten-rich clusters due to progressive loss of oxygen atoms. The overall intermolecular reaction can therefore be described as a step-wise reductive polycondensation of POM molecules, via an intermediate state of an oxide nanowire. Kinetic analysis enabled by controlled variation of the electron flux in TEM revealed the reaction to be highly flux-dependent, which leads to reaction rates too fast to follow under the standard TEM imaging conditions. Although this presents a challenge for traditional structural characterisation of POM molecules, we harness this effect by controlling the conditions around the molecules and tuning the imaging parameters in TEM, which combined with theoretical modelling and image simulation, can shed light on the atomistic mechanisms of the reactions of POMs. This approach, based on the direct space and real time chemical reaction analysis by TEM, adds a new method to the arsenal of single-molecule kinetics techniques.
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Apr 2021
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Sergio
Celis
,
Fruzsina
Hobor
,
Thomas
James
,
Gail J.
Bartlett
,
Amaurys A.
Ibarra
,
Deborah K.
Shoemark
,
Zsofia
Hegedus
,
Kristina
Hetherington
,
Derek N.
Woolfson
,
Richard B.
Sessions
,
Thomas A.
Edwards
,
David M.
Andrews
,
Adam
Nelson
,
Andrew J.
Wilson
Diamond Proposal Number(s):
[19248]
Open Access
Abstract: Protein–protein interactions (PPIs) are central to biological mechanisms, and can serve as compelling targets for drug discovery. Yet, the discovery of small molecule inhibitors of PPIs remains challenging given the large and typically shallow topography of the interacting protein surfaces. Here, we describe a general approach to the discovery of orthosteric PPI inhibitors that mimic specific secondary protein structures. Initially, hot residues at protein–protein interfaces are identified in silico or from experimental data, and incorporated into secondary structure-based queries. Virtual libraries of small molecules are then shape-matched against the queries, and promising ligands docked to target proteins. The approach is exemplified experimentally using two unrelated PPIs that are mediated by an α-helix (p53/hDM2) and a β-strand (GKAP/SHANK1-PDZ). In each case, selective PPI inhibitors are discovered with low μM activity as determined by a combination of fluorescence anisotropy and 1H–15N HSQC experiments. In addition, hit expansion yields a series of PPI inhibitors with defined structure–activity relationships. It is envisaged that the generality of the approach will enable discovery of inhibitors of a wide range of unrelated secondary structure-mediated PPIs.
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Mar 2021
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I19-Small Molecule Single Crystal Diffraction
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Aaron J
Scott
,
Euan K.
Brechin
,
Stergios
Piligkos
,
Gopalan
Rajaraman
,
Mark
Murrie
,
Simon
Coles
,
Wim T.
Klooster
,
Gary S.
Nichol
,
Paul
Lusby
,
Lucy
Smythe
,
Arup
Sarkar
,
Julia
Vallejo
,
Emma
Regincos Marti
Diamond Proposal Number(s):
[22240]
Open Access
Abstract: Reaction of Ni(OTf)2 with the bisbidentate quaterpyridine ligand L results in the self-assembly of a tetrahedral, paramagnetic cage [NiII4L6]8+. By selectively exchanging the bound triflate from [OTf⊂NiII4L6](OTf)7 (1), we have been able to prepare a series of host-guest complexes that feauture an encapsulated paramagnetic tetrahalometallate ion inside this paramagnetic host giving [MIIX4⊂NiII4L6](OTf)6, where MIIX42− = MnCl42− (2), CoCl42− (5), CoBr42− (6), NiCl42− (7), CuBr42− (8) or [MIIIX4⊂NiII4L6](OTf)7, where MIIIX4− = FeCl4− (3), FeBr4− (4). Triflate-to-tetrahalometallate exchange occurs in solution and can also be accomplished through single-crystal-to-single-crystal transformations. Host-guest complexes 1-8 all crystallise as homochiral racemates in monoclinic space groups, wherein the four {NiN6} vertex within a single Ni4L6 unit possess the same Δ or Λ stereochemistry. Magnetic susceptibility and magnetisation data show that the magnetic exchange between metal ions in the host [NiII4] complex, and between the host and the MX4n- guest, are of comparable magnitude and antiferromagnetic in nature. Theoretically derived values for the magnetic exchange are in close agreement with experiment, revealing that large spin densities on the electronegative X-atoms of particular {MX4}n− guest molecules leads to stronger host-guest magnetic exchange interactions.
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Mar 2021
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Husam Sabah
Auhim
,
Bella L.
Grigorenko
,
Tessa K.
Harris
,
Ozan E.
Aksakal
,
Igor V.
Polyakov
,
Colin
Berry
,
Gabriel Dos Passos
Gomes
,
Igor V.
Alabugin
,
Pierre J.
Rizkallah
,
Alexander V.
Nemukhin
,
D. Dafydd
Jones
Diamond Proposal Number(s):
[18812]
Open Access
Abstract: Fluorescent proteins (FPs) have revolutionised the life sciences, but the mechanism of chromophore maturation is still not fully understood. Here we show that incorporation of a photo-responsive non-canonical amino acid within the chromophore stalls maturation of Venus, a yellow FP, at an intermediate stage; a crystal structure indicates the presence of O2 located above a dehydrated enolate form of the imidazolone ring, close to the strictly conserved Gly67 that occupies a twisted conformation. His148 adopts an “open” conformation so forming a channel that allows O2 access to the immature chromophore. Absorbance spectroscopy supported by QM/MM simulations suggests that the first oxidation step involves formation of a hydroperoxyl intermediate in conjunction with dehydrogenation of the methylene bridge. A fully conjugated mature chromophore is formed through release of H2O2, both in vitro and in vivo. The possibility of interrupting and photochemically restarting chromophore maturation and the mechanistic insights open up new approaches for engineering optically controlled fluorescent proteins.
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Mar 2021
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I11-High Resolution Powder Diffraction
I12-JEEP: Joint Engineering, Environmental and Processing
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Kieran W. P.
Orr
,
Sean M.
Collins
,
Emily M.
Reynolds
,
Frank
Nightingale
,
Hanna L. B.
Bostroem
,
Simon J.
Cassidy
,
Daniel M.
Dawson
,
Sharon E.
Ashbrook
,
Oxana
Magdysyuk
,
Paul A.
Midgley
,
Andrew L.
Goodwin
,
Hamish H.-M.
Yeung
Diamond Proposal Number(s):
[20946, 18786]
Open Access
Abstract: Control over the spatial distribution of components in metal–organic frameworks has potential to unlock improved performance and new behaviour in separations, sensing and catalysis. We report an unprecedented single-step synthesis of multi-component metal–organic framework (MOF) nanoparticles based on the canonical ZIF-8 (Zn) system and its Cd analogue, which form with a core–shell structure whose internal interface can be systematically tuned. We use scanning transmission electron microscopy, X-ray energy dispersive spectroscopy and a new composition gradient model to fit high-resolution X-ray diffraction data to show how core–shell composition and interface characteristics are intricately controlled by synthesis temperature and reaction composition. Particle formation is investigated by in situ X-ray diffraction, which reveals that the spatial distribution of components evolves with time and is determined by the interplay of phase stability, crystallisation kinetics and diffusion. This work opens up new possibilities for the control and characterisation of functionality, component distribution and interfaces in MOF-based materials.
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Feb 2021
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I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[23459]
Open Access
Abstract: 2-Oxoglutarate (2OG) is involved in biological processes including oxidations catalyzed by 2OG oxygenases for which it is a cosubstrate. Eukaryotic 2OG oxygenases have roles in collagen biosynthesis, lipid metabolism, DNA/RNA modification, transcriptional regulation, and the hypoxic response. Aspartate/asparagine-β-hydroxylase (AspH) is a human 2OG oxygenase catalyzing post-translational hydroxylation of Asp/Asn-residues in epidermal growth factor-like domains (EGFDs) in the endoplasmic reticulum. AspH is of chemical interest, because its Fe(II) cofactor is complexed by two rather than the typical three residues. AspH is upregulated in hypoxia and is a prognostic marker on the surface of cancer cells. We describe studies on how derivatives of its natural 2OG cosubstrate modulate AspH activity. An efficient synthesis of C3- and/or C4-substituted 2OG derivatives, proceeding via cyanosulfur ylid intermediates, is reported. Mass spectrometry-based AspH assays with >30 2OG derivatives reveal that some efficiently inhibit AspH via competing with 2OG as evidenced by crystallographic and solution analyses. Other 2OG derivatives can substitute for 2OG enabling substrate hydroxylation. The results show that subtle changes, e.g. methyl- to ethyl-substitution, can significantly alter the balance between catalysis and inhibition. 3-Methyl-2OG, a natural product present in human nutrition, was the most efficient alternative cosubstrate identified; crystallographic analyses reveal the binding mode of (R)-3-methyl-2OG and other 2OG derivatives to AspH and inform on the balance between turnover and inhibition. The results will enable the use of 2OG derivatives as mechanistic probes for other 2OG utilizing enzymes and suggest 2-oxoacids other than 2OG may be employed by some 2OG oxygenases in vivo.
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Feb 2021
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[19248]
Open Access
Abstract: β-Strand mediated protein–protein interactions (PPIs) represent underexploited targets for chemical probe development despite representing a significant proportion of known and therapeutically relevant PPI targets. β-Strand mimicry is challenging given that both amino acid side-chains and backbone hydrogen-bonds are typically required for molecular recognition, yet these are oriented along perpendicular vectors. This paper describes an alternative approach, using GKAP/SHANK1 PDZ as a model and dynamic ligation screening to identify small-molecule replacements for tranches of peptide sequence. A peptide truncation of GKAP functionalized at the N- and C-termini with acylhydrazone groups was used as an anchor. Reversible acylhydrazone bond exchange with a library of aldehyde fragments in the presence of the protein as template and in situ screening using a fluorescence anisotropy (FA) assay identified peptide hybrid hits with comparable affinity to the GKAP peptide binding sequence. Identified hits were validated using FA, ITC, NMR and X-ray crystallography to confirm selective inhibition of the target PDZ-mediated PPI and mode of binding. These analyses together with molecular dynamics simulations demonstrated the ligands make transient interactions with an unoccupied basic patch through electrostatic interactions, establishing proof-of-concept that this unbiased approach to ligand discovery represents a powerful addition to the armory of tools that can be used to identify PPI modulators.
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Jan 2021
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