I02-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Marta
Artola
,
Liang
Wu
,
Maria J.
Ferraz
,
Chi-Lin
Kuo
,
Lluís
Raich
,
Imogen Z.
Breen
,
Wendy A.
Offen
,
Jeroen D. C.
Codée
,
Gijsbert A.
Van Der Marel
,
Carme
Rovira
,
Johannes M. F. G.
Aerts
,
Gideon J.
Davies
,
Herman S.
Overkleeft
Diamond Proposal Number(s):
[13587]
Open Access
Abstract: The essential biological roles played by glycosidases, coupled to the diverse therapeutic benefits of pharmacologically targeting these enzymes, provide considerable motivation for the development of new inhibitor classes. Cyclophellitol epoxides and aziridines are recently established covalent glycosidase inactivators. Inspired by the application of cyclic sulfates as electrophilic equivalents of epoxides in organic synthesis, we sought to test whether cyclophellitol cyclosulfates would similarly act as irreversible glycosidase inhibitors. Here we present the synthesis, conformational analysis, and application of novel 1,6-cyclophellitol cyclosulfates. We show that 1,6-epi-cyclophellitol cyclosulfate (α-cyclosulfate) is a rapidly reacting α-glucosidase inhibitor whose 4C1 chair conformation matches that adopted by α-glucosidase Michaelis complexes. The 1,6-cyclophellitol cyclosulfate (β-cyclosulfate) reacts more slowly, likely reflecting its conformational restrictions. Selective glycosidase inhibitors are invaluable as mechanistic probes and therapeutic agents, and we propose cyclophellitol cyclosulfates as a valuable new class of carbohydrate mimetics for application in these directions.
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Jul 2017
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Maria-Agustina
Rossi
,
Veronica
Martinez
,
Philip
Hinchliffe
,
Maria F.
Mojica
,
Valerie
Castillo
,
Diego M.
Moreno
,
Ryan
Smith
,
Brad
Spellberg
,
George L.
Drusano
,
Claudia
Banchio
,
Robert A.
Bonomo
,
James
Spencer
,
Alejandro J.
Vila
,
Graciela
Mahler
Diamond Proposal Number(s):
[17212]
Open Access
Abstract: Infections caused by multidrug resistant (MDR) bacteria are a major public health threat. Carbapenems are among the most potent antimicrobial agents that are commercially available to treat MDR bacteria. Bacterial production of carbapenem-hydrolysing metallo-β-lactamases (MBLs) challenges their safety and efficacy, with subclass B1 MBLs hydrolysing almost all β-lactam antibiotics. MBL inhibitors would fulfil an urgent clinical need by prolonging the lifetime of these life-saving drugs. Here we report the synthesis and activity of a series of 2-mercaptomethyl-thiazolidines (MMTZs), designed to replicate MBL interactions with reaction intermediates or hydrolysis products. MMTZs are potent competitive inhibitors of B1 MBLs in vitro (e.g., Ki = 0.44 μM vs. NDM-1). Crystal structures of MMTZ complexes reveal similar binding patterns to the most clinically important B1 MBLs (NDM-1, VIM-2 and IMP-1), contrasting with previously studied thiol-based MBL inhibitors, such as bisthiazolidines (BTZs) or captopril stereoisomers, which exhibit lower, more variable potencies and multiple binding modes. MMTZ binding involves thiol coordination to the Zn(II) site and extensive hydrophobic interactions, burying the inhibitor more deeply within the active site than D/L-captopril. Unexpectedly, MMTZ binding features a thioether–π interaction with a conserved active-site aromatic residue, consistent with their equipotent inhibition and similar binding to multiple MBLs. MMTZs penetrate multiple Enterobacterales, inhibit NDM-1 in situ, and restore carbapenem potency against clinical isolates expressing B1 MBLs. Based on their inhibitory profile and lack of eukaryotic cell toxicity, MMTZs represent a promising scaffold for MBL inhibitor development. These results also suggest sulphur–π interactions can be exploited for general ligand design in medicinal chemistry.
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Jan 2021
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Krios I-Titan Krios I at Diamond
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Pu
Qian
,
Alastair T.
Gardiner
,
Ivana
Šímová
,
Katerina
Naydenova
,
Tristan I.
Croll
,
Philip J.
Jackson
,
Nupur
Nupur
,
Miroslav
Kloz
,
Petra
Čubáková
,
Marek
Kuzma
,
Yonghui
Zeng
,
Pablo
Castro-Hartmann
,
Bart
Van Knippenberg
,
Kenneth N.
Goldie
,
David
Kaftan
,
Pavel
Hrouzek
,
Jan
Hájek
,
Jon
Agirre
,
C. Alistair
Siebert
,
David
Bína
,
Kasim
Sader
,
Henning
Stahlberg
,
Roman
Sobotka
,
Christopher J.
Russo
,
Tomáš
Polívka
,
C. Neil
Hunter
,
Michal
Koblížek
Diamond Proposal Number(s):
[29785]
Open Access
Abstract: Phototrophic Gemmatimonadetes evolved the ability to use solar energy following horizontal transfer of photosynthesis-related genes from an ancient phototrophic proteobacterium. The electron cryo-microscopy structure of the Gemmatimonas phototrophica photosystem at 2.4 Å reveals a unique, double-ring complex. Two unique membrane-extrinsic polypeptides, RC-S and RC-U, hold the central type 2 reaction center (RC) within an inner 16-subunit light-harvesting 1 (LH1) ring, which is encircled by an outer 24-subunit antenna ring (LHh) that adds light-gathering capacity. Femtosecond kinetics reveal the flow of energy within the RC-dLH complex, from the outer LHh ring to LH1 and then to the RC. This structural and functional study shows that G. phototrophica has independently evolved its own compact, robust, and highly effective architecture for harvesting and trapping solar energy.
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Feb 2022
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I12-JEEP: Joint Engineering, Environmental and Processing
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Chun
Huang
,
Matthew
Wilson
,
Kosuke
Suzuki
,
Enzo
Liotti
,
Thomas
Connolley
,
Oxana
Magdysyuk
,
Stephen
Collins
,
Frederic
Van Assche
,
Matthieu N
Boone
,
Matthew C.
Veale
,
Andrew
Lui
,
Rhian-Mair
Wheater
,
Chu Lun Alex
Leung
Diamond Proposal Number(s):
[23400]
Open Access
Abstract: The performance of Li+ ion batteries (LIBs) is hindered by steep Li+ ion concentration gradients in the electrodes. Although thick electrodes (≥300 µm) have the potential for reducing the proportion of inactive components inside LIBs and increasing battery energy density, the Li+ ion concentration gradient problem is exacerbated. Most understanding of Li+ ion diffusion in the electrodes is based on computational modeling because of the low atomic number (Z) of Li. There are few experimental methods to visualize Li+ ion concentration distribution of the electrode within a battery of typical configurations, for example, coin cells with stainless steel casing. Here, for the first time, an interrupted in situ correlative imaging technique is developed, combining novel, full-field X-ray Compton scattering imaging with X-ray computed tomography that allows 3D pixel-by-pixel mapping of both Li+ stoichiometry and electrode microstructure of a LiNi0.8Mn0.1Co0.1O2 cathode to correlate the chemical and physical properties of the electrode inside a working coin cell battery. An electrode microstructure containing vertically oriented pore arrays and a density gradient is fabricated. It is shown how the designed electrode microstructure improves Li+ ion diffusivity, homogenizes Li+ ion concentration through the ultra-thick electrode (1 mm), and improves utilization of electrode active materials.
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Apr 2022
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I13-2-Diamond Manchester Imaging
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Diamond Proposal Number(s):
[15444]
Abstract: Inorganic/organic hybrids have co-networks of inorganic and organic components, with the aim of obtaining synergy of the properties of those components. Here, a silica-gelatin sol-gel hybrid “ink” was directly 3D printed to produce 3D grid-like scaffolds, using a coupling agent, 3-glycidyloxypropyl)trimethoxysilane (GPTMS), to form covalent bonds between the silicate and gelatin co-networks. Scaffolds were printed with 1 mm strut separation, but the drying method affected the final architecture and properties. Freeze drying produced <40 μm struts and large ~700 μm channels. Critical point drying enabled strut consolidation and optimal mechanical properties, with ~160 μm struts and ~200 μm channels, which improved mechanical properties. This architecture was critical to cellular response: when chondrocytes were seeded on the scaffolds with 200 μm wide pore channels in vitro, collagen Type II matrix was preferentially produced (negligible amount of Type I or X were observed), indicative of hyaline-like cartilaginous matrix formation, but when pore channels were 700 μm wide, Type I collagen was prevalent. This was supported by Sox9 and Aggrecan expression. The scaffolds have potential for regeneration of articular cartilage regeneration, particularly in sports medicine cases.
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Feb 2021
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I12-JEEP: Joint Engineering, Environmental and Processing
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Diamond Proposal Number(s):
[9036, 7730]
Open Access
Abstract: The combined use of high resolution X-ray computed tomography with digital image correlation allows quantitative observations of the three-dimensional deformations that occur within a material when it is strained. In suitable microstructures, the displacement resolution is sub-voxel (a voxel is the three-dimensional equivalent of a pixel), and both elastic and plastic deformations can be studied. This paper reviews recent work in which three-dimensional in situ observations of deformation have provided unique insights that support both continuum and heterogeneous microstructure-dependent models of damage development in a range of materials. The examples presented include; crack propagation in a quasi-brittle porous material (polygranular graphite), sub-indentation radial and lateral cracking in a brittle polycrystalline ceramic (alumina); plastic deformation and damage development underneath indentations in a ductile metal (Al-SiC composite) and a ceramic matrix composite (SiC-SiCfibre). These examples show how material properties can be obtained by analysis of the displacement fields, how such measurements can be used to better define the applied loading on small test specimens and how crack opening magnitude and mode may be extracted also. Some new directions for research are outlined, including the combined use of diffraction and imaging techniques on synchrotron X-ray facilities to map both elastic and inelastic strains.
Keywords: Computed Tomography; Damage; Deformation; Digital Image Correlation
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Aug 2014
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Paolo
Ruzza
,
Giuliano
Siligardi
,
Arianna
Donella-Deana
,
Andrea
Calderan
,
Rohanah
Hussain
,
Chiara
Rubini
,
Luca
Cesaro
,
Alessio
Osler
,
Andrea
Guiotto
,
Lorenzo A.
Pinna
,
Gianfranco
Borin
Abstract: Eukaryotic signal transduction involves the assembly of transient protein–protein complexes mediated by modular interaction domains. Specific Pro-rich sequences with the consensus core motif PxxP adopt the PPII helix conformation upon binding to SH3 domains. For short Pro-rich peptides, little or no ordered secondary structure is usually observed before binding interactions. The association of a Pro-rich peptide with the SH3 domain involves unfavorable binding entropy due to the loss of rotational freedom on forming the PPII helix. With the aim of stabilizing the PPII helix conformation in the Pro-rich HPK1 decapeptide PPPLPPKPKF (P2), a series of P2 analogues was prepared, in which specific Pro positions were alternatively occupied by 4(S)- or 4(R)-4-fluoro-L-proline. The interactions of these peptides with the SH3 domain of the HPK1-binding partner HS1 were quantitatively analyzed by the NILIA-CD approach. A CD thermal analysis of the P2 analogues was performed to assess their propensity to adopt the PPII helix conformation. Contrary to our expectations, the Kd values of the analogues were lower than that of the parent peptide P2. These results clearly show that the induction of a stable PPII helix conformation in short Pro-rich peptides is not sufficient to increase their affinity toward the SH3 domain and that the effect of 4-fluoroproline strongly depends on the position of this residue in the sequence and the chirality of the substituent in the pyrrolidine ring.
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Jul 2006
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[987]
Abstract: The single-crystal diffraction structures of 38 salt forms of the base tyramine (4-hydroxyphenethylamine) are reported for the first time. Together with literature examples, these structures are discussed with respect to cation conformation, cation packing, hydrogen bonding and hydrate formation. It is found that isostructural cation packing can occur even with structurally different anions, with different hydration states and with different hydrogen bonding. Hydrate formation is found to be more likely both (i) when there is an increase in the total number of potential hydrogen bond acceptor and donor atoms; and (ii) when the ratio of potential hydrogen bond donor to acceptor atoms is low.
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Aug 2012
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I13-2-Diamond Manchester Imaging
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Diamond Proposal Number(s):
[11078]
Open Access
Abstract: Four dimensional (4D, or 3D plus time) X-ray tomographic imaging of phase
changes in materials is quickly becoming an accepted tool for quantifying the development of
microstructures to both inform and validate models. However, most of the systems studied
have been relatively simple binary compositions with only two phases. In this study we present
a quantitative dataset of the phase evolution in a complex three-phase material, ice cream. The
microstructure of ice cream is an important parameter in terms of sensorial perception, and
therefore quantification and modelling of the evolution of the microstructure with time and
temperature is key to understanding its fabrication and storage. The microstructure consists of
three phases, air cells, ice crystals, and unfrozen matrix. We perform in situ synchrotron X-ray
imaging of ice cream samples using in-line phase contrast tomography, housed within a
purpose built cold-stage (-40 to +20o
C) with finely controlled variation in specimen
temperature. The size and distribution of ice crystals and air cells during programmed
temperature cycling are determined using 3D quantification. The microstructural evolution of
three-phase materials has many other important applications ranging from biological to
structural and functional material, hence this dataset can act as a validation case for numerical
investigations on faceted and non-faceted crystal growth in a range of materials.
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Jun 2015
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I04-Macromolecular Crystallography
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A.
Cruz-Migoni
,
G. M.
Hautbergue
,
P. J.
Artymiuk
,
P. J.
Baker
,
M.
Bokori-Brown
,
C.-T.
Chang
,
M. J.
Dickman
,
A.
Essex-Lopresti
,
S. V.
Harding
,
N. M.
Mahadi
,
L. E.
Marshall
,
G.
Mobbs
,
R.
Mohamed
,
S.
Nathan
,
S. A.
Ngugi
,
C.
Ong
,
W. F.
Ooi
,
L. J.
Partridge
,
H. L.
Phillips
,
M. F.
Raih
,
S.
Ruzheinikov
,
M.
Sarkar-Tyson
,
S. E.
Sedelnikova
,
S. J.
Smither
,
P.
Tan
,
R. W.
Titball
,
S. A.
Wilson
,
D. W.
Rice
Abstract: The structure of BPSL1549, a protein of unknown function from Burkholderia pseudomallei, reveals a similarity to Escherichia coli cytotoxic necrotizing factor 1. We found that BPSL1549 acted as a potent cytotoxin against eukaryotic cells and was lethal when administered to mice. Expression levels of bpsl1549 correlate with conditions expected to promote or suppress pathogenicity. BPSL1549 promotes deamidation of glutamine-339 of the translation initiation factor eIF4A, abolishing its helicase activity and inhibiting translation. We propose to name BPSL1549 Burkholderia lethal factor 1.
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Nov 2011
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