I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[2373]
Open Access
Abstract: The design of completely synthetic proteins from first principles—de novo protein design—is challenging. This is because, despite recent advances in computational protein–structure prediction and design, we do not understand fully the sequence-to-structure relationships for protein folding, assembly, and stabilization. Antiparallel 4-helix bundles are amongst the most studied scaffolds for de novo protein design. We set out to re-examine this target, and to determine clear sequence-to-structure relationships, or design rules, for the structure. Our aim was to determine a common and robust sequence background for designing multiple de novo 4-helix bundles. In turn, this could be used in chemical and synthetic biology to direct protein–protein interactions and as scaffolds for functional protein design. Our approach starts by analyzing known antiparallel 4-helix coiled-coil structures to deduce design rules. In terms of the heptad repeat, abcdefg—i.e., the sequence signature of many helical bundles—the key features that we identify are: a = Leu, d = Ile, e = Ala, g = Gln, and the use of complementary charged residues at b and c. Next, we implement these rules in the rational design of synthetic peptides to form antiparallel homo- and heterotetramers. Finally, we use the sequence of the homotetramer to derive in one step a single-chain 4-helix-bundle protein for recombinant production in E. coli. All of the assembled designs are confirmed in aqueous solution using biophysical methods, and ultimately by determining high-resolution X-ray crystal structures. Our route from peptides to proteins provides an understanding of the role of each residue in each design.
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Sep 2022
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I15-Extreme Conditions
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Diamond Proposal Number(s):
[20310, 13678, 11768, 9873, 9696]
Abstract: The pressure-induced structural phase transitions in the lanthanide elements provide insight into changes in their electronic structures at high densities. After a series of transitions via close-packed structures, the regular trivalent lanthanides (La to Lu, excluding Ce, Eu and Yb) undergo first-order transitions to so-called collapsed phases, the structures of which have long been reported as monoclinic. However, the diffraction data from these phases are not well fitted by this monoclinic structure, and the patterns from Nd and Sm are distinctly different to those from the higher-Z lanthanides (Gd→). Here we present results from recent diffraction studies on Tb, Gd, Sm, Nd and Y to above 300 GPa, which reveal that there are two different collapsed structures, neither of which is monoclinic. High-precision equation of state studies of the same elements reveal distinct changes in compressibility once the collapsed phases are obtained. We also show that these new structures are strikingly similar to those observed in the higher-Z actinides at high pressure, greatly strengthening the structural systematics of the 4f and 5f elements.
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Sep 2022
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I09-Surface and Interface Structural Analysis
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Hongxia
Wang
,
Meiyan
Cui
,
Gaoliang
Fu
,
Jiaye
Zhang
,
Xingyu
Ding
,
Irene
Azaceta
,
Matthew
Bugnet
,
Demie M.
Kepaptsoglou
,
Vlado K.
Lazarov
,
Víctor A.
De La Pena O'Shea
,
Freddy E.
Oropeza
,
Kelvin H. L.
Zhang
Abstract: The design of heterostructured transition metal-based electrocatalysts with controlled composition and interfaces is key to increasing the efficiency of the water electrolysis and the elucidation of reaction mechanisms. In this work, we report the synthesis of well-controlled vertically aligned Ni/NiO nanocomposites consisting of Ni nanoclusters embedded in NiO, which result in highly efficient electrocatalysts for overall water splitting. We show that such a high catalytic efficiency toward both the hydrogen evolution reaction (HER) and the oxygen evolution reaction (OER) originates from a synergetic effect at Ni/NiO interfaces that significantly reduces the energy barrier for water dissociation, and favours the formation of reactive H* intermediates on the Ni side of the interface, and OHads on the NiO side of the interface. A study of water chemisorption based on near-ambient pressure photoelectron spectroscopy indicates that the abundant hetero-interfaces in Ni/NiO nanocomposite promote the dissociation of water with a three-fold increase in the surface concentration of OHads compared with pure NiO. Density functional theory calculations indicate that Ni/NiO interface leads to the reduction of the water dissociation energy barrier due to a high concentration of oxygen vacancies at NiO side of the interface, whereas the formation of highly active metallic Ni sites with an optimal value of Gibbs free energy of H* (ΔGH* = −0.16 eV) owes to a favourable adjustment of the electron energetics at the interface, thus accelerating the overall electrochemical water splitting.
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Sep 2022
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[15246, 15478]
Abstract: Improving the performance of polyurethane is a crucial endeavor due to its versatile properties that make it suitable for various uses, especially as a matrix in the field of composite materials. The current work investigates the influence of the addition of two types of graphene derivatives, graphene oxide (GO) and reduced graphene oxide (rGO), to hard copolymer polyurethane (HCPU). HCPUs as nanocomposites were synthesized using melt-mixing approaches with different weight ratios of nanofiller additives. The transmission electron microscopy and scanning electron microscopy displayed the morphology through the incorporation of nanofillers within the HCPU structure. Thermogravimetric analysis (TGA) testing showed an increase in the thermal stability of HCPU with the addition of GO and rGO. Herein, the overall HCPU crystallinity/microphase separation decreased after the addition of GO and rGO compared to unfilled HCPU samples. The thermal stability test showed significant enhancement with increasing GO and rGO incorporated weight ratio due to the barrier and tortuous path effects of nanofillers. A clear increase in thermal and electrical conductivity is found, in particular at greater content of addition (5 wt%) of rGO in comparison with neat HCPU. The rheological behavior showed that the storage modulus of HCPU nanocomposites increased from that of pure HCPU, proving the formation of a filler-polymer network interaction within the HCPU chain structure. Dispersion and physical and/or chemical interaction of the GO and rGO within polyurethane chains plays a major role in enhancing the morphology and thermal and rheological properties, and thus represents a significant improvement for the final properties of HCPU nanocomposites.
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Sep 2022
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I13-2-Diamond Manchester Imaging
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Diamond Proposal Number(s):
[25453]
Open Access
Abstract: Bush-crickets (or katydids) have sophisticated and ultrasonic ears located in the tibia of their forelegs, with a working mechanism analogous to the mammalian auditory system. Their inner-ears are endowed with an easily accessible hearing organ, the crista acustica (CA), possessing a spatial organisation that allows for different frequencies to be processed at specific graded locations within the structure. Similar to the basilar membrane in the mammalian ear, the CA contains mechanosensory receptors which are activated through the frequency dependent displacement of the CA. While this tonotopical arrangement is generally attributed to the gradual stiffness and mass changes along the hearing organ, the mechanisms behind it have not been analysed in detail. In this study, we take a numerical approach to investigate this mechanism in the Copiphora gorgonensis ear. In addition, we propose and test the effect of the different vibration transmission mechanisms on the displacement of the CA. The investigation was carried out by conducting finite-element analysis on a three-dimensional, idealised geometry of the C. gorgonensis inner-ear, which was based on precise measurements. The numerical results suggested that (i) even the mildest assumptions about stiffness and mass gradients allow for tonotopy to emerge, and (ii) the loading area and location for the transmission of the acoustic vibrations play a major role in the formation of tonotopy.
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Aug 2022
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I14-Hard X-ray Nanoprobe
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Yeseul
Park
,
Zohar
Eyal
,
Péter
Pekker
,
Daniel M.
Chevrier
,
Christopher T.
Lefèvre
,
Pascal
Arnoux
,
Jean
Armengaud
,
Caroline L.
Monteil
,
Assaf
Gal
,
Mihály
Pósfai
,
Damien
Faivre
Diamond Proposal Number(s):
[23693]
Open Access
Abstract: Metal sulfides are a common group of extracellular bacterial biominerals. However, only a few cases of intracellular biomineralization are reported in this group, mostly limited to greigite (Fe3S4) in magnetotactic bacteria. Here, a previously unknown periplasmic biomineralization of copper sulfide produced by the magnetotactic bacterium Desulfamplus magnetovallimortis strain BW-1, a species known to mineralize greigite (Fe3S4) and magnetite (Fe3O4) in the cytoplasm is reported. BW-1 produces hundreds of spherical nanoparticles, composed of 1–2 nm substructures of a poorly crystalline hexagonal copper sulfide structure that remains in a thermodynamically unstable state. The particles appear to be surrounded by an organic matrix as found from staining and electron microscopy inspection. Differential proteomics suggests that periplasmic proteins, such as a DegP-like protein and a heavy metal-binding protein, could be involved in this biomineralization process. The unexpected periplasmic formation of copper sulfide nanoparticles in BW-1 reveals previously unknown possibilities for intracellular biomineralization that involves intriguing biological control and holds promise for biological metal recovery in times of copper shortage.
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Aug 2022
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I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[28349]
Open Access
Abstract: Metal–organic frameworks (MOFs) are among the most promising materials for next-generation energy storage systems. However, the impact of particle morphology on the energy storage performances of these frameworks is poorly understood. To address this, here we use coordination modulation to synthesise three samples of the conductive MOF Cu3(HHTP)2 (HHTP = 2,3,6,7,10,11-hexahydroxytriphenylene) with distinct microstructures. Supercapacitors assembled with these samples conclusively demonstrate that sample microstructure and particle morphology have a significant impact on the energy storage performances of MOFs. Samples with ‘flake-like’ particles, with a pore network comprised of many short pores, display superior capacitive performances than samples with either ‘rod-like’ or strongly agglomerated particles. The results of this study provide a target microstructure for conductive MOFs for energy storage applications.
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Aug 2022
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[19884]
Open Access
Abstract: Homomers are prevalent in bacterial proteomes, particularly among core metabolic enzymes. Homomerization is often key to function and regulation, and interfaces that facilitate the formation of homomeric enzymes are subject to intense evolutionary change. However, our understanding of the molecular mechanisms that drive evolutionary variation in homomeric complexes is still lacking. How is the diversification of protein interfaces linked to variation in functional regulation and structural integrity of homomeric complexes? To address this question, we studied quaternary structure evolution of bacterial methionine S-adenosyltransferases (MATs)—dihedral homotetramers formed along a large and conserved dimeric interface harboring two active sites, and a small, recently evolved, interdimeric interface. Here, we show that diversity in the physicochemical properties of small interfaces is directly linked to variability in the kinetic stability of MAT quaternary complexes and in modes of their functional regulation. Specifically, hydrophobic interactions within the small interface of Escherichia coli MAT render the functional homotetramer kinetically stable yet impose severe aggregation constraints on complex assembly. These constraints are alleviated by electrostatic interactions that accelerate dimer-dimer assembly. In contrast, Neisseria gonorrhoeae MAT adopts a nonfunctional dimeric state due to the low hydrophobicity of its small interface and the high flexibility of its active site loops, which perturbs small interface integrity. Remarkably, in the presence of methionine and ATP, N. gonorrhoeae MAT undergoes substrate-induced assembly into a functional tetrameric state. We suggest that evolution acts on the interdimeric interfaces of MATs to tailor the regulation of their activity and stability to unique organismal needs.
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Jul 2022
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I03-Macromolecular Crystallography
I23-Long wavelength MX
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Christian M.
Orr
,
Hayden
Fisher
,
Xiaojie
Yu
,
Claude H.-T.
Chan
,
Yunyun
Gao
,
Patrick J.
Duriez
,
Steven G.
Booth
,
Isabel
Elliott
,
Tatyana
Inzhelevskaya
,
Ian
Mockridge
,
Christine A.
Penfold
,
Armin
Wagner
,
Martin J.
Glennie
,
Ann L.
White
,
Jonathan W.
Essex
,
Arwen R.
Pearson
,
Mark S.
Cragg
,
Ivo
Tews
Diamond Proposal Number(s):
[22563]
Open Access
Abstract: Antibodies protect from infection, underpin successful vaccines and elicit therapeutic responses in otherwise untreatable cancers and autoimmune conditions. The human IgG2 isotype displays a unique capacity to undergo disulfide shuffling in the hinge region, leading to modulation of its ability to drive target receptor signaling (agonism) in a variety of important immune receptors, through hitherto unexplained molecular mechanisms. To address the underlying process and reveal how hinge disulfide orientation affects agonistic activity, we generated a series of cysteine to serine exchange variants in the hinge region of the clinically relevant monoclonal antibody ChiLob7/4, directed against the key immune receptor CD40. We report how agonistic activity varies with disulfide pattern and is afforded by the presence of a disulfide crossover between F(ab) arms in the agonistic forms, independently of epitope, as observed in the determined crystallographic structures. This structural “switch” affects directly on antibody conformation and flexibility. Small-angle x-ray scattering and ensemble modeling demonstrated that the least flexible variants adopt the fewest conformations and evoke the highest levels of receptor agonism. This covalent change may be amenable for broad implementation to modulate receptor signaling in an epitope-independent manner in future therapeutics.
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Jul 2022
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[20876]
Abstract: A new metastable phase in flash-frozen disordered Prussian blue analogues is reported. The phase is characterised by the appearance of diffuse scattering clouds and the reduction of the local structure symmetry: from cubic to a tetragonal or lower space group. The phase transition is characterised by the translational modulation of the structure and is likely caused by the freezing of the water confined in the pores of the structure.
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Jun 2022
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