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Open Access
Abstract: The adsorption configurations of a technologically relevant model organic adsorbate on the silicon (001) surface were studied using energy scanned X-ray photoelectron diffraction (PhD). Previous work has established the existence of an interesting vertically-aligned ("flagpole") configuration, where the acetophenone attaches to Si(001) via the acetyl group carbon and oxygen atoms. DFT calculations have predicted two energetically similar variants of this structure, where the phenyl ring is orientated parallel or perpendicular to the rows of silicon dimers on this reconstructed surface. However, previously published experimental measurements, including scanning tunnelling microscopy, X-ray photoelectron spectroscopy, and near-edge X-ray absorption fine structure investigations were unable to distinguish between these two configurations. Here, we apply the unique experimental capabilities of the PhD technique to this system and demonstrate that the dominant adsorption configuration has the phenyl ring parallel to the dimer rows (the end-bridge structure). This information in turn facilitates the determination of the dominant reaction pathway for acetophenone on Si(001), which has remained elusive until now. Information about subtle preferences in reaction pathways that affect the alignment and orientation of organic adsorbates such as acetophenone on technologically-relevant semiconductor surfaces such as Si(001) is critical for the fabrication of future atomically-precise atomic and molecular-scale electronic devices utilising the organic-silicon interface, and this work demonstrates the unique and complementary capabilities of PhD for providing this information.
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Feb 2021
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[15833]
Open Access
Abstract: The solid state supramolecular interactions of diketopyrrolopyrrole derivatives (DPPs) and their correlation with thin film optical properties are of particular interest because of the applications of these materials in organic electronics. In this study, we report the single crystal X-ray structures of several phenyl DPP derivatives, containing 4-methoxyphenyl, 4-hydroxyphenyl and 4-((tetrahydro-2H-pyran-2-yl)oxy)phenyl aryl units, and show how subtle changes in the substituent chains at side or end positions of the chromophore can lead to very different packing. They are compared to their phenyl counterpart to explore how the nature of both the alkyl chain and the aryl unit influence the optical properties that have been measured in solid and solution states. Importantly, for the three families of N-substituted compounds studied, the structures are changed by the conformation of the molecules and are apparently dominated by crystal packing effects where edge-to-face interactions are favoured rather than π stacking, with only one of the compounds showing a flat form, promoted by intermolecular contacts between the aromatic regions. It is therefore possible that the twist between DPP and phenyl units in crystals of DPPs results from edge-to-face interactions (rather than steric interactions between the N-substituent and the protons attached to the aromatic ring) that might be overcome in more extended structures. Hydrogen bonding dominates the packing to generate chains of DPP units for phenol derivatives. Remote bulky groups do affect the core conformation. The emission of the materials as thin films is dominated by local effects in the packing of the materials that are unique for each case as the structures are distinct from one another. Charge mobility (as calculated from the crystal structures) is not favoured because of twisted conformations and large displacement, but the sometimes high emission and large Stokes shift could make the materials interesting for other purposes, such as light emitters.
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Feb 2021
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I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[19800]
Abstract: Cooperative ligand binding is an important phenomenon in biological systems where ligand binding influences the binding of another ligand at an alternative site of the protein via an intramolecular network of interactions. The underlying mechanisms behind cooperative binding remain poorly understood, primarily due to the lack of structural data of these ternary complexes. Using time-resolved fluorescence resonance energy transfer (TR-FRET) studies, we show that cooperative ligand binding occurs for RORγt, a nuclear receptor associated with the pathogenesis of autoimmune diseases. To provide the crucial structural insights, we solved 12 crystal structures of RORγt simultaneously bound to various orthosteric and allosteric ligands. The presence of the orthosteric ligand induces a clamping motion of the allosteric pocket via helices 4 to 5. Additional molecular dynamics simulations revealed the unusual mechanism behind this clamping motion, with Ala355 shifting between helix 4 and 5. The orthosteric RORγt agonists regulate the conformation of Ala355, thereby stabilizing the conformation of the allosteric pocket and cooperatively enhancing the affinity of the allosteric inverse agonists.
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Feb 2021
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[25402]
Open Access
Abstract: For several centuries, microorganisms and enzymes have been used for many different applications. Although many enzymes with industrial applications have already been reported, different screening technologies, methods and approaches are constantly being developed in order to allow the identification of enzymes with even more interesting applications. In our work, we have performed data mining on the Chitinophaga sp. genome, a gram-negative bacterium isolated from a bacterial consortium of sugarcane bagasse isolated from an ethanol plant. The analysis of 8 Mb allowed the identification of the chtcp gene, previously annotated as putative Cht4039. The corresponding codified enzyme, denominated as ChtCP, showed the HEXXH conserved motif of family M32 from thermostable carboxypeptidases. After expression in E. coli, the recombinant enzyme was characterized biochemically. ChtCP showed the highest activity versus benziloxicarbonil Ala-Trp at pH 7.5, suggesting a preference for hydrophobic substrates. Surprisingly, the highest activity of ChtCP observed was between 55 °C and 75 °C, and 62% activity was still displayed at 100 °C. We observed that Ca2+, Ba2+, Mn2+ and Mg2+ ions had a positive effect on the activity of ChtCP, and an increase of 30 °C in the melting temperature was observed in the presence of Co2+. These features together with the structure of ChtCP at 1.2 Å highlight the relevance of ChtCP for further biotechnological applications.
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Feb 2021
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[27906]
Open Access
Abstract: Multicomponent hydrogels offer a tremendous opportunity to prepare useful and exciting materials that cannot be accessed using a single component. Here, we describe an unusual multi‐component low molecular weight gelling system that exhibits pH‐responsive behavior involving cooperative hydrogen bonding between the components, allowing it to maintain a gel phase across a wide pH range. Unlike traditional acid‐triggered gels, our system undergoes a change in the underlying molecular packing and maintains the β‐sheet structure both at acidic and basic pH. We further establish that autonomous programming between these two gel states is possible by an enzymatic reaction which allows us to prepare gels with improved mechanical properties.
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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):
[27011]
Abstract: A two-phase near-β titanium alloy (Ti–10V–2Fe–3Al, or Ti-1023) in its as-forged state is employed to illustrate the feasibility of a Bayesian framework to identify single-crystal elastic constants (SEC). High Energy X-ray diffraction (HE-XRD) obtained at the Diamond synchrotron source are used to characterize the evolution of lattice strains for various grain orientations during in situ specimen loading in the elastic regime. On the other hand, specimen behavior and grain deformation are estimated using the elastic self-consistent (ELSC) homogenization scheme. The XRD data and micromechanical modelling are revisited with a Bayesian framework. The effect of different material parameters (crystallographic and morphological textures, phase volume fraction) of the micromechanical model and the biases introduced by the XRD data on the identification of the SEC of the β phase are systematically investigated. In this respect, all the three cubic elastic constants of the β phase (
) in the Ti-1023 alloy have been derived with their uncertainties. The grain aspect ratio in the ELSC model, which is often not considered in the literature, is found to be an important parameter in affecting the identified SEC. The Bayesian inference suggests a high probability for non-spherical grains (aspect ratio of
):
. The uncertainty obtained by Bayesian approach lies in the range of ∼1-3 GPa for the shear modulus
, and ∼7 GPa for the shear modulus
, while it is significantly larger in the case of the bulk modulus
(∼17-24 GPa).
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Feb 2021
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Shanshan
Zhou
,
Hussain
Bhukya
,
Nicolas
Malet
,
Peter J.
Harrison
,
Dean
Rea
,
Matthew J.
Belousoff
,
Hariprasad
Venugopal
,
Paulina K.
Sydor
,
Kathryn M.
Styles
,
Lijiang
Song
,
Max J.
Cryle
,
Lona M.
Alkhalaf
,
Vilmos
Fulop
,
Gregory L.
Challis
,
Christophe
Corre
Diamond Proposal Number(s):
[8359, 8388]
Abstract: Actinobacteria produce numerous antibiotics and other specialized metabolites that have important applications in medicine and agriculture1. Diffusible hormones frequently control the production of such metabolites by binding TetR family transcriptional repressors (TFTRs), but the molecular basis for this remains unclear2. The production of methylenomycin antibiotics in Streptomyces coelicolor A3(2) is initiated by the binding of 2-alkyl-4-hydroxymethylfuran-3-carboxylic acid (AHFCA) hormones to the TFTR MmfR3. Here we report the X-ray crystal structure of an MmfR–AHFCA complex, establishing the structural basis for hormone recognition. We also elucidate the mechanism for DNA release upon hormone binding through the single-particle cryo-electron microscopy structure of an MmfR–operator complex. DNA binding and release assays with MmfR mutants and synthetic AHFCA analogues define the role of individual amino acid residues and hormone functional groups in ligand recognition and DNA release. These findings will facilitate the exploitation of actinobacterial hormones and their associated TFTRs in synthetic biology and in the discovery of new antibiotics.
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Feb 2021
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B21-High Throughput SAXS
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Yoshifumi
Itoh
,
Michael
Ng
,
Akira
Wiberg
,
Katsuaki
Inoue
,
Narumi
Hirata
,
Katiucia Batista Silva
Paiva
,
Noriko
Ito
,
Kim
Dzobo
,
Nanami
Sato
,
Valentina
Gifford
,
Yasuyuki
Fujita
,
Masaki
Inada
,
Dominic
Furniss
Abstract: Dupuytren's Disease (DD) is a common fibroproliferative disease of the palmar fascia. We previously identified a causal association with a non-synonymous variant (rs1042704, p.D273N) in MMP14 (encoding MT1-MMP). In this study, we investigated the functional consequences of this variant, and demonstrated that the variant MT1-MMP (MT1-N273) exhibits only 17% of cell surface collagenolytic activity compared to the ancestral enzyme (MT1-D273). Cells expressing both MT1-D273 and MT1-N273 in a 1:1 ratio, mimicking the heterozygous state, possess 38% of the collagenolytic activity compared to the cells expressing MT1-D273, suggesting that MT1-N273 acts in a dominant negative manner. Consistent with the above observation, patient-derived DD myofibroblasts with the alternate allele demonstrated around 30% of full collagenolytic activity detected in ancestral G/G genotype cells, regardless of the heterozygous (G/A) or homozygous (A/A) state. Small angle X-ray scattering analysis of purified soluble Fc-fusion enzymes allowed us to construct a 3D-molecular envelope of MT1-D273 and MT1-N273, and demonstrate altered flexibility and conformation of the ectodomains due to D273 to N substitution. Taking together, rs1042704 significantly reduces collagen catabolism in tissue, which tips the balance of homeostasis of collagen in tissue, contributing to the fibrotic phenotype of DD. Since around 30% of the worldwide population have at least one copy of the low collagenolytic alternate allele, further investigation of rs1042704 across multiple pathologies is needed.
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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):
[24685]
Open Access
Abstract: This paper presents a diamond gammavoltaic cell – a solid state device which converts gamma radiation into electricity - with a novel design and promising capabilities. Gammavoltaics pose a unique challenge among radiovoltaics due to the highly penetrating nature of gamma rays. Adapting existing radiovoltaic and dosimeter designs by increasing their thickness risks throttling the flowing current, due to an attendant increase in series resistance. The presented design partially decouples this relationship, by creating a low-coverage hydrogen-terminated collection volume around the device, exploiting the transfer doping effect. This paper proves that hydrogen termination is necessary for the gammavoltaism exhibited. Data are then presented from current-voltage curves taken using synchrotron radiation, over the range 50 – 150 keV. A drop in series resistance over the range is discovered, and linked to the transition from the photoelectric effect to Compton scattering. The cell produces an open-circuit voltage VOC = 0.8 V. Its short-circuit current ISC and maximum power Pmax are found to also depend on photon energy, reaching maxima at ∼ 150 keV, where ISC > 10 μA and Pmax > 3 μW, normalised in flux to 2 × 1011 γ.s-1. Groundwork is hence laid for developing this type of cell for micropower applications.
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Feb 2021
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[17251]
Open Access
Abstract: Acquisition of foreign DNA by Staphylococcus aureus, including vancomycin resistance genes, is thwarted by the ATP-dependent endonuclease SauUSI. Deciphering the mechanism of action of SauUSI could unravel the reason how it singularly plays a major role in preventing horizontal gene transfer (HGT) in S. aureus. Here, we report a detailed biochemical and structural characterization of SauUSI, which reveals that in the presence of ATP, the enzyme can cleave DNA having a single or multiple target site/s. Remarkably, in the case of multiple target sites, the entire region of DNA flanked by two target sites is shred into smaller fragments by SauUSI. Crystal structure of SauUSI reveals a stable dimer held together by the nuclease domains, which are spatially arranged to hydrolyze the phosphodiester bonds of both strands of the duplex. Thus, the architecture of the dimeric SauUSI facilitates cleavage of either single-site or multi-site DNA. The structure also provides insights into the molecular basis of target recognition by SauUSI. We show that target recognition activates ATP hydrolysis by the helicase-like ATPase domain, which powers active directional movement (translocation) of SauUSI along the DNA. We propose that a pile-up of multiple translocating SauUSI molecules against a stationary SauUSI bound to a target site catalyzes random double-stranded breaks causing shredding of the DNA between two target sites. The extensive and irreparable damage of the foreign DNA by shredding makes SauUSI a potent barrier against HGT.
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Feb 2021
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