I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Diamond Proposal Number(s):
[22891, 18136]
Abstract: Among several proteins participating in the olfactory perception process of insects, Odorant Binding Proteins (OBPs) are today considered valid targets for the discovery of compounds that interfere with their host-detection behavior. The 3D structures of Anopheles gambiae mosquito AgamOBP1 in complex with the known synthetic repellents DEET and Icaridin have provided valuable information on the structural characteristics that govern their selective binding.
However, no structure of a plant-derived repellent bound to an OBP has been available until now. Herein, we present the novel three-dimensional crystal structures of AgamOBP5 in complex with two natural phenolic monoterpenoid repellents, Carvacrol and Thymol, and the MPD molecule.
Structural analysis revealed that both monoterpenoids occupy a binding site (Site-1) by adopting two alternative conformations. An additional Carvacrol was also bound to a secondary site (Site-2) near the central cavity entrance. A protein-ligand hydrogen-bond network supplemented by van der Waals interactions spans the entire binding cavity, bridging α4, α6, and α3 helices and stabilizing the overall structure.
Fluorescence competition and Differential Scanning Calorimetry experiments verified the presence of two binding sites and the stabilization effect on AgamOBP5. While Carvacrol and Thymol bind to Site-1 with equal affinity in the submicromolar range, they exhibit a significantly lower and distinct binding capacity for Site-2 with Kd's of ~7 μΜ and ~18 μΜ, respectively.
Finally, a comparison of AgamOBP5 complexes with the AgamOBP4-Indole structure revealed that variations of ligand-interacting aminoacids such as A109T, I72M, A112L, and A105T cause two structurally similar and homologous proteins to display different binding specificities.
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Mar 2023
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E02-JEM ARM 300CF
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William J.
Cull
,
Stephen T.
Skowron
,
Ruth
Hayter
,
Craig T.
Stoppiello
,
Graham A.
Rance
,
Johannes
Biskupek
,
Zakhar R.
Kudrynskyi
,
Zakhar D.
Kovalyuk
,
Christopher S.
Allen
,
Thomas J.
Slater
,
Ute
Kaiser
,
Amalia
Patanè
,
Andrei N.
Khlobystov
Diamond Proposal Number(s):
[25251]
Open Access
Abstract: Indium selenides (InxSey) have been shown to retain several desirable properties, such as ferroelectricity, tunable photoluminescence through temperature-controlled phase changes, and high electron mobility when confined to two dimensions (2D). In this work we synthesize single-layer, ultrathin, subnanometer-wide InxSey by templated growth inside single-walled carbon nanotubes (SWCNTs). Despite the complex polymorphism of InxSey we show that the phase of the encapsulated material can be identified through comparison of experimental aberration-corrected transmission electron microscopy (AC-TEM) images and AC-TEM simulations of known structures of InxSey. We show that, by altering synthesis conditions, one of two different stoichiometries of sub-nm InxSey, namely InSe or β-In2Se3, can be prepared. Additionally, in situ AC-TEM heating experiments reveal that encapsulated β-In2Se3 undergoes a phase change to γ-In2Se3 above 400 °C. Further analysis of the encapsulated species is performed using X-ray photoelectron spectroscopy (XPS), thermogravimetric analysis (TGA), energy dispersive X-ray analysis (EDX), and Raman spectroscopy, corroborating the identities of the encapsulated species. These materials could provide a platform for ultrathin, subnanometer-wide phase-change nanoribbons with applications as nanoelectronic components.
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Mar 2023
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I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[18786]
Open Access
Abstract: The crystallization of a new series of A-site substituted lanthanum ferrite materials (La1–xREx)FeO3 was explored by the hydrothermal method at 240 °C, for rare earth (RE) = Nd, Sm, Gd, Ho, Er, Yb, and Y, with 0 ≤ x ≤ 1. The effect of elemental substitution on the morphological, structural, and magnetic properties of the materials was studied using high-resolution powder X-ray diffraction, energy dispersive spectroscopy (EDS) on the scanning electron microscope, Raman spectroscopy, and SQUID magnetometry. If the radius of the La3+ and the substituent ions is similar, such as for Nd3+, Sm3+, and Gd3+, homogeneous solid solutions are formed, with the orthorhombic GdFeO3-type structure, and a continuous evolution of Raman spectra with composition and distinct magnetic behavior from the end members. When the radius difference between substituents and La3+ is large, such as for Ho3+, Er3+, Yb3+, and Y3+, then instead of forming solid solutions, crystallization in separate phases is found. However, low levels of element mixing are found and intergrowths of segregated regions give composite particles. In this case, the Raman spectra and magnetic behavior are characteristic of mixtures of phases, while EDS shows distinctive elemental segregation. A-site replacement induces an evolution in the crystallite shape with an increasing amount of substituent ions and this is most evident for RE = Y from cube-shaped crystals seen for LaFeO3 to multipodal crystals for (La1–xYx)FeO3, providing evidence for a phase-separation-driven evolution of morphology.
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Mar 2023
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I04-Macromolecular Crystallography
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Martina
Durcik
,
Andrej Emanuel
Cotman
,
Žan
Toplak
,
Štefan
Možina
,
Žiga
Skok
,
Petra Eva
Szili
,
Márton
Czikkely
,
Elvin
Maharramov
,
Thu Hien
Vu
,
Maria Vittoria
Piras
,
Nace
Zidar
,
Janez
Ilaš
,
Anamarija
Zega
,
Jurij
Trontelj
,
Luis A.
Pardo
,
Diarmaid
Hughes
,
Douglas
Huseby
,
Tália
Berruga-Fernández
,
Sha
Cao
,
Ivailo
Simoff
,
Richard
Svensson
,
Sergiy V.
Korol
,
Zhe
Jin
,
Francisca
Vicente
,
Maria C.
Ramos
,
Julia E. A.
Mundy
,
Anthony
Maxwell
,
Clare E. M.
Stevenson
,
David M.
Lawson
,
Björn
Glinghammar
,
Eva
Sjöström
,
Martin
Bohlin
,
Joanna
Oreskär
,
Sofie
Alvér
,
Guido V.
Janssen
,
Geert Jan
Sterk
,
Danijel
Kikelj
,
Csaba
Pal
,
Tihomir
Tomašič
,
Lucija
Peterlin Mašič
Diamond Proposal Number(s):
[25108]
Open Access
Abstract: A new series of dual low nanomolar benzothiazole inhibitors of bacterial DNA gyrase and topoisomerase IV were developed. The resulting compounds show excellent broad-spectrum antibacterial activities against Gram-positive Enterococcus faecalis, Enterococcus faecium and multidrug resistant (MDR) Staphylococcus aureus strains [best compound minimal inhibitory concentrations (MICs): range, <0.03125–0.25 μg/mL] and against the Gram-negatives Acinetobacter baumannii and Klebsiella pneumoniae (best compound MICs: range, 1–4 μg/mL). Lead compound 7a was identified with favorable solubility and plasma protein binding, good metabolic stability, selectivity for bacterial topoisomerases, and no toxicity issues. The crystal structure of 7a in complex with Pseudomonas aeruginosa GyrB24 revealed its binding mode at the ATP-binding site. Expanded profiling of 7a and 7h showed potent antibacterial activity against over 100 MDR and non-MDR strains of A. baumannii and several other Gram-positive and Gram-negative strains. Ultimately, in vivo efficacy of 7a in a mouse model of vancomycin-intermediate S. aureus thigh infection was also demonstrated.
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Mar 2023
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B18-Core EXAFS
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Diamond Proposal Number(s):
[25120]
Open Access
Abstract: The development of multielectron redox-active cathode materials is a top priority for achieving high energy density with long cycle life in the next-generation secondary battery applications. Triggering anion redox activity is regarded as a promising strategy to enhance the energy density of polyanionic cathodes for Li/Na-ion batteries. Herein, K2Fe(C2O4)2 is shown to be a promising new cathode material that combines metal redox activity with oxalate anion (C2O42–) redox. This compound reveals specific discharge capacities of 116 and 60 mAh g–1 for sodium-ion batterie (NIB) and lithium-ion batterie (LIB) cathode applications, respectively, at a rate of 10 mA g–1, with excellent cycling stability. The experimental results are complemented by density functional theory (DFT) calculations of the average atomic charges.
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Mar 2023
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[28511]
Open Access
Abstract: The contents of biological cells are retained within compartments formed of phospholipid membranes. The movement of material within and between cells is often mediated by the fusion of phospholipid membranes, which allows mixing of contents or excretion of material into the surrounding environment. Biological membrane fusion is a highly regulated process that is catalyzed by proteins and often triggered by cellular signaling. In contrast, the controlled fusion of polymer-based membranes is largely unexplored, despite the potential application of this process in nanomedicine, smart materials, and reagent trafficking. Here, we demonstrate triggered polymersome fusion. Out-of-equilibrium polymersomes were formed by ring-opening metathesis polymerization-induced self-assembly and persist until a specific chemical signal (pH change) triggers their fusion. Characterization of polymersomes was performed by a variety of techniques, including dynamic light scattering, dry-state/cryogenic-transmission electron microscopy, and small-angle X-ray scattering (SAXS). The fusion process was followed by time-resolved SAXS analysis. Developing elementary methods of communication between polymersomes, such as fusion, will prove essential for emulating life-like behaviors in synthetic nanotechnology.
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Mar 2023
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Open Access
Abstract: The most advanced antiviral molecules addressing major SARS-CoV-2 targets (Main protease, Spike protein, and RNA polymerase), compared with proteins of other human pathogenic coronaviruses, may have a short-lasting clinical efficacy. Accumulating knowledge on the mechanisms underlying the target structural basis, its mutational progression, and the related biological significance to virus replication allows envisaging the development of better-targeted therapies in the context of COVID-19 epidemic and future coronavirus outbreaks. The identification of evolutionary patterns based solely on sequence information analysis for those targets can provide meaningful insights into the molecular basis of host–pathogen interactions and adaptation, leading to drug resistance phenomena. Herein, we will explore how the study of observed and predicted mutations may offer valuable suggestions for the application of the so-called “synthetic lethal” strategy to SARS-CoV-2 Main protease and Spike protein. The synergy between genetics evidence and drug discovery may prioritize the development of novel long-lasting antiviral agents.
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Mar 2023
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Mona M.
Katariya
,
Matthew
Snee
,
Richard B.
Tunnicliffe
,
Madeline E.
Kavanagh
,
Helena I. M.
Boshoff
,
Cecilia N.
Amadi
,
Colin W.
Levy
,
Andrew W.
Munro
,
Chris
Abell
,
David
Leys
,
Anthony G.
Coyne
,
Kirsty J.
Mclean
Diamond Proposal Number(s):
[17773, 24447]
Open Access
Abstract: Mycobacterium tuberculosis (Mtb) was responsible for approximately 1.6 million deaths in 2021. With the emergence of extensive drug resistance, novel therapeutic agents are urgently needed, and continued drug discovery efforts required. Host-derived lipids such as cholesterol support Mtb growth, and are also suspected to function in immunomodulation, with links to persistence and immune evasion. Mtb cytochrome P450 (CYP) enzymes facilitate key steps in lipid catabolism and thus present potential targets for inhibition. Here we present a series of compounds based on an ethyl 5-(pyridin-4-yl)-1H-indole-2-carboxylate pharmacophore which bind strongly to both Mtb cholesterol oxidases CYP125 and CYP142. Using a structure-guided approach, combined with biophysical characterization, compounds with micromolar range in-cell activity against clinically relevant drug-resistant isolates were obtained. These will support further development of much-needed additional treatment options and provide routes to probe the role of CYP125 and CYP142 in Mtb pathogenesis.
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Mar 2023
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[19127, 18027]
Open Access
Abstract: Hybrid vesicles consisting of phospholipids and block-copolymers are increasingly finding applications in science and technology. Herein, small angle X-ray scattering (SAXS) and cryo-electron tomography (cryo-ET) are used to obtain detailed structural information about hybrid vesicles with different ratios of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and poly(1,2-butadiene-block-ethylene oxide) (PBd22-PEO14, Ms = 1800 g mol−1). Using single particle analysis (SPA) the authors are able to further interpret the information gained from SAXS and cryo-ET experiments, showing that increasing PBd22-PEO14 mole fraction increases the membrane thickness from 52 Å for a pure lipid system to 97 Å for pure PBd22-PEO14 vesicles. Two vesicle populations with different membrane thicknesses in hybrid vesicle samples are found. As these lipids and polymers are reported to homogeneously mix, bistability is inferred between weak and strong interdigitation regimes of PBd22-PEO14 within the hybrid membranes. It is hypothesized that membranes of intermediate structure are not energetically favorable. Therefore, each vesicle exists in one of these two membrane structures, which are assumed to have comparable free energies. The authors conclude that, by combining biophysical methods, accurate determination of the influence of composition on the structural properties of hybrid membranes is achieved, revealing that two distinct membranes structures can coexist in homogeneously mixed lipid-polymer hybrid vesicles.
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Mar 2023
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I03-Macromolecular Crystallography
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Rob
Barringer
,
Alice E.
Parnell
,
Aleix
Lafita
,
Vivian
Monzon
,
Catherine R.
Back
,
Mariusz
Madej
,
Jan
Potempa
,
Angela H.
Nobbs
,
Steven G.
Burston
,
Alex
Bateman
,
Paul R.
Race
Diamond Proposal Number(s):
[23269]
Abstract: Bacterial fibrillar adhesins are specialised extracellular polypeptides that promote the attachment of bacteria to the surfaces of other cells or materials. Adhesin-mediated interactions are critical for the establishment and persistence of stable bacterial populations within diverse environmental niches and are important determinants of virulence. The fibronectin (Fn) binding fibrillar adhesin CshA, and its paralogue CshB, play important roles in host colonisation by the oral commensal and opportunistic pathogen Streptococcus gordonii. As paralogues are often catalysts for functional diversification, we have probed the early stages of structural and functional divergence in Csh proteins by determining the X-ray crystal structure of the CshB adhesive domain NR2 and characterising its Fn binding properties in vitro. Despite sharing a common fold, CshB_NR2 displays an ~1.7-fold reduction in Fn binding affinity relative to CshA_NR2. This correlates with reduced electrostatic charge in the Fn binding cleft. Complementary bioinformatic studies reveal that homologues of CshA/B_NR2 domains are widely distributed in both Gram-positive and Gram-negative bacteria, where they are found housed within functionally cryptic multi-domain polypeptides. Our findings are consistent with the classification of Csh adhesins and their relatives as members of the recently defined Polymer Adhesin Domain (PAD) family of bacterial proteins.
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Mar 2023
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