School of Chemistry - Research Publications
Now showing items 1-12 of 841
Altered structure and dynamics of pathogenic cytochrome c variants correlate with increased apoptotic activity.
(Portland Press Ltd., 2021-02-12)
Mutation of cytochrome c in humans causes mild autosomal dominant thrombocytopenia. The role of cytochrome c in platelet formation, and the molecular mechanism underlying the association of cytochrome c mutations with thrombocytopenia remains unknown, although a gain-of-function is most likely. Cytochrome c contributes to several cellular processes, with an exchange between conformational states proposed to regulate changes in function. Here, we use experimental and computational approaches to determine whether pathogenic variants share changes in structure and function, and to understand how these changes might occur. Three pathogenic variants (G41S, Y48H, A51V) cause an increase in apoptosome activation and peroxidase activity. Molecular dynamics simulations of these variants, and two non-naturally occurring variants (G41A, G41T), indicate that increased apoptosome activation correlates with the increased overall flexibility of cytochrome c, particularly movement of the Ω loops. Crystal structures of Y48H and G41T complement these studies which overall suggest that the binding of cytochrome c to apoptotic protease activating factor-1 (Apaf-1) may involve an 'induced fit' mechanism which is enhanced in the more conformationally mobile variants. In contrast, peroxidase activity did not significantly correlate with protein dynamics. Thus, the mechanism by which the variants increase peroxidase activity is not related to the conformational dynamics of the native hexacoordinate state of cytochrome c. Recent molecular dynamics data proposing conformational mobility of specific cytochrome c regions underpins changes in reduction potential and alkaline transition pK was not fully supported. These data highlight that conformational dynamics of cytochrome c drive some but not all of its properties and activities.
Collagen-Targeted Peptides for Molecular Imaging of Diffuse Cardiac Fibrosis
Background Cardiac fibrosis is the excessive deposition of extracellular matrix in the heart, triggered by a cardiac insult, aging, genetics, or environmental factors. Molecular imaging of the cardiac extracellular matrix with targeted probes could improve diagnosis and treatment of heart disease. However, although this technology has been used to demonstrate focal scarring arising from myocardial infarction, its capacity to demonstrate extracellular matrix expansion and diffuse cardiac fibrosis has not been assessed. Methods and Results Here, we report the use of collagen-targeted peptides labeled with near-infrared fluorophores for the detection of diffuse cardiac fibrosis in the β2-AR (β-2-adrenergic receptor) overexpressing mouse model and in ischemic human hearts. Two approaches were evaluated, the first based on a T peptide that binds matrix metalloproteinase-2-proteolyzed collagen IV, and the second on the cyclic peptide EP-3533, which targets collagen I. The systemic and cardiac uptakes of both peptides (intravenously administered) were quantified ex vivo by near-infrared imaging of whole organs, tissue sections, and heart lysates. The peptide accumulation profiles corresponded to an immunohistochemically-validated increase in collagen types I and IV in hearts of transgenic mice versus littermate controls. The T peptide could encouragingly demonstrate both the intermediate (7 months old) and severe (11 months old) cardiomyopathic phenotypes. Co-immunostainings of fluorescent peptides and collagens, as well as reduced collagen binding of a control peptide, confirmed the collagen specificity of the tracers. Qualitative analysis of heart samples from patients with ischemic cardiomyopathy compared with nondiseased donors supported the collagen-enhancement capabilities of these peptides also in the clinical settings. Conclusions Together, these observations demonstrate the feasibility and translation potential of molecular imaging with collagen-binding peptides for noninvasive imaging of diffuse cardiac fibrosis.
Selective crystallization via vibrational strong coupling
(ROYAL SOC CHEMISTRY, 2021-08-10)
The coupling of (photo)chemical processes to optical cavity vacuum fields is an emerging method for modulating molecular and material properties. Recent reports have shown that strong coupling of the vibrational modes of solvents to cavity vacuum fields can influence the chemical reaction kinetics of dissolved solutes. This suggests that vibrational strong coupling might also effect other important solution-based processes, such as crystallization from solution. Here we test this hitherto unexplored notion, investigating pseudopolymorphism in the crystallization from water of ZIF metal-organic frameworks inside optical microcavities. We find that ZIF-8 crystals are selectively obtained from solution inside optical microcavities, where the OH stretching vibration of water is strongly coupled to cavity vacuum fields, whereas mixtures of ZIF-8 and ZIF-L are obtained otherwise. Moreover, ZIF crystallization is accelerated by solvent vibrational strong coupling. This work suggests that cavity vacuum fields might become a tool for materials synthesis, biasing molecular self-assembly and driving macroscopic material outcomes.
Sound methods for the synthesis of nanoparticles from biological molecules
(ROYAL SOC CHEMISTRY, 2021-07-19)
Low and high frequency ultrasonic techniques offer a green strategy to synthesize multifunctional nanoparticles from small aromatic biological molecules and proteins with tunable size, morphology, and optical and bio-functional properties.
Toward an Understanding of the Propensity for Crystalline Hydrate Formation by Molecular Compounds. Part 2
(AMER CHEMICAL SOC, 2021-09-01)
The propensity of molecular organic compounds to form stoichiometric or nonstoichiometric crystalline hydrates remains a challenging aspect of crystal engineering and is of practical relevance to fields such as pharmaceutical science. In this work, we address the propensity for hydrate formation of a library of eight compounds comprised of 5- and 6-membered N-heterocyclic aromatics classified into three subgroups: linear dipyridyls, substituted Schiff bases, and tripodal molecules. Each molecular compound studied possesses strong hydrogen bond acceptors and is devoid of strong hydrogen bond donors. Four methods were used to screen for hydrate propensity using the anhydrate forms of the molecular compounds in our library: water slurry under ambient conditions, exposure to humidity, aqueous solvent drop grinding (SDG), and dynamic water vapor sorption (DVS). In addition, crystallization from mixed solvents was studied. Water slurry, aqueous SDG, and exposure to humidity were found to be the most effective methods for hydrate screening. Our study also involved a structural analysis using the Cambridge Structural Database, electrostatic potential (ESP) maps, full interaction maps (FIMs), and crystal packing motifs. The hydrate propensity of each compound studied was compared to a compound of the same type known to form a hydrate through a previous study of ours. Out of the eight newly studied compounds (herein numbered 4-11), three Schiff bases were observed to form hydrates. Three crystal structures (two hydrates and one anhydrate) were determined. Compound 6 crystallized as an isolated site hydrate in the monoclinic space group P21/a, while 7 and 10 crystallized in the monoclinic space group P21/c as a channel tetrahydrate and an anhydrate, respectively. Whereas we did not find any direct correlation between the number of H-bond acceptors and either hydrate propensity or the stoichiometry of the resulting hydrates, analysis of FIMs suggested that hydrates tend to form when the corresponding anhydrate structure does not facilitate intermolecular interactions.
Substituted 1,2,3-triazoles: a new class of nitrification inhibitors
(NATURE PORTFOLIO, 2021-07-22)
Nitrogen (N) fertilisers amended with nitrification inhibitors can increase nitrogen use efficiencies in agricultural systems but the effectiveness of existing commercial inhibitor products, including 3,4-dimethylpyrazole phosphate (DMPP), is strongly influenced by climatic and edaphic factors. With increasing pressure to reduce the environmental impact of large-scale agriculture it is important to develop new nitrogen-stabilising products that can give reliable and consistent results, particularly for warmer climatic conditions. We synthesised a library of 17 compounds featuring a substituted 1,2,3-triazole motif and performed laboratory incubations in two south-eastern Australian soils. In the neutral (pH 7.3) soil, the compounds N002, N013, N016 and N017, which possess short non-polar alkyl or alkynyl substituents at the triazole ring, retained NH4+-N concentrations at 35 °C soil temperature to a better extent (P < 0.001) than DMPP. In the alkaline soil (pH 8.8) N013 performed better with regards to NH4+-N retention (P = 0.004) than DMPP at 35 °C soil temperature. Overall, our data suggest that substituted 1,2,3-triazoles, which can be synthesized with good yields and excellent atom economy through 1,3-dipolar cycloaddition from readily available starting materials, are promising nitrification inhibitors performing similar to, or better than DMPP, particularly at elevated soil temperatures.
Preparation of MgTi2O5 nanoparticles for sonophotocatalytic degradation of triphenylmethane dyes
MgTi2O5 (magnesium dititanate) nanoparticles were prepared by a simple hydrothermal assisted post-annealing method and characterized with various analytical techniques. The catalytic properties (sonocatalytic, photocatalytic and sonophotocatalytic activity) were evaluated using the degradation of triphenylmethane dyes (crystal violet, basic fuchsin, and acid fuchsin). The sonophotocatalytic activity of MgTi2O5 nanoparticles towards crystal violet was found to be ~2.9 times higher than the photocatalytic activity and ~20 times higher than that of the sonocatalytic processes. In addition, the sonophotocatalytic efficiency of MgTi2O5 nanoparticles was found to be remarkable for the degradation of basic fuchsin (cationic dye) and acid fuchsin (anionic dye). The mechanism of these catalytic activities has been discussed in detail.
Ultrasound-Assisted Microencapsulation of Soybean Oil and Vitamin D Using Bare Glycogen Nanoparticles
Ultrasonically synthesized core-shell microcapsules can be made of synthetic polymers or natural biopolymers, such as proteins and polysaccharides, and have found applications in food, drug delivery and cosmetics. This study reports on the ultrasonic synthesis of microcapsules using unmodified (natural) and biodegradable glycogen nanoparticles derived from various sources, such as rabbit and bovine liver, oyster and sweet corn, for the encapsulation of soybean oil and vitamin D. Depending on their source, glycogen nanoparticles exhibited differences in size and 'bound' proteins. We optimized various synthetic parameters, such as ultrasonic power, time and concentration of glycogens and the oil phase to obtain stable core-shell microcapsules. Particularly, under ultrasound-induced emulsification conditions (sonication time 45 s and sonication power 160 W), native glycogens formed microcapsules with diameter between 0.3 μm and 8 μm. It was found that the size of glycogen as well as the protein component play an important role in stabilizing the Pickering emulsion and the microcapsules shell. This study highlights that native glycogen nanoparticles without any further tedious chemical modification steps can be successfully used for the encapsulation of nutrients.
Graphene/fluorescein dye-based sensor for detecting As(III) in drinking water
(NATURE PORTFOLIO, 2021-08-27)
A complex of reduced graphene oxide (rGO) and fluorescein (FL) dye nanoparticles of size between 50 and 100 nm has been prepared and its sensing performance for detection of As(III) in drinking water has been reported. When As(III) binds to the rGO-FL nanoparticles the relative quenching of fluorescence was increased with increase in As(III) concentration thus provide two linear calibration ranges (0-4.0 mmol L-1 and 4.0-10 mmol L-1). The fluorescence quenching mechanism was investigated by using time-resolved fluorescence spectroscopy and molecular modeling. The detection limit of this sensor has been determined as equal to 0.96 µg L-1 which is about 10 times lower than the WHO stipulated standard for As(III) in drinking water (10 µg L-1). The analytical performance and potential application of the nanosensor was compared to commercial field kits used in arsenic monitoring. The sensor proposed in this study is fast, sensitive and accurate for detection of As(III) in drinking water and environmental samples.
The structural basis of bacterial manganese import
(AMER ASSOC ADVANCEMENT SCIENCE, 2021-08-01)
Metal ions are essential for all forms of life. In prokaryotes, ATP-binding cassette (ABC) permeases serve as the primary import pathway for many micronutrients including the first-row transition metal manganese. However, the structural features of ionic metal transporting ABC permeases have remained undefined. Here, we present the crystal structure of the manganese transporter PsaBC from Streptococcus pneumoniae in an open-inward conformation. The type II transporter has a tightly closed transmembrane channel due to "extracellular gating" residues that prevent water permeation or ion reflux. Below these residues, the channel contains a hitherto unreported metal coordination site, which is essential for manganese translocation. Mutagenesis of the extracellular gate perturbs manganese uptake, while coordination site mutagenesis abolishes import. These structural features are highly conserved in metal-specific ABC transporters and are represented throughout the kingdoms of life. Collectively, our results define the structure of PsaBC and reveal the features required for divalent cation transport.
Antibacterial mechanism of ultrasound against Escherichia coli: Alterations in membrane microstructures and properties
This study was aimed at providing new insights on the response of bacterial cell membranes to ultrasound exposure. Escherichia coli (E. coli) O157:H7 cells were exposed to different ultrasound treatments (power intensities of 64, 191, 372, and 573 W/cm2, frequency of 20 kHz, pulsed mode of 2 sec: 2 sec) and the dynamic changes in cell viability within 27 min were assessed. With an increase in ultrasonic intensity and prolonged duration, a 0.76-3.52 log CFU/mL reduction in E. coli populations was attained. The alterations in the sensitivity of ultrasound-treated cells to antimicrobial compounds were evaluated by exposure to thyme essential oil nanoemulsion (TEON). The treatment reduced the E. coli population by 2.16-7.10 log CFU/mL, indicating the effects of ultrasonic field on facilitating the antibacterial efficacy of TEON. Ultrasonic-treated E. coli cells also displayed remarkable morphological and ultrastructural damages with destroyed membrane integrity and misshaped cell structures, which was observed by electron microscopy analysis. Significant increase in outer and inner membrane permeability, along with the cytoplasmic leakage and membrane depolarization were assessed utilizing spectrophotometry. For the first time, significant reduction in the membrane fluidity in response to ultrasound exposure were investigated. Additional efforts in exploring the effect of ultrasonic field on some bacterial membrane compositions were performed with infrared spectroscopy. In this study, multiple lines of evidence effectively served to elucidate the alterations on cellular membrane structure and property during exposure to sonication that could extend our understanding of the antimicrobial molecular mechanisms of ultrasound.