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The human sliding clamp protein known as proliferating cell nuclear antigen (PCNA) orchestrates DNA-replication and -repair and as such is an ideal therapeutic target for proliferative diseases, including cancer. Peptides derived from the human p21 protein bind PCNA with high affinity via a 310-helical binding conformation and are known to shut down DNA-replication. Here, we present studies on short analogues of p21 peptides (143–151) conformationally constrained with a covalent linker between i, i + 4 separated cysteine residues at positions 145 and 149 to access peptidomimetics that target PCNA. The resulting macrocycles bind PCNA with KD values ranging from 570 nM to 3.86 μM, with the bimane-constrained peptide 7 proving the most potent. Subsequent X-ray crystallography and computational modelling studies of the macrocyclic peptides bound to PCNA indicated only the high-affinity peptide 7 adopted the classical 310-helical binding conformation. This suggests the 310-helical conformation is critical to high affinity PCNA binding, however NMR secondary shift analysis of peptide 7 revealed this secondary structure was not well-defined in solution. Peptide 7 is cell permeable and localised to the cell cytosol of breast cancer cells (MDA-MB-468), revealed by confocal microscopy showing blue fluorescence of the bimane linker. The inherent fluorescence of the bimane moiety present in peptide 7 allowed it to be directly imaged in the cell uptake assay, without attachment of an auxiliary fluorescent tag. This highlights a significant benefit of using a bimane constraint to access conformationally constrained macrocyclic peptides. This study identifies a small peptidomimetic that binds PCNA with higher affinity than previous reported p21 macrocycles, and is cell permeable, providing a significant advance toward development of a PCNA inhibitor for therapeutic applications., A small, inherently fluorescent macrocyclic peptide constrained with a bimane-linker is cell permeable, and binds the human sliding clamp protein, PCNA, in a 310-helical conformation with nanomolar affinity.

We present a new coating procedure to prepare optical fibre sensors suitable for use with protein analytes. We demonstrate this through the detection of AlexaFluor-532 tagged streptavidin by its binding to D-biotin that is functionalised onto an optical fibre, via incorporation in a silk fibroin fibre coating. The D-biotin was covalently attached to a silk-binding peptide to provide SBP–biotin, which adheres the D-biotin to the silk-coated fibre tip. These optical fibre probes were prepared by two methods. The first involves dip-coating the fibre tip into a mixture of silk fibroin and SBP–biotin, which distributes the SBP–biotin throughout the silk coating (method A). The second method uses two steps, where the fibre is first dip-coated in silk only, then SBP–biotin added in a second dip-coating step. This isolates SBP–biotin to the outer surface of the silk layer (method B). A series of fluorescence measurements revealed that only the surface bound SBP–biotin detects streptavidin with a detection limit of 15 μg mL−1. The fibre coatings are stable to repeated washing and long-term exposure to water. Formation of silk coatings on fibres using commercial aqueous silk fibroin was found to be inhibited by a lithium concentration of 200 ppm, as determined by atomic absorption spectroscopy. This was reduced to less than 20 ppm by dialysis against water, and was found to successfully form a coating on optical fibres.

A new class of semiconductor photonic crystals composed of titanium dioxide (TiO2)-functionalized nanoporous anodic alumina (NAA) broadband-distributed Bragg reflectors (BDBRs) for visible-light-driven photocatalysis is presented. NAA-BDBRs produced by double exponential pulse anodization (DEPA) show well-resolved, spectrally tunable, broad photonic stop bands (PSBs), the width of which can be precisely tuned from 70 ± 6 to 153 ± 9 nm (in air) by progressive modification of the anodization period in the input DEPA profile. Photocatalytic efficiency of TiO2-NAA-BDBRs with tunable PSB width upon visible-NIR illumination is studied using three model photodegradation reactions of organics with absorbance bands across the visible spectral regions. Analysis of these reactions allows us to elucidate the interplay of spectral distance between red edge of TiO2-NAA-BDBRs' PSB, electronic bandgap, and absorbance band of model organics in harnessing visible photons for photocatalysis. Photodegradation reaction efficiency is optimal when the PSB's red edge is spectrally close to the electronic bandgap of the functional semiconductor coating. Photocatalytic performance decreases dramatically when the red edge of the PSB is shifted toward visible wavelengths. However, a photocatalytic recovery is observed when the PSB's red edge is judiciously positioned within the proximity of the absorption band of model organics, indicating that TiO2-NAA-BDBRs can harness visible electromagnetic waves to speed up photocatalytic reactions by drastically slowing the group velocity of incident photons at specific spectral regions. Our advances provide new opportunities to better understand and engineer light-matter interactions for photocatalysis, using TiO2-NAA-BDBRs as model nanoporous semiconductor platforms. These high-performing photocatalysts could find broad applicability in visible-NIR light harvesting for environmental remediation, green energy generation, and chemical synthesis.

Enzymes involved in Staphylococcus aureus amino acid metabolism have recently gained traction as promising targets for the development of new antibiotics, however, not all aspects of this process are understood. The ATP-grasp superfamily includes enzymes that predominantly catalyze the ATP-dependent ligation of various carboxylate and amine substrates. One subset, ʟ-amino acid ligases (LALs), primarily catalyze the formation of dipeptide products in Gram-positive bacteria, however, their involvement in S. aureus amino acid metabolism has not been investigated. Here, we present the characterization of the putative ATP-grasp enzyme (SAOUHSC_02373) from S. aureus NCTC 8325 and its identification as a novel LAL. First, we interrogated the activity of SAOUHSC_02373 against a panel of ʟ-amino acid substrates. As a result, we identified SAOUHSC_02373 as an LAL with high selectivity for ʟ-aspartate and ʟ-methionine substrates, specifically forming an ʟ-aspartyl-ʟ-methionine dipeptide. Thus, we propose that SAOUHSC_02373 be assigned as ʟ-aspartate-ʟ-methionine ligase (LdmS). To further understand this unique activity, we investigated the mechanism of LdmS by X-ray crystallography, molecular modeling, and site-directed mutagenesis. Our results suggest that LdmS shares a similar mechanism to other ATP-grasp enzymes but possesses a distinctive active site architecture that confers selectivity for the ʟ-Asp and ʟ-Met substrates. Phylogenetic analysis revealed LdmS homologs are highly conserved in Staphylococcus and closely related Gram-positive Firmicutes. Subsequent genetic analysis upstream of the ldmS operon revealed several trans-acting regulatory elements associated with control of Met and Cys metabolism. Together, these findings support a role for LdmS in Staphylococcal sulfur amino acid metabolism.

Amyloid beta peptide (Aβ42) aggregation in the brain is thought to be responsible for the onset of Alzheimer's disease, an insidious condition without an effective treatment or cure. Hence, a strategy to prevent aggregation and subsequent toxicity is crucial. Bio-inspired peptide-based molecules are ideal candidates for the inhibition of Aβ42 aggregation, and are currently deemed to be a promising option for drug design. In this study, a hexapeptide containing a self-recognition component unique to Aβ42 was designed to mimic the β-strand hydrophobic core region of the Aβ peptide. The peptide is comprised exclusively of D-amino acids to enhance specificity towards Aβ42, in conjunction with a C-terminal disruption element to block the recruitment of Aβ42 monomers on to fibrils. The peptide was rationally designed to exploit the synergy between the recognition and disruption components, and incorporates features such as hydrophobicity, β-sheet propensity, and charge, that all play a critical role in the aggregation process. Fluorescence assays, native ion-mobility mass spectrometry (IM-MS) and cell viability assays were used to demonstrate that the peptide interacts with Aβ42 monomers and oligomers with high specificity, leading to almost complete inhibition of fibril formation, with essentially no cytotoxic effects. These data define the peptide-based inhibitor as a potentially potent anti-amyloid drug candidate for this hitherto incurable disease.

The antioxidant nuclear factor erythroid 2-related factor 2 (Nrf2) is a desirable therapeutic target for a broad range of pathologies, including chronic diseases of the lung and liver, and autoimmune, neurodegenerative, and cardiovascular disorders. However, current Nrf2 activators are limited by unwanted effects due to non-specificity, and systemic distribution and action. Here we report that a 1,2-dicarbonyl moiety masks the electrophilic reactivity of the Nrf2 activator monomethyl fumarate (MMF), otherwise responsible for its non-specific effects. The 1,2-dicarbonyl compound is highly susceptible to Baeyer-Villiger oxidation, with generation of MMF specifically on exposure to pathological levels of hydrogen peroxide or peroxynitrite. Oral treatment with the MMF generating 1,2-dicarbonyl compound reversed chronic neuropathic and osteoarthritis pain in mice, and selectively activated Nrf2 at sites of oxidative stress. This 1,2-dicarbonyl platform may be used to treat additional disorders of oxidative stress, and to selectively target other therapeutics to sites of redox imbalance.

The primary sequence and secondary structure of a peptide are crucial to charge migration, not only in solution (electron transfer, ET), but also in the solid-state (electron transport, ETp). Hence, understanding the charge migration mechanisms is fundamental to the development of biomolecular devices and sensors. We report studies on four Aib-containing helical peptide analogues: two acyclic linear peptides with one and two electron-rich alkene-based side chains, respectively, and two peptides that are further rigidified into a macrocycle by a side bridge constraint, containing one or no alkene. ETp was investigated across Au/peptide/Au junctions, between 80 and 340 K in combination with the molecular dynamic (MD) simulations. The results reveal that the helical structure of the peptide and electron-rich side chain both facilitate the ETp. As temperature increases, the loss of helical structure, change of monolayer tilt angle, and increase of thermally activated fluctuations affect the conductance of peptides. Specifically, room temperature conductance across the peptide monolayers correlates well with previously observed ET rate constants, where an interplay between backbone rigidity and electron-rich side chains was revealed. Our findings provide new means to manipulate electronic transport across solid-state peptide junctions.

The rapidly expanding field of photoswitchable biomolecules is a major frontier in scientific research and provides unparalleled opportunities for studying biological pathways and disease progression. In particular, the development of photochromic peptides has delivered both scientific tools and candidates for photopharmaceuticals. The action and function of the peptide can be remotely altered using light, allowing detection of its biological role in complex biological settings, while also enabling folding studies that provide greater understanding of protein structure dynamics. In this review we provide a key, comprehensive overview of the different types of photoswitches that have been used to control peptide structure, excluding the already extensively reviewed azobenzene. This will help address the question as to which synthetic photoswitch to use in a given study.

A comprehensive study on the engineering of titanium dioxide-functionalized nanoporous anodic alumina distributed Bragg reflectors (TiO2–NAA-DBRs) for photocatalysis enhanced by the “slow photon” effect is presented. The photocatalytic performance of these composite photonic crystals (PCs) is assessed by monitoring photodegradation of a variety of organic molecules with absorbance bands across the spectral regions. This study demonstrates that photocatalytic performance of TiO2–NAA-DBRs is enhanced by the “slow photon” effect when the edges of the PC’s photonic stopband (PSB) fall within the absorbance band of the organic molecules. The photocatalytic performance is significantly enhanced when the PSB’s red edge is in close proximity to the absorbance band of the organic molecules. Overall photocatalytic degradation is also dependent on the total pore length of the PC structure, charge of the organic molecules, percentage of vis–near-IR irradiation, and matrix complexity (i.e., interfering ions and molecules) when the PC’s PSB is partially or entirely misaligned with respect to the absorbance band of the organic molecules. Finally, the real-life application of TiO2–NAA-DBRs to degrade pollutants such as pesticides in environmental matrices is demonstrated. This study provides new insights into the development of rationally engineered, high-performing, safe, and reusable photocatalyst systems. This is peer-reviewed version of the article: ACS Applied Energy Materials, 2019, 2, 2, 1169-1184, [https://doi.org/10.1021/acsaem.8b01721] [http://cer.ihtm.bg.ac.rs/handle/123456789/2988]

Sabrina Heng, Xiaozhou Zhang, Jinxin Pei, Alaknanda Adwal, Philipp Reineck, Brant C. Gibson, Mark R. Hutchinson and Andrew D. Abell

Refereed/Peer-reviewed Local activation of an anti-cancer drug when and where needed can improve selectivity and reduce undesirable side effects. Photoswitchable drugs can be selectively switched between active and inactive states by illumination with light; however, the clinical development of these drugs has been restricted by the difficulty in delivering light deep into tissue where needed. Optical fibres have great potential for light delivery in vivo, but their use in facilitating photoswitching in anti-cancer compounds has not yet been explored. In this paper, a photoswitchable chemotherapeutic is switched using an optical fibre, and the cytotoxicity of each state is measured against HCT-116 colorectal cancer cells. The performance of optical-fibre-enabled photoswitching is characterised through its dose response. The UV–Vis spectra confirm light delivered by an optical fibre effectively enables photoswitching. The activated drug is shown to be twice as effective as the inactive drug incausing cancer cell death, characterised using an MTT assay and fluorescent microscopy. This is the first study in which a photoswitchable anti-cancer compound is switched using an optical fibre and demonstrates the feasibility of using optical fibres to activate photoswitchable drugs for potential future clinical applications.

Fumarates are successfully used for the treatment of psoriasis and multiple sclerosis. Their antioxidative, immunomodulatory, and neuroprotective properties make fumarates attractive therapeutic candidates for other pathologies. The exact working mechanisms of fumarates are, however, not fully understood. Further elucidation of the mechanisms is required if these drugs are to be successfully repurposed for other diseases. Towards this, administration route, dosage, and treatment timing, frequency, and duration are important parameters to consider and optimize with clinical paradigms in mind. Here, we summarize the rapidly expanding literature on the pharmacokinetics and pharmacodynamics of fumarates, including a discussion on two recently FDA-approved fumarates VumerityTM and BafiertamTM. We review emerging applications of fumarates, focusing on neurological and cardiovascular diseases.

High-quality nanoporous anodic alumina gradient-index filters (NAA-GIFs) are realized by sinusoidal pulse anodisation (SPA) of aluminum. A three-level factorial design of experiments is used to determine the effect of three critical anodization parameters –electrolyte temperature, concentration of the electrolyte and anodization time– on the quality of light control in these photonic crystal (PC) structures. Quantitative analysis of the effect of these anodization parameters on the quality of the characteristic photonic stopband (PSB) of NAA-GIFs reveals that all three anodization parameters and their respective combinations have statistically significant effects. However, anodization time is found to have the highest impact on the quality of light control in NAA-GIFs, followed by the electrolyte concentration and its temperature. Our findings demonstrate that NAA-GIFs fabricated under optimal conditions achieve an outstanding quality factor of ∼86 (i.e. ∼18% superior to that of other NAA-based PCs reported in the literature). This study provides new insight into optimal anodization conditions to fabricate high-quality NAA-based PC structures, opening new exciting opportunities to integrate these nanoporous PCs as platform materials for light-based technologies requiring a precise control over photons such as ultra-sensitive optical sensors and biosensors, photocatalysts for green energy generation and environmental remediation, optical encoding and lasing.

Three photoswitchable tetrapeptides, based on a known synthetic antibacterial, were designed and synthesized to determine activity against Staphylococcus aureus ( S. aureus ). Each peptide contains an azobenzene photoswitch incorporated into either the N‐terminal side chain ( 1 ), C‐terminal side chain ( 2 ), or the C‐terminus ( 3 ), to allow reversible switching between cis ‐enriched and trans ‐enriched photostationary states (PSS). Biological assays revealed the C‐terminal azobenzene ( 3 ) possessed the most potent antibacterial activity, with an MIC of 1 µg/mL. In this study, net positive charge, hydrophobicity, position of the azobenzene, secondary structure, and amphiphilicity were all found to contribute to antibacterial activity, with each of these factors likely facilitating the peptide to disrupt the negatively charged bacterial lipid membrane. Hence, these short photoswitchable antibacterial tetrapeptides provide insights for the future design and synthesis of antibiotics for S. aureus infections. Refereed/Peer-reviewed

The development of amorphous films with a wide transmission window and high refractive index is of growing significance due to the strong demand of integrating functional nanoparticles for the next-generation hybrid optoelectronic films. High-index TeO2-based glass films made via the sol–gel process are particularly suitable as their low temperature preparation process promises high compatibility with a large variety of nanoparticles and substrates that suffer from low thermal stability. However, due to the lack of in-depth understanding of the mechanisms of the formation of undesired metallic-Te (highly absorbing species) in the films, the preparation of high-transmission TeO2-based sol–gel films has been severely hampered. Here, by gaining insight into the mechanistic chemistry of metallic-Te formation at different stages during the non-hydrolytic sol–gel process, we identify the chemical route to prevent the generation of metallic-Te in a TeO2-based film. The as-prepared TeO2-based film exhibits a high transmission that is close to the theoretical limit. This opens up a new avenue for advancing the performance of hybrid optoelectronic films via incorporating a large variety of unique nanoparticles. Refereed/Peer-reviewed

Neuronal nitric oxide synthase (nNOS) is an enzyme responsible for catalyzing the production of the crucial cellular signalling molecule, nitric oxide (NO), through its interaction with the PDZ domain of α-syntrophin protein. In this study, a novel light-driven photoswitchable peptide-based biosensor, modelled on the nNOS β-finger, is used to detect and control its interaction with α-syntrophin. An azobenzene photoswitch incorporated into the peptide backbone allows reversible switching between a trans photostationary state devoid of secondary structure, and a cis photostationary state possessing a well-defined antiparallel β-strand geometry, as revealed by molecular modelling. Electrochemical impedance spectroscopy (EIS) is used to successfully detect the interaction between the gold electrode bound peptide in its cis photostationary state and a wide range of concentrations of α-syntrophin protein, highlighting both the qualitative and quantitative properties of the sensor. Furthermore, EIS demonstrates that the probe in its random trans photostationary state does not bind to the target protein. The effectiveness of the biosensor is further endorsed by the high thermal stability of the photostationary state of the cis-isomer, and the ability to actively control biomolecular interactions using light. This approach allows detection and control of binding to yield a regenerable on-off biosensor.

Molecular electronics is at the forefront of interdisciplinary research, offering a significant extension of the capabilities of conventional silicon-based technology as well as providing a possible stand-alone alternative. Bio-inspired molecular electronics is a particularly intriguing paradigm, as charge transfer in proteins/peptides, for example, plays a critical role in the energy storage and conversion processes for all living organisms. However, the structure and conformation of even the simplest protein is extremely complex, and therefore, synthetic model peptides comprising well-defined geometry and predetermined functionality are ideal platforms to mimic nature for the elucidation of fundamental biological processes while also enhancing the design and development of single-peptide electronic components. In this Account, we first present intramolecular electron transfer within two synthetic peptides, one with a well-defined helical conformation and the other with a random geometry, using electrochemical techniques and computational simulations. This study reveals two definitive electron transfer pathways (mechanisms), the natures of which are dependent on secondary structure. Following on from this, electron transfer within a series of well-defined helical peptides, constrained by either Huisgen cycloaddition, ring-closing metathesis, or a lactam bridge, was determined. The electrochemical results indicate that each constrained peptide, in contrast to a linear counterpart, exhibits a remarkable shift of the formal potential to the positive (>460 mV) and a significant reduction of the electron transfer rate constant (up to 15-fold), which represent two distinct electronic "on/off" states. High-level calculations demonstrate that the additional backbone rigidity provided by the side-bridge constraints leads to an increased reorganization energy barrier, which impedes the vibrational fluctuations necessary for efficient intramolecular electron transfer through the peptide backbone. Further calculations reveal a clear mechanistic transition from hopping to superexchange (tunneling) stemming from side-bridge gating. We then extended our research to fine-tuning of the electronic properties of peptides through both structural and chemical manipulation, to reveal an interplay between electron-rich side chains and backbone rigidity on electron transfer. Further to this, we explored the possibility that the side-bridge constraints present in our synthetic peptides provide an additional electronic transport pathway, which led to the discovery of two distinct forms of quantum interferometer. The effects of destructive quantum interference appear essentially through both the backbone and an alternative tunneling pathway provided by the side bridge in the constrained β-strand peptide, as evidenced by a correlation between electrochemical measurements and conductance simulations for both linear and constrained β-strand peptides. In contrast, an interplay between quantum interference effects and vibrational fluctuations is revealed in the linear and constrained 310-helical peptides. Collectively, these exciting findings augment our fundamental knowledge of charge transfer dynamics and kinetics in peptides and also open up new avenues to design and develop functional bio-inspired electronic devices, such as on/off switches and quantum interferometers, for practical applications in molecular electronics.

We have demonstrated that an optical fibre-based pH sensor can be utilised to accurately assess pH in a biological environment. Initial measurements were performed on 5 μL drops of culture medium containing individual female mouse reproductive cells (cumulus-oocyte-complexes, COCs), with the goal of obtaining a biomarker of individual cell health during assisted reproductive processes. Improvements to the measurement procedure were found to reduce fluorescence signal variability, enabling improved measurement precision compared to previous studies. Results show the application of treatments which serve to increase lactic acid production by the COC, and thus induce an acidification of the local microenvironment, are detectable by the pH sensor. This optical technology presents a promising platform for the measurement of pH and the detection of other extracellular biomarkers to assess cell health during assisted reproduction.

Unfertilised eggs (oocytes) release chemical biomarkers into the medium surrounding them. This provides an opportunity to monitor cell health and development during assisted reproductive processes if detected in a non-invasive manner. Here we report the measurement of pH using an optical fibre probe, OFP1, in 5 μL drops of culture medium containing single mouse cumulus oocyte complexes (COCs). This allowed for the detection of statistically significant differences in pH between COCs in culture medium with no additives and those incubated with either a chemical (cobalt chloride) or hormonal treatment (follicle stimulating hormone); both of which serve to induce the release of lactic acid into the medium immediately surrounding the COC. Importantly, OFP1 was shown to be cell-safe with no inherent cell toxicity or light-induced phototoxicity indicated by negative DNA damage staining. Pre-measurement photobleaching of the probe reduced fluorescence signal variability, providing improved measurement precision (0.01-0.05 pH units) compared to previous studies. This optical technology presents a promising platform for the measurement of pH and the detection of other extracellular biomarkers to assess cell health during assisted reproduction. Refereed/Peer-reviewed

Glycosylated human leukocyte elastase (HLE) was crystallized and structurally analysed in complex with a 1,3-thiazolidine-2,4-dione derivative that had been identified as an HLE inhibitor in preliminary studies. In contrast to previously described HLE structures with small-molecule inhibitors, in this structure the inhibitor does not bind to the S1 and S2 substrate-recognition sites; rather, this is the first HLE structure with a synthetic inhibitor in which the S2′ site is blocked that normally binds the second side chain at the C-terminal side of the scissile peptide bond in a substrate protein. The inhibitor also induces the formation of crystalline HLE dimers that block access to the active sites and that are also predicted to be stable in solution. Neither such HLE dimers nor the corresponding crystal packing have been observed in previous HLE crystal structures. This novel crystalline environment contributes to the observation that comparatively large parts of the N-glycan chains of HLE are defined by electron density. The final HLE structure contains the largest structurally defined carbohydrate trees among currently available HLE structures.

In this study, we explore for the first time the capabilities of nanoporous anodic alumina gradient-index filters (NAA-GIFs) functionalized with titanium dioxide (TiO2) photoactive layers to enhance photon-to-electron conversion rates and improve the efficiency of photocatalytic reactions by “slow photon” effect. A set of NAA-GIFs was fabricated by sinusoidal pulse anodization, in which a systematic modification of various anodization parameters (i.e., pore widening time, anodization period, and anodization time) enables the fine-tuning of the photonic stopband (PSB) of these nanoporous photonic crystals (PCs) across the spectral regions. The surface of NAA-GIFs was chemically modified with photoactive layers of TiO2 to create a composite photoactive material with precisely engineered optical properties. The photocatalytic performance of TiO2-functionalized NAA-GIFs was assessed by studying the photodegradation of three model organic dyes (i.e., methyl orange, Rhodamine B, and methylene blue) with well-de...

Biologically compatible fluorescent ion sensors, particularly those that are reversible, represent a key tool for answering a range of fundamental biological questions. We report a rationally designed probe with a 6′-fluoro spiropyran scaffold (5) for the reversible sensing of zinc (Zn 2+ ) in cells. The 6′-fluoro substituent overcomes several limitations normally associated with spiropyran-based sensors to provide an improved signal-To-background ratio and faster photoswitching times in aqueous solution. In vitro studies were performed with 5 and the 6′-nitro analogues (6) in HEK 293 and endothelial cells. The new spiropyran (5) can detect exogenous Zn 2+ inside both cell types and without affecting the proliferation of endothelial cells. Studies were also performed on dying HEK 293 cells, with results demonstrating the ability of the key compound to detect endogenous Zn 2+ efflux from cells undergoing apoptosis. Biocompatibility and photoswitching of 5 were demonstrated within endothelial cells but not with 6, suggesting the future applicability of sensor 5 to study intracellular Zn 2+ efflux in these systems. Refereed/Peer-reviewed

Can we separate embryos cultured under either 7% or 20% oxygen atmospheres by measuring their metabolic heterogeneity?Metabolic heterogeneity and changes in metabolic profiles in morula exposed to two different oxygen concentrations were not detectable using traditional fluorophore and two-channel autofluorescence but were detectable using hyperspectral microscopy.Increased genetic and morphological blastomere heterogeneity is associated with compromised developmental competence of embryos and currently forms the basis for embryo scoring within the clinic. However, there remains uncertainty over the accuracy of current techniques, such as PGS and time-lapse microscopy, to predict subsequent pregnancy establishment.The impact of two oxygen concentrations (7% = optimal and 20% = stressed) during post-fertilisation embryo culture was assessed. Cattle embryos were exposed to the different oxygen concentrations for 8 days (D8; embryo developmental competence) or 5 days (D5; metabolism measurements). Between 3 and 4 experimental replicates were performed, with 40-50 embryos per replicate used for the developmental competency experiment, 10-20 embryos per replicate for the fluorophore and two-channel autofluorescence experiments and a total of 21-22 embryos used for the hyperspectral microscopy study.In-vitro produced (IVP) cattle embryos were utilised for this study. Post-fertilisation, embryos were exposed to 7% or 20% oxygen. To determine impact of oxygen concentrations on embryo viability, blastocyst development was assessed on D8. On D5, metabolic heterogeneity was assessed in morula (on-time) embryos using fluorophores probes (active mitochondria, hydrogen peroxide and reduced glutathione), two-channel autofluorescence (FAD and NAD(P)H) and 18-channel hyperspectral microscopy.Exposure to 20% oxygen following fertilisation significantly reduced total blastocyst, expanded and hatched blastocyst rates by 1.4-, 1.9- and 2.8-fold, respectively, compared to 7% oxygen (P0.05), demonstrating that atmospheric oxygen was a viable model for studying mild metabolic stress. The metabolic profiles of D5 embryos was determined and although metabolic heterogeneity was evident within the cleavage stage (i.e. arrested) embryos exposed to fluorophores, there were no detectable difference in fluorescence intensity and pattern localisation in morula exposed to the two different oxygen concentrations (P0.05). While there were no significant differences in two-channel autofluorescent profiles of morula exposed to 7% and 20% oxygen (main effect, P0.05), morula that subsequently progressed to the blastocyst stage had significantly higher levels of FAD and NAD(P)H fluorescence compared to arrested morula (P0.05), with no change in the redox ratio. Hyperspectral autofluorescence imaging (in 18-spectral channels) of the D5 morula revealed highly significant differences in four features of the metabolic profiles of morula exposed to the two different oxygen concentrations (P0.001). These four features were weighted and their linear combination revealed clear discrimination between the two treatment groups.Metabolic profiles were assessed at a single time point (morula), and as such further investigation is required to determine if differences in hyperspectral signatures can be detected in pre-compaction embryos and oocytes, using both cattle and subsequently human models. Furthermore, embryo transfers should be performed to determine the relationship between metabolic profiles and pregnancy success.Advanced autofluorescence imaging techniques, such as hyperspectral microscopy, may provide clinics with additional tools to improve the assessment of embryos prior to transfer.This study was funded by the Australian Research Council Centre of Excellence for Nanoscale BioPhotonics (CE140100003). The Fluoview FV10i confocal microscope was purchased as part of the Sensing Technologies for Advanced Reproductive Research (STARR) facility, funded by the South Australian Premier's Science and Research Fund. The authors declare there are no conflict of interest.

We explore new approaches to engineering the surface chemistry of interferometric sensing platforms based on nanoporous anodic alumina (NAA) and reflectometric interference spectroscopy (RIfS). Two surface engineering strategies are presented, namely (i) selective chemical functionalization of the inner surface of NAA pores with amine-terminated thiol molecules and (ii) selective chemical functionalization of the top surface of NAA with dithiol molecules. The strong molecular interaction of Au3+ ions with thiol-containing functional molecules of alkane chain or peptide character provides a model sensing system with which to assess the sensitivity of these NAA platforms by both molecular feature and surface engineering. Changes in the effective optical thickness of the functionalized NAA photonic films (i.e., sensing principle), in response to gold ions, are monitored in real-time by RIfS. 6-Amino-1-hexanethiol (inner surface) and 1,6-hexanedithiol (top surface), the most sensitive functional molecules fro...

The fluorescence spectra and photostability under 532 nm laser excitation of four different common photoswitches (an azobenzene, spiropyran, indolylfulgide, and a diarylperfluorocyclopentene) were investigated in a silica microstructured optical fibre. An example of each photoswitch was examined in solution and physically adsorbed to the silica fibre surface. This comparison was made to define fluorescence behaviour in these two states and to determine which photoswitch has the best performance in this light intense microenvironment. The azobenzene and the spiropyran switches demonstrated the strongest fluorescence response and the least degradation of the fluorescence signal. Refereed/Peer-reviewed

Electron transfer in peptides provides an opportunity to mimic nature for applications in bio-inspired molecular electronics. However, quantum interference effects, which become significant at the molecular level, have yet to be addressed in this context. Electrochemical and theoretical studies are reported on a series of cyclic and linear peptides of both β-strand and helical conformation, to address this shortfall and further realize the potential of peptides in molecular electronics. The introduction of a side-bridge into the peptides provides both additional rigidity to the backbone, and an alternative pathway for electron transport. Electronic transport studies reveal an interplay between quantum interference and vibrational fluctuations. We utilize these findings to demonstrate two distinctive peptide-based quantum interferometers, one exploiting the tunable effects of quantum interference (β-strand) and the other regulating the interplay between the two phenomena (310-helix).

Understanding the electronic properties inherent to peptides is crucial for controlling charge transfer, and precursory to the design and fabrication of bio-inspired next generation electronic components. However, to achieve this objective one must first be able to predict and control the associated charge transfer mechanisms. Here we demonstrate for the first time a controllable mechanistic transition in peptides resulting directly from the introduction of a side-bridge. High level computational studies on two similar 310-helical hexapeptides, one further constrained into this geometry by linking the i to i + 3 residues with a lactam side-bridge, highlight the effects of the bridge on electron transfer parameters, i.e. thermodynamic driving forces, reorganization energies, and electronic coupling factors. The additional backbone rigidity imparted by the bridge significantly alters the molecular dynamics of the peptide to such an extent as to induce a mechanistic transition from hopping in the linear peptide, to superexchange in the constrained peptide. This exciting finding not only advances our fundamental knowledge of the mechanisms governing charge transfer in peptides, but also reveals novel approaches to design and develop new functional devices that are tailored for applications in molecular electronics.

Nitric oxide (NO) is a key regulator of endothelial cell and vascular function. The direct measurement of NO is challenging due to its short half-life, and as such surrogate measurements are typically used to approximate its relative concentrations. Here we demonstrate that ruthenium-based [Ru(bpy)2(dabpy)]2+ is a potent sensor for NO in its irreversible, NO-bound active form, [Ru(bpy)2(T-bpy)]2+. Using spectrophotometry we established the sensor’s ability to detect and measure soluble NO in a concentration-dependent manner in cell-free media. Endothelial cells cultured with acetylcholine or hydrogen peroxide to induce endogenous NO production showed modest increases of 7.3 ± 7.1% and 36.3 ± 25.0% respectively in fluorescence signal from baseline state, while addition of exogenous NO increased their fluorescence by 5.2-fold. The changes in fluorescence signal were proportionate and comparable against conventional NO assays. Rabbit blood samples immediately exposed to [Ru(bpy)2(dabpy)]2+ displayed 8-fold higher mean fluorescence, relative to blood without sensor. Approximately 14% of the observed signal was NO/NO adduct-specific. Optimal readings were obtained when sensor was added to freshly collected blood, remaining stable during subsequent freeze-thaw cycles. Clinical studies are now required to test the utility of [Ru(bpy)2(dabpy)]2+ as a sensor to detect changes in NO from human blood samples in cardiovascular health and disease.

One of the biggest challenges associated with exposed core glass optical fiber-based sensing is the availability of techniques that can be used to generate reproducible, homogeneous and stable surface coating. We report a one step, solvent free method for surface functionalization of exposed core glass optical fiber that allows achieving binding of fluorophore of choice for metal ion sensing. The plasma polymerization-based method yielded a homogeneous, reproducible and stable coating, enabling high sensitivity aluminium ion sensing. The sensing platform reported in this manuscript is versatile and can be used to bind different sensing molecules opening new avenues for optical fiber-based sensing. Refereed/Peer-reviewed

This study explores the potential of gold-coated titania-functionalized nanoporous anodic alumina distributed Bragg reflectors (Au-TiO2-NAA-DBRs) as platforms to enhance photocatalytic reactions by integrating “slow photons” and surface plasmon resonance (SPR). The photocatalytic degradation rate of methylene blue – a model organic compound with a well-defined absorption band in the visible spectral region – by these composite photonic crystals (PCs) upon visible-NIR light irradiation is used as an indicator to identify coupling effects between the “slow photon” effect and SPR. Our study demonstrates that the photocatalytic enhancement in Au-TiO2-NAA-DBRs is strongly associated with “slow photon” effect, while the contribution of SPR to the overall photocatalytic enhancement is weak due to the localized generation of surface plasmons on the top surface of the composite PC structure. Photocatalytic enhancement is optimal when the characteristic photonic stopband of these PCs partially overlaps with the absorption band of methylene blue, which results in edges being positioned away from the absorption maximum of the organic dye. The overall photocatalytic degradation for methylene blue is also correlated to the type of noble metal coating and the geometric features of the PC structures. These results establish a rationale for further development of noble metal-coated NAA-based hybrid plasmonic–photonic crystal photocatalyst platforms to optimally integrate “slow photons” and SPR for enhancing the efficiency of photocatalytic reactions and other light harvesting applications. Related: [http://cer.ihtm.bg.ac.rs/handle/123456789/3007] This is peer-reviewed version of the article: Law, L. Liu, M. Markovic, A. D. Abell and A. Santos, Catalysis Science & Technology, 2019, 9, 12, 3158-3176 [https://dx.doi.org/10.1039/C9CY00627C]

This is the first work to use a newly designed Li+-selective photoswitchable probe Sabrina Heng Lithium (SHL) in living colon cancer cells to noninvasively monitor cation channel activity in real time by the appearance of lithium hot spots detected by confocal microscopy. Punctate Li+ hot spots are clustered in the lamellipodial leading edges of HT29 human colon cancer cells and are colocalized with aquaporin-1 (AQP1) channels. AQP1 is a dual water and cyclic-nucleotide-gated cation channel located in lamellipodia and is essential for rapid cell migration in a subset of aggressive cancers. Both the Li+ hot spots and cell migration are blocked in HT29 cells by the AQP1 ion channel antagonist AqB011. In contrast, Li+ hot spots are not evident in a poorly migrating colon cancer cell line, SW620, which lacks comparable membrane expression of AQP1. Knockdown of AQP1 by RNA interference in HT29 cells significantly impairs Li+ hot spot activity. The SHL probe loaded in living cells shows signature chemical properties of ionic selectivity and reversibility. Dynamic properties of the Li+ hot spots, turning on and off, are confirmed by time-lapse imaging. SHL is a powerful tool for evaluating cation channel function in living cells in real time, with particular promise for studies of motile cells or interlinked networks not easily analyzed by electrophysiological methods. The ability to reset SHL by photoswitching allows monitoring of dynamic signals over time. Future applications of the Li+ probe could include high-throughput optical screening for discovering new classes of channels, or finding new pharmacological modulators for nonselective cation channels.

The human sliding clamp, Proliferating Cell Nuclear Antigen (hPCNA), interacts with over 200 proteins through a conserved binding motif, the PIP-box, to orchestrate DNA replication and repair. It is not clear how changes to the features of a PIP-box modulate protein binding and thus how they fine-tune downstream processes. Here, we present a systematic study of each position within the PIP-box to reveal how hPCNA-interacting peptides bind with drastically varied affinities. We synthesized a series of 27 peptides derived from the native protein p21 with small PIP-box modifications and another series of 19 peptides containing PIP-box binding motifs from other proteins. The hPCNA-binding affinity of all peptides, characterized as KD values determined by surface plasmon resonance, spanned a 4000-fold range, from 1.83 nM to 7.59 μM. The hPCNA-bound peptide structures determined by X-ray crystallography and modeled computationally revealed intermolecular and intramolecular interaction networks that correlate with high hPCNA affinity. These data informed rational design of three new PIP-box sequences, testing of which revealed the highest affinity hPCNA-binding partner to date, with a KD value of 1.12 nM, from a peptide with PIP-box QTRITEYF. This work showcases the sequence-specific nuances within the PIP-box that are responsible for high-affinity hPCNA binding, which underpins our understanding of how nature tunes hPCNA affinity to regulate DNA replication and repair processes. In addition, these insights will be useful to future design of hPCNA inhibitors.

Replacing the labile adenosinyl-substituted phosphoanhydride of biotinyl-5′-AMP with a N1-benzyl substituted 1,2,3-triazole gave a new truncated series of inhibitors of Staphylococcus aureus biotin protein ligase (SaBPL). The benzyl group presents to the ribose-binding pocket of SaBPL based on in silico docking. Halogenated benzyl derivatives (12t, 12u, 12w, and 12x) proved to be the most potent inhibitors of SaBPL. These derivatives inhibited the growth of S. aureus ATCC49775 and displayed low cytotoxicity against HepG2 cells. Refereed/Peer-reviewed