Integrating airway microbiome and blood proteomics data to identify multi-omic networks associated with response to pulmonary infection.

Host response to airway infections can vary widely. Cystic fibrosis (CF) pulmonary exacerbations provide an opportunity to better understand the interplay between respiratory microbes and the host. This study aimed to investigate the observed heterogeneity in airway infection recovery by analyzing microbiome and host response (i.

Localising individual atoms of tryptophan side chains in the metallo--lactamase IMP-1 by pseudocontact shifts from paramagnetic lanthanoid tags at multiple sites.

The metallo--lactamase IMP-1 features a flexible loop near the active site that assumes different conformations in single crystal structures, which may assist in substrate binding and enzymatic activity. To probe the position of this loop, we labelled the tryptophan residues of IMP-1 with 7-C-indole and the protein with lanthanoid tags at three different sites. The magnetic susceptibility anisotropy () tensors were determined by measuring pseudocontact shifts (PCSs) of backbone amide protons.

A lipid-anchored neurokinin 1 receptor antagonist prolongs pain relief by a three-pronged mechanism of action targeting the receptor at the plasma membrane and in endosomes.

G-protein-coupled receptors (GPCRs) are traditionally known for signaling at the plasma membrane, but they can also signal from endosomes after internalization to control important pathophysiological processes. In spinal neurons, sustained endosomal signaling of the neurokinin 1 receptor (NKR) mediates nociception, as demonstrated in models of acute and neuropathic pain. An NKR antagonist, Spantide I (Span), conjugated to cholestanol (Span-Chol), accumulates in endosomes, inhibits endosomal NKR signaling, and causes prolonged antinociception.

A molecular sensor to quantify the localization of proteins, DNA and nanoparticles in cells.

Intracellular trafficking governs receptor signaling, pathogenesis, immune responses and fate of nanomedicines. These processes are typically tracked by observing colocalization of fluorescent markers using confocal microscopy. However, this method is low throughput, limited by the resolution of microscopy, and can miss fleeting interactions.

Hexaarylbiimidazoles(HABI)-functionalized lyotropic liquid crystalline systems as visible light-responsive materials.

Hexaarylbiimidazoles (HABIs) are a promising class of photoswitchable molecule that have received little attention in the literature. Among them, (2,2'-dimethoxydiphenylimidazole)-1,1'-binaphthyl (HABI1) displays unusual negative photochromism and is responsive to green light. This study investigates the potential of HABIs to serve as photo-responsive actuators controlling the structure of lyotropic liquid crystalline (LLC) materials.

Probing the solution structure of the E. coli multidrug transporter MdfA using DEER distance measurements with nitroxide and Gd(III) spin labels.

Methodological and technological advances in EPR spectroscopy have enabled novel insight into the structural and dynamic aspects of integral membrane proteins. In addition to an extensive toolkit of EPR methods, multiple spin labels have been developed and utilized, among them Gd(III)-chelates which offer high sensitivity at high magnetic fields. Here, we applied a dual labeling approach, employing nitroxide and Gd(III) spin labels, in conjunction with Q-band and W-band double electron-electron resonance (DEER) measurements to characterize the solution structure of the detergent-solubilized multidrug transporter MdfA from E.

Visible light-triggered cargo release from donor acceptor Stenhouse adduct (DASA)-doped lyotropic liquid crystalline nanoparticles.

Light-responsive nanocarriers are applicable as non-invasive, highly tunable and precisely controlled drug delivery systems. Here, we report a new nanocarrier system, achieved by doping D1, a type of green light-responsive donor acceptor Stenhouse adduct (DASA), into a lipid-based lyotropic liquid crystalline system. Time-resolved small angle X-ray scattering was used to confirm that the matrix underwent a rapid and fully reversible phase transition from lamellar to inverse cubic phase upon irradiation with green light (532 nm), reverting back on removal of light.

Linker chemistry dictates the delivery of a phototoxic organometallic rhenium(i) complex to human cervical cancer cells from core crosslinked star polymer nanoparticles.

We have investigated core-crosslinked star polymer nanoparticles designed with tunable release chemistries as potential nanocarriers for a photoactive Re(i) organometallic complex. The nanoparticles consisted of a brush poly(oligo-ethylene glycol)methyl ether acrylate (POEGA) corona and a cross-linked core of non-biodegradable N,N'-methylenebis(acrylamide) (MBAA) and either pentafluorophenyl acrylate (PFPA), 3-vinyl benzaldehyde (VBA) or diacetone acrylamide (DAAM). Each star was modified with an amine functionalized photodynamic agent (i.

Interaction of Nucleotides with a Trinuclear Terbium(III)-Dizinc(II) Complex: Efficient Sensitization of Terbium Luminescence by Guanosine Monophosphate and Application to Real-Time Monitoring of Phosphodiesterase Activity.

An in-depth study of the interaction of a trinuclear terbium(III)-dizinc(II) complex with an array of nucleotides differing in the type of nucleobase and number of phosphate groups, as well as cyclic versus acyclic variants, is presented. The study examined the nature of the interaction and the efficiency at which guanine was able to sensitize terbium(III) luminescence. Competitive binding and titration studies were performed to help establish the nature/mode of the interactions.

Towards Utilising Photocrosslinking of Polydiacetylenes for the Preparation of "Stealth" Upconverting Nanoparticles.

We demonstrate a novel strategy for preparing hydrophilic upconverting nanoparticles (UCNPs) by harnessing the photocrosslinking ability of diacetylenes. Replacement of the hydrophobic oleate coating on the UCNPs with 10,12-pentacosadiynoic acid, followed by overcoating with diacetylene phospholipid and subsequent photocrosslinking under 254 nm irradiation produces water-dispersible polydiacetylene-coated UCNPs. These UCNPs resist the formation of a biomolecular corona and show great colloidal stability.

Small neutral Gd(iii) tags for distance measurements in proteins by double electron-electron resonance experiments.

Spin labels containing a Gd(iii) ion have become important for measuring nanometer distances in proteins by double electron-electron resonance (DEER) experiments at high EPR frequencies. The distance resolution and sensitivity of these measurements strongly depend on the Gd(iii) tag used. Here we report the performance of two Gd(iii) tags, propargyl-DO3A and C11 in DEER experiments carried out at W-band (95 GHz).

Site-Specific Incorporation of Selenocysteine by Genetic Encoding as a Photocaged Unnatural Amino Acid.

Selenocysteine (Sec) is a naturally occurring amino acid that is also referred to as the 21st amino acid. Site-specific incorporation of Sec into proteins is attractive, because the reactivity of a selenol group exceeds that of a thiol group and thus allows site-specific protein modifications. It is incorporated into proteins by an unusual enzymatic mechanism which, in E.

Facile preparation of multifunctionalisable 'stealth' upconverting nanoparticles for biomedical applications.

Pure hexagonal (β-phase) NaYF-based hydrophobic upconverting nanoparticles (UCNPs) were surface-modified with O-phospho-l-threonine (OPLT), alendronic acid, and PEG-phosphate ligands to generate water-dispersible UCNPs. Fourier-transform infrared (FTIR) spectroscopy was used to establish the presence of the ligands on the UCNP surface. These UCNPs exhibit great colloidal stability and a near-neutral surface at physiological pH, as confirmed by dynamic light scattering (DLS) and zeta potential (ζ) measurements, respectively.

Quantifying Cellular Internalization with a Fluorescent Click Sensor.

The ability to determine the amount of material endocytosed by a cell is important for our understanding of cell biology and in the design of effective carriers for drug delivery. To quantify internalization by fluorescence, the signal from material remaining on the cell surface must be differentiated from endocytosed material. Sensors for internalization offer advantages over traditional methods for achieving this as they exhibit improved sensitivity, allow for multiple fluorescent markers to be used simultaneously, and are amenable to high-throughput analysis.

Small Gd(III) Tags for Gd(III)-Gd(III) Distance Measurements in Proteins by EPR Spectroscopy.

The C7-Gd and C8-Gd tags are compact hydrophilic cyclen-based lanthanide tags for conjugation to cysteine residues in proteins. The tags are enantiomers, which differ in the configuration of the 2-hydroxylpropyl pendant arms coordinating the lanthanide ion. Here, we report the electron paramagnetic resonance (EPR) performance of the C7-Gd ( S configuration) and C8-Gd ( R configuration) tags loaded with Gd(III) on two mutants of the homodimeric ERp29 protein.

Trimethylsilyl tag for probing protein-ligand interactions by NMR.

Protein-ligand titrations can readily be monitored with a trimethylsilyl (TMS) tag. Owing to the intensity, narrow line shape and unique chemical shift of a TMS group, dissociation constants can be determined from straightforward 1D H-NMR spectra not only in the fast but also in the slow exchange limit. The tag is easily attached to cysteine residues and a sensitive reporter of ligand binding also at sites where it does not interfere with ligand binding or catalytic efficiency of the target protein.

Spectroscopic Studies on Photoinduced Reactions of the Anticancer Prodrug, trans,trans,trans-[Pt(N ) (OH) (py) ].

The photodecomposition mechanism of trans,trans,trans-[Pt(N ) (OH) (py) ] (1, py=pyridine), an anticancer prodrug candidate, was probed using complementary Attenuated Total Reflection Fourier Transform Infrared (ATR-FTIR), transient electronic absorption, and UV/Vis spectroscopy. Data fitting using Principal Component Analysis (PCA) and Multi-Curve Resolution Alternating Least Squares, suggests the formation of a trans-[Pt(N )(py) (OH/H O)] intermediate and trans-[Pt(py) (OH/H O) ] as the final product upon 420 nm irradiation of 1 in water. Rapid disappearance of the hydroxido ligand stretching vibration upon irradiation is correlated with a -10 cm shift to the antisymmetric azido vibration, suggesting a possible second intermediate.

Fluorescently Labeled Morphine Derivatives for Bioimaging Studies.

Opioids, like morphine, are the mainstay analgesics for the treatment and control of pain. Despite this, they often exhibit severe side effects that limit dose; patients often become tolerant and dependent on these drugs, which remains a major health concern. The analgesic actions of opioids are primarily mediated via the μ-opioid receptor, a member of the G protein-coupled receptor superfamily.

Genetically encoded amino acids with tert-butyl and trimethylsilyl groups for site-selective studies of proteins by NMR spectroscopy.

The amino acids 4-(tert-butyl)phenylalanine (Tbf) and 4-(trimethylsilyl)phenylalanine (TMSf), as well as a partially deuterated version of Tbf (dTbf), were chemically synthesized and site-specifically incorporated into different proteins, using an amber stop codon, suppressor tRNA and the broadband aminoacyl-tRNA synthetase originally evolved for the incorporation of p-cyano-phenylalanine. The H-NMR signals of the tert-butyl and TMS groups were compared to the H-NMR signal of tert-butyltyrosine (Tby) in protein systems with molecular weights ranging from 8 to 54 kDa. The H-NMR resonance of the TMS group appeared near 0 ppm in a spectral region with few protein resonances, facilitating the observation of signal changes in response to ligand binding.

8-Mercaptoguanine Derivatives as Inhibitors of Dihydropteroate Synthase.

Dihydropteroate synthase (DHPS) is an enzyme of the folate biosynthesis pathway, which catalyzes the formation of 7,8-dihydropteroate (DHPt) from 6-hydroxymethyl-7,8-dihydropterin pyrophosphate (DHPPP) and para-aminobenzoic acid (pABA). DHPS is the long-standing target of the sulfonamide class of antibiotics that compete with pABA. In the wake of sulfa drug resistance, targeting the structurally rigid (and more conserved) pterin site has been proposed as an alternate strategy to inhibit DHPS in wild-type and sulfa drug resistant strains.

Short two-armed lanthanide-binding tags for paramagnetic NMR spectroscopy based on chiral 1,4,7,10-tetrakis(2-hydroxypropyl)-1,4,7,10-tetraazacyclododecane scaffolds.

A new pair of enantiomeric two-armed lanthanide-binding tags have been developed for paramagnetic NMR studies of proteins. The tags produce large and significantly different paramagnetic effects to one another when bound to the same tagging site. Additionally, they are less sensitive to sample pH than our previous two-armed tag designs.

Novel agrochemical conjugates with self-assembling behaviour.

Hypothesis: That conjugation of agrichemicals to pro-assembly hydrophobic moieties will enable enhanced compatibility and loading with host lyotropic liquid crystalline carrier matrix, and potentially self-assemble in their own right in aqueous environments.

Experiments: A series of lipid-like agrochemical-conjugates were synthesized using specific amphiphilic entities conjugated onto the agrochemicals, picloram and 2,4-dichlorophenoxyacetic acid (2,4-D). The self-assembly behaviour and compatibility of the novel entities when incorporated into phytantriol and monoolein-based liquid crystalline systems were examined using small angle X-ray scattering, cryo-TEM and polarized optical microscopy.

Selective Distance Measurements Using Triple Spin Labeling with Gd, Mn, and a Nitroxide.

Distance measurements by pulse electron paramagnetic resonance techniques, such as double electron-electron resonance (DEER, also called PELDOR), have become an established tool to explore structural properties of biomacromolecules and their assemblies. In such measurements a pair of spin labels provides a single distance constraint. Here we show that by employing three different types of spin labels that differ in their spectroscopic and spin dynamics properties it is possible to extract three independent distances from a single sample.

Chemical Tagging with tert-Butyl and Trimethylsilyl Groups for Measuring Intermolecular Nuclear Overhauser Effects in a Large Protein-Ligand Complex.

Intermolecular H- H nuclear Overhauser effects (NOE) present a powerful tool to assess contacts between proteins and binding partners, but are difficult to identify for complexes of high molecular weight. This report shows that intermolecular NOEs can readily be observed following chemical labeling with tert-butyl or trimethylsilyl (TMS) groups. Proteins can be furnished with tert-butyl or TMS groups site-specifically using genetically encoded unnatural amino acids or by chemical modification of single cysteine residues.