Conotoxin Prediction: New Features to Increase Prediction Accuracy.

Conotoxins are toxic, disulfide-bond-rich peptides from cone snail venom that target a wide range of receptors and ion channels with multiple pathophysiological effects. Conotoxins have extraordinary potential for medical therapeutics that include cancer, microbial infections, epilepsy, autoimmune diseases, neurological conditions, and cardiovascular disorders. Despite the potential for these compounds in novel therapeutic treatment development, the process of identifying and characterizing the toxicities of conotoxins is difficult, costly, and time-consuming. This challenge requires a series of diverse, complex, and labor-intensive biological, toxicological, and analytical techniques for effective characterization. While recent attempts, using machine learning based solely on primary amino acid sequences to predict biological toxins (e.g., conotoxins and animal venoms), have improved toxin identification, these methods are limited due to peptide conformational flexibility and the high frequency of cysteines present in toxin sequences. This results in an enumerable set of disulfide-bridged foldamers with different conformations of the same primary amino acid sequence that affect function and toxicity levels. Consequently, a given peptide may be toxic when its cysteine residues form a particular disulfide-bond pattern, while alternative bonding patterns (isoforms) or its reduced form (free cysteines with no disulfide bridges) may have little or no toxicological effects. Similarly, the same disulfide-bond pattern may be possible for other peptide sequences and result in different conformations that all exhibit varying toxicities to the same receptor or to different receptors. We present here new features, when combined with primary sequence features to train machine learning algorithms to predict conotoxins, that significantly increase prediction accuracy.

On the effects of quadrupolar relaxation in Earth's field NMR spectra.

There is growing interest in using low-field magnetic resonance experiments for routine chemical characterization. Earth's field NMR is one such technique that can garner structural information and enable sample differentiation with low cost and highly portable designs. The resulting NMR spectra are primarily influenced by J-couplings, resulting in so-called J-coupled spectra (JCS). Many small molecules include atoms with NMR-active nuclei that are quadrupolar either at natural abundance or are often isotopically enriched (e.g.,2H, 6Li, 11B, 14N, 17O, etc.) where the effects of quadrupolar J-couplings and relaxation on JCS of strongly- and weakly-coupled spin systems have not been explored to date. Herein, using a set of seven fluoropyridine samples with unique substitution and J-couplings, we demonstrate that the 14N relaxation rates can induce drastic line-broadening in the JCS. This includes a previously unexplored unique line broadening mechanism enabled by strongly coupled spins at low-field. Numerical simulations are used to model and refine the magnitudes and signs of J-couplings, as well as indirectly determine the 14N relaxation rates in a single 1D experiment that has a higher fidelity than observed in high-field NMR experiments.

Reactivity of [(PNP)Mn(CO)2] with Organophosphates.

Organophosphorus nerve agents (OPAs) are a toxic class of synthetic compounds that cause adverse effects with many biological systems. Development of methods for environmental remediation and passivation has been ongoing for years. However, little progress has been made in therapeutic development for exposure victims. Given the postexposure behavior of OPA materials in enzymes such as acetylcholinesterase (AChE), development of electrophilic compounds as therapeutics may be more beneficial than the currently employed nucleophilic countermeasures. In this report, we present our studies with an electrophilic, 16-electron manganese complex (iPrPNP)Mn(CO)2 (1) and the nucleophilic hydroxide derivative (iPrPNHP)Mn(CO)2(OH) (2). The reactivity of 1 with phosphorus acids and the reactivity of 2 with the P-F bond of diisopropylfluorophosphate (DIPF) were studied. The role of water in both nucleophilic and electrophilic reactivity was investigated with the use of 17O-labeled water. Promising results arising from reactions of both 1 and 2 with organophosphorus substrates are reported.

Backbone and side chain chemical shift assignment of diisopropyl fluorophosphatase (DFPase) from Loligo vulgaris, an organophosphorus-degrading enzyme.

NMR chemical shift assignments are reported for backbone (15N, 1H) and partial side chain (13Cα and ß, side chain 1H) atoms of diisopropyl fluorophosphatase (DFPase), a calcium-dependent phosphotriesterase capable of hydrolyzing phosphorus - fluorine bonds in a variety of toxic organophosphorus compounds. Analysis of residues lining the active site of DFPase highlight a number of residues whose chemical shifts can be used as a diagnostic of binding and detection of organophosphorus compounds.

Detection of natural abundance 13C J-couplings at Earth's magnetic field for spin system differentiation of small organic molecules.

Nuclear magnetic resonance (NMR) spectroscopy routinely characterizes the unique spin systems of molecules using a combination of chemical shift and J-coupling interactions for the 1H and 13C nuclei. However, at Earth's magnetic field, chemical shifts are unresolvable and the ability to characterize structure relies solely on the J-couplings. Fortuitously, the J-couplings at Earth's field provides the same spin system information as high field, but only requires detection of the 1H nucleus. We report the first identification of the multiple natural abundance 1H-13C spin systems on organic molecules detected at Earth's magnetic field. The results clearly demonstrate the feasibility of Earth's field NMR to characterize small organic molecules without costly enrichment strategies.

Quantitation of Nuclear Magnetic Resonance Spectra at Earth's Magnetic Field.

The inherently quantitative nature of nuclear magnetic resonance (NMR) spectroscopy is one of the most attractive aspects of this analytical technique. Quantitative NMR analyses have typically been limited to high-field (>1 T) applications. The aspects for quantitation at low magnetic fields (<1 mT) have not been thoroughly investigated and are shown to be impacted by the complex signatures that arise at these fields from strong heteronuclear J-couplings. This study investigates quantitation at Earth's magnetic field (∼50 µT) for a variety of samples in strongly, weakly, and uncoupled spin systems. To achieve accurate results in this regime, the instrumentation, experimental acquisition, processing, and theoretical aspects must be considered and reconciled. Of particular note is the constant field nuclear receptivity equation, which has been re-derived in this study to account for strong coupling and quality factor effects. The results demonstrate that the quantitation of homonuclear molecular groups, determination of heteronuclear pseudoempirical formulas, and mixture analysis are all feasible at Earth's magnetic field in a greatly simplified experimental system.

Conformational control via sequence for a heteropeptoid in water: coupled NMR and Rosetta modelling.

We report a critical advance in the generation and characterization of peptoid hetero-oligomers. A library of sub-monomers with amine and carboxylate side-chains are combined in different sequences using microwave-assisted synthesis. Their sequence-structure propensity is confirmed by circular dichroism, and conformer subtypes are enumerated by NMR. Biasing the ψ-angle backbone to trans (180°) in Monte Carlo modelling favors i to i + 3 naphthyl-naphthyl stacking, and matches experimental ensemble distributions. Taken together, high-yield synthesis of heterooligomers and NMR with structure prediction enables rapid determination of sequences that induce secondary structural propensities for predictive design of hydrophilic peptidomimetic foldamers and their future libraries.

The 1H T1 dispersion curve of fentanyl citrate to identify NQR parameters.

We report the 1H T1 dispersion curve between 0 and 5 â€‹MHz for the synthetic opioid fentanyl citrate (C28H36N2O8). The structures in the curve can be used to estimate the 14N nuclear quadrupole resonance (NQR) frequencies of the material. Density functional theory predictions of the NQR parameters of several fentanyl citrate compounds are also reported. The predictions for the aniline nitrogen are consistent with structures in the observed T1 data. To help interpret the fentanyl citrate results the T1 dispersion curve for the explosive ammonium nitrate is also presented.

Design and implementation of a J-coupled spectrometer for multidimensional structure and relaxation detection at low magnetic fields.

In recent years, it has been realized that low and ultra-low field (mT-nT magnetic field range) nuclear magnetic resonance spectroscopy can be used for molecular structural analysis. However, spectra are often hindered by lengthy acquisition times or require large sample volumes and high concentrations. Here, we report a low field (50 µT) instrument that employs a linear actuator to shuttle samples between a 1 T prepolarization field and a solenoid detector in a laboratory setting. The current experimental setup is benchmarked using water and 13C-methanol with a single scan detection limit of 2 × 1020 spins (3 µl, 55M H2O) and detection limit of 2.9 × 1019 (200 µl, 617 mM 13C-methanol) spins with signal averaging. The system has a dynamic range of >3 orders of magnitude. Investigations of room-temperature relaxation dynamics of 13C-methanol show that sample dilution can be used in lieu of sample heating to acquire spectra with linewidths comparable to high-temperature spectra. These results indicate that the T1 and T2 mechanisms are governed by both the proton exchange rate and the dissolved oxygen in the sample. Finally, a 2D correlation spectroscopy experiment is reported, performed in the strong coupling regime that resolves the multiple resonances associated with the heteronuclear J-coupling. The spectrum was collected using 10 times less sample and in less than half the time from previous reports in the strong coupling limit.

Correction of Q Factor Effects for Simultaneous Collection of Elemental Analysis and Relaxation Times by Nuclear Magnetic Resonance.

A new method for measurement of elemental analysis by nuclear magnetic resonance (NMR) of unknown samples is discussed here as a quick and robust means to measure elemental ratios without the use of internal or external calibration standards. The determination of elemental ratios was done by normalizing the signal intensities by the frequency dependent quality factor (Q) and the gyromagnetic ratios (γ) for each measured nucleus. The correction for the frequency dependence was found by characterizing the output signal of the probe as a function of the quality factor (Q) and the frequency, and the correction for γ was discussed in a previous study. A Carr-Purcell-Meiboom-Gill (CPMG) pulse sequence was used for evaluation of the relative signal intensities, which allows for derivation of elemental ratios, and was correspondingly used to simultaneously measure the T2* of samples for an added parameter for more accurate identification of unknown samples.

Synthesis of stable isotope-labeled chloroquine and amodiaquine and their metabolites.

Anti-malaria drugs chloroquine and amodiaquine and their metabolites were synthesized to incorporate 13 C and 15 N starting from U-13 C-labeled benzene to give M + 7 isotopomers. Chloroquine and its metabolites were prepared from 7-chloro-1,2,3,4-tetrahydroquinolin-4-one through an aryl substitution with the corresponding amines; and the amodiaquine and its metabolites were prepared from 4,7-dichloroquinoline in a similar fashion.

A general route for 13C-labeled fluorenols and phenanthrenols via palladium-catalyzed cross-coupling and one-carbon homologation.

A series of (13)C-labeled polyaromatic hydrocarbons (PAHs), fluorenols and phenanthrenols were synthesized from commercially available (13)C-labeled starting material giving rise to M + 6 isotopomers. This was accomplished using key palladium-catalyzed cross-coupling and one-carbon homologation strategies. The conditions for these reactions were optimized, and the new chemical routes are efficient in the number of chemical steps, can be scaled to afford gram quantities and occur in good yields based on the (13)C label. These labeled compounds as precursors for more complex PAHs and are useful as internal standards in mass spectrometry and NMR spectroscopy studies for monitoring environmental contamination and biological exposure to PAHs and their metabolites.

Immunomagnetic separation and quantification of butyrylcholinesterase nerve agent adducts in human serum.

A novel method for extracting butyrylcholinesterase (BuChE) from serum as a means of identifying and measuring nerve agent adducts to human BuChE is presented here. Antibutyrylcholinesterase monoclonal antibodies were conjugated to protein-G ferromagnetic particles and mixed with 500 microL serum samples. The particle-antibody-BuChE product was rinsed and directly digested with pepsin. Native and isotopically enriched nonapeptides corresponding to the pepsin digest products for uninhibited BuChE, and sarin, cyclohexylsarin, VX, and Russian VX nerve agent-inhibited BuChE were synthesized for use as calibrators and internal standards, respectively. Internal standards were added to the filtered digest sample, and the samples were quantified via high performance liquid chromatography-isotope dilution-tandem mass spectrometry. The ratio of adducted to total BuChE nonapeptides was calculated for each nerve agent-exposed serum sample using data collected in a single chromatogram. Nerve agent-inhibited quality control serum pools were characterized as part of method validation; the method was observed to have extremely low background noise. The measurement of both uninhibited and inhibited BuChE peptides compensated for any variations in the pepsin digestion before the internal standard peptide was added to the sample and may prove useful in individualizing patient results following a nerve agent exposure.

Carbon-fate maps for metabolic reactions.

MOTIVATION: Stable isotope labeling of small-molecule metabolites (e.g. (13)C-labeling of glucose) is a powerful tool for characterizing pathways and reaction fluxes in a metabolic network. Analysis of isotope labeling patterns requires knowledge of the fates of individual atoms and moieties in reactions, which can be difficult to collect in a useful form when considering a large number of enzymatic reactions. RESULTS: We report carbon-fate maps for 4605 enzyme-catalyzed reactions documented in the KEGG database. Every fate map has been manually checked for consistency with known reaction mechanisms. A map includes a standardized structure-based identifier for each reactant (namely, an InChI string); indices for carbon atoms that are uniquely derived from the metabolite identifiers; structural data, including an identification of homotopic and prochiral carbon atoms; and a bijective map relating the corresponding carbon atoms in substrates and products. Fate maps are defined using the BioNetGen language (BNGL), a formal model-specification language, which allows a set of maps to be automatically translated into isotopomer mass-balance equations. AVAILABILITY: The carbon-fate maps and software for visualizing the maps are freely available (http://cellsignaling.lanl.gov/FateMaps/).

A microfluidic SELEX prototype.

Aptamers are nucleic acid binding species capable of recognizing a wide variety of targets ranging from small organic molecules to supramolecular structures, including organisms. They are isolated from combinatorial libraries of synthetic nucleic acid by an iterative process referred to as SELEX (Systematic Evolution of Ligands by Exponential Enrichment). Here we describe an automated microfluidic, microline-based assembly that uses LabView-controlled actuatable valves and a PCR machine, and which is capable of the selection and synthesis of an anti-lysozyme aptamer as verified by sequence analysis. The microfluidic prototype described is 1) a simple apparatus that is relatively inexpensive to assemble, making automated aptamer selection accessible to many investigators, and 2) useful for the continued "morphing" of macro-->meso-->microfabricated structures until a convergence to a few functional systems evolves and emerges, partly or completely achieving simpler, smaller and more rapid SELEX applications.

Endometrial microstructure after long-term use of a 91-day extended-cycle oral contraceptive regimen.

OBJECTIVE: To assess the effect on the endometrial microstructure of an extended-cycle oral contraceptive (OC) regimen containing ethinyl estradiol (EE) and levonorgestrel (LNG). METHODOLOGY: Subjects received up to four cycles of a 91-day extended-cycle OC regimen (84 consecutive days of monophasic 30 microg EE/150 microg LNG followed by 7 days of placebo). Endometrial biopsies were performed prior to the initiation and at the completion of therapy. All endometrial samples were processed centrally and reviewed by three independent pathologists blinded to treatment groups. RESULTS: Endometrial biopsies were performed in 50 women. In general, samples taken after completion of therapy with no further hormonal exposure demonstrated rapid return to normal endometrial cycling. In contrast, the majority of subjects still on active extended hormonal OC therapy at the time of biopsy had inactive or atrophic endometrium. No intravascular blood clots were observed in any of the specimens. CONCLUSION: The endometrial findings observed in this cohort of women treated with a 91-day extended-cycle OC regimen for up to 1 year showed no significant pathology. Additionally, the endometrium reverted quickly to normal cyclic changes in those subjects who, after completing therapy, elected not to continue with hormonal contraception.

Hemispheric asymmetries and joke comprehension.

Joke comprehension deficits in patients with right hemisphere (RH) damage raise the question of the role of the intact RH in understanding jokes. One suggestion is that semantic, or meaning, activations are different in the RH and LH, and RH meanings are particularly important for joke comprehension. To assess whether hypothesized differences in semantic activation in the two hemispheres were relevant to joke comprehension, we recorded event-related brain potentials (ERPs) as healthy adults read laterally presented "punch words" to one-line jokes and nonjoke controls. Jokes presented to the RVF/LH elicited larger amplitude N400 than the nonjoke endings; when presented to the LVF/RH, the joke and nonjoke endings elicited N400s of equal amplitude. This finding suggests that semantic activations in the two hemispheres do differ, with RH semantic activation facilitating joke comprehension.