Accurate de novo design of membrane-traversing macrocycles.

We use computational design coupled with experimental characterization to systematically investigate the design principles for macrocycle membrane permeability and oral bioavailability. We designed 184 6-12 residue macrocycles with a wide range of predicted structures containing noncanonical backbone modifications and experimentally determined structures of 35; 29 are very close to the computational models. With such control, we show that membrane permeability can be systematically achieved by ensuring all amide (NH) groups are engaged in internal hydrogen bonding interactions. 84 designs over the 6-12 residue size range cross membranes with an apparent permeability greater than 1 × 10-6 cm/s. Designs with exposed NH groups can be made membrane permeable through the design of an alternative isoenergetic fully hydrogen-bonded state favored in the lipid membrane. The ability to robustly design membrane-permeable and orally bioavailable peptides with high structural accuracy should contribute to the next generation of designed macrocycle therapeutics.

Magic angle spinning NMR of proteins: high-frequency dynamic nuclear polarization and (1)H detection.

Magic angle spinning (MAS) NMR studies of amyloid and membrane proteins and large macromolecular complexes are an important new approach to structural biology. However, the applicability of these experiments, which are based on (13)C- and (15)N-detected spectra, would be enhanced if the sensitivity were improved. Here we discuss two advances that address this problem: high-frequency dynamic nuclear polarization (DNP) and (1)H-detected MAS techniques. DNP is a sensitivity enhancement technique that transfers the high polarization of exogenous unpaired electrons to nuclear spins via microwave irradiation of electron-nuclear transitions. DNP boosts NMR signal intensities by factors of 10(2) to 10(3), thereby overcoming NMR's inherent low sensitivity. Alternatively, it permits structural investigations at the nanomolar scale. In addition, (1)H detection is feasible primarily because of the development of MAS rotors that spin at frequencies of 40 to 60 kHz or higher and the preparation of extensively (2)H-labeled proteins.

Sensitivity-enhanced NMR reveals alterations in protein structure by cellular milieus.

Biological processes occur in complex environments containing a myriad of potential interactors. Unfortunately, limitations on the sensitivity of biophysical techniques normally restrict structural investigations to purified systems, at concentrations that are orders of magnitude above endogenous levels. Dynamic nuclear polarization (DNP) can dramatically enhance the sensitivity of nuclear magnetic resonance (NMR) spectroscopy and enable structural studies in biologically complex environments. Here, we applied DNP NMR to investigate the structure of a protein containing both an environmentally sensitive folding pathway and an intrinsically disordered region, the yeast prion protein Sup35. We added an exogenously prepared isotopically labeled protein to deuterated lysates, rendering the biological environment "invisible" and enabling highly efficient polarization transfer for DNP. In this environment, structural changes occurred in a region known to influence biological activity but intrinsically disordered in purified samples. Thus, DNP makes structural studies of proteins at endogenous levels in biological contexts possible, and such contexts can influence protein structure.

A genome-wide Drosophila screen for heat nociception identifies α2δ3 as an evolutionarily conserved pain gene.

Worldwide, acute, and chronic pain affects 20% of the adult population and represents an enormous financial and emotional burden. Using genome-wide neuronal-specific RNAi knockdown in Drosophila, we report a global screen for an innate behavior and identify hundreds of genes implicated in heat nociception, including the α2δ family calcium channel subunit straightjacket (stj). Mice mutant for the stj ortholog CACNA2D3 (α2δ3) also exhibit impaired behavioral heat pain sensitivity. In addition, in humans, α2δ3 SNP variants associate with reduced sensitivity to acute noxious heat and chronic back pain. Functional imaging in α2δ3 mutant mice revealed impaired transmission of thermal pain-evoked signals from the thalamus to higher-order pain centers. Intriguingly, in α2δ3 mutant mice, thermal pain and tactile stimulation triggered strong cross-activation, or synesthesia, of brain regions involved in vision, olfaction, and hearing.

1H detection and dynamic nuclear polarization-enhanced NMR of Aß1-42 fibrils.

Several publications describing high-resolution structures of amyloid-ß (Aß) and other fibrils have demonstrated that magic-angle spinning (MAS) NMR spectroscopy is an ideal tool for studying amyloids at atomic resolution. Nonetheless, MAS NMR suffers from low sensitivity, requiring relatively large amounts of samples and extensive signal acquisition periods, which in turn limits the questions that can be addressed by atomic-level spectroscopic studies. Here, we show that these drawbacks are removed by utilizing two relatively recent additions to the repertoire of MAS NMR experiments-namely, 1H detection and dynamic nuclear polarization (DNP). We show resolved and sensitive two-dimensional (2D) and three-dimensional (3D) correlations obtained on 13C,15N-enriched, and fully protonated samples of M0Aß1-42 fibrils by high-field 1H-detected NMR at 23.4 T and 18.8 T, and 13C-detected DNP MAS NMR at 18.8 T. These spectra enable nearly complete resonance assignment of the core of M0Aß1-42 (K16-A42) using submilligram sample quantities, as well as the detection of numerous unambiguous internuclear proximities defining both the structure of the core and the arrangement of the different monomers. An estimate of the sensitivity of the two approaches indicates that the DNP experiments are currently ∼6.5 times more sensitive than 1H detection. These results suggest that 1H detection and DNP may be the spectroscopic approaches of choice for future studies of Aß and other amyloid systems.

Metabolism and Excretion of [14C]Mobocertinib, a Selective Covalent Inhibitor of Epidermal Growth Factor Receptor (EGFR) Exon 20 Insertion Mutations, in Healthy Male Subjects.

Mobocertinib (formerly known as TAK-788) is a targeted covalent tyrosine kinase inhibitor of epidermal growth factor receptor with exon 20 insertion mutations. This article describes the metabolism and excretion of mobocertinib in healthy male subjects after a single oral administration of [14C]mobocertinib. Mobocertinib-related materials were highly covalently bound to plasma proteins such as human serum albumin. The mean extraction recovery of total radioactivity was only 3.9% for six individual Hamilton pooled plasma samples. After extraction, mobocertinib was the most abundant component accounting for 7.7% of total extracted circulating radioactivity (TECRA) in the supernatant. Each of identified metabolites accounted for <10% of TECRA. Mobocertinib underwent extensive first-pass metabolism with the fraction of the dose absorbed estimated to be approximately 91.7%. Fecal excretion of mobocertinib metabolites was the major elimination route. Mobocertinib was mainly eliminated via oxidative metabolism with a fraction of approximately 88% metabolized by CYP3A4/5. The other minor elimination pathways included cysteine conjugation, metabolism by other cytochrome P450s, and renal excretion of unchanged mobocertinib. SIGNIFICANCE STATEMENT: This article describes the metabolism and excretion of a targeted covalent inhibitor mobocertinib in humans after a single oral administration of [14C]mobocertinib. Mobocertinib was highly covalently bound to human plasma proteins. No metabolite accounted for >10% of total extracted circulating radioactivity in human plasma. Mobocertinib was mainly eliminated via CYP3A4/5 mediated oxidative metabolism followed by fecal excretion after approximately 91.7% of the dose was absorbed.

A phase 1 study to assess the absolute bioavailability, mass balance, pharmacokinetics, metabolism, and excretion of [14C]-mobocertinib, an oral inhibitor of EGFR exon 20 insertion mutations, in healthy participants.

Mobocertinib (TAK-788) is a first-in-class oral epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor that received accelerated approval for the treatment of patients with non-small cell lung cancer with EGFR exon 20 insertion mutations previously treated with platinum-based chemotherapy. This phase 1, 2-period, study was conducted to assess the absolute bioavailability of mobocertinib (Period 1), as well as mass balance, pharmacokinetics, metabolism, and excretion of [14C]-mobocertinib (Period 2) in healthy adult males. In Period 1, participants received a single oral capsule dose of 160 mg mobocertinib, followed by a 15-minute intravenous infusion of 50 µg (~ 2 µCi) [14C]-mobocertinib administered from 3.75 to 4 h after the capsule dose. In Period 2, a single oral dose of 160 mg (~ 100 µCi) [14C]-mobocertinib was administered as an oral solution. The geometric mean absolute bioavailability of mobocertinib was determined to be 36.7%. After oral administration of [14C]-mobocertinib, mobocertinib and its active metabolites, AP32960 and AP32914, were minor components in plasma, accounting for only 0.275% of total plasma radioactivity as the majority of mobocertinib-related material was covalently bound to plasma proteins. The geometric mean percentage of the administered radioactive dose recovered in the urine and feces was 3.57% and 76.0%, respectively. Only 0.39% of the oral dose of [14C]-mobocertinib was recovered in the urine as mobocertinib; thus, indicating that renal excretion of unchanged drug was a very minor pathway of elimination. In both treatment periods, mobocertinib was generally safe and well-tolerated as all adverse events were Grade 1 in severity. (Trial registration number ClinicalTrials.gov NCT03811834. Registration date January 22, 2019).

Peptidic "Molecular Beacon" for Collagen.

Collagen-mimetic peptides (CMP) have been invaluable tools for understanding the structure and function of collagen, which is the most abundant protein in animals. CMPs have also been developed as probes that detect damaged collagen because of the specificity required to form a collagen triple helix. These probes are not, however, ratiometric. Here, we used EPR spectroscopy to determine the end-to-end distances of CMPs that do not form stable homotrimeric helices. We found that those distances are shorter than the distances in the context of a collagen triple helix, suggesting their potential utility as a "molecular beacon" and guiding the choice and location of a pendant fluorophore-quencher pair. We then showed that a molecular beacon based on a glycine-(2S,4S)-4-fluoroproline-(2S,4R)-4-hydroxyproline tripeptide repeat and EDANS-DABCYL pair enabled the ratiometric detection of its binding to both other CMPs and natural mammalian collagen. These results provide guidance for the development of a new modality for detecting damaged collagen in physiological settings.

Structural characterization of E22G Aß1-42 fibrils via1H detected MAS NMR.

Amyloid fibrils have been implicated in the pathogenesis of several neurodegenerative diseases, the most prevalent example being Alzheimer's disease (AD). Despite the prevalence of AD, relatively little is known about the structure of the associated amyloid fibrils. This has motivated our studies of fibril structures, extended here to the familial Arctic mutant of Aß1-42, E22G-Aß1-42. We found E22G-AßM0,1-42 is toxic to Escherichia coli, thus we expressed E22G-Aß1-42 fused to the self-cleavable tag NPro in the form of its EDDIE mutant. Since the high surface activity of E22G-Aß1-42 makes it difficult to obtain more than sparse quantities of fibrils, we employed 1H detected magic angle spinning (MAS) nuclear magnetic resonance (NMR) experiments to characterize the protein. The 1H detected 13C-13C methods were first validated by application to fully protonated amyloidogenic nanocrystals of GNNQQNY, and then applied to fibrils of the Arctic mutant of Aß, E22G-Aß1-42. The MAS NMR spectra indicate that the biosynthetic samples of E22G-Aß1-42 fibrils comprise a single conformation with 13C chemical shifts extracted from hCH, hNH, and hCCH spectra that are very similar to those of wild type Aß1-42 fibrils. These results suggest that E22G-Aß1-42 fibrils have a structure similar to that of wild type Aß1-42.

Economic evaluation of sea-level rise adaptation strongly influenced by hydrodynamic feedbacks.

Coastal communities rely on levees and seawalls as critical protection against sea-level rise; in the United States alone, $300 billion in shoreline armoring costs are forecast by 2100. However, despite the local flood risk reduction benefits, these structures can exacerbate flooding and associated damages along other parts of the shoreline-particularly in coastal bays and estuaries, where nearly 500 million people globally are at risk from sea-level rise. The magnitude and spatial distribution of the economic impact of this dynamic, however, are poorly understood. Here we combine hydrodynamic and economic models to assess the extent of both local and regional flooding and damages expected from a range of shoreline protection and sea-level rise scenarios in San Francisco Bay, California. We find that protection of individual shoreline segments (5 to 75 km) can increase flooding in other areas by as much as 36 million m3 and damages by $723 million for a single flood event and in some cases can even cause regional flood damages that exceed the local damages prevented from protection. We also demonstrate that strategic flooding of certain shoreline segments, such as those with gradually sloping baylands and space for water storage, can help alleviate flooding and damages along other stretches of the coastline. By matching the scale of the economic assessment to the scale of the threat, we reveal the previously uncounted costs associated with uncoordinated adaptation actions and demonstrate that a regional planning perspective is essential for reducing shared risk and wisely spending adaptation resources in coastal bays.

Design of proteasome inhibitors with oral efficacy in vivo against Plasmodium falciparum and selectivity over the human proteasome.

The Plasmodium falciparum proteasome is a potential antimalarial drug target. We have identified a series of amino-amide boronates that are potent and specific inhibitors of the P. falciparum 20S proteasome (Pf20S) ß5 active site and that exhibit fast-acting antimalarial activity. They selectively inhibit the growth of P. falciparum compared with a human cell line and exhibit high potency against field isolates of P. falciparum and Plasmodium vivax They have a low propensity for development of resistance and possess liver stage and transmission-blocking activity. Exemplar compounds, MPI-5 and MPI-13, show potent activity against P. falciparum infections in a SCID mouse model with an oral dosing regimen that is well tolerated. We show that MPI-5 binds more strongly to Pf20S than to human constitutive 20S (Hs20Sc). Comparison of the cryo-electron microscopy (EM) structures of Pf20S and Hs20Sc in complex with MPI-5 and Pf20S in complex with the clinically used anti-cancer agent, bortezomib, reveal differences in binding modes that help to explain the selectivity. Together, this work provides insights into the 20S proteasome in P. falciparum, underpinning the design of potent and selective antimalarial proteasome inhibitors.

Waterborne amino acids: uptake and functional roles in aquatic animals.

Dissolved organic matter is a ubiquitous component of freshwater and marine environments, and includes small nutrient molecules, such as amino acids, which may be available for uptake by aquatic biota. Epithelial transporters, including cotransporters, uniporters and antiporters, facilitate the absorption of dissolved amino acids (often against concentration gradients). Although there is a lack of mechanistic and molecular characterization of such transporters, pathways for the direct uptake of amino acids from the water appear to exist in a wide range of marine phyla, including Porifera, Cnidaria, Platyhelminthes, Brachiopoda, Mollusca, Nemertea, Annelida, Echinodermata, Arthropoda and Chordata. In these animals, absorbed amino acids have several putative roles, including osmoregulation, hypoxia tolerance, shell formation and metabolism. Therefore, amino acids dissolved in the water may play an important, but overlooked, role in aquatic animal nutrition.

Marine Submicron Aerosols from the Gulf of Mexico: Polluted and Acidic with Rapid Production of Sulfate and Organosulfates.

We measured submicron aerosols (PM1) at a beachfront site in Texas in Spring 2021 to characterize the "background" aerosol chemical composition advecting into Texas and the factors controlling this composition. Observations show that marine "background" aerosols from the Gulf of Mexico were highly processed and acidic; sulfate was the most abundant component (on average 57% of total PM1 mass), followed by organic material (26%). These chemical characteristics are similar to those observed at other marine locations globally. However, Gulf "background" aerosols were much more polluted; the average non-refractory (NR-) PM1 mass concentration was 3-70 times higher than that observed in other clean marine atmospheres. Anthropogenic shipping emissions over the Gulf of Mexico explain 78.3% of the total measured "background" sulfate in the Gulf air. We frequently observed haze pollution in the air mass from the Gulf, with significantly elevated concentrations of sulfate, organosulfates, and secondary organic aerosol associated with sulfuric acid. Analysis suggests that aqueous oxidation of shipping emissions over the Gulf of Mexico by peroxides in the particles might potentially be an important pathway for the rapid production of acidic sulfate and organosulfates during the haze episodes under acidic conditions.

Frontiers in the Application of RF Vacuum Electronics.

The application of radio frequency (RF) vacuum electronics for the betterment of the human condition began soon after the invention of the first vacuum tubes in the 1920s and has not stopped since. Today, microwave vacuum devices are powering important applications in health treatment, material and biological science, wireless communication-terrestrial and space, Earth environment remote sensing, and the promise of safe, reliable, and inexhaustible energy. This article highlights some of the exciting application frontiers of vacuum electronics.

Exosomal MicroRNA and Protein Profiles of Hepatitis B Virus-Related Hepatocellular Carcinoma Cells.

Infection with hepatitis B virus (HBV) is a main risk factor for hepatocellular carcinoma (HCC). Extracellular vesicles, such as exosomes, play an important role in tumor development and metastasis, including regulation of HBV-related HCC. In this study, we have characterized exosome microRNA and proteins released in vitro from hepatitis B virus (HBV)-related HCC cell lines SNU-423 and SNU-182 and immortalized normal hepatocyte cell lines (THLE2 and THLE3) using microRNA sequencing and mass spectrometry. Bioinformatics, including functional enrichment and network analysis, combined with survival analysis using data related to HCC in The Cancer Genome Atlas (TCGA) database, were applied to examine the prognostic significance of the results. More than 40 microRNAs and 200 proteins were significantly dysregulated (p < 0.05) in the exosomes released from HCC cells in comparison with the normal liver cells. The functional analysis of the differentially expressed exosomal miRNAs (i.e., mir-483, mir-133a, mir-34a, mir-155, mir-183, mir-182), their predicted targets, and exosomal differentially expressed proteins (i.e., POSTN, STAM, EXOC8, SNX9, COL1A2, IDH1, FN1) showed correlation with pathways associated with HBV, virus activity and invasion, exosome formation and adhesion, and exogenous protein binding. The results from this study may help in our understanding of the role of HBV infection in the development of HCC and in the development of new targets for treatment or non-invasive predictive biomarkers of HCC.

Room-Temperature Quantitative Quantum Sensing of Lithium Ions with a Radical-Embedded Metal-Organic Framework.

Recent advancements in quantum sensing have sparked transformative detection technologies with high sensitivity, precision, and spatial resolution. Owing to their atomic-level tunability, molecular qubits and ensembles thereof are promising candidates for sensing chemical analytes. Here, we show quantum sensing of lithium ions in solution at room temperature with an ensemble of organic radicals integrated in a microporous metal-organic framework (MOF). The organic radicals exhibit electron spin coherence and microwave addressability at room temperature, thus behaving as qubits. The high surface area of the MOF promotes accessibility of the guest analytes to the organic qubits, enabling unambiguous identification of lithium ions and quantitative measurement of their concentration through relaxometric and hyperfine spectroscopic methods based on electron paramagnetic resonance (EPR) spectroscopy. The sensing principle presented in this work is applicable to other metal ions with nonzero nuclear spin.

Observing Nearby Nuclei on Paramagnetic Trityls and MOFs via DNP and Electron Decoupling.

Dynamic nuclear polarization (DNP) is an NMR sensitivity enhancement technique that mediates polarization transfer from unpaired electrons to NMR-active nuclei. Despite its success in elucidating important structural information on biological and inorganic materials, the detailed polarization-transfer pathway from the electrons to the nearby and then the bulk solvent nuclei, and finally to the molecules of interest-remains unclear. In particular, the nuclei in the paramagnetic polarizing agent play significant roles in relaying the enhanced NMR polarizations to more remote nuclei. Despite their importance, the direct NMR observation of these nuclei is challenging because of poor sensitivity. Here, we show that a combined DNP and electron decoupling approach can facilitate direct NMR detection of these nuclei. We achieved an ∼80 % improvement in NMR intensity via electron decoupling at 0.35 T and 80 K on trityl radicals. Moreover, we recorded a DNP enhancement factor of ϵ ${\varepsilon{} }$ ∼90 and ∼11 % higher NMR intensity using electron decoupling on paramagnetic metal-organic framework, magnesium hexaoxytriphenylene (MgHOTP MOF).

Disparities in air quality downscaler model uncertainty across socioeconomic and demographic indicators in North Carolina.

Studies increasingly use output from the Environmental Protection Agency's Fused Air Quality Surface Downscaler ("downscaler") model, which provides spatial predictions of daily concentrations of fine particulate matter (PM2.5) and ozone (O3) at the census tract level, to study the health and societal impacts of exposure to air pollution. Downscaler outputs have been used to show that lower income and higher minority neighborhoods are exposed to higher levels of PM2.5 and lower levels of O3. However, the uncertainty of the downscaler estimates remains poorly characterized, and it is not known if all subpopulations are benefiting equally from reliable predictions. We examined how the percent errors (PEs) of daily concentrations of PM2.5 and O3 between 2002 and 2016 at the 2010 census tract centroids across North Carolina were associated with measures of racial and educational isolation, neighborhood disadvantage, and urbanicity. Results suggest that there were socioeconomic and demographic disparities in surface concentrations of PM2.5 and O3, as well as their prediction uncertainties. Neighborhoods characterized by less reliable downscaler predictions (i.e., higher PEPM2.5 and PEO3) exhibited greater levels of aerial deprivation as well as educational isolation, and were often non-urban areas (i.e., suburban, or rural). Between 2002 and 2016, predicted PM2.5 and O3 levels decreased and O3 predictions became more reliable. However, the predictive uncertainty for PM2.5 has increased since 2010. Substantial spatial variability was observed in the temporal changes in the predictive uncertainties; educational isolation and neighborhood deprivation levels were associated with smaller increases in predictive uncertainty of PM2.5. In contrast, racial isolation was associated with a greater decline in the reliability of PM2.5 predictions between 2002 and 2016; it was associated with a greater improvement in the predictive reliability of O3 within the same time frame.

Observation of a four-spin solid effect.

The two-spin solid effect (2SSE) is one of the established continuous wave dynamic nuclear polarization mechanisms that enables enhancement of nuclear magnetic resonance signals. It functions via a state-mixing mechanism that mediates the excitation of forbidden transitions in an electron-nuclear spin system. Specifically, microwave irradiation at frequencies ωµw ∼ ω0S ± ω0I, where ω0S and ω0I are electron and nuclear Larmor frequencies, respectively, yields enhanced nuclear spin polarization. Following the recent rediscovery of the three-spin solid effect (3SSE) [Tan et al., Sci. Adv. 5, eaax2743 (2019)], where the matching condition is given by ωµw = ω0S ± 2ω0I, we report here the first direct observation of the four-spin solid effect (4SSE) at ωµw = ω0S ± 3ω0I. The forbidden double- and quadruple-quantum transitions were observed in samples containing trityl radicals dispersed in a glycerol-water mixture at 0.35 T/15 MHz/9.8 GHz and 80 K. We present a derivation of the 4SSE effective Hamiltonian, matching conditions, and transition probabilities. Finally, we show that the experimental observations agree with the results from numerical simulations and analytical theory.

Team IHMC at the 2020 Cybathlon: a user-centered approach towards personal mobility exoskeletons.

BACKGROUND: The past few decades have seen rapid advancements in exoskeleton technology, with a considerable shift towards applications involving users with gait pathologies. Commercial devices from ReWalk, Ekso Bionics, and Indego, mainly designed for rehabilitation purposes, have inspired the development of many research platforms aimed at extending capabilities for use as safe and effective personal mobility devices. The 2016 Cybathlon featured an impressive demonstration of exoskeletons designed to enable mobility for individuals with spinal cord injury, however, not a single team completed every task and only two completed the stairs. Major improvements were showcased at the 2020 Cybathlon, with seven of the nine teams completing a similar set of tasks. Team IHMC built upon its silver-medal success from 2016 with an upgraded device, Quix. METHODS: Quix features several notable improvements including an additional powered degree of freedom for hip ab/adduction to laterally shift the device and reduce user effort while walking, custom-tailored cuffs and soft goods based on 3D body scans to optimize user comfort, and a streamlined testing pipeline for online tuning of gait parameters. RESULTS: Team IHMC finished in fourth place behind the teams from EPFL and Angel Robotics. Although we suffered from a considerably slower flat-ground walking speed, our pilot reported marked improvements in overall effort, comfort, and ease-of-use compared to our previous device. CONCLUSIONS: Clear progress in exoskeleton development has been exhibited since the inaugural Cybathlon, with tasks involving rough terrain, stairs, and ramps now posing little threat to most of the competitors. As a result, the layout of the powered exoskeleton course will likely undergo significant modifications to further push the devices towards suitability for personal everyday use. The current tasks do not address the issue of donning and doffing, nor do they simulate a scenario similar to maneuvering a kitchen to prepare a meal, for example. An additional limitation that may be more difficult to test in a competition setting is the required upper-body effort to manipulate the device in an effective manner.