Stereospecific recognition of a chiral centre over multiple flexible covalent bonds by 19F-NMR.

High performance in chiral recognition by a reactive 19F-tag was demonstrated for a variety of enantiomers. The analytes with up to five flexible covalent bonds from the chiral center can be discriminated by a sensitive chiral reporter manifested in the 19F-NMR spectrum. Simultaneous identification of chiral amines in a mixture and high accuracy ee determination were achieved.

Development and validation of machine learning models for nonalcoholic fatty liver disease.

BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) had become the most prevalent liver disease worldwide. Early diagnosis could effectively reduce NAFLD-related morbidity and mortality. This study aimed to combine the risk factors to develop and validate a novel model for predicting NAFLD. METHODS: We enrolled 578 participants completing abdominal ultrasound into the training set. The least absolute shrinkage and selection operator (LASSO) regression combined with random forest (RF) was conducted to screen significant predictors for NAFLD risk. Five machine learning models including logistic regression (LR), RF, extreme gradient boosting (XGBoost), gradient boosting machine (GBM), and support vector machine (SVM) were developed. To further improve model performance, we conducted hyperparameter tuning with train function in Python package 'sklearn'. We included 131 participants completing magnetic resonance imaging into the testing set for external validation. RESULTS: There were 329 participants with NAFLD and 249 without in the training set, while 96 with NAFLD and 35 without were in the testing set. Visceral adiposity index, abdominal circumference, body mass index, alanine aminotransferase (ALT), ALT/AST (aspartate aminotransferase), age, high-density lipoprotein cholesterol (HDL-C) and elevated triglyceride (TG) were important predictors for NAFLD risk. The area under curve (AUC) of LR, RF, XGBoost, GBM, SVM were 0.915 [95% confidence interval (CI): 0.886-0.937], 0.907 (95% CI: 0.856-0.938), 0.928 (95% CI: 0.873-0.944), 0.924 (95% CI: 0.875-0.939), and 0.900 (95% CI: 0.883-0.913), respectively. XGBoost model presented the best predictive performance, and its AUC was enhanced to 0.938 (95% CI: 0.870-0.950) with further parameter tuning. CONCLUSIONS: This study developed and validated five novel machine learning models for NAFLD prediction, among which XGBoost presented the best performance and was considered a reliable reference for early identification of high-risk patients with NAFLD in clinical practice.

Highly Selective and Fast Response/Recovery Cataluminescence Sensor Based on SnO2 for H2S Detection.

In the present work, three kinds of nanosized SnO2 samples were successfully synthesized via a hydrothermal method with subsequent calcination at temperatures of 500 °C, 600 °C, and 700 °C. The morphology and structure of the as-prepared samples were characterized using X-ray diffraction, transmission electron microscopy, selected area electron diffraction, Brunauer-Emmett-Teller analysis, and X-ray photoelectron spectroscopy. The results clearly indicated that the SnO2 sample calcined at 600 °C had a higher amount of chemisorbed oxygen than the SnO2 samples calcined at 500 °C and 700 °C. Gas sensing investigations revealed that the cataluminescence (CTL) sensors based on the three SnO2 samples all exhibited high selectivity toward H2S, but the sensor based on SnO2-600 °C exhibited the highest response under the same conditions. At an operating temperature of 210 °C, the SnO2-600 °C sensor showed a good linear response to H2S in the concentration range of 20-420 ppm, with a detection limit of 8 ppm. The response and recovery times were 3.5 s/1.5 s for H2S gas within the linear range. The study on the sensing mechanism indicated that H2S was oxidized into excited states of SO2 by chemisorbed oxygen on the SnO2 surface, which was mainly responsible for CTL emission. The chemisorbed oxygen played an important role in the oxidation of H2S, and, as such, the reason for the SnO2-600 °C sensor showing the highest response could be ascribed to the highest amount of chemisorbed oxygen on its surface. The proposed SnO2-based gas sensor has great potential for the rapid monitoring of H2S.

Distinct stereospecific effect of chiral tether between a tag and protein on the rigidity of paramagnetic tag.

Flexibility between the paramagnetic tag and its protein conjugates is a common yet unresolved issue in the applications of paramagnetic NMR spectroscopy in biological systems. The flexibility greatly attenuates the magnetic anisotropy and compromises paramagnetic effects especially for pseudocontact shift and residual dipolar couplings. Great efforts have been made to improve the rigidity of paramagnetic tag in the protein conjugates, however, the effect of local environment vicinal to the protein ligation site on the paramagnetic effects remains poorly understood. In the present work, the stereospecific effect of chiral tether between the protein and a tag on the paramagnetic effects produced by the tag attached via a D- and L-type linker between the protein and paramagnetic metal chelating moiety was assessed. The remarkable chiral effect of the D- and L-type tether between the tag and the protein on the rigidity of paramagnetic tag is disclosed in a number of protein-tag-Ln complexes. The chiral tether formed between the D-type tag and L-type protein surface minimizes the effect of the local environment surrounding the ligation site on the averaging of paramagnetic tag, which is helpful to preserve the rigidity of a paramagnetic tag in the protein conjugates.

Simultaneous Discrimination and Quantification of Enantiomeric Amino Acids under Physiological Conditions by Chiral 19F NMR Tag.

Enantiomeric analysis is of great significance in chemistry, chemical biology and pharmaceutical research. We herein propose a chiral 19F NMR tag containing an amino reactive NHS group to discriminate the enantiomeric amino acids under physiological conditions by NMR spectroscopy. The chiral 19F NMR tag readily forms stable amide products with the amino acids in aqueous solution. The stereospecific chemistry of enantiomeric amino acids is discriminated by a stereogenic carbon bonded with a 19F atom and is therefore decoded by the 19F reporter and manifested in the distinct 19F chemical shift. The chemical shift difference (ΔΔδ) of the chiral 19F NMR tag derived enantiomeric amino acids variants has a broad chemical shift range between -1.13 to 1.68 ppm, indicating the high sensitivity of the chiral 19F NMR tag to the stereospecific environment surrounding the individual amino acids. The distinguishable chemical shift produced by the chiral 19F NMR tag permits simultaneous discrimination and quantification of the enantiomeric amino acids in a mixture. The high fidelity of the chiral 19F NMR tag affords high-accuracy determination of the enantiomeric composition of amino acids by simple 1D NMR under physiological conditions.

Simultaneous Quantification of Biothiols and Deciphering Diverse GSH Stability in Different Live Cells by 19F-Tag.

GSH, Cys, Hcy, and H2S are important biothiols and play important roles in the living systems. Quantitative and simultaneous determination of these biothiols under physiological conditions is still a challenge. Herein, we developed an effective 19F-reactive tag that readily interacts with these four biothiols for the generation of stable thioether products that have distinguishable 19F-chemical shifts. These thioester compounds encode the characteristic fingerprint profiles of each biothiols, allowing one to simultaneously quantify and determine these biothiols by 1D 19F NMR spectroscopy. The intra-/extracellular GSH in live cells was assessed by the established strategy, and remarkable variations in the GSH stability were determined between the normal mammalian cells and cancer cells. It is notable that GSH hydrolyzes efficiently in the out-membrane of the cancer cells and the lysates. In contrast, GSH remains stable in the tested normal cells.

Efficient Protein-Protein Couplings Mediated by Small Molecules under Mild Conditions.

Protein-protein coupling reactions under physiological conditions that do not impact the three-dimensional structures of the proteins are in high demand. Owing to the combination of phenylsulfonyl and aldehyde groups in 5-fluoro-4-(phenylsulfonyl)picolinaldehyde (FPPA), the fluorine substituent shows high reactivity toward free thiols. In FPPA, the fluorine is more reactive than phenylsulfonyl for free thiols. Thus the first quantitative nucleophilic substitution can be followed by selective substitution of phenylsulfonyl by an additional thiol or cyclization of aldehyde with a 1,2-aminothiol molecule. The FPPA mediated protein-protein coupling proceeds efficiently under mild conditions, resulting in stable protein conjugates. This coupling method has negligible 3D structural perturbations on the target proteins, and it produces overall intact, nearly traceless, and native structural folds of proteins. It is highly suitable for reconstruction of proteins that are difficult to make and segmental isotopic labeling of multidomain proteins.

Rigid, Highly Reactive and Stable DOTA-like Tags Containing a Thiol-Specific Phenylsulfonyl Pyridine Moiety for Protein Modification and NMR Analysis*.

Site specific installation of a paramagnetic ion with magnetic anisotropy in a biomolecule generates valuable structural restraints, such as pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs). These paramagnetic effects can be used to characterize the structures, interactions and dynamics of biological macromolecules and their complexes. Two single-armed DOTA-like tags, BrPSPy-DO3M(S)A-Ln and BrPSPy-6M-DO3M(S)A-Ln, each containing a thiol-specific reacting group, that is, a phenylsulfonyl pyridine moiety, are demonstrated as rigid, reactive and stable paramagnetic tags for protein modification by formation of a reducing resistant thioether bond between the protein and the tag. The two tags present high reactivity with the solvent exposed thiol group in aqueous solution at room temperature. The introduction of Br at the meta-position in pyridine enhances the reactivity of 4-phenylsulfonyl pyridine towards the solvent exposed thiol group in a protein, whereas the ortho-methyl group in pyridine increases the rigidity of the tag in the protein conjugates. The high performance of these two tags has been demonstrated in different cysteine mutants of ubiquitin and GB1. The high reactivity and rigidity of these two tags can be added in the toolbox of paramagnetic tags suitable for the high-resolution NMR measurements of biological macromolecules and their complexes.

Normalization of magnesium deficiency attenuated mechanical allodynia, depressive-like behaviors, and memory deficits associated with cyclophosphamide-induced cystitis by inhibiting TNF-α/NF-κB signaling in female rats.

BACKGROUND: Bladder-related pain symptoms in patients with bladder pain syndrome/interstitial cystitis (BPS/IC) are often accompanied by depression and memory deficits. Magnesium deficiency contributes to neuroinflammation and is associated with pain, depression, and memory deficits. Neuroinflammation is involved in the mechanical allodynia of cyclophosphamide (CYP)-induced cystitis. Magnesium-L-Threonate (L-TAMS) supplementation can attenuate neuroinflammation. This study aimed to determine whether and how L-TAMS influences mechanical allodynia and accompanying depressive symptoms and memory deficits in CYP-induced cystitis. METHODS: Injection of CYP (50 mg/kg, intraperitoneally, every 3 days for 3 doses) was used to establish a rat model of BPS/IC. L-TAMS was administered in drinking water (604 mg·kg-1·day-1). Mechanical allodynia in the lower abdomen was assessed with von Frey filaments using the up-down method. Forced swim test (FST) and sucrose preference test (SPT) were used to measure depressive-like behaviors. Novel object recognition test (NORT) was used to detect short-term memory function. Concentrations of Mg2+ in serum and cerebrospinal fluid (CSF) were measured by calmagite chronometry. Western blot and immunofluorescence staining measured the expression of tumor necrosis factor-α/nuclear factor-κB (TNF-α/NF-κB), interleukin-1ß (IL-1ß), and N-methyl-D-aspartate receptor type 2B subunit (NR2B) of the N-methyl-D-aspartate receptor in the L6-S1 spinal dorsal horn (SDH) and hippocampus. RESULTS: Free Mg2+ was reduced in the serum and CSF of the CYP-induced cystitis rats on days 8, 12, and 20 after the first CYP injection. Magnesium deficiency in the serum and CSF correlated with the mechanical withdrawal threshold, depressive-like behaviors, and short-term memory deficits (STMD). Oral application of L-TAMS prevented magnesium deficiency and attenuated mechanical allodynia (n = 14) and normalized depressive-like behaviors (n = 10) and STMD (n = 10). The upregulation of TNF-α/NF-κB signaling and IL-1ß in the L6-S1 SDH or hippocampus was reversed by L-TAMS. The change in NR2B expression in the SDH and hippocampus in the cystitis model was normalized by L-TAMS. CONCLUSIONS: Normalization of magnesium deficiency by L-TAMS attenuated mechanical allodynia, depressive-like behaviors, and STMD in the CYP-induced cystitis model via inhibition of TNF-α/NF-κВ signaling and normalization of NR2B expression. Our study provides evidence that L-TAMS may have therapeutic value for treating pain and comorbid depression or memory deficits in BPS/IC patients.

Site-Specific Tagging of Proteins with Paramagnetic Ions for Determination of Protein Structures in Solution and in Cells.

High-resolution NMR spectroscopy is sensitive to local structural variations and subtle dynamics of biomolecules and is an important technique for studying the structures, dynamics, and interactions of these molecules. Small-molecule probes, including paramagnetic tags, have been developed for this purpose. Paramagnetic effects manifested in magnetic resonance spectra have long been recognized as valuable tools for chemical analysis of small molecules, and these effects were later applied in the fields of chemical biology and structural biology. However, such applications require the installation of a paramagnetic center in the biomolecules of interest. Paramagnetic metal ions and stable free radicals are the most widely used paramagnetic probes for biological magnetic resonance spectroscopy, and therefore mild, high-yielding approaches for chemically attaching paramagnetic tags to biomolecules are in high demand. In this Account, we begin by discussing paramagnetic species, especially transition metal ions and lanthanide ions, that are suitable for NMR and EPR studies, particularly for in-cell applications. Thereafter, we describe approaches for site-specific tagging of proteins with paramagnetic ions and discuss considerations involved in designing high-quality paramagnetic tags, including the strength of the binding between the metal-chelating moiety and the paramagnetic ion, the chemical stability, and the flexibility of the tether between the paramagnetic tag and the target protein. The flexibility of a tag correlates strongly with the averaging of paramagnetic effects observed in NMR spectra, and we describe methods for increasing tag rigidity and applications of such tags in biological systems. We also describe specific applications of established site-specific tagging approaches and newly developed paramagnetic tags for the elucidation of protein structures and dynamics at atomic resolution both in solution and in cells. First, we describe the determination of the 3D structure of a short-lived, low-abundance enzyme intermediate complex in real time by using pseudocontact shifts as structural restraints. Second, we demonstrate the utility of stable paramagnetic tags for determining 3D structures of proteins in live cells, and pseudocontact shifts are shown to be valuable structural restraints for in-cell protein analysis. Third, we show that a NMR optimized paramagnetic tag allows one to determine distance restraints on proteins by double electron-electron resonance (DEER) measurements with high spatial resolution both in vitro and in cells. Finally, we summarize recent advances in site-specific tagging of proteins to achieve atomic-resolution information about structural changes of proteins, and the advantages and challenges of magnetic resonance spectroscopy in biological systems.

Resonance Assignments of Lowly Populated and Unstable Enzyme Intermediate Complex under Real-Time Conditions.

Unstable and low-abundance protein complexes represent a large family of transient protein complexes that are difficult to characterize, even by means of high-resolution NMR spectroscopy. A method to assign the NMR signals of these unstable complexes through a combination of selective isotope labeling of amino acids in a protein and site-specific labeling the protein with a paramagnetic tag is presented herein. By using this method, the resonances of unstable thioester intermediate complex (lifetime <5 h and highest concentration ≈20 µm) generated by Staphylococcus aureus sortase A and its peptide substrate under a real-time reaction have been assigned.

Neuregulin-1-ErbB signaling promotes microglia activation contributing to mechanical allodynia of cyclophosphamide-induced cystitis.

AIMS: Central sensitization playsimportant roles in cyclophosphamide (CYP)-induced cystitis. In addition, as a visceral pain, CYP-induced chronic pain shares common pathophysiological mechanisms with neuropathic pain. Previous studies demonstrated that neuregulin-1 (Nrg1)-ErbB signaling contributes to neuropathic pain, but whether and how this signaling influences mechanical allodynia in CYP-induced cystitis is unclear. This study aimed to determine whether and how Nrg1-ErbB signaling modulates mechanical allodynia in a CYP-induced cystitis rat model. METHODS: Systemic injection with CYP was used to establish a rat model of bladder pain syndrome/interstitial cystitis (BPS/IC). An irreversible ErbB family receptor inhibitor, PD168393, and exogenous Nrg1 were intrathecally injected to modulate Nrg1-ErbB signaling. Mechanical allodynia in the lower abdomen was assessed with von-Frey filaments using the up-down method. Western blot analysis and immunofluorescence staining were used to measure the expression of Nrg1-ErbB signaling, Iba-1, p-p38, and IL-1ß in the L6-S1 spinal dorsal horn (SDH). RESULTS: We observed upregulation of Nrg1-ErbB signaling as well as overexpression of the microglia activation markers Iba-1 and p-p38 and the proinflammatory factor, interleukin-1ß (IL-1ß), in the SDH of the cystitis group. Further, treatment with PD168393 attenuated mechanical allodynia in CYP-induced cystitis and inhibited microglia activation, leading to decreased production of IL-1ß. The inhibitor PD168393 reversed the algesic effect of exogenous Nrg1 on the cystitis model. CONCLUSIONS: Nrg1-ErbB signaling may promote microglia activation, contributing to mechanical allodynia of CYP-induced cystitis. Our study showed that modulation of Nrg1-ErbB signaling may have therapeutic value for treating pain symptoms in BPS/IC.

Stable and rigid DTPA-like paramagnetic tags suitable for in vitro and in situ protein NMR analysis.

Organic synthesis of a ligand with high binding affinities for paramagnetic lanthanide ions is an effective way of generating paramagnetic effects on proteins. These paramagnetic effects manifested in high-resolution NMR spectroscopy are valuable dynamic and structural restraints of proteins and protein-ligand complexes. A paramagnetic tag generally contains a metal chelating moiety and a reactive group for protein modification. Herein we report two new DTPA-like tags, 4PS-PyDTTA and 4PS-6M-PyDTTA that can be site-specifically attached to a protein with a stable thioether bond. Both protein-tag adducts form stable lanthanide complexes, of which the binding affinities and paramagnetic tensors are tunable with respect to the 6-methyl group in pyridine. Paramagnetic relaxation enhancement (PRE) effects of Gd(III) complex on protein-tag adducts were evaluated in comparison with pseudocontact shift (PCS), and the results indicated that both 4PS-PyDTTA and 4PS-6M-PyDTTA tags are rigid and present high-quality PREs that are crucially important in elucidation of the dynamics and interactions of proteins and protein-ligand complexes. We also show that these two tags are suitable for in-situ protein NMR analysis.

Deciphering the Multisite Interactions of a Protein and Its Ligand at Atomic Resolution by Using Sensitive Paramagnetic Effects.

Quantitative analysis of multisite interactions between a protein and its binding partner at atomic resolution is complicated because locating the binding sites is difficult and differentiating the flexibility of each binding site is even more elusive. Introduction of a paramagnetic metal center close to the binding pocket greatly attenuates the signals in the NMR spectrum upon binding. Herein, the multisite binding of hen egg white lysozyme (HEWL) with lanthanide complexes [Ln(DPA)3 ]3- (DPA=dipicolinic acid) was analyzed with sensitive paramagnetic NMR spectroscopy. Paramagnetic relaxation enhancement (PRE) revealed that HEWL interacts with [Ln(DPA)3 ]3- at four major binding sites in aqueous solution, which is in contrast to a previous X-ray structural analysis. The varied binding affinities for the ligands and different flexibilities at each binding site were in good agreement with atomistic molecular dynamics (MD) simulations. The present work demonstrates that a combination of paramagnetic NMR spectroscopy and MD simulations is a powerful tool to delineate the multisite interactions of a protein with its binding partner at atomic resolution, in terms of both affinity and flexibility.

Transconjunctival Orbital Septum Fat Release and Preservation for Orbitopalpebral Sulcus in Lower Eyelid Blepharoplasty.

BACKGROUND: Compared to the traditional transcutaneous approach, a safe and effective lower eyelid blepharoplasty has been recognized. In 2007, Sadove first reported a series of patients treated with transconjunctival septal suturing, but the inferior orbitopalpebral sulcus was not totally improved. PURPOSE: Orbital septal fat release and preservation through the transconjunctival approach was used to treat 20 young patients with bulging bags and inferior orbitopalpebral sulcus. METHOD: The orbital septal fat was released and transferred to infraorbital rim to be a base for the inferior orbitopalpebral sulcus. RESULT: Obvious bulging fat was released, and the orbitopalpebral sulcus was flattened by released and excessive orbital septal fat. Satisfactory results were achieved. CONCLUSION: The results achieved from this series of patients indicate that orbital septal fat release and preservation through the transconjunctival approach for reducing the orbitopalpebral sulcus is a safe and effective treatment for bulging fat and orbitopalpebral sulcus in young patients. LEVEL OF EVIDENCE IV: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

A Reactive, Rigid GdIII Labeling Tag for In-Cell EPR Distance Measurements in Proteins.

The cellular environment of proteins differs considerably from in vitro conditions under which most studies of protein structures are carried out. Therefore, there is a growing interest in determining dynamics and structures of proteins in the cell. A key factor for in-cell distance measurements by the double electron-electron resonance (DEER) method in proteins is the nature of the used spin label. Here we present a newly designed GdIII spin label, a thiol-specific DOTA-derivative (DO3MA-3BrPy), which features chemical stability and kinetic inertness, high efficiency in protein labelling, a short rigid tether, as well as favorable spectroscopic properties, all are particularly suitable for in-cell distance measurements by the DEER method carried out at W-band frequencies. The high performance of DO3MA-3BrPy-GdIII is demonstrated on doubly labelled ubiquitin D39C/E64C, both in vitro and in HeLa cells. High-quality DEER data could be obtained in HeLa cells up to 12 h after protein delivery at in-cell protein concentrations as low as 5-10 µm.

Analysis of the solution conformations of T4 lysozyme by paramagnetic NMR spectroscopy.

A large number of crystal structures of bacteriophage T4 lysozyme (T4-L) have shown that it contains two subdomains, which can arrange in a compact conformation (closed state) or, in mutants of T4-L, more extended structures (open state). In solution, wild-type T4-L displays only a single set of nuclear magnetic resonance (NMR) signals, masking any conformational heterogeneity. To probe the conformational space of T4-L, we generated a site-specific lanthanide binding site by attaching 4-mercaptomethyl dipicolinic acid via a disulfide bond to Cys44 in the triple-mutant C54T/C97A/S44C of T4-L and measured pseudocontact shifts (PCS) and magnetically induced residual dipolar couplings (RDC). The data indicate that, in solution and in the absence of substrate, the structure of T4-L is on average more open than suggested by the closed conformation of the crystal structure of wild-type T4-L. A slightly improved fit was obtained by assuming a population-weighted two-state model involving an even more open conformation and the closed state, but paramagnetic relaxation enhancements measured with Gd(3+) argue against such a conformational equilibrium. The fit could not be improved by including a third conformation picked from the hundreds of crystal structures available for T4-L mutants.

3D Structure Determination of an Unstable Transient Enzyme Intermediate by Paramagnetic NMR Spectroscopy.

Enzyme catalysis relies on conformational plasticity, but structural information on transient intermediates is difficult to obtain. We show that the three-dimensional (3D) structure of an unstable, low-abundance enzymatic intermediate can be determined by nuclear magnetic resonance (NMR) spectroscopy. The approach is demonstrated for Staphylococcus aureus sortase A (SrtA), which is an established drug target and biotechnological reagent. SrtA is a transpeptidase that converts an amide bond of a substrate peptide into a thioester. By measuring pseudocontact shifts (PCSs) generated by a site-specific cysteine-reactive paramagnetic tag that does not react with the active-site residue Cys184, a sufficient number of restraints were collected to determine the 3D structure of the unstable thioester intermediate of SrtA that is present only as a minor species under non-equilibrium conditions. The 3D structure reveals structural changes that protect the thioester intermediate against hydrolysis.