Formation of hydrogen bonding network of methane sulfonic acid at low degree of hydration (MSA)m·(H2O)n (m = 1-2 and n = 1-5)

This study employs ab initio calculations based on density functional theory (DFT) to investigate the structural properties, 1H-NMR spectra, and vibrational spectra of methane sulfonic acid (MSA) at low degree of hydration. The findings reveal that energetically stable structures are formed by small clusters consisting of one or two MSA molecules (m = 1 and 2) and one or two water molecules in (MSA)m·(H2O)n (m = 1-2 and n = 1-5).These stable structures arise from the formation of strong cyclic hydrogen bonds between the proton of the hydroxyl (OH) group in MSA and the water molecules. However, clusters containing three or more water molecules (n > 2) exhibit proton transfer from MSA to water, resulting in the formation of ion-pairs composed of CH3SO3- and H3O+species. The measured 1H-NMR spectra demonstrate the presence of hydrogen-bonded interactions between MSA and water, with a single MSA molecule interacting with water molecules. This interaction model accurately represents the hydrogen bonding network, as supported by the agreement between the experimental and calculated NMR chemical shift results.

Brookite TiO2 as an active photocatalyst for photoconversion of plastic wastes to acetic acid and simultaneous hydrogen production: Comparison with anatase and rutile

Photoreforming is a clean photocatalytic technology for simultaneous plastic waste degradation and hydrogen fuel production, but there are still limited active and stable catalysts for this process. This work introduces the brookite polymorph of TiO2 as an active photocatalyst for photoreforming with an activity higher than anatase and rutile polymorphs for both hydrogen production and plastic degradation. Commercial brookite successfully converts polyethylene terephthalate (PET) plastic to acetic acid under light. The high activity of brookite is attributed to good charge separation, slow decay and moderate electron trap energy, which lead to a higher generation of hydrogen and hydroxyl radicals and accordingly enhanced photo-oxidation of PET plastic. These results introduce brookite as a stable and active catalyst for the photoconversion of water contaminated with microplastics to value-added organic compounds and hydrogen.

NMR sugar-profile in genuine grape must

The wine market has always faced the problem of fraud, including the addition of exogenous sugar solutions to grape musts to increase the final alcohol content. Since in some countries the practice of chaptalization is prohibited (except by adding concentrated must) it is necessary to broaden the analytical techniques that allow the identification of this type of fraud. The aim of this study was to define an NMR-based sugar profile of genuine grape must to set concentration limits for each sugar as parameters of authenticity. Glucose, fructose, together with eleven minor sugars were quantified in 82 genuine Italian grape musts, developing an analytical procedure based on highly selective chemical shift filters followed by TOCSY. Alongside the characteristic myo- and scyllo-inositol, significant contents of mannose, galactose, and trehalose were also found. Otherwise, maltose, rhamnose, arabinose, sucrose and lactose are present in lower concentrations and show great concentration variability.

The role of magnesium ion in the interactions between humic acid and tetracycline in solution

Coexisting tetracycline (TC), dissolved organic matter (DOM), and metal cations in aqueous environments might form complexes and consequently affect the environmental fate of TC. In this study, the interactions among coexisting humic acid (HA), TC, and Mg(II) in solutions were investigated by equilibrium dialysis batch experiments and nuclear magnetic resonance hydrogen spectroscopy (1H NMR) characterization. In the binary systems, the dimethylamine (4Me2NH+) functional group on the A-ring of TC bound to the oxygen-containing functional groups of HA via hydrogen bond. The solution pH affected the agglomeration morphology and dissociation of the oxygen-containing functional groups of HA as well as protonation and spatial conformation of TC, which in turn affected the HA-TC interactions. The complexation sites and ratio of Mg(II) on TC affect the binding mode in the ternary system. When the TC-Mg(II) complexation ratio is 1:1, the B, C, and D rings of TC preferentially complex with Mg(II), resulting in the change of TC from an extended to a twisted conformation. At this time, Mg(II) had a weaker inhibitory effect on binding affinity between HA and TC. When the complexation ratio was 1:2, the second Mg(II) complexation deactivated the 4Me2NH + on the A ring and further stabilized TC twisted conformation, resulting in a stronger inhibitory effect on the binding of TC to HA. Under acidic conditions, the solution pH mainly caused the difficulty in forming TC-Mg(II) complexes. The inhibitory effect of Mg(II) on the binding between HA and TC is weaker than that under alkaline conditions.

1H, 31P NMR, Raman and FTIR spectroscopies for investigating phosphoric acid dissociation to understand phosphate ion kinetics in body fluids

The study investigates the formation and transportation of ionic charge carriers in phosphoric acid-water system. This investigation encompasses an analysis of 1H and 31P NMR chemical shifts, self-diffusion coefficients, spin-lattice relaxation rates, spin-spin relaxation rates, activation energies, dissociation constants, electrical conductivity, and Raman shifts, along with FTIR spectra across various water concentrations. Significantly, the maxima observed in these curves at around 0.8 water molar fraction predominantly from the unique molecular arrangement between phosphoric acid and water molecules, influenced by a hydrogen bonding network. These findings yield valuable insights into phosphate ion kinetics within body fluids, covering essential aspects like hydrogen bonding networks, ionization processes, and the energy kinetics of phosphoric dissociation. A customized semiempirical model is applied to calculate dissociated species (water, phosphoric acid, and hydronium ion) at different water contents within a wide range of water mole fraction. Furthermore, this investigation extends to the dissociation of phosphoric acid in DMEM cell culture media, offering a more precise model for phosphate ionic kinetics within body fluids, especially at nominal phosphate concentrations of approximately 1:700μL.

The Complementarity of Nuclear Magnetic Resonance and Native Mass Spectrometry in Probing Protein-Protein Interactions

Nuclear magnetic resonance (NMR) and native mass spectrometry (MS) are mature physicochemical techniques with long histories and important applications. NMR spectroscopy provides detailed information about the structure, dynamics, interactions, and chemical environment of biomolecules. MS is an effective approach for determining the mass of biomolecules with high accuracy, sensitivity, and speed. The two techniques offer unique advantages and provide solid tools for structural biology. In the present review, we discuss their individual merits in the context of their applications to structural studies in biology with specific focus on protein interactions and evaluate their limitations. We provide specific examples in which these techniques can complement each other, providing new information on the same scientific case. We discuss how the field may develop and what challenges are expected in the future. Overall, the combination of NMR and MS plays an increasingly important role in integrative structural biology, assisting scientists in deciphering the three-dimensional structure of composite macromolecular assemblies.

Evidence of residual micellar structures in a lipid nanocapsule dispersion. A multi-technique approach

Nanoemulsions are metastable emulsions in the nanometric range which can be obtained using low-energy processes. A decade ago, it was demonstrated that a non-negligible amount of residual surfactant micelles may coexist with the oil nanodroplets in a model oil/surfactant system. Those micelles were called "wasted" micelles as they did not participate in the formation of the nanodroplets. Little attention has been focused on the potential presence or effect of such secondary structures in nanoemulsions used as drug delivery systems. Here, we present an extensive characterization of lipid nanocapsules, a nanoemulsion obtained from a medium-chain triglyceride mixed with a pegylated surfactant by a process comprising a temperature-dependent phase inversion followed by a cold-water quench. Lipid nanocapsules demonstrate a very good shelf stability. First, for clarity and academic purposes, we briefly present the pros and the cons of the various diffusion-based characterization techniques used i.e., multi-angle and single-angle dynamic light scattering, nanoparticle tracking analysis, fluorescence recovery after photobleaching, and diffusometry nuclear magnetic resonance. Then, combining all these techniques, we show that up to 40 wt% of the surfactant is not involved in the lipid nanocapsule construction but forms residual micellar structures. Those micelles also contain a small quantity of medium-chain triglyceride (2 wt% of the initial amount) and encapsulate around 40 wt% of a fluorescent dye originally dispersed in the oily phase.

The sensitivity of mechanical properties and pore structures of Beishan granite to large variation of temperature in nuclear waste storage sites

Granite is the host rock of the Beishan Underground Research Laboratory (URL) for geological disposal of high-level radioactive waste in China. The mechanical behavior of Beishan granite is the key in determining whether the repository can serve safely for a long time. The surrounding rock of the repository will be exposed to thermal environment induced by radionuclide decay, resulting in significant changes in the physical and mechanical properties of the Beishan granite. This study investigated the pore structure and mechanical properties of Beishan granite after thermal treatment. The T₂ spectrum distribution, pore size distribution, porosity, and magnetic resonance imaging (MRI) were obtained through nuclear magnetic resonance (NMR); uniaxial compressive strength (UCS) and acoustic emission (AE) signal characteristic of granite were investigated through uniaxial compression tests. The results showed that high temperature significantly affected the T₂ spectrum distribution, pore size distribution, porosity, compressive strength, and elastic modulus of granite, and porosity gradually increases, whereas the strength and elastic modulus gradually decline with increasing temperature. The porosity of granite has a linear relationship with UCS and elastic modulus, indicating that the essential mechanism for the deterioration of macroscopic mechanical properties lies in changes of microstructure. In addition, the thermal damage mechanism of granite was revealed, and a damage variable was defined based on porosity and uniaxial compressive strength.

CPMG pulse sequence for relaxation dispersion that cancels artifacts independently of spin states

The relaxation dispersion (rd) of nuclear magnetic resonance provides thermodynamic and kinetic information regarding molecules for which the conformations are exchanging in equilibrium. Experiments have often been implemented with Carr-Purcell-Meiboom-Gill (CPMG) pulse sequences for heteronuclear S-spin in SI and SI₃ spin systems. One of the most common CPMG sequences contains a sequence called a P-element in the middle to average the different relaxation rates of anti-phase and in-phase coherences; however, its drawback is that the artifacts that can be compensated for are only those in one of the two S-spin doublet magnetization components, for example, SI_α or SI_β in an SI spin system. Thus, when the CPMG sequence is followed by a normal heteronuclear single-quantum correlation (HSQC) sequence, the detected signal will also include the other component with accumulated artifacts. To overcome this issue, we developed a new pulse sequence (AFTAC) that can suppress artifacts in both the magnetization components. Its effectiveness was demonstrated by simulations and actual measurements targeting the methyl groups of dimethylsulfoxide and N, N-dimethyltrichloroacetamide. The results demonstrated that the AFTAC sequence sufficiently suppressed the artifacts, despite being followed by an HSQC sequence that detects both components. AFTAC is particularly suitable for the rd measurements of small molecules, which are usually not deuterated and are not subject to transverse relaxation optimized spectroscopy (TROSY) sequences. AFTAC does not require ¹H continuous wave irradiation for I-spin decoupling, which is necessary for certain CPMG methods that maintain S-spin in-phase coherence during the CPMG period (T_cpmg). Therefore, AFTAC places less burden on the probe, even with a long T_cpmg. Furthermore, the AFTAC method achieves a similar artifact suppression quality not only in SI but also in SI₂ and SI₃ spin systems.

NMR-based metabolomics to determine the fluctuation of metabolites in hydroponic purslane crops at different harvesting times

Purslane (Portulaca oleracea L.) has a high content of nutrients and medicinal effects that depend on the genotype, harvesting time, and production system. The objective of the present research work was to elucidate the NMR-based metabolomics profiling of three native purslane cultivars from Mexico (Xochimilco, Mixquic, and Cuautla) grown under hydroponic conditions and harvested in three different times (32, 39, and 46 days after emergence). Thirty-nine metabolites identified in the ¹H NMR spectra of aerial parts of purslane, 5 sugars, 15 amino acids, 8 organic acids, 3 caffeoylquinic acids, as well as 2 alcohols and 3 nucleosides, choline, O-phosphocholine and trigonelline were also detected. A total of 37 compounds were detected in native purslane from Xochimilco and Cuautla, whereas 39 compounds were detected in purslane from Mixquic. Principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) separated the cultivars into three clusters. Mixquic cultivar had the highest number of differential compounds (amino acids and carbohydrates), followed by Xochimilco and Cuautla cultivars, respectively. Changes in the metabolome were observed in latest times of harvest for all the cultivars studied. The differential compounds were glucose, fructose, galactose, pyruvate, choline, and 2-hydroxysobutyrate. The results obtained in this investigation may contribute to selecting the best cultivar of purslane and the best time in which the levels of nutrients are optimal.

The effect of methylated phosphatidylethanolamine derivatives on the ionization properties of signaling phosphatidic acid

Phosphatidylethanolamine (PE) and Phosphatidylcholine (PC) are the most abundant glycerophospholipids in eukaryotic membranes. The differences in the physicochemical properties of their headgroups have contrasting modulatory effects on their interaction with intracellular macromolecules. As such, their overall impact on membrane structure and function differs significantly. Enzymatic methylation of PE's amine headgroup produces two methylated derivatives namely monomethyl PE (MMPE) and dimethyl PE (DMPE) which have physicochemical properties that generally range between that of PE and PC. Additionally, their influence on membrane properties differs from both PE and PC. Although variations in headgroup methylation have been reported to affect signaling pathways, the direct influence that these differences exert on the ionization properties of signaling phospholipids have not been investigated. Here, we briefly review membrane function and structure that are mediated by the differences in headgroup methylation between PE, MMPE, DMPE and PC. In addition, using ³¹P MAS NMR, we investigate the effect of these four phospholipids on the ionization properties of the ubiquitous signaling anionic lipid phosphatidic acid (PA). Our results show that PA's ionization properties are differentially affected by changes in phospholipid headgroup methylation. This could have important implications for PA-protein binding and hence physiological functions in cells where signaling events lead to changes in abundance of methylated PE derivatives in the membrane.

Quantitative NMR Methods in Metabolomics

Nuclear Magnetic Resonance (NMR) spectroscopy is one of the two major analytical platforms in the field of metabolomics, the other being mass spectrometry (MS). NMR is less sensitive than MS and hence it detects a relatively small number of metabolites. However, NMR exhibits numerous unique characteristics including its high reproducibility and non-destructive nature, its ability to identify unknown metabolites definitively, and its capabilities to obtain absolute concentrations of all detected metabolites, sometimes even without an internal standard. These characteristics outweigh the relatively low sensitivity and resolution of NMR in metabolomics applications. Since biological mixtures are highly complex, increased demand for new methods to improve detection, better identify unknown metabolites, and provide more accurate quantitation continues unabated. Technological and methodological advances to date have helped to improve the resolution and sensitivity and detection of a larger number of metabolite signals. Efforts focused on measuring unknown metabolite signals have resulted in the identification and quantitation of an expanded pool of metabolites including labile metabolites such as cellular redox coenzymes, energy coenzymes, and antioxidants. This chapter describes quantitative NMR methods in metabolomics with an emphasis on recent methodological developments, while highlighting the benefits and challenges of NMR-based metabolomics.

Qualitative and Quantitative Characterization of Protein-Carbohydrate Interactions by NMR Spectroscopy

Solution-state nuclear magnetic resonance (NMR) spectroscopy can be used to monitor protein-carbohydrate interactions. Two-dimensional ¹H-¹⁵N heteronuclear single quantum coherence (HSQC)-based techniques described in this chapter can be used quickly and effectively to screen a set of possible carbohydrate-binding partners, to quantify the dissociation constant (K_d) of any identified interactions, and to the map the carbohydrate-binding site on the structure of a protein. Here, we describe the titration of a family 32 carbohydrate-binding module from Clostridium perfringens (CpCBM32) with the monosaccharide N-acetylgalactosamine (GalNAc), in which we calculate the apparent dissociation of the interaction and map the GalNAc binding site onto the structure of CpCBM32. This approach can be applied to other CBM- and protein-ligand systems.

Detecting and Characterizing Interactions of Metabolites with Proteins by Saturation Transfer Difference Nuclear Magnetic Resonance (STD NMR) Spectroscopy

Saturation transfer difference (STD) nuclear magnetic resonance (NMR) spectroscopy is an established technique for detecting and characterizing the binding of small molecules, such as metabolites, to biological macromolecules like proteins and nucleic acids. STD NMR allows detection of binding in complex mixtures of potential ligands, which is often used for library screening in the pharmaceutical industry but may also be beneficial for binding studies with metabolite mixtures. The nature of the ligand is normally restricted to small molecules in terms of NMR spectroscopy, and the size of the macromolecule on the other side should be larger than 10-15 kDa. This technique is especially applicable to detecting binders of intermediate to low affinity with the dissociation constant (K_D) above 1 μM. In this chapter, we focus on recent developments and the applications of STD NMR to studying interactions of natural products and metabolites, in particular. The reader is also referred to excellent reviews of the field and the literature cited therein. This chapter also provides a detailed experimental protocol for performing the STD NMR measurement based on the example of the subunit A of the Na⁺-transporting NADH/ubiquinone oxidoreductase (Na⁺-NQR) from V. cholerae interacting with its natural quinone substrate and inhibitors.

Isolated murine skeletal muscles utilize pyruvate over glucose for oxidation

INTRODUCTION

Fuel sources for skeletal muscle tissue include carbohydrates and fatty acids, and utilization depends upon fiber type, workload, and substrate availability. The use of isotopically labeled substrate tracers combined with nuclear magnetic resonance (NMR) enables a deeper examination of not only utilization of substrates by a given tissue, but also their contribution to tricarboxylic acid (TCA) cycle intermediates.

OBJECTIVES

The goal of this study was to determine the differential utilization of substrates in isolated murine skeletal muscle, and to evaluate how isopotomer anlaysis provided insight into skeletal muscle metabolism.

METHODS

Isolated C57BL/6 mouse hind limb muscles were incubated in oxygenated solution containing uniformly labeled 13C6 glucose, 13C3 pyruvate, or 13C2 acetate at room temperature. Isotopomer analysis of 13C labeled glutamate was performed on pooled extracts of isolated soleus and extensor digitorum longus (EDL) muscles.

RESULTS

Pyruvate and acetate were more avidly consumed than glucose with resultant increases in glutamate labeling in both muscle groups. Glucose incubation resulted in glutamate labeling, but with high anaplerotic flux in contrast to the labeling by pyruvate. Muscle fiber type distinctions were evident by differences in lactate enrichment and extent of substrate oxidation.

CONCLUSION

Isotope tracing experiments in isolated muscles reveal that pyruvate and acetate are avidly oxidized by isolated soleus and EDL muscles, whereas glucose labeling of glutamate is accompanied by high anaplerotic flux. We believe our results may set the stage for future examination of metabolic signatures of skeletal muscles from pre-clinical models of aging, type-2 diabetes and neuromuscular disease.

Distinct mode of membrane interaction and disintegration by diverse class of antimicrobial peptides

The exploitation of conventional antibiotics in conjunction with the adeptness of microbes has led to the emergence of multi-drug-resistant pathogens. This has posed a severe threat to combating life-threatening infectious diseases. Antimicrobial peptides (AMP), which are considered to be the first line of defense in all living organisms, are being developed for therapeutic use. Herein, we determined the NMR solution structure of Rhesus macaque Myeloid Alpha Defensin-4 (RMAD4), a defensin AMP. Additionally, the distinct modes of membrane perturbation for two structurally dissimilar classes of AMPs was studied using biophysical methods namely, Solid-state ³¹P NMR, DSC and cryo-TEM. The cathelicidin - Bovine myeloid antimicrobial peptide (BMAP-28 (1-18)), which adopts a helical conformation, and the defensin RMAD4 peptide that natively folds to form β-sheets appeared to engage differently with the bacterial membrane. The helical BMAP-28 (1-18) peptide initiates lipid segregation and membrane thinning followed by pore formation, while the β-stranded RMAD4 peptide demonstrates fragmentation of the bilayer by the carpet or detergent-like mechanism of action. Molecular dynamics studies sufficiently corroborated these findings. The structure and mechanism of action of the AMPs studied using experimental and computational approaches are believed to help in providing a platform for the rational design of new competent and cost-effective antimicrobial peptides for therapeutic applications.

Triticonazole enantiomers induced enantioselective metabolic phenotypes in Fusarium graminearum and HepG2 cells

The management of Fusarium head blight relies heavily on triazole fungicides. Most of triazole fungicides are chiral, and their enantioselective effects on metabolic phenotypes are poorly understood. Herein, we analyzed the bioactivity of triticonazole against Fusarium graminearum, and ¹H-nuclear magnetic resonance-based metabolomics was used to assess the metabolic disturbances of triticonazole enantiomers in Fusarium graminearum and human hepatocarcinoma cells. Results indicated that the bioactivity of R-triticonazole was 4.28-fold higher than its antipode since it bound stronger with fungal CYP51B and induced more abnormal metabolic processes of Fusarium graminearum, including lipid metabolism, glycolysis, and amino acid metabolism. In human hepatocarcinoma cells, pathways of "alanine, aspartic acid and glutamate metabolism" and "pyruvate metabolism" were disturbed significantly by R-triticonazole; "phenylalanine metabolism" and "taurine-hypotaurine metabolism" were abnormal in the exposure of S-triticonazole. These results suggested that R- and S-triticonazole could affect different metabolic pathways of human hepatocarcinoma cells, and the massively use of inefficient S-triticonazole should be avoided. Our data will help to better understand the enantioselectivity of chiral pesticides and provide a reference for the development of green pesticides.

Enzyme kinetics by real-time quantitative NMR (qNMR) spectroscopy with progress curve analysis

This review article summarizes how the experimental data obtained using quantitative nuclear magnetic resonance (qNMR) spectroscopy can be combined with progress curve analysis to determine enzyme kinetic parameters. The qNMR approach enables following the enzymatic conversion of the substrate to the product in real-time by a continuous collection of spectra. The Lambert-W function, a closed-form solution to the time-dependent substrate/product kinetics of the rate equation, can estimate the Michaelis-Menten constant (K_M.) and the maximum velocity (V_max) from a single experiment. This article highlights how the qNMR data is well suited for analysis using the Lambert-W function with three different applications. Results from studies on acetylcholinesterase (acetylcholine to acetic acid and choline), β-Galactosidase (lactose to glucose and galactose), and invertase (sucrose to glucose and fructose) are presented. Furthermore, an additional example of how the progress curve analysis is applied to understand the inhibitory role of the artificial sweetener sucralose on sucrose's enzymatic conversion by invertase is discussed. With the wide availability of NMR spectrometers in academia and industries, including bench-top systems with permanent magnets, and the potential to enhance sensitivity using dynamic nuclear polarization in combination with ultrafast methods, the NMR-based enzyme kinetics could be considered a valuable tool for broader applications in the field of enzyme kinetics.

Association between remnant lipoprotein cholesterol, high-sensitivity C-reactive protein, and risk of atherosclerotic cardiovascular disease events in the Multi-Ethnic Study of Atherosclerosis (MESA)

BACKGROUND

Elevated remnant-lipoprotein (RLP)-cholesterol (RLP-C) and high-sensitivity C-reactive protein (hsCRP) are each individually associated with atherosclerotic cardiovascular disease (ASCVD).

OBJECTIVE

To evaluate the interplay of nuclear magnetic resonance (NMR)-derived RLP-C and hsCRP and their association with ASCVD in the Multi-Ethnic Study of Atherosclerosis (MESA).

METHODS

Lipoprotein particles were measured using NMR spectroscopic analysis at baseline. RLP-C includes very-low-density lipoprotein cholesterol and intermediate-density lipoprotein cholesterol. Four groups were created as follows: Group 1: RLP-C ≤ median (≤29.14 mg/dL) and hsCRP < 2 mg/L; Group 2: RLP-C ≤ median and hsCRP≥ 2 mg/L; Group 3: RLP-C > median and hsCRP level < 2 mg/L; and Group 4: RLP-C > median and hsCRP level ≥ 2 mg/L. Kaplan-Meier survival curves and multivariable-adjusted Cox proportional hazard models were used to examine the relationship between RLP-C and hsCRP with incident ASCVD.

RESULTS

A total of 6,720 MESA participants (mean age 62.2 y, 53% female) with a median follow-up of 15.6 years were included. In the fully adjusted model, compared to those in the reference group (Group 1), participants in Group 2, Group 3, and Group 4 demonstrated a 20% (95% CI, -2%-48%), 18% (-4%-44%), and 43% (18%-76%) increased risk of incident ASCVD events, respectively (p < 0.01). An additive and multiplicative interaction between RLP-C and hsCRP was not statistically significant.

CONCLUSION

NMR-derived RLP-C and hsCRP showed a similar independent association with incident ASCVD. Notably, the combination of increased RLP-C and hsCRP was associated with an increased risk of future ASCVD events.

Structural determination of the cell wall polysaccharide LCPS-1 in Lacticaseibacillus paracasei strain Shirota YIT 9029

The neutral polysaccharides LCPS-1 and LCPS-2 play functional roles in the cell wall of the lactic acid bacterium Lacticaseibacillus paracasei strain Shirota YIT 9029 (LcS; formerly Lactobacillus casei strain Shirota YIT 9029), which has long been used as a probiotic food product. Studies have shown that LCPS-1 is associated with the immunomodulatory functions of LcS. We hypothesized that the structure of LCPS-1 is crucial for elucidating the mechanism of action of LcS on host immune responses and aimed to solve the undetermined primary structure of LCPS-1. Our results showed that LCPS-1 has a molecular weight of >400 kDa and is composed of Glc, Rha, Gal, and GlcNAc, with a repeating structure. Using limited degradation reactions, including controlled Smith and deamination degradations, we obtained key fragments with low molecular weight. Subsequently, their structures were analyzed using NMR spectra and other analytical techniques. Further, we integrated the results for each key fragment to derive the complete structure of LCPS-1. Our results indicated that the most probable structure of LCPS-1 is composed of two types of units (X, Y), each with a basic structure of seven sugars in which the C2-position of Rha is substituted with an acetyl group. The structure of X is {6[Glcβ1-2] Galα1-3[2-OAc] Rhaβ1-4Glcβ1-4[Rhaα1-3] [Glcα1-6] Glcβ1-} and that of Y is {6[Glcβ1-2] Galα1-3[2-OAc] Rhaβ1-4Glcβ1-4[Rhaα1-3] [Glcα1-6)] GlcNAcβ1-}, which can be expressed as (X₆Y₁₂)_n. In this study, we identified the primary structure of LCPS-1, and our results may enable an improved understanding of the immunomodulatory abilities of LcS.

Cross-correlated relaxation rates provide facile exchange signature in selectively labeled RNA

Gerhard Wagner has made numerous contributions to NMR spectroscopy, particularly his developments in the field of spin-relaxation stand out in directly mapping the spectral density functions of proteins. He and his group developed experimental techniques to reveal the importance of dynamics to protein biological function and drug discovery. On his 75th birthday, we take this opportunity to highlight how some of those seminal ideas developed for proteins are being extended to RNAs. The role of dynamics in the structure and function of RNA has been a major interest in drug design and therapeutics. Here we present the use of cross-correlated relaxation rates (η_xy) from anti-TROSY (R_2α) and TROSY (R_2β) to rapidly obtain qualitative information about the chemical exchange taking place within the bacterial and human A-site RNA system while reducing the sets of relaxation experiments required to map dynamics. We show that η_xy correlates with the order parameter which gives information on how flexible or rigid a residue is. We further show R_2β/η_xy can rapidly be used to probe chemical exchange as seen from its agreement with R_ex. In addition, we report the ability of R_2β/η_xy to determine chemical exchange taking place within the bacterial A-site RNA during structural transitions at pH 6.2 and 6.5. Finally, comparison of the R_2β/η_xy ratios indicates bacterial A-site has greater R_2β/η_xy values for G19 (1.34 s^-1), A20 (1.38 s^-1), U23 (1.63 s^-1) and C24 (1.51 s^-1) than human A-site [A19 (0.76 s^-1), A20 (1.01 s^-1), U23 (0.74 s^-1) and C24 (0.71 s^-1)]. Taken together, we have shown that the chemical exchange can quickly be analyzed for RNA systems from cross-correlated relaxation rates.

Solution NMR Spectroscopy for Characterizing Protein-Glycosaminoglycan Interactions

Solution nuclear magnetic resonance (NMR) spectroscopy and, in particular, chemical shift perturbation (CSP) titration experiments are ideally suited for mapping and characterizing the binding interface of macromolecular complexes. ¹H-¹⁵N-HSQC-based CSP studies have become the method of choice due to their simplicity, short-time requirements, and minimal working knowledge of NMR. CSP studies for characterizing protein-glycosaminoglycan (GAG) interactions can be challenging due to binding-induced aggregation/precipitation and/or poor quality data. In this chapter, we discuss how optimizing experimental conditions such as protein concentration, choice of buffer pH, ionic strength, and GAG size, as well as sensitivity of NMR instrumentation can overcome these roadblocks to obtain meaningful structural insights into protein-GAG interactions.

Post-translational modifications within tau paired helical filament nucleating motifs perturb microtubule interactions and oligomer formation

Post-translationally modified tau is the primary component of tau neurofibrillary tangles, a pathological hallmark of Alzheimer's disease and other tauopathies. Post-translational modifications within the tau microtubule binding domain (MBD), which encompasses two hexapeptide motifs that act as critical nucleating regions for tau aggregation, can potentially modulate tau aggregation as well as interactions with microtubules (MTs) and membranes. Here we characterize the effects of a recently discovered tau PTM, lysine succinylation, on tau-tubulin interactions, and compare these to the effects of two previously reported MBD modifications, lysine acetylation and tyrosine phosphorylation. As generation of site-specific PTMs in proteins is challenging, we used short synthetic peptides to quantify the effects on tubulin binding of three site-specific PTMs located within the PHF6* (residues 275-280) and PHF6 (residues 306-311) hexapeptide motifs: K280 acetylation, Y310 phosphorylation and K311 succinylation. We compared these effects to those observed for MBD PTM-mimetic point mutations K280Q, Y310E and K311E. Finally, we evaluated the effects of these PTM-mimetic mutations on MBD membrane binding and membrane-induced fibril and oligomer formation. We found that all three PTMs perturb tau MT binding, with Y310 phosphorylation exerting the strongest effect. PTM mimetic mutations partially recapitulated the effects of the PTMs on MT binding and also disrupted tau membrane binding and membrane induced oligomer and fibril formation. These results imply that these PTMs, including the novel and AD-specific succinylation of tau K311, may influence both the physiological and pathological interactions of tau and thus represent targets for therapeutic intervention.

Infrared spectroscopy quantification of functional carbon groups in kerogens and coals: A calibration procedure

The determination of the abundances of the CH_x, C = O and aromatic groups in chondritic Insoluble Organic Matter (IOM) and coals by Infrared (IR) spectroscopy is a challenging issue due to insufficient knowledge on the absorption cross-sections and their sensitivity to the molecular environment. Here, we report a calibration approach based on a ¹³C synthetic model material whose composition was unambiguously determined by Direct-Pulse/Magic Angle Spinning Nuclear Magnetic Resonance (DP/MAS NMR). Ratios of the cross-sections of the CH_x, C = O and aromatic groups have been determined, and the method has been applied to IOM samples extracted from four chondrites as Orgueil (CI), Murchison (CM), Tagish Lake (C2-ungrouped) and EET 92042 (CR2), and to a series of coals. The estimate of the aliphatic to aromatic carbon ratio (n_CHx/n_Aro) in IOM samples from Orgueil, Murchison and Tagish Lake chondrites is in good agreement with Single-Pulse/NMR estimates earlier published, and is lower by a factor of 1.3 in the case of the CR chondrite EET 92042 (but the error bars overlap). In contrast, the aliphatic to carbonyl ratio (n_CHx/n_C=O) is overestimated for the four chondrites. These discrepancies are likely due to the control of the absorption cross-section of the C = O and C = C bonds by the local molecular environment. Regarding coals, the use of published NMR analyses has brought to light that the integrated cross-section ratio A_CHx/A_Aro varies with the vitrinite reflectance over an order of magnitude. Here as well, the local oxygen speciation plays a critical control in A_Aro, which decreases with increasing the vitrinite reflectance. We provide an analytical law that links A_CHx/A_Aro and vitrinite reflectance, which will allow the determination of n_CHx/n_Aro for any coal sample, provided its vitrinite reflectance is known.

THz-enhanced dynamic nuclear polarized liquid spectrometer

Dynamic nuclear polarization (DNP) technology can be utilized to dramatically enhance NMR signal. In this paper, we report on the development of a self-constructed 5 T DNP spectrometer for liquid samples and the ¹³C DNP enhancement achieved with this spectrometer. The DNP spectrometer is comprised of a wide-bore superconducting magnet, a home-made console, a dual resonance probe and a self-built 140 GHz microwave source for the spectrometer. Specifically, a microwave source of traveling wave tube (TWT) amplifier has been developed, which can provide a maximum power output of 4.4 W and a wide frequency tuning range of 1 GHz. The excellent performance of our built liquid-state DNP spectrometer is verified by the observation of more than 100-fold DNP enhancement of the ¹³C NMR signal for liquid ¹³CCl₄ sample. Our result shows the superiority of DNP technology in the liquid-state high-field NMR spectrometer.

Schistocins: Novel antimicrobial peptides encrypted in the Schistosoma mansoni Kunitz Inhibitor SmKI-1

BACKGROUND

Here we describe a new class of cryptides (peptides encrypted within a larger protein) with antimicrobial properties, named schistocins, derived from SmKI-1, a key protein in Shistosoma mansoni survival. This is a multi-functional protein with biotechnological potential usage as a therapeutic molecule in inflammatory diseases and to control schistosomiasis.

METHODS

We used our algorithm enCrypted, to perform an in silico proteolysis of SmKI-1 and a screening for potential antimicrobial activity. The selected peptides were chemically synthesized, tested in vitro and evaluated by both structural (CD, NMR) and biophysical (ITC) studies to access their structure-function relationship.

RESULTS

EnCrypted was capable of predicting AMPs in SmKI-1. Our biophysical analyses described a membrane-induced conformational change from random coil-to-α-helix and a peptide-membrane equilibrium for all schistocins. Our structural data allowed us to suggest a well-known mode of peptide-membrane interaction in which electrostatic attraction between the cationic peptides and anionic membranes results in the bilayer disordering. Moreover, the NMR exchange H/D data with the higher entropic contribution observed for the peptide-membrane interaction showed that shistocins have different orientations upon the membrane.

CONCLUSIONS

This work demonstrate the robustness for using the physicochemical features of predicted peptides in the identification of new bioactive cryptides besides the relevance of combining these analyses with biophysical methods to understand the peptide-membrane affinity and improve further algorithms.

GENERAL SIGNIFICANCE

Bioprospecting cryptides can be conducted through data mining of protein databases demonstrating the success of our strategy. The peptides-based agents derived from SmKI-1 might have high impact for system-biology and biotechnology.

Commensal Streptococcus mitis produces two different lipoteichoic acids of type I and type IV

The opportunistic pathogen Streptococcus mitis possesses, like other members of the Mitis group of viridans streptococci, phosphorylcholine (P-Cho)-containing teichoic acids (TAs) in its cell wall. Bioinformatic analyses predicted the presence of TAs that are almost identical with those identified in the pathogen S. pneumoniae, but a detailed analysis of S. mitis lipoteichoic acid (LTA) was not performed to date. Here we determined the structures of LTA from two S. mitis strains, the high-level beta-lactam and multiple antibiotic resistant strain B6 and the penicillin-sensitive strain NCTC10712. In agreement with bioinformatic predictions we found that the structure of one LTA (type IV) was like pneumococcal LTA, except the exchange of a glucose moiety with a galactose within the repeating units. Further genome comparisons suggested that the majority of S. mitis strains should contain the same type IV LTA as S. pneumoniae, providing a more complete understanding of the biosynthesis of these P-Cho-containing TAs in members of the Mitis group of streptococci. Remarkably, we observed besides type IV LTA an additional polymer belonging to LTA type I in both investigated S. mitis strains. This LTA consists of β-galactofuranosyl-(1,3)-diacylglycerol as glycolipid anchor and a poly-glycerol-phosphate chain at the O-6 position of the furanosidic galactose. Hence, these bacteria are capable of synthesizing two different LTA polymers, most likely produced by distinct biosynthesis pathways. Our bioinformatics analysis revealed the prevalence of the LTA synthase LtaS, most probably responsible for the second LTA version (type I), amongst S. mitis and S. pseudopneumoniae strains.

Ionization properties of monophosphoinositides in mixed model membranes

Phosphoinositides are found in low concentration in cellular membranes but perform numerous functions such as signaling, membrane trafficking, protein recruitment and modulation of protein activity. Spatiotemporal regulation by enzymes that phosphorylate and dephosphorylate the inositol ring results in the production of seven distinct and functionally diverse derivatives. Ionization properties of the phosphorylated headgroups of anionic lipids have been shown to impact how they interact with proteins and lipids in the membrane. While the ionization properties of the three bis and one tris phosphorylated forms have been studied in physiologically relevant model membranes, that of the monophosphorylated forms (i.e., phosphatidylinositol-3-phosphate (PI3P), phosphatidylinositol-4-phosphate (PI4P), phosphatidylinositol-5-phosphate (PI5P)) has received less attention. Here, we used ³¹P MAS NMR to determine the charge of 5 mol% of the monophosphorylated derivatives in pure dioleoylphosphatidylcholine (DOPC) and DOPC/dioleoylphosphatidylethanolamine (DOPE) bilayers as a function of pH. We find that PI3P, PI4P and PI5P each have unique pKa2 values in a DOPC bilayer, and each is reduced in DOPC/DOPE model membranes through the interaction of their headgroups with DOPE according to the electrostatic-hydrogen bond switch model. In this study, using model membranes mimicking the plasma membrane (inner leaflet), Golgi, nuclear membrane, and endosome (outer leaflet), we show that PI3P, PI4P or PI5P maximize their charge at neutral pH. Our results shed light on the electrostatics of the monophosphorylated headgroups of PI3P, PI4P, and PI5P and form the basis of their intracellular functions.

An atomic perspective on improving daptomycin's activity

BACKGROUND

Recently, through comprehensive medicinal chemistry efforts, we have found a new daptomycin analogue, termed kynomycin, showing enhanced activity against both methicillin-resistant S. aureus and vancomycin-resistant Enterococcus in vitro and in vivo, with improved pharmacokinetics and lower cytotoxicity than daptomycin.

METHODS

In this study we compared the physicochemical properties of kynomycin with those of daptomycin from an atomic perspective by using Nuclear Magnetic Resonance spectroscopy and Molecular Dynamics simulations.

RESULTS AND CONCLUSION

We observed that kynurenine methylation changes daptomycin's key physicochemical properties; its calcium dependent oligomerization efficiency is improved and the modified kynurenine strengths contacts with the lipid tail and tryptophan residues. In addition, it is observed that, compared to daptomycin, kynomycin tetramer is more stable and binds stronger to calcium. The combined experiments provide key clues for the improved antibacterial activity of kynomycin.

GENERAL SIGNIFICANCE

We expect that this approach will help study the calcium binding and oligomerization features of new calcium dependent peptide antibiotics.

NMR-Based Metabolomics in Cancer Research

Nuclear magnetic resonance (NMR) spectroscopy offers reproducible quantitative analysis and structural identification of metabolites in various complex biological samples, such as biofluids (plasma, serum, and urine), cells, tissue extracts, and even intact organs. Therefore, NMR-based metabolomics, a mainstream metabolomic platform, has been extensively applied in many research fields, including pharmacology, toxicology, pathophysiology, nutritional intervention, disease diagnosis/prognosis, and microbiology. In particular, NMR-based metabolomics has been successfully used for cancer research to investigate cancer metabolism and identify biomarker and therapeutic targets. This chapter highlights the innovations and challenges of NMR-based metabolomics platform and its applications in cancer research.

A simple data post-processing method for axial peaks free 2D PSYCHEDELIC NMR spectra

Homonuclear scalar coupling plays an important role in the elucidation of molecular structure and dynamics. However, complex multiplets due to ¹H-¹H scalar coupling splittings complicate the assignment of peaks in overcrowded spectral regions. Although many methods focusing on disentangling couplings have been proposed in recent years, some defects like intense axial peaks and dispersive components still exist. Herein, a simple data post-processing method based on the interleaved acquisition mode PSYCHEDELIC (Pure Shift Yielded by CHirp Excitation to DELiver Individual Couplings) is designed to acquire absorption-mode 2D J spectrum while eradicating axial peaks. This approach provides a high resolution and pure absorptive spectrum, permitting unambiguous and accurate measurement of scalar coupling constants involving a given proton.

Conservation tillage for 17 years alters the molecular composition of organic matter in soil profile

Conservation tillage is considered as a potential measure to mitigate climate change by sequestering soil organic matter (SOM), however its stabilization mechanisms remain elusive. In this study, we revealed the molecular composition of SOM in soil profile (~50 cm depth) from a 17-yr tillage experiment in North China. The soils were collected from 0-10, 10-20, 20-30 and 30-50 cm layers under conventional tillage (CT), and conservation tillage such as rotary tillage (RT) and no-tillage (NT). The sequential solvent extraction and CuO oxidation methods were used to quantify free lipids and lignin-derived phenols. The results showed that NT (cf. CT) increased labile compounds (i.e., carbohydrates) and plant-derived SOM (i.e., long-chain (≥C₂₀) aliphatic lipids and steroids) in the 0-10 and 30-50 cm layers. The RT (cf. CT) increased the total free lipids by 72-133% in the sublayers (>10 cm). The RT (cf. CT and NT) resulted in higher preservation of plant-derived (≥C₂₀ aliphatic lipids and steroids) and microbial-derived compounds (<C₂₀ aliphatic lipids and trehalose) SOM in deep soils (i.e., ≥10 cm). Conservation tillage suppressed lignin degradation, as reflected by 32-137% higher total lignin-derived phenols under RT and NT than CT in the 0-10 and 30-50 cm layers. The NMR revealed higher aliphatic to aromatic C ratio under NT and RT in the whole soil profile, suggesting more aliphatic lipids accumulated. Conservation tillage increased SOC stocks by 10-14% in 0-10 cm layer but not in deeper profiles. These results suggest that conservation tillage have increased plant-derived lipids and lignin accumulation. Our study highlights that conservation tillage (particularly the RT) after 17 years alters SOM molecular compositions and degradation processes in the soil profile. These findings have implications for improving our understanding of C stabilization mechanisms in agroecosystems.

Unambiguous and accurate measurement of scalar coupling constants through a selective refocusing NMR experiment

Scalar coupling plays an important role in the analysis of molecular structure and dynamics. A great number of nuclear magnetic resonance (NMR) selective refocusing experiments, such as 2D G-SERF and PSYCHEDELIC, were developed to extract scalar coupling constants involving a selected proton from overlapped spectra. However, intense axial peaks occur in this type of experiments, leading to possible ambiguity in the assignment of spectral peaks and subsequent accurate measurement of ¹H-¹H scalar coupling constants. Here, a method based on selective coherence transfer and PSYCHEDELIC module is designed to acquire absorption-mode selective refocusing spectrum while suppressing intense axial peaks. Therefore, unambiguous and accurate measurement of scalar coupling constants involving the selectively excited proton can be achieved. The performances of the proposed method are demonstrated on several samples.

Biophysical characterization of two commercially available preparations of the drug containing Escherichia coli L-Asparaginase 2

The hydrolysis of asparagine and glutamine by L-asparaginase has been used to treat acute lymphoblastic leukemia for over four decades. Each L-asparaginase monomer has a long loop that closes over the active site upon substrate binding, acting as a lid. Here we present a comparative study of two commercially available preparations of the drug containing Escherichia coli L-Asparaginase 2 (EcA2), performed by a comprehensive array of biophysical and biochemical approaches. We report the oligomeric landscape and conformational and dynamic plasticity of E. coli type 2 L-asparaginase present in two different formulations, and its relationship with L-aspartic acid, which is present in Aginasa, but not in Leuginase. The L-Asp present in Aginasa formulation was found to provide to EcA2 a resistance to in vitro proteolysis. EcA2 shows a composition of monomers and oligomers up to tetramers, which is mostly not altered in the presence of L-Asp. Ion-mobility spectrometry-mass spectrometry reveals two conformers for the monomeric EcA2, and that monomeric species has sufficient capacity for selective binding to L-Asp and L-Glu. The N-terminal loop of the EcA2 present in Leuginase, which is part of the active site is disordered, but it gets ordered in the presence of L-Asp, while L-Glu only does so to a limited extent. These data provide new insights on the mechanistic of ligand recognition by EcA2, and the impact of formulation in its conformational diversity landscape.

High Sensitivity Detection of a Solubility Limiting Surface Transformation of Drug Particles by DNP SENS

We investigate the presence of a surface species for the active pharmaceutical ingredient (API) AZD9496 with dynamic nuclear polarization surface enhanced nuclear spectroscopy (DNP SENS). We show that using DNP we can elucidate the presence of an amorphous form of the API at the surface of crystalline particles of the salt form. The amorphous form of the API has distinguishable ¹³C chemical shifts when compared to the salt form under various acidic conditions. The predominant form in frozen particles of AZD9496 is the salt, and we provide evidence to suggest that the amorphous layer at the surface is mainly made up of the dissociated free form.

NMR-Based Metabolomics

Nuclear magnetic resonance (NMR) spectroscopy is a major analytical method used in the growing field of metabolomics. Although NMR is relatively less sensitive than mass spectrometry, this analytical platform has numerous characteristics including its high reproducibility and quantitative abilities, its nonselective and noninvasive nature, and the ability to identify unknown metabolites in complex mixtures and trace the downstream products of isotope labeled substrates ex vivo, in vivo, or in vitro. Metabolomic analysis of highly complex biological mixtures has benefitted from the advances in both NMR data acquisition and analysis methods. Although metabolomics applications span a wide range of disciplines, a majority has focused on understanding, preventing, diagnosing, and managing human diseases. This chapter describes NMR-based methods relevant to the rapidly expanding metabolomics field.

Nuclear magnetic resonance reveals postprandial low-density lipoprotein cholesterol determined by enzymatic method could be a misleading indicator

BACKGROUND

Serum concentration of low-density lipoprotein cholesterol (LDL-C) is markedly reduced after a meal. Does postprandial cholesterol in LDL truly decline via clearance of LDL particles or is there simply a redistribution of cholesterol in LDL subclasses? Thus, we sought to evaluate whether postprandial decline of LDL-C reflects a reduction of LDL particle and to assess the correlation between proprotein convertase subtilisin/kexin type 9 (PCSK9) concentration and postprandial atherogenic lipoproteins profile.

METHODS

Eighty-seven persons were enrolled in this study. We measured lipid profiles by enzymatic and nuclear magnetic resonance (NMR)-based methods and serum PCSK9 concentration by enzyme-linked immunosorbent assays before and after a meal. Plasma samples were collected after a 10-h fasting and 2 and 4 h post-meal.

RESULTS

Compared to the fasting status, there was significant postprandial decline of LDL-C measured enzymatically (LDL-Ce) at 2nd and 4th h [99.38 (80.43, 120.65) vs 95.51 (74.25, 117.17) vs 87.01 (69.99, 108.28) mg/dl, p < 0.000]. But there was no significant reduction in LDL particle and its cholesterol content (LDL-Cn) determined by NMR. Just the postprandial large LDL particle [186.45 (151.36, 229.42) vs 176.92 (147.43, 220.91) vs 181.77 (149.05, 224.17), p < 0.000] and its cholesterol content [19.10 (15.09, 22.37) vs 18.28 (14.59, 21.84) vs 17.79 (14.62, 22.14), p < 0.000] were greatly decreased at 2nd and 4th h compared to the fasting one. Interestingly, postprandial serum PCSK9 was decreased at 2nd and 4th h compared with fasting concentration [298.75 (233.25, 396.92) vs 257.34 (207.52, 342.36) vs 250.57 (215.02, 339.66) ng/ml, p < 0.000]. The postprandial percent decrease in serum PCSK9 at 4th h was positively correlated to the percent decline in postprandial LDL-Ce (r = 0.252, p = 0.019) but was independently associated with the percent increase in remnant cholesterol (r = 0.262, p = 0.016).

CONCLUSIONS

Postprandial decline of LDL-C determined enzymatically was not confirmed by NMR-based methods. Indeed, there exists cholesterol redistribution in LDL subclasses following a meal. The decrease of postprandial PCSK9 may be secondary to the increase in intrahepatic lipids following food intake.

1H NMR-based water-soluble lower molecule characterization and fatty acid composition of Chinese native chickens and commercial broiler

The aim of this study was to compare the water-soluble low molecular weight (WLMW) compounds and fatty acids (FAs) in raw meat and chicken soup between the two Chinese native chickens (Wuding chicken and Yanjin silky fowl chicken) and one typical commercial broiler (Cobb chicken). The WLMW compounds of chicken meat was studied using ¹H nuclear magnetic resonance spectroscopy (¹H NMR) and the FAs were identified and quantified using gas chromatography-mass spectrometry (GC-MS). Compared with typical commercial broiler, the main flavor substances (WLMW compounds and FAs) content were significantly higher in the breast and leg meat of the two Chinese native chickens (P < 0.05). Instead, the content of main flavor compounds was significantly higher in chicken soup of typical commercial broiler (P < 0.05). These results contribute to a further understanding the distinction of the flavor compounds between the typical commercial broiler and Chinese native chickens, which could be used to help assess the meat quality of different local broilers.

Metabolomic understanding of pod removal effect in soybean plants and potential association with their health benefit

Since natural materials, such as phytochemicals in plants, are increasingly being used for foods and skincare due to their beneficial functions, it is important for developing the cultivation practices to increase the contents of phytochemicals. We here explored metabolite perturbations in the leaves of soybean plants when their pods were removed during growth through 1H NMR-based metabolomics approach. There were obvious metabolic differences in the leaves between normal and pod-removed soybean plants. High amounts of primary metabolites in pod-removed soybean leaves, including amino acids, sugars, and fatty acids, reflected a delay of leaf senescence caused by pod removal. In particular, amounts of isoflavones, coumestrol, and apigenin derivatives in pod-removed soybean leaves were substantially increased. These were considered as distinct metabolic influences of pod removal in soybean plants. These results indicate that pod removal of soybean plants can induce significant perturbations of various metabolites in their soybean leaves, providing useful information to improve the quality of soybean leaves by increasing amounts of bioactive components.

Molecular insights into the differential structure-dynamics-stability features of interleukin-8 orthologs: Implications to functional specificity

Chemokines are a sub-group of chemotactic cytokines that regulate the leukocyte migration by binding to G-protein coupled receptors (GPCRs) and cell surface glycosaminoglycans (GAGs). Interleukin-8 (CXCL8/IL8) is one of the most essential CXC chemokine that has been reported to be involved in various pathophysiological conditions. Structure-function relationships of human IL8 have been studied extensively. However, no such detailed information is available on IL8 orthologs, although they exhibit significant functional divergence. In order to unravel the differential structure-dynamics-stability-function relationship of IL8 orthologs, comparative molecular analysis was performed on canine (laurasians) and human (primates) IL8 proteins using in-silico molecular evolutionary analysis and solution NMR spectroscopy methods. The residue level NMR studies suggested that, although the overall structural architecture of canine IL8 is similar to that of human IL8, systematic differences were observed in their backbone dynamics and low-energy excited states due to amino acid substitutions. Further, these substitutions also resulted in attenuation of stability and heparin binding affinity in the canine IL8 as compared to its human counterpart. Indeed, structural and sequence analysis evidenced for specificity of molecular interactions with cognate receptor (CXCR1) and glycosaminoglycan (heparin), thus providing evidence for a noticeable functional specificity and divergence between the two IL8 orthologs.

Optimizing the properties of Zodo gum and examining its potential for amino acid binding by periodate oxidation

In this study, the Zodo gum exudated by Amygdalus scoparia spach underwent the periodate oxidation process for chemical modification and the formation of dialdehyde groups. Modification of the Zodo gum properties was done using the periodate oxidation method, response surface methodology (RSM) and central composite design (CCD), with 4 factors of sodium periodate volume (6.4-19.2 mL), temperature (35-55 °C), pH (3-5) and time (2-4 h). Dialdehyde Zodo gum (DZG) was produced by controlling test variables and measuring some responses including dialdehyde content and efficacy, in addition to evaluating the rheological parameters. Quadratic, linear polynomial equations were then fitted with the insignificant Lack of fit and high R² to address the relationship between the mentioned variables and responses. Optimal test conditions, including pH = 3.9, T = 43 °C and Time = 3.5 h, were also determined for the production of DZG₁₀, DZG₂₀ and DZG₃₀ samples. The results of ¹H-¹³C NMR, FTIR and determination of the aldehyde content indicated the formation of dialdehyde groups in equilibrium with the dominant hemiacetal form. The AFM study of the DZG₃₀ sample also showed over-oxidation and depolymerization, which could be associated with increased hydrophobic properties and the reduced viscosity. Although the DZG₃₀ sample had the highest amount of the dialdehyde factor group with the tendency to combine with the amino group of proteins, DZG₁₀ and DZG₂₀ samples could be recommended for industrial applications due to the nonoccurrence of overoxidation.

Metabotyping of different soybean genotypes and distinct metabolism in their seeds and leaves

The metabolome of three soybean genotypes, Glycine max Hwangkeum (elite or domesticated cultivar), Glycine max Napjakong (landrace or semi-wild cultivar) and Glycine soja Dolkong (wild cultivar), were characterized in seeds and leaves using a 1H NMR-based metabolomics approach. Expression of primary and secondary metabolites were different in seeds and leaves as well as amongst soybean genotypes. Different kaempferol glycosides were observed in the leaves but not in the seeds, and quercetin derivatives were found only in G. max Napjakong and G. soja Dolkong. Moreover, epicatechin was found only in the seeds of G. max Napjakong and G. soja Dolkong. These results demonstrate distinct adaptations of different soybean genotypes to given environmental conditions. The current study, therefore, provides useful information on global metabolic compositions that might be used to develop soybean-based products through better understanding of the metabolic phenotypes of existing soybean genotypes.

Principal component analysis for automated classification of 2D spectra and interferograms of protein therapeutics: influence of noise, reconstruction details, and data preparation

Protein therapeutics have numerous critical quality attributes (CQA) that must be evaluated to ensure safety and efficacy, including the requirement to adopt and retain the correct three-dimensional fold without forming unintended aggregates. Therefore, the ability to monitor protein higher order structure (HOS) can be valuable throughout the lifecycle of a protein therapeutic, from development to manufacture. 2D NMR has been introduced as a robust and precise tool to assess the HOS of a protein biotherapeutic. A common use case is to decide whether two groups of spectra are substantially different, as an indicator of difference in HOS. We demonstrate a quantitative use of principal component analysis (PCA) scores to perform this decision-making, and demonstrate the effect of acquisition and processing details on class separation using samples of NISTmAb monoclonal antibody Reference Material subjected to two different oxidative stress protocols. The work introduces an approach to computing similarity from PCA scores based upon the technique of histogram intersection, a method originally developed for retrieval of images from large databases. Results show that class separation can be robust with respect to random noise, reconstruction method, and analysis region selection. By contrast, details such as baseline distortion can have a pronounced effect, and so must be controlled carefully. Since the classification approach can be performed without the need to identify peaks, results suggest that it is possible to use even more efficient measurement strategies that do not produce spectra that can be analyzed visually, but nevertheless allow useful decision-making that is objective and automated.

Fast reconstruction of non-uniform sampling multidimensional NMR spectroscopy via a deep neural network

Multidimensional nuclear magnetic resonance (NMR) spectroscopy is used to examine the chemical structures of the studied systems. Unfortunately, the application of NMR spectra is limited by their long acquisition time, especially for 3D, 4D, and higher dimensional spectra. Non-uniform sampling (NUS) has been widely recognized as a powerful tool to reduce the NMR experimental time. But the quality of NUS spectra depends on appropriate reconstruction algorithms. As an effective data processing method, deep learning has been widely used in many fields in recent years. In this work, a deep learning-based strategy for fast reconstruction of non-uniform sampling NMR spectra is proposed. In our experiments, the proposed deep neural network has better performance in removing artifacts and preserving weak peaks than typical convolutional neural networks of U-Net and DenseNet. Besides, a novel approach of generating training data is utilized to reduce the computational burden of neural networks, and thus training our network can be easier and faster than previous deep learning-based works. Compared with the two currently available methods, SMILE and hmsIST, our strategy can provide comparable reconstruction quality in terms of peak intensities and the fidelity of peak shape. The reconstruction time of our methods is also comparable to or faster than the two methods, especially for 3D spectra.

Dissecting the differential structural and dynamics features of CCL2 chemokine orthologs

Chemokines are a sub-group of cytokines that regulate the leukocyte migration. Monocyte chemoattractant protein-1 (MCP/CCL2) is one of the essential CC chemokine that regulates the migration of monocytes into inflamed tissues. It has been observed that the primary sequences of CCL2 orthologs among rodents and primates vary significantly at the C-terminal region. However, no structural details are available for the rodentia family CCL2 proteins. The current study unravelled the structural, dynamics and in-silico functional characteristics of murine CCL2 chemokine using a comprehensive set of NMR spectroscopy techniques and evolutionary approaches. The study unravelled that the N-terminal portion of the murine CCL2 forms a canonical CC chemokine dimer similar to that of human CCL2. However, unlike human CCL2, the murine ortholog exhibits extensive dynamics in the μs-ms timescales. The presence of C-terminal region of the murine CCL2 protein/rodentia family is highly glycosylated, completely disordered, and inhibits the folding of the structured CCL2 regions. Further, it has been observed that the glycosaminoglycan binding surfaces of these orthologs proteins are greatly differed. In a nut shell, this comparative study provided the role of molecular evolution in generating orthologous proteins with differential structural and dynamics characteristics to engage them in specific molecular interactions.

Isoelectric point-amyloid formation of α-synuclein extends the generality of the solubility and supersaturation-limited mechanism

Proteins in either a native or denatured conformation often aggregate at an isoelectric point (pI), a phenomenon known as pI precipitation. However, only a few studies have addressed the role of pI precipitation in amyloid formation, the crystal-like aggregation of denatured proteins. We found that α-synuclein, an intrinsically disordered protein of 140 amino acid residues associated with Parkinson's disease, formed amyloid fibrils at pI (= 4.7) under the low-sodium phosphate conditions. Although α-synuclein also formed amyloid fibrils at a wide pH range under high concentrations of sodium phosphate, the pI-amyloid formation was characterized by marked amyloid-specific thioflavin T fluorescence and clear fibrillar morphology, indicating highly ordered structures. Analysis by heteronuclear NMR in combination with principal component analysis suggested that amyloid formation under low and high phosphate conditions occurred by distinct mechanisms. The former was likely to be caused by the intermolecular attractive charge-charge interactions, where α-synuclein has +17 and −17 charges even with the zero net charge. On the other hand, the latter was caused by the phosphate-dependent salting-out effects. pI-amyloid formation may play a role in the membrane-dependent amyloid formation of α-synuclein, where the negatively charged membrane surface reduces the local pH to pI and the membrane hydrophobic environment enhances electrostatic interactions. The results extend the supersaturation-limited mechanism of amyloid formation: Amyloid fibrils are formed under a variety of conditions of decreased solubility of denatured proteins triggered by the breakdown of supersaturation.

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pI precipitation of α-synuclein led to the formation of amyloid fibrils.

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Fibrils formed at pI were more organized than those formed under other conditions.

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Attractive charge-charge interactions are responsible for the pI-amyloid formation.

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pI-amyloid formation may lead to the amyloid formation upon phospholipid membranes.

Boosting resolution in NMR spectroscopy by chemical shift upscaling

Resolution is an essential challenge in NMR spectroscopy. Narrow chemical shift range and extensive signal splittings due to scalar couplings often give rise to spectral congestion and even overlap in NMR spectra. Magnetic field strength is directly responsible for spectral resolution as higher magnetic field strength offers better signal dispersion. However, the process of further increasing magnetic field strength of NMR instruments is slow and expensive. Methodology aimed at resolution issue has long been developing. Here, we present a chemical shift upscaling method, in which chemical shifts are upscaled by a given factor while scalar couplings are unchanged. As a result, signal dispersion and hence the resolution are improved. Therefore, it is possible to separate multiplets which originally overlap with each other and to extract their integrals for quantitative analysis. Improved signal dispersion and the preservation of scalar couplings also facilitate multiplet analysis and signal assignment. Chemical shift upscaling offers a method for enhancing resolution limited by magnetic field strength.

On the Differential Roles of Mg2+, Zn2+, and Cu2+ in the Equilibrium of β-N-Methyl-Amino-L-Alanine (BMAA) and its Carbamates

β-N-methyl-amino-L-alanine (BMAA) in the presence of bicarbonate (HCO₃^-) undergoes structural modifications generating two carbamate species, α-carbamate and β-carbamate forms of BMAA. The chemical structure of BMAA and BMAA-carbamate adducts strongly suggest they may interact with divalent metal ions. The ability of BMAA to cross the blood-brain barrier and possibly interact with divalent metal ions may augment the neurotoxicity of these molecules. To understand the effects of divalent metal ions (Mg²⁺, Zn²⁺, and Cu²⁺) on the overall dynamic equilibrium between BMAA and its carbamate adducts, a systematic study using nuclear magnetic resonance (NMR) is presented. The chemical equilibria between BMAA, its carbamate adducts, and each of the divalent ions were studied using two-dimensional chemical exchange spectroscopy (EXSY). The NMR results demonstrate that BMAA preferentially interacts with Zn²⁺ and Cu²⁺, causing an overall reduction in the production of carbamate species by altering the dynamic equilibria. The NMR-based spectral changes due to the BMAA interaction with Cu²⁺ is more drastic than with the Zn²⁺, under the same stoichiometric ratios of BMAA and the individual divalent ions. However, the presence of Mg²⁺ does not significantly alter the dynamic equilibria between BMAA and its carbamate adducts. The NMR-based results are further validated using circular dichroism (CD) spectroscopy, observing the n ➔ π interaction in the complex formation of BMAA and the divalent metal ions, with additional verification of the interaction with Cu²⁺ using UV-Vis spectroscopy. Our results demonstrate that BMAA differentially interacts with divalent metal ions (Mg²⁺ < Zn²⁺ < Cu²⁺), and thus alters the rate of formation of carbamate products. The equilibria between BMAA, the bicarbonate ions, and the divalent metal ions may alter the total population of a specific form of BMAA-ion complex at physiological conditions and, therefore, add a level of complexity of the mechanisms by which BMAA acts as a neurotoxin.

Nuclear magnetic resonance T1-T2 inversion with double objective functions

We report an effective and robust method for nuclear magnetic resonance (NMR) longitudinal relaxation time-transverse relaxation time (T₁-T₂) inversion with double objective functions. First, we develop the first objective function based on L1 regularization, proposed an effective method to choose the optimum L1 regularization parameter, and solve the objective function employing a two-step iterative shrinkage/thresholding algorithm. Subsequently, we update the kernel matrix based on the solution of the first objective function, and then develop the second objective function using the measured data and updated kernel matrix based on the least-squares principle, and we use the conjugate gradient algorithm for the first time to solve the objective function about NMR data inversion. To improve the speed of NMR T₁-T₂ inversion, we present a Gaussian-based random SVD method. Finally, numerical and experimental examples are done to test the robustness of the proposed inversion method. The results indicate that the proposed inversion method can effectively achieve NMR T₁-T₂ inversion at a low data SNR.

PE-SERF: A sensitivity-improved experiment to measure JHH in crowded spectra

Aiming at facilitating the analysis of molecular structure, the gradient-encoded selective refocusing methods (G-SERF) and a great number of its variants for measuring proton-proton coupling constants have been proposed. However, the sensitivity is an issue in the 2D gradient-encoded experiments, because the signal intensity is determined by the slice thickness of the sample that depends on encoding gradient and the bandwidth of selective pulses which is limited by the smallest chemical shift difference of any two coupled protons. Here, we present a method dubbed PE-SERF (perfect echo selective refocusing) which can determine all J_HH values involving a selected proton with improved sensitivity compared to original G-SERF experiment. The modules of perfect echo involving selective pulses and gradient-encoded selective refocusing are combined in the method, so that the unwanted J couplings arising from coupled spin pairs in the same sample slice would be nullified. In this way, instead of single proton, a pair of coupled protons is allowed to share a sample slice, and thus the slice thickness can be increased and the spectral sensitivity can be improved. The performance of the method is demonstrated by experiments on quinine and strychnine.