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.