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Yakugaku Zasshi : Journal of the... 2024Quantitative NMR (qNMR), particularly H-qNMR, is useful for determining the absolute purity of organic molecules. However, identifying the target signal(s) for...
Quantitative NMR (qNMR), particularly H-qNMR, is useful for determining the absolute purity of organic molecules. However, identifying the target signal(s) for quantification is difficult, because of the overlap and complexity of organic molecules. Therefore, we focused on the P nucleus, owing to the simplicity of its signals, and investigated the P-qNMR absolute determination method by using organophosphorus drugs, water-soluble cyclophosphamide hydrate (CP), and water-insoluble sofosbuvir (SOF). The optimized and reproducible P-qNMR conditions, such as qNMR sample preparation [i.e., selecting suitable deuterated solvents and a reference standard (RS) for P-qNMR], hygroscopicity and solution stability of the analyte and RS, and qNMR measurements-such as acquisition time, relaxation delay time, and spectral width-were examined. The CP purities determined using P-qNMR agreed well with those for the established H-qNMR method in DO. In contrast, the SOF purity determined using P-qNMR was 1.6% higher than that for H-qNMR in the protic solvent CDOD. Therefore, using a protic solvent, such as CDOD, was not suitable for P-qNMR; the deuterium exchange with the RS for P-qNMR (i.e., phosphonoacetic acid) resulted in a small integrated intensity. Consequently, the aprotic solvent DMSO-d was employed to determine the SOF purity. The data revealed that the SOF purities determined using P-qNMR agreed well with the established H-qNMR values, indicating that the absolute quantification of SOF using both P-qNMR and H-qNMR is possible in DMSO-d. Thus, we established an optimized and reproducible P-qNMR method in validation study across multiple laboratories.
Topics: Organophosphorus Compounds; Dimethyl Sulfoxide; Water; Solvents; Pharmaceutical Preparations
PubMed: 38556308
DOI: 10.1248/yakushi.23-00151-3 -
The Journal of Biological Chemistry May 2024The complement system serves as the first line of defense against invading pathogens by promoting opsonophagocytosis and bacteriolysis. Antibody-dependent activation of...
The complement system serves as the first line of defense against invading pathogens by promoting opsonophagocytosis and bacteriolysis. Antibody-dependent activation of complement occurs through the classical pathway and relies on the activity of initiating complement proteases of the C1 complex, C1r and C1s. The causative agent of Lyme disease, Borrelia burgdorferi, expresses two paralogous outer surface lipoproteins of the OspEF-related protein family, ElpB and ElpQ, that act as specific inhibitors of classical pathway activation. We have previously shown that ElpB and ElpQ bind directly to C1r and C1s with high affinity and specifically inhibit C2 and C4 cleavage by C1s. To further understand how these novel protease inhibitors function, we carried out a series of hydrogen-deuterium exchange mass spectrometry (HDX-MS) experiments using ElpQ and full-length activated C1s as a model of Elp-protease interaction. Comparison of HDX-MS profiles between unbound ElpQ and the ElpQ/C1s complex revealed a putative C1s-binding site on ElpQ. HDX-MS-guided, site-directed ElpQ mutants were generated and tested for direct binding to C1r and C1s using surface plasmon resonance. Several residues within the C-terminal region of ElpQ were identified as important for protease binding, including a single conserved tyrosine residue that was required for ElpQ- and ElpB-mediated complement inhibition. Collectively, our study identifies key molecular determinants for classical pathway protease recognition by Elp proteins. This investigation improves our understanding of the unique complement inhibitory mechanism employed by Elp proteins which serve as part of a sophisticated complement evasion system present in Lyme disease spirochetes.
Topics: Humans; Bacterial Outer Membrane Proteins; Borrelia burgdorferi; Complement C1r; Complement C1s; Complement Pathway, Classical; Lipoproteins; Lyme Disease; Protein Binding
PubMed: 38552741
DOI: 10.1016/j.jbc.2024.107236 -
Journal of Cheminformatics Mar 2024DGet! is an open-source analysis package written in Python for calculating the degree of deuterium enrichment in isotopically labelled molecules using mass spectrometric...
DGet! is an open-source analysis package written in Python for calculating the degree of deuterium enrichment in isotopically labelled molecules using mass spectrometric data. The nuclear properties of deuterium make it a valuable tracer in metabolic studies and an excellent contrast agent in nuclear spectroscopies. Determination of molecular deuteration levels is typically performed using mass spectrometry, however software options to perform these calculations are scarce. The in-house scripts and spreadsheets currently used rarely account for isotopic interferences from C or multi-isotopic elements that impact deuteration calculations. DGet! removes isotopic interferences using de-convolution and both the isotopological makeup and overall deuteration level can be accurately recovered. The software is available as command line and web applications that take a molecular formula and mass spectrometry data and output a graphical representation of the degree of deuteration as well as the distribution of partially deuterated analogues. These applications are designed to be easy to use and enable superior characterisation of deuterated molecules for users of all levels of expertise, without the limitations of techniques currently used by the majority of deuteration laboratories and researchers.
PubMed: 38549134
DOI: 10.1186/s13321-024-00828-x -
Polymers Mar 2024The peculiarities of crystal growth on a Nafion polymeric substrate from supersaturated aqueous solutions of initial substances were studied. The solutions were prepared...
The peculiarities of crystal growth on a Nafion polymeric substrate from supersaturated aqueous solutions of initial substances were studied. The solutions were prepared based on deionized natural water and deuterium-depleted water. As was found earlier, in natural water (deuterium content 157 ± 1 ppm) polymer fibers are capable of unwinding towards the bulk of the liquid, while in deuterium-depleted water (deuterium content ≤ 3 ppm) there is no such effect. Since the distance between the unwound fibers falls in a nanometer range (which is close to the size of the unit cell of the crystal lattice), and these fibers are directed normally to the polymeric substrate, the unwinding can affect crystal growth on the polymer substrate. As was obtained in experiments with X-ray diffractometry, the unwound polymer fibers predetermine syngony of crystals, for which the unit cell is either a rectangular parallelepiped (monoclinic system) or an oblique parallelepiped (triclinic system). A quantitative theoretical model that describes the local interaction of the polymer substrate with the crystalline complexes is presented. Within this model, the polymer substrate can be considered as a flexible matrix for growing crystals.
PubMed: 38543350
DOI: 10.3390/polym16060744 -
Biomolecules Mar 2024Japanese encephalitis virus (JEV) remains a global public health concern due to its epidemiological distribution and the existence of multiple strains. Neutralizing...
Japanese encephalitis virus (JEV) remains a global public health concern due to its epidemiological distribution and the existence of multiple strains. Neutralizing antibodies against this infection have shown efficacy in in vivo studies. Thus, elucidation of the epitopes of neutralizing antibodies can aid in the design and development of effective vaccines against different strains of JEV. Here, we describe a combination of native mass spectrometry (native-MS) and hydrogen/deuterium exchange mass spectrometry (HDX-MS) to complete screening of eight mouse monoclonal antibodies (MAbs) against JEV E-DIII to identify epitope regions. Native-MS was used as a first pass to identify the antibodies that formed a complex with the target antigen, and it revealed that seven of the eight monoclonal antibodies underwent binding. Native mass spectra of a MAb (JEV-27) known to be non-binding showed broad native-MS peaks and poor signal, suggesting the protein is a mixture or that there are impurities in the sample. We followed native-MS with HDX-MS to locate the binding sites for several of the complex-forming antibodies. This combination of two mass spectrometry-based approaches should be generally applicable and particularly suitable for screening of antigen-antibody and other protein-protein interactions when other traditional approaches give unclear results or are difficult, unavailable, or need to be validated.
Topics: Animals; Mice; Epitope Mapping; Hydrogen; Encephalitis Virus, Japanese; Deuterium; Antibodies, Viral; Epitopes; Antibodies, Neutralizing; Mass Spectrometry; Antibodies, Monoclonal
PubMed: 38540792
DOI: 10.3390/biom14030374 -
ELife Mar 2024Activation of the extracellular signal-regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by...
Activation of the extracellular signal-regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states of the active kinase, named 'L' and 'R,' where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site. However, the features of inhibitors important for R-state selection are unknown. Here, we survey a panel of ATP-competitive ERK inhibitors using HDX-MS and NMR and identify 14 new molecules with properties of R-state selection. They reveal effects propagated to distal regions in the +1 and helix αF segments surrounding the activation loop, as well as helix αL16. Crystal structures of inhibitor complexes with ERK2 reveal systematic shifts in the Gly loop and helix αC, mediated by a Tyr-Tyr ring stacking interaction and the conserved Lys-Glu salt bridge. The findings suggest a model for the R-state involving small movements in the N-lobe that promote compactness within the kinase active site and alter mobility surrounding the activation loop. Such properties of conformation selection might be exploited to modulate the protein docking interface used by ERK substrates and effectors.
Topics: Adenosine Triphosphate; Catalytic Domain; Phosphorylation; Protein Conformation
PubMed: 38537148
DOI: 10.7554/eLife.91507 -
Gels (Basel, Switzerland) Mar 2024This study aims to evaluate the percutaneous permeation profiles of caffeic acid (CA) from the cubic and hexagonal liquid crystalline phases of Pluronic P123/water...
BACKGROUND
This study aims to evaluate the percutaneous permeation profiles of caffeic acid (CA) from the cubic and hexagonal liquid crystalline phases of Pluronic P123/water mixtures.
METHOD
The resulting drug-loaded mesophases were subjected to characterisation through deuterium nuclear magnetic resonance spectroscopy and polarised optical microscopy observations. These analyses aimed to evaluate the structural changes that occurred in the mesophases loading with CA. Additionally, steady and dynamic rheology studies were conducted to further explore their mechanical properties and correlate them to the supramolecular structure. Finally, CA release experiments were carried out at two different temperatures to examine the behaviour of the structured systems in a physiological or hyperthermic state.
RESULTS
As the concentration of the polymer increases, an increase in the viscosity of the gel is noted; however, the addition of caffeic acid increases microstructure fluidity. It is observed that the temperature effect conforms to expectations. The increase in temperature causes a decrease in viscosity and, consequently, an increase in the rate of permeation of caffeic acid.
CONCLUSIONS
The CA permeation profile from the prepared formulations is mostly dependent on the structural organisation and temperature. Cubic mesophase LLC 30/CA showed greater skin permeation with good accumulation in the skin at both tested temperatures.
PubMed: 38534599
DOI: 10.3390/gels10030181 -
The Journal of Biological Chemistry May 2024Sensor-effector proteins integrate information from different stimuli and transform this into cellular responses. Some sensory domains, like red-light responsive...
Sensor-effector proteins integrate information from different stimuli and transform this into cellular responses. Some sensory domains, like red-light responsive bacteriophytochromes, show remarkable modularity regulating a variety of effectors. One effector domain is the GGDEF diguanylate cyclase catalyzing the formation of the bacterial second messenger cyclic-dimeric-guanosine monophosphate. While critical signal integration elements have been described for different phytochromes, a generalized understanding of signal processing and communication over large distances, roughly 100 Å in phytochrome diguanylate cyclases, is missing. Here we show that dynamics-driven allostery is key to understanding signal integration on a molecular level. We generated protein variants stabilized in their far-red-absorbing Pfr state and demonstrated by analysis of conformational dynamics using hydrogen-deuterium exchange coupled to mass spectrometry that single amino acid replacements are accompanied by altered dynamics of functional elements throughout the protein. We show that the conformational dynamics correlate with the enzymatic activity of these variants, explaining also the increased activity of a non-photochromic variant. In addition, we demonstrate the functional importance of mixed Pfr/intermediate state dimers using a fast-reverting variant that still enables wild-type-like fold-changes of enzymatic stimulation by red light. This supports the functional role of single protomer activation in phytochromes, a property that might correlate with the non-canonical mixed Pfr/intermediate-state spectra observed for many phytochrome systems. We anticipate our results to stimulate research in the direction of dynamics-driven allosteric regulation of different bacteriophytochrome-based sensor-effectors. This will eventually impact design strategies for the creation of novel sensor-effector systems for enriching the optogenetic toolbox.
Topics: Allosteric Regulation; Bacterial Proteins; Light; Phosphorus-Oxygen Lyases; Phytochrome; Protein Multimerization; Red Light; Alteromonadaceae; Models, Molecular
PubMed: 38522512
DOI: 10.1016/j.jbc.2024.107217 -
Communications Biology Mar 2024Muscarinic acetylcholine receptor M3 (M3) and its downstream effector Gq/11 are critical drug development targets due to their involvement in physiopathological...
Muscarinic acetylcholine receptor M3 (M3) and its downstream effector Gq/11 are critical drug development targets due to their involvement in physiopathological processes. Although the structure of the M3-miniGq complex was recently published, the lack of information on the intracellular loop 3 (ICL3) of M3 and extensive modification of Gαq impedes the elucidation of the molecular mechanism of M3-Gq coupling under more physiological condition. Here, we describe the molecular mechanism underlying the dynamic interactions between full-length wild-type M3 and Gq using hydrogen-deuterium exchange mass spectrometry and NanoLuc Binary Technology-based cell systems. We propose a detailed analysis of M3-Gq coupling through examination of previously well-defined binding interfaces and neglected regions. Our findings suggest potential binding interfaces between M3 and Gq in pre-assembled and functionally active complexes. Furthermore, M3 ICL3 negatively affected M3-Gq coupling, and the Gαq AHD underwent unique conformational changes during M3-Gq coupling.
Topics: Receptors, Muscarinic; GTP-Binding Protein alpha Subunits, Gq-G11
PubMed: 38521872
DOI: 10.1038/s42003-024-06056-1 -
Journal of Animal Science Jan 2024The aim of the present study was to determine the optimal concentration of dietary protein required in transition diets for multiparous sows that enhance the farrowing...
The aim of the present study was to determine the optimal concentration of dietary protein required in transition diets for multiparous sows that enhance the farrowing process, colostrum production, and subsequent lactation performance. Forty-eight multiparous sows were allotted to one of six dietary treatments according to body weight (290 ± 3 kg) and parity (3.8 ± 0.2) from day 108 of gestation until 24 h after the onset of farrowing. The diets were isoenergetic and contained increasing concentrations of dietary protein (expressed as standardized ileal digestible [SID] Lys) and were supplied at a daily feed supply of 3.8 kg. On day 108 of gestation and days 2, 7, 14, 21, and 28 of lactation, body weight, and back fat thickness were recorded, and blood was sampled on day 108 of gestation, at the onset of farrowing, and days 3, 10, 17, and 24 of lactation from the sows for analysis of plasma metabolites. On day 115 of gestation, urine, and feces were collected for nitrogen (N) balance. The number of liveborn and stillborn piglets and time of birth were recorded and blood from every fourth piglet was sampled at birth for blood gas analysis. Piglets were weighed individually from birth until weaning, to estimate the colostrum and milk yield of the sows. Colostrum and milk samples were collected, and their compositions were determined. On days 3 and 28 of lactation, sows were injected with deuterium oxide to estimate body composition. The N utilization was maximized when the concentration of SID Lys in the transition diet was 6.06 g/kg (P < 0.01). When urinary concentrations of urea were expressed relative to creatinine, the relative concentration of urea remained low until a dietary concentration of 6.08 g SID Lys/kg, above which the relative concentration of urea increased (P < 0.01). Stillbirth rate increased linearly with increasing SID Lys concentration in the transition diet (P < 0.001), thus the concentration of SID Lys should be kept as low as possible without impairing sow performance excessively. A carry-over effect on milk yield was observed, showing that a dietary SID Lys concentration of 5.79 g/kg during transition optimized milk production at an average yield of 13.5 kg/d (P = 0.04). Increasing loss of body fat in lactation was observed with increasing SID Lys concentration in the transition diet (P = 0.03). In conclusion, the transition diet of multiparous sows should contain 5.79 g SID Lys/kg when fed 3.8 kg/d (13.0 MJ ME/kg), for a total SID Lys intake of 22 g/d.
Topics: Pregnancy; Animals; Swine; Female; Diet; Lactation; Body Weight; Dietary Proteins; Urea; Animal Feed
PubMed: 38517473
DOI: 10.1093/jas/skae082