Combination Of Nuclear Magnetic Resonance Research Articles

Synthesis and Functionalization of a 1,2-Bis(trimethylsilyl)-1,2-disilacyclohexene That Can Serve as a Unit of cis-1,2-Dialkyldisilene

π-Electron compounds that include multiple bonds between silicon atoms have received much attention as novel functional silicon compounds. In the present paper, 1,2-bis(trimethylsilyl)-1,2-disilacyclohexene 1 was successfully synthesized as thermally stable yellow crystals. Disilene 1 was easily converted to the corresponding potassium disilenide 4, which furnished novel functionalized disilenes after the subsequent addition of an electrophile. Interestingly, two trimethylsilyl groups in 1 can be stepwise converted to anthryl groups. The novel disilenes derived from 1 were characterized by a combination of nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), elemental analyses, and X-ray single crystal diffraction analysis. The present study demonstrates that disilene 1 can serve as a unit of cis-1,2-dialkyldisilene.

A Measured Method for In Situ Viscosity of Fluid in Porous Media by Nuclear Magnetic Resonance

At present, the existing measuring methods for viscosity of fluid can only obtain the viscosity of bulk fluid, while the in situ viscosity of fluid in porous media cannot be acquired. In this paper, with the combination of nuclear magnetic resonance (NMR) and physical simulation experiment, a testing method for in situ viscosity of fluid in porous media is established, and the in situ viscosity spectra of water in tight cores under different displacement conditions is obtained. The experimental results show that the in situ viscosity distribution of water in porous media is inhomogeneous, and it is not a constant but is related to the distance between water and rock walls. When the distance between fluid and rock walls is close enough (e.g., T2 relaxation time is less than 1 ms), the viscosity of fluid increases rapidly, and the in situ viscosity is greater than the bulk viscosity. Moreover, after the rock samples are saturated with water, the in situ viscosity of water is distributed as a double-peak structure. The left peak is characterized mainly by the in situ viscosity distribution of movable fluid, whose in situ viscosity is smaller, and the right peak mainly represents the in situ viscosity distribution characteristics of immovable fluid, whose in situ viscosity is larger and increases gradually. Under a relatively large driving force, the in situ viscosity amplitude of movable fluid decreases greatly, and the average in situ viscosity of residual water in the core is much higher than that of saturated water in initial state.

A combination of NMR and liquid chromatography to characterize the protective effects of Rhus tripartita extracts on ethanol-induced toxicity and inflammation on intestinal cells

Consumption of ethanol may have severe effects on human organs and tissues and lead to acute and chronic inflammation of internal organs. The present study aims at investigating the potential protective effects of three different extracts prepared from the leaves, root, and stem of the sumac, Rhus tripartita, against ethanol-induced toxicity and inflammation using intestinal cells as a cell culture system, in vitro model of the intestinal mucosa. The results showed an induction of cytotoxicity by ethanol, which was partially reversed by co-administration of the plant extracts. As part of investigating the cellular response and the mechanism of toxicity, the role of reduced thiols and glutathione-S-transferases were assessed. In addition, intestinal cells were artificially imposed to an inflammation state and the anti-inflammatory effect of the extracts was estimated by determination of interleukin-8. Finally, a detailed characterization of the contents of the three plant extracts by high resolution Nuclear Magnetic Resonance (NMR) spectroscopy and mass spectrometry revealed significant differences in their chemical compositions.

Structural analysis of the complex between influenza B nucleoprotein and human importin-\u03b1

Influenza viruses are negative strand RNA viruses that replicate in the nucleus of the cell. The viral nucleoprotein (NP) is the major component of the viral ribonucleoprotein. In this paper we show that the NP of influenza B has a long N-terminal tail of 70 residues with intrinsic flexibility. This tail contains the Nuclear Location Signal (NLS). The nuclear trafficking of the viral components mobilizes cellular import factors at different stages, making these host-pathogen interactions promising targets for new therapeutics. NP is imported into the nucleus by the importin-α/β pathway, through a direct interaction with importin-α isoforms. Here we provide a combined nuclear magnetic resonance and small-angle X-ray scattering (NMR/SAXS) analysis to describe the dynamics of the interaction between influenza B NP and the human importin-α. The NP of influenza B does not have a single NLS nor a bipartite NLS but our results suggest that the tail harbors several adjacent NLS sequences, located between residues 30 and 71.

Synthesis and characterization of aluminum diboride products using 27Al, 11B NMR and ab initio studies

Understanding different bonding environments in various metal borides provides insight into their structures and physical properties. Polycrystalline aluminum diboride (AlB2) samples have been synthesized and compared both with a commercial sample and with the literature. One issue that arose is the relative ease with which boron-rich and aluminum deficient phases of aluminum borides can be presented in AlB2. Here, we report 27Al, 11B nuclear magnetic resonance (NMR) spectroscopy and first-principles calculations on AlB2 in order to shed light on these different bonding environments at the atomic level and compare the structural and electronic properties of the products of different preparations. Along with the aforementioned, the present study also takes an in-depth look at the nature of the 11B and 27Al nuclear spin–lattice relaxation recovery data for the AlB2 and other superhard materials. The nuclear spin–lattice relaxation has been measured for a static sample and with magic-angle spinning. The combination of NMR and band structure calculations highlights the synthetic challenges with superhard materials.

USP7-Specific Inhibitors Target and Modify the Enzyme's Active Site via Distinct Chemical Mechanisms

USP7 is a deubiquitinating enzyme that plays a pivotal role in multiple oncogenic pathways and therefore is a desirable target for new anti-cancer therapies. However, the lack of structural information about the USP7-inhibitor interactions has been a critical gap in the development of potent inhibitors. USP7 is unique among USPs in that its active site is catalytically incompetent, and is postulated to rearrange into a productive conformation only upon binding to ubiquitin. Surprisingly, we found that ubiquitin alone does not induce an active conformation in solution. Using a combination of nuclear magnetic resonance, mass spectrometry, computational modeling, and cell-based assays, we found that DUB inhibitors P22077 and P50429 covalently modify the catalytic cysteine of USP7 and induce a conformational switch in the enzyme associated with active site rearrangement. This work represents the first experimental insights into USP7 activation and inhibition and provides a structural basis for rational development of potent anti-cancer therapeutics.

Compositional analysis of multi-element magnetic nanoparticles with a combined NMR and TEM approach

The increasing interest in nanoscale materials goes hand in hand with the challenge to reliably characterize the chemical compositions and structural features of nanosized objects in order to relate those to their physical properties. Despite efforts, the analysis of the chemical composition of individual multi-element nanoparticles remains challenging—from the technical point of view as well as from the point of view of measurement statistics. Here, we demonstrate that zero-field solid-state nuclear magnetic resonance (NMR) complements local, single particle transmission electron microscopy (TEM) studies with information on a large assembly of chemically complex nanoparticles. The combination of both experimental techniques gives information on the local composition and structure and provides an excellent measurement statistic through the corresponding NMR ensemble measurement. This analytical approach is applicable to many kinds of magnetic materials and therefore may prove very versatile in the future research of particulate magnetic nanomaterials.

Metal-Free [2 + 2]-Photocycloaddition of (Z)-4-Aryliden-5(4H)-Oxazolones as Straightforward Synthesis of 1,3-Diaminotruxillic Acid Precursors: Synthetic Scope and Mechanistic Studies

The direct [2 + 2]-photocycloaddition of (Z)-2-phenyl-4-aryliden-5(4H)-oxazolones 1 to give 1,3-diaminotruxillic cyclobutane derivatives 2 in very good yields (75–100%) is reported. The reaction takes place by irradiation of CH2Cl2 solutions of 1 with blue light (465 nm) provided by light-emitting diode (LED) lamps of low power (around 1 W) for 72 h. Four isomers of the 1,3-diaminotruxillic cyclobutanes 2 were obtained; all of them fully characterized by a combination of nuclear magnetic resonance (NMR) spectroscopy and X-ray diffraction analysis. The reaction shows a certain selectivity, since one of the isomers (the epsilon) is obtained preferentially, and works for electron-releasing and electron-withdrawing substituents at the arylidene ring. A novel setup is presented for the in-line monitoring of the continuous flow photoassisted synthesis of the cyclobutane derivatives 2 by NMR spectroscopy, with the microreactor dramatically reducing reaction times to only 30 min with clear product distribution of...

Structural and Dynamic "Portraits" of Recombinant and Native Cytotoxin I from Naja oxiana: How Close Are They?

Today, recombinant proteins are quite widely used in biomedical and biotechnological applications. At the same time, the question about their full equivalence to the native analogues remains unanswered. To gain additional insight into this problem, intimate atomistic details of a relatively simple protein, small and structurally rigid recombinant cardiotoxin I (CTI) from cobra Naja oxiana venom, were characterized using nuclear magnetic resonance (NMR) spectroscopy and atomistic molecular dynamics (MD) simulations in water. Compared to the natural protein, it contains an additional Met residue at the N-terminus. In this work, the NMR-derived spatial structure of uniformly 13C- and 15N-labeled CTI and its dynamic behavior were investigated and subjected to comparative analysis with the corresponding data for the native toxin. The differences were found in dihedral angles of only a single residue, adjacent to the N-terminal methionine. Microsecond-long MD traces of the toxins reveal an increased flexibility in the residues spatially close to the N-Met. As the detected structural and dynamic changes of the two CTI models do not result in substantial differences in their cytotoxicities, we assume that the recombinant protein can be used for many purposes as a reasonable surrogate of the native one. In addition, we discuss general features of the spatial organization of cytotoxins, implied by the results of the current combined NMR and MD study.

Conformational Heterogeneity in the Activation Mechanism of Bax

Bax is known for its pro-apoptotic role within the mitochondrial pathway of apoptosis. However, the mechanism for transitioning Bax from cytosolic to membrane-bound oligomer remains elusive. Previous nuclear magnetic resonance (NMR) and electronparamagnetic resonance (EPR) studies defined monomeric Bax as conformationally homogeneous. Yet it has recently been proposed that monomeric Bax exists in equilibrium with a minor state that is distinctly different from its NMR structure. Here, we revisited the structural analysis of Bax using methods uniquely suited for unveiling "invisible" states of proteins, namely, NMR paramagnetic relaxation enhancements and EPR double electron-electron resonance (DEER). Additionally we examined the effect of glycerol, the co-solvent of choice in DEER studies, on the structure of Bax using NMR chemical-shift perturbations and residual dipolar couplings. Based on our combined NMR and EPR results, Bax is a conformationally homogeneous protein prior to its activation.

Modeling compressive strength of cement asphalt composite based on pore size distribution

Cement asphalt composite is a porous material with various connected and closed pores, and pore structure is the major factor affecting its strength. In this paper, the pore structure of cement asphalt composites with different asphalt contents were analyzed by the combination of Nuclear Magnetic Resonance (NMR) and modified image analysis methods. The former one mainly detects the smaller and open pores, and the latter one mainly measures the larger and spherical closed pores. The total porosity is the sum of open and closed porosities. A model, based on Griffith theory and complete pore structure, was developed to predict the compressive strength of cement asphalt composites with high and low asphalt contents. It is demonstrated that the proposed models predict the compressive strength of cement and asphalt composite quite well.

Carbohydrate–Polypeptide Contacts in the Antibody Receptor CD16A Identified through Solution NMR Spectroscopy

Asparagine-linked carbohydrates (N-glycans) are common modifications of eukaryotic proteins that confer multiple properties, including the essential stabilization of therapeutic monoclonal antibodies. Here we present a rapid and efficient strategy for identifying N-glycans that contact polypeptide residues and apply the method to profile the five N-glycans attached to the human antibody receptor CD16A (Fc γ receptor IIIA). Human embryonic kidney 293S cells expressed CD16A with 13CU-labeled N-glycans using standard protein expression techniques and medium supplemented with 3 g/L [13CU]glucose. Anomeric resonances on the protein-linked N-acetylglucosamine residue at the reducing end of the glycan are particularly well suited to studies of multiply glycosylated N-glycoproteins because only one reducing end and nitrogen-linked residue is present in each N-glycan. Correlations between anomeric 1H1 and 13C1 nuclei on the reducing end residue generate crosspeaks in a conventional two-dimensional heteronuclear single-quantum coherence nuclear magnetic resonance (NMR) experiment that appear in a region of the spectrum devoid of other carbohydrate peaks or background protein signals. Two N-glycan peaks corresponding to the N45 and N162 N-glycans were dispersed from the rapidly averaged peaks corresponding to the N38, N74, and N169 N-glycans. We used a combination of NMR and 1 μs all-atom computational simulations to identify unexpected contacts between the N45 N-glycan and CD16A polypeptide residues.

Formation, characterization and pH dependence of rifampicin: heptakis(2,6-di-O-methyl)-β-cyclodextrin complexes

Rifampicin (Rif) is a broad spectrum antibiotic used as a first line agent in the treatment of mycobacterial infections. However, its low solubility and reduced stability in water limit its bioavailability, thus requiring the use of complex formulations. Here, we present a systematic study of Rif in complex with a methylated cyclodextrin, heptakis(2,6-di-O-methyl)-β-cyclodextrin (DIMEB), in phosphate buffer using a combination of nuclear magnetic resonance (NMR) and steady-state UV–vis spectroscopic methods. An increase in the stability and solubility of Rif in complex with DIMEB was observed in buffered solutions (phosphate, PBS). At neutral pH the presence of three distinguishable binding sites was revealed, demonstrating that DIMEB forms predominantly a stable 1:1 (K∼3000M−1) complex at the piperazine site of Rif, while at acidic pH the binding constant decreases significantly (K∼400M−1) due to protonation of the piperazine, thus inducing a release of Rif. The reported results provide new and relevant information for the stability and solubility of Rif in aqueous solution when forming a complex with DIMEB. Furthermore they contribute to clarify Rif interactions with cyclodextrin carriers, thus providing the basis for the development of new methylated cyclodextrin that can efficiently encapsulate and deliver Rif and derivatives of its family.

Effects of naturally occurring charged mutations on the structure, stability, and binding of the Pin1 WW domain

Pin1 is a peptidyl-prolyl cis-trans isomerase, whose WW domain specifically recognizes the pSer/Thr-Pro motif. Pin1 is involved in multiple phosphorylation events that regulate the activities of various substrates, and Pin1 deregulation has been reported in various diseases, including cancer and Alzheimer's disease. The WW domain of Pin1 has been used as a small model protein to investigate the folding mechanisms of the β-sheet structure by studying the effect of mutations or its naturally occurring variants. However, only a few studies have investigated the structure and binding of Pin1 WW mutants. In the present work, two naturally occurring Pin1 WW variants, namely, G20D and S16R, derived from the cynomolgus monkey and African green monkey, respectively, were selected to investigate the influence of charge mutation on the structure, stability, and binding properties of the Pin1 WW domain. Analysis using a combination of nuclear magnetic resonance (NMR) and chemical shift-based calculations revealed that the G20D and S16R mutants had high structural similarity to the wild-type Pin1 WW domain. However, the presence of a charge mutation significantly decreased the stability of the Pin1 WW domain. Both the wild-type and G20D forms of the Pin1 WW domain utilized a three-site mode to bind to a phosphorylated Tau peptide, pT231, whereas the S16R mutant binds to the pT231 peptide either in a non-specific manner or through a totally different binding mechanism. Correspondingly, the wild-type and two mutant Pin1 WW domains showed different binding affinities to the Tau phosphopeptide. Considering that the WW domain participates in the catalytic activity of the Pin1 isomerase, our study represents a novel approach for studying Pin1 function through the analysis of its naturally occurring mutants.

Insights into HuR RRM1–2 tandem domains self‐association and mRNA recognition

Human antigen R (HuR) employs its mRNA stabilizing activity to function as a major post‐transcriptional regulator of gene expression. This protein plays a central role in the outcome of the inflammatory response as it may stabilize mRNAs of key components of the immune system. HuR comprises three functionally distinct RNA Recognition Motifs: RRM1, RRM2, and RRM3. The two N‐terminal tandem RRM domains can selectively bind AU‐rich elements (AREs), while the third RRM domain (RRM3) contributes to interactions with the poly‐A tail of target mRNA. Here, we characterized the structure, dynamics, and binding properties of HuR RRM11‐99 and RRM1–21‐189 tandem domains using a combination of Nuclear Magnetic Resonance and ion mobility‐mass spectrometry. RRM11‐99 adopts a typical RRM fold, composed of two α‐helices and a 4‐stranded β‐sheet (β1α1β2β3α2β4 topology and a β‐hairpin between α2 and β4). 15N relaxation measurements demonstrate that the N‐terminal intrinsically disordered region (residues 1–19) and the RRM1‐RRM2 linker region (residues 95–106) are highly flexible, suggesting that RRM1 and RRM2 domains behave as independent structural modules in solution. NMR titration experiments show that residues on the β‐sheet surface (β1 and β3) and the C‐terminus of RRM11‐99 mediate mRNA binding. An increase in R2/R1 values further confirms the mRNA interaction site, which is compatible with a low μM binding affinity. Both the single RRM11‐99 and the tandem RRM1–21‐189 have the ability to self‐associate, although representing a minor population. Ion mobility‐mass spectrometry identified the presence of oligomers (dimers, trimers and tetramers) with at least three different conformations for the apo forms of RRM11‐99 and RRM1–21‐189. However, only the monomeric species was able to interact with RNA, suggesting that ligand binding shifts the oligomeric/conformational equilibrium of HuR N‐terminal RRM domains. Our results show that the tandem RRM1–2 domains of HuR adopt three distinct conformations in the absence of RNA, suggesting that conformational selection may underlie the mechanism by which HuR recognizes and stabilizes mRNA.Support or Funding InformationThis work was supported by grants from Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), and by a Brazil Initiative Collaboration Grant from Brown University to A.S.P.

Characterization of a New Trioxilin and a Sulfoquinovosyl Diacylglycerol with Anti-Inflammatory Properties from the Dinoflagellate Oxyrrhis marina.

Two new compounds—a trioxilin and a sulfoquinovosyl diacylglycerol (SQDG)—were isolated from the methanolic extract of the heterotrophic dinoflagellate Oxyrrhis marina cultivated by feeding on dried yeasts. The trioxilin was identified as (4Z,8E,13Z,16Z,19Z) -7(S),10(S),11(S)-trihydroxydocosapentaenoic acid (1), and the SQDG was identified as (2S)-1-O-hexadecanosy-2-O-docosahexaenoyl-3-O-(6-sulfo-α-d-quinovopyranosyl)-glycerol (2) by a combination of nuclear magnetic resonance (NMR) spectra, mass analyses, and chemical reactions. The two compounds were associated with docosahexaenoic acid, which is a major component of O. marina. The two isolated compounds showed significant nitric oxide inhibitory activity on lipopolysaccharide-induced RAW264.7 cells. Compound 2 showed no cytotoxicity against hepatocarcinoma (HepG2), neuroblastoma (Neuro-2a), and colon cancer (HCT-116) cells, while weak cytotoxicity was observed for compound 1 against Neuro-2a cells.

From basic apoptosis discoveries to advanced selective BCL-2 family inhibitors.

Members of the B cell lymphoma 2 (BCL-2) gene family have a central role in regulating programmed cell death by controlling pro-apoptotic and anti-apoptotic intracellular signals. In cancer, apoptosis evasion through dysregulation of specific BCL-2 family genes is a recurring event; accordingly, selective inhibition of specific anti-apoptotic BCL-2 family proteins represents an exciting therapeutic opportunity. A combination of nuclear magnetic resonance (NMR)-based screening and structure-based drug design has yielded the first bona fide BCL-2 homology 3 (BH3) mimetics, including the BCL-2 and BCL-XL dual antagonist navitoclax, which is the first BCL-2 family inhibitor to show efficacy in patients with cancer. Clinical experience with navitoclax prompted the generation of the highly selective BCL-2 inhibitor venetoclax, which is now approved in the United States for the treatment of patients with chronic lymphocytic leukaemia with 17p deletion who have received at least one prior therapy. Recent advances have also been made in the development of potent and selective inhibitors of BCL-XL and myeloid cell leukaemia 1 (MCL1), which are additional BCL-2 family members with established anti-apoptotic roles in cancer. Here we review the latest progress in direct and selective targeting of BCL-2 family proteins for cancer therapy.

Unusual Topological RNA Architecture with an Eight-Stranded Helical Fragment Containing A-, G-, and U-Tetrads.

Human telomeric RNA performs various cellular functions such as telomere length regulation, heterochromatin formation, and chromosome end protection. Using a combination of nuclear magnetic resonance, circular dichroism, and gel electrophoresis, we observed an unusual topological structure formed by human telomere RNA r(GUUAGGGU). Our results showed that every set of four strands formed a parallel G-quadruplex as symmetry-related units containing four G-tetrads, two U-tetrads, and one A-tetrad. An eight-stranded helical fragment containing A-, G-, and U-tetrads provided a central intercalated scaffold that connected two G-quadruplex units in an alternating antiparallel arrangement, giving rise to a novel RNA architecture. This higher order RNA structure is so stable that it would be surprising if similar structures do not occur in nature. Our findings provide a new insight into the behavior of human telomeric RNA molecules.

A Preliminary Investigation Into the Characterization of Asphaltenes Extracted From an Oil Sand and Two Vacuum Residues From Petroleum Refining Using Nuclear Magnetic Resonance, DEPT, and MALDI-TOF

This paper reports the findings of an investigation into the molecular structures and properties of three asphaltene samples, namely, an asphaltene sample extracted from Buton Oil Sand (Indonesia), and two asphaltene samples extracted from vacuum residues from Liaohe Refinery (China) and Vene Refinery (Venezuela), respectively. The average molecular structural parameters, including the average polycyclic aromatic hydrocarbon (PAH) size, average side chain length, and average molecular weight (AMW), of the three asphaltene samples were estimated using data from nuclear magnetic resonance (NMR) in combination with distortionless enhancement by polarization transfer (DEPT), and then compared against each other. The molecular weight distributions (MWDs) of the three asphaltene samples were measured using a matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. The results indicated that the island molecular architecture predominated in all three asphaltenes and the average polycyclic aromatic hydrocarbon size was found to be six rings. The average molecular weight of the Buton asphaltene sample was found to be ca. 800 Da while those of the two petroleum asphaltene samples were approximately 600 Da. In comparison, the Buton asphaltene sample contained a much higher level of oxygen and sulfur, but a lower aromaticity than those of the two petroleum asphaltene samples. The use of liquid NMR in combination with DEPT was shown to provide an effective method for characterization and estimation of the molecular structures of asphaltenes, supported by MALDI-TOF mass spectra.

Integration of CuAAC Polymerization and Controlled Radical Polymerization into Electron Transfer Mediated "Click-Radical" Concurrent Polymerization.

The successful chain-growth copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) polymerization employing Cu(0)/pentamethyldiethylenetriamine (PMDETA) and alkyl halide as catalyst is first investigated by a combination of nuclear magnetic resonance, gel-permeation chromatography, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. In addition, the electron transfer mediated "click-radical" concurrent polymerization utilizing Cu(0)/PMDETA as catalyst is successfully employed to generate well-defined copolymers, where controlled CuAAC polymerization of clickable ester monomer is progressed in the main chain acting as the polymer backbone, the controlled radical polymerization (CRP) of acrylic monomer is carried out in the side chain. Furthermore, it is found that there is strong collaborative effect and compatibility between CRP and CuAAC polymerization to improve the controllability.