Labeling Strategy and Signal Broadening Mechanism of Protein NMR Spectroscopy in Xenopus laevis Oocytes

We used Xenopus laevis oocytes, a paradigm for a variety of biological studies, as a eukaryotic model system for in‐cell protein NMR spectroscopy. The small globular protein GB1 was one of the first studied in Xenopus oocytes, but there have been few reports since then of high‐resolution spectra in oocytes. The scarcity of data is at least partly due to the lack of good labeling strategies and the paucity of information on resonance broadening mechanisms. Here, we systematically evaluate isotope enrichment and labeling methods in oocytes injected with five different proteins with molecular masses of 6 to 54 kDa. ¹⁹F labeling is more promising than ¹⁵N, ¹³C, and ²H enrichment. We also used ¹⁹F NMR spectroscopy to quantify the contribution of viscosity, weak interactions, and sample inhomogeneity to resonance broadening in cells. We found that the viscosity in oocytes is only about 1.2 times that of water, and that inhomogeneous broadening is a major factor in determining line width in these cells.     

NMR and Molecular Genetics as Tools for Investigating Protein Interactions in Membrane Systems

In our laboratory, we have applied the tools of nuclear magnetic resonance (NMR) spectroscopy and molecular genetics to investigate the structural and dynamic properties of membrane-associated proteins and their interactions with membrane components. There are two general classes of membrane proteins, i.e., intrinsic and peripheral ones. For the intrinsic membrane proteins, we have chosen the membranebound D-lactate dehydrogenase (D-LDH) of Escherichia coli as a model to study protein-lipid interactions in membranes. D-LDH is a respiratory enzyme of molecularweight 65, 000 containing flavin adenine dinucleotide (FAD) as a cofactor. The activity of purified D-LDH is enhanced up to 100-fold by lipids and detergents. The gene for D-LDH has been sequenced, and production of the enzyme amplified up to 300-times normal levels. We have biosynthetically incorporated 5-fluorotryptophan (5F-Trp) into D-LDH and studied the five Trp residues by ¹⁹F-NMR spectroscopy. In order to gain additional information using ¹⁹F-NMR, site-specific, oligonucleotide-directed mutagenesis has been used to insert a sixth Trp into D-LDH at various positions throughout the 571-amino acid chain. These mutant D-LDHs are being characterized biochemically and through NMR. For peripheral membrane proteins, we have chosen two periplasmic binding proteins, histidine-binding protein J (J protein) of Salmonella Typhimurium and glutamine-binding protein (GlnBP) of E. coli as models to investigate the structure-function relationship in periplasmic binding protein-mediated active transport systems. These two proteins both have molecular weights of approximately 25, 000. By using mutant J proteins and GlnBPs and site-specific, oligonucleotide-directed mutagenesis techniques, we have assigned several resonances to specific amino acid residues. We are investigating the relationship between ligand-induced conformational changes in these two proteins and their roles in the active transport of ligand across the cell membrane. We have found that a combination of isotopic labeling, biochemistry, molecular biology, and NMR is a very useful approach to investigate various interactions of membrane-associated protein systems.     

Evaluation of Relative Aptamer Binding to Campylobacter jejuni Bacteria Using Affinity Probe Capillary Electrophoresis

Abstract

A qualitative capillary electrophoresis immunoassay was developed for the first-time to evaluate aptamer binding to bacterial cells. Binding affinity of aptamers developed against a Campylobacter jejuni bacterial cell target, relative to other common food-borne pathogens was investigated and specific binding affinity was evidenced by pronounced mobility shift and peak broadening with increasing bacteria concentration for both aptamers. Little to no mobility shift was observed for food-borne pathogens, Salmonella typhirium and Escherichia coli, even when increasing concentrations 10-fold over target. These results suggest that affinity probe capillary electrophoresis could be useful for qualitative screening of aptamer candidates for bacterial cell targets.     

Application of whole cell NMR techniques to study the interaction of arsenic compounds with catharanthus roseus cell suspension cultures

¹H spin–echo NMR spectroscopy of intact cells of C. roseus facilitates monitoring changes inside the cells on treatment with arsenicals. This in situ detection method is non-invasive and non-destructive in comparison to other available biochemical methods. Short term uptake of the arsinicals, methylarsinate MMA and dimethylarsenate DMA, by C. roseus cells that have reached stationary phase in 1-B5 medium, is followed by using NMR spectroscopy, and in particular, the Carr–Purcell–Meiboom–Gill pulse sequence. An increase in the peak height of the methylarsenic resonance over a period of 11 h is indicative of uptake of each arsenical. However, there is no evidence of any biotransformation products in the ¹H NMR spectra. The accumulation site of DMA is probably the vacuole as is seen from the change in the chemical shift of DMA as it moves into a compartment of lower pH. Biochemical changes associated with the presence of arsenicals are evident in the ¹H NMR spectra of C. roseus cells isolated at different stages in the growth cycle. Although uptake has been demonstrated by other analytical techniques, the resonances corresponding to both MMA and DMA are not observed in the ¹H NMR spectra of cells growing in media containing each arsenical. The association of these arsenicals with large biomolecules in the cell may account for these absences. In this event, the spins–spin relaxation time of the arsenic species would shorten and the signals would not be seen in the spin–echo NMR spectrum. In cells growing in the presence of MMA, a new resonance is observed at a chemical shift position 2.2 ppm after 15 days of growth. The shift in position of the resonance, from 1.75 ppm expected at physiological pH, may indicate an altered environment around the arsenic species such as high intracellular acidity.     

Visualizing Proteins in Human Cells at Near-Physiological Concentrations with Sensitive 19F NMR Chemical Tags

In-cell NMR spectroscopy is an effective tool for observing proteins at atomic resolution in their native cellular environment. However, its utility is limited by its low sensitivity and the extensive line broadening caused by nonspecific interactions in the cells, which is even more pronounced in human cells due to the difficulty of overexpressing or delivering high concentrations of isotopically labeled proteins. Here, we present a high-sensitivity tag (wPSP-6F) containing two trifluoromethyl groups that can efficiently label globular proteins with molecular weights in the 6–40 kDa range under mild conditions. This tag allowed us to detect globular proteins in human cells at concentrations as low as 1.0 μM, which would not have been achievable with ¹⁵N or 3-fluorotyrosine labeling. Moreover, we detected conformational changes and interactions of proteins in the cellular environment. The new sensitive ¹⁹F NMR tag may significantly expand the scope of protein NMR in human cells.     

Target‐Based Whole‐Cell Screening by 1H NMR Spectroscopy

An NMR‐based approach marries the two traditional screening technologies (phenotypic and target‐based screening) to find compounds inhibiting a specific enzymatic reaction in bacterial cells. Building on a previous study in which it was demonstrated that hydrolytic decomposition of meropenem in living Escherichia coli cells carrying New Delhi metallo‐β‐lactamase subclass 1 (NDM‐1) can be monitored in real time by NMR spectroscopy, we designed a cell‐based NMR screening platform. A strong NDM‐1 inhibitor was identified with cellular IC₅₀ of 0.51 μM , which is over 300‐fold more potent than captopril, a known NDM‐1 inhibitor. This new screening approach has great potential to be applied to targets in other cell types, such as mammalian cells, and to targets that are only stable or functionally competent in the cellular environment.     

Real‐Time Monitoring of New Delhi Metallo‐β‐Lactamase Activity in Living Bacterial Cells by 1H NMR Spectroscopy

Disconnections between in vitro responses and those observed in whole cells confound many attempts to design drugs in areas of serious medical need. A method based on 1D ¹H NMR spectroscopy is reported that affords the ability to monitor the hydrolytic decomposition of the carbapenem antibiotic meropenem inside Escherichia coli cells expressing New Delhi metallo‐β‐lactamase subclass 1 (NDM‐1), an emerging antibiotic‐resistance threat. Cell‐based NMR studies demonstrated that two known NDM‐1 inhibitors, L ‐captopril and ethylenediaminetetraacetic acid (EDTA), inhibit the hydrolysis of meropenem in vivo. NDM‐1 activity in cells was also shown to be inhibited by spermine, a porin inhibitor, although in an in vitro assay, the influence of spermine on the activity of isolated NDM‐1 protein is minimal. This new approach may have generic utility for monitoring reactions involving diffusible metabolites in other complex biological matrices and whole‐cell settings, including mammalian cells.     

Weak Attractive Ligand–Polymer and Related Interactions in Catalysis and Reactivity: Impact,Applications, and Modeling

The notion of weak attractive ligand–polymer interactions is introduced, and its potential application, importance, and conceptual links with “cooperative” ligand–substrate interactions are discussed. Synthetic models of weak attractive ligand–polymer interactions are described, in which intramolecular weak C? H???F? C interactions (the existence of which remains contentious) have been detected by NMR spectroscopy and neutron and X‐ray diffraction experiments. These C? H???F? C interactions carry important implications for the design of catalysts for olefin polymerization, because they provide support for the practical feasibility of ortho‐F???H_β ligand–polymer contacts proposed for living Group 4 fluorinated phenoxyimine catalysts. The notion of weak attractive noncovalent interactions between an “active” ligand and the growing polymer chain is a novel concept in polyolefin catalysis.     

3‐Mercapto‐2,6‐Pyridinedicarboxylic Acid: A Small Lanthanide‐Binding Tag for Protein Studies by NMR Spectroscopy

Paramagnetic effects from lanthanide ions present powerful tools for protein studies by nuclear magnetic resonance (NMR) spectroscopy provided that the lanthanide can be site‐specifically and rigidly attached to the protein. A new, particularly small and rigid lanthanide‐binding tag, 3‐mercapto‐2,6‐pyridinedicarboxylic acid (3MDPA), was synthesized and attached to two different proteins via a disulfide bond. The complexes of the N‐terminal domain of the E. coli arginine repressor (ArgN) with seven different paramagnetic lanthanide ions and Co²⁺ were analyzed in detail by NMR spectroscopy. The magnetic susceptibility anisotropy (Δχ) tensors and metal position were determined from pseudocontact shifts. The 3MDPA tag generated very different Δχ tensor orientations compared to the previously studied 4‐mercaptomethyl‐DPA tag, making it a highly complementary and useful tool for protein NMR studies.     

Recent advances in protein NMR spectroscopy and their implications in protein therapeutics research

Nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography are the two main methods for protein three-dimensional structure determination at atomic resolution. According to the protein structures deposited in the Protein Data Bank, X-ray crystallography has become the dominant method for structure determination, particularly for large proteins and complexes. However, with the developments of isotope labeling, increase of magnetic field strength, common use of a cryogenic probe, and ingenious pulse sequence design, the applications of NMR spectroscopy have expanded in biological research, especially in characterizing protein dynamics, sparsely populated transient structures, weak protein interactions, and proteins in living cells at atomic resolution, which is difficult if not impossible by other biophysical methods. Although great advances have been made in protein NMR spectroscopy, its applications in protein therapeutics, which represents the fastest growing segment of the pharmaceutical industry, are still limited. Here we review the recent advances in the use of NMR spectroscopy in studies of large proteins or complexes, posttranslation modifications, weak interactions, and aggregation, and in-cell NMR spectroscopy. The potential applications of NMR spectroscopy in protein therapeutic assays are discussed.     

Synthesis,Photophysical Properties,and Antimicrobial Activity of Novel Styryl Colorants Derived from 7‐Methoxy‐1,4‐diphenethyl‐1,2,3,4‐tetrahydroquinoxaline‐6‐carbaldehyde

The novel 1,4‐diphenethyl‐1,2,3,4‐tetrahydro‐7‐methoxyquinoxalin‐6‐carbaldehyde was synthesized by reductive alkylation of 6‐methoxy quinoxaline with phenyl acetic acid and was further subjected to Knoevenagel condensation with various active methylene compounds to synthesize novel styryl colorants. Photophysical properties of styryl colorants were studied using UV–visible and fluorescence spectroscopy. These colorants displayed orange to violet hue and showed fluorescence emission maxima in the region of 560–640 nm, and displayed a large Stokes shift (85–104 nm). Compounds were subjected to thermogravimetric analysis which showed excellent stability up to 310°C. These styryl compounds were evaluated for their antimicrobial study as antifungal against Candida albicans C. albicans and Aspergillus niger and antibacterial against Escherichia coli and Staphylococcus aureus. The results revealed good antimicrobial activity against tested organisms. The synthesized chromophores were characterized using elemental analysis, FTIR, ¹³C‐NMR and ¹H‐NMR spectroscopy and mass spectrometry.     

Full polysaccharide chitosan‐CMC membrane and silver nanocomposite: synthesis,characterization, and antibacterial behaviors

Chitosan‐carboxymethyl cellulose (CMC) full polysaccharide membrane was prepared by cross‐linking of chitosan with CMC dialdehyde and subsequent reductive amination. CMC dialdehyde molecule was prepared by periodate oxidation of CMC and then applied as a cross‐linking agent to form a new membrane network. The properties of oxidized CMC were investigated by various methods such as Fourier transform infrared (FT‐IR) spectroscopy, ¹H NMR spectroscopy, and viscosity test. Then, novel chitosan‐CMC silver nanocomposite was prepared using chitosan‐CMC as a carrier. The structure of the chitosan‐CMC membrane and the silver nanocomposite were confirmed by FT‐IR spectroscopy, scanning electron microscopy (SEM), transmission electron microscopy (TEM), and thermogravimetric analysis (TGA). TEM images indicate that the chitosan‐CMC nanocomposite comprises silver nanoparticles with diameters in the range of about 5–20 nm. The antibacterial studies of the nanocomposite were also evaluated. The chitosan‐CMC silver nanocomposite demonstrates good antibacterial activity against Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli. Copyright © 2016 John Wiley & Sons, Ltd.     

Novel Cr (III), Fe (III) and Ru (III) Vanillin Based Metallo‐Pharmaceuticals for Cancer and Inflammation Treatment: Experimental and Theoretical Studies

In this study, three novel complexes comprising trivalent Cr (III), Fe (III) and Ru (III) with imine ligand derived from 2‐amino‐3‐hydroxypyridine and o‐vanillin (H₂L) have been synthesized and characterized via wide range of spectroscopic and analytical tools such as ¹H NMR and ¹³C NMR, infrared (IR) and UV–Vis spectrophotometry, conductivity and magnetic measurements. The obtained results along with DFT data confirmed a 1:1 (metal: ligand) stoichiometry with non‐planner geometries for the three complexes. The binding action and the docking study of the prepared metal‐complexes to calf thymus DNA was also studied by absorption spectra and viscosity technique, which revealed that the three complexes interact strongly with DNA through intercalative binding mode. Significantly, these metal‐imine complexes showed strong and efficient anti‐inflammatory and antimicrobial activities against various gram‐positive (Microccus luteus), gram‐negative (Escherichia coli and Serratia marcescence) bacteria, and three strains of fungus. Moreover, all complexes exhibited more potent cytotoxicity effect on the outgrowth of different types of carcinoma cells, including human colon (HCT‐116 cell line), breast (MCF‐7 cell line), and hepatic cellular (HepG‐2), than the clinically‐proven Vinblastine standard.     

Visualizing an Ultra‐Weak Protein–Protein Interaction in Phosphorylation Signaling

Proteins interact with each other to fulfill their functions. The importance of weak protein–protein interactions has been increasingly recognized. However, owing to technical difficulties, ultra‐weak interactions remain to be characterized. Phosphorylation can take place via a K_D≈25 mM interaction between two bacterial enzymes. Using paramagnetic NMR spectroscopy and with the introduction of a novel Gd^III‐based probe, we determined the structure of the resulting complex to atomic resolution. The structure accounts for the mechanism of phosphoryl transfer between the two enzymes and demonstrates the physical basis for their ultra‐weak interaction. Further, molecular dynamics (MD) simulations suggest that the complex has a lifetime in the micro‐ to millisecond regimen. Hence such interaction is termed a fleeting interaction. From mathematical modeling, we propose that an ultra‐weak fleeting interaction enables rapid flux of phosphoryl signal, providing a high effective protein concentration.     

Uniaxial Movements of a Metal–Cyanide Framework Switched by Weak Interactions through Dehydration and Rehydration

A metal–cyanide framework undergoes a dehydration–rehydration triggered reversible single‐crystal‐to‐single‐crystal transformation. The resulting accordion‐like contraction–expansion corresponds to a size change along the c axis as much as 24 %. This anisotropic response arises from the cooperativity among the water molecules, K ions, and CN groups between the unique two‐dimensional bimetallic layers through weak interactions of hydrogen bonds and electrostatic (ionic) interactions. The key role of the water molecules in the dehydration–rehydration process is revealed by solid‐state ¹H NMR spectroscopy and dielectric measurements.     

Synthesis,antifungal and antibacterial activity of calix[4]arene-based 1,3,4-oxadiazole derivatives

We describe the synthesis of some novel p-tert-butylcalix[4]arene-based (5-aryl-1,3,4-oxadiazol-2-yl)2-chloroethanethioate derivatives ( 4a–e ). These compounds were synthesized by the reaction of tetra-tert-butyl calix[4]arene ( 1 ) with (5-aryl-1,3,4-oxadiazol-2-yl)2-chloroethanethioate ( 3a–e ) in the presence of potassium carbonate as a weak base and dry acetone as the solvent. All the newly synthesized calix[4]arene derivatives were characterized by elemental analysis and various spectroscopic methods such as FT-IR, ¹H NMR,¹³C NMR, DEPT, and ESI-MS. The synthesized compounds were tested in vitro for their antibacterial and antifungal activities against Escherichia coli and Aspergillus fumigates in comparison with enrofloxacin and amphotericin as reference drugs, which are normally used for treating such infections. The synthesized compounds showed different inhibition zones against the tested bacteria and fungi. Compound 4c was found to be most effective against A. fumigates, whereas compound 4e was found to be equally effective against E. coli and A. fumigates.     

Controlled/living copolymerization of styrene and acrylamide in DMF with Fe/TMEDA complex as catalyst

In this work, Fe(0)‐mediated single electron‐living radical copolymerization of styrene (St) and acrylamide (AM) was investigated at ambient temperature in N,N‐dimethylformamide using carbon tetrachloride as initiator and tetramethylethylenediamine as ligand. Kinetic studies showed that the copolymerization followed the first‐order kinetics model. The resulting copolymers of St and AM possessed predetermined molecular weights and narrow molecular weight distribution, which agreed with the character of controlled/living polymerization. On the basis of Fourier transform infrared spectroscopy (FTIR), proton nuclear magnetic resonance (NMR), the monomer reactivity ratios were calculated. The amount of ligand played an important role in copolymerization. The obtained polymer was characterized by FTIR, ¹H NMR, ¹³C NMR, and gel permeation chromatography. The living characteristics were demonstrated by chain extension experiment. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 2919–2924     

Synthesis,characterization, antimicrobial activity, 3D-QSAR,DFT, and molecular docking of some ciprofloxacin derivatives and their copper(II) complexes

Six new derivatives of ciprofloxacin compounds and their copper(II) complexes were synthesized, characterized by spectroscopic methods (ultraviolet–visible [UV–vis], Fourier transform infrared [FTIR], nuclear magnetic resonance [NMR], mass spectrometry [MS], and electron paramagnetic resonance [EPR]), and tested for antibacterial activities against gram-negative and gram-positive bacteria. The data showed that ciprofloxacin derivatives act as bidentate ligands and the metal ions coordinate through the pyridone carbonyl and the carboxylate oxygen atoms. Tetragonally distorted octahedral ligand fields were assumed for all complexes based on their spectral studies. Copper(II) complexes of the synthesized ciprofloxacin derivatives revealed higher antibacterial activities against gram-positive and gram-negative bacterial species than the parent ciprofloxacin antibiotic. Furthermore, three-dimensional quantitative structure–activity relationship (3D-QSAR) models were evaluated by studying 30 antibiotic compounds of the quinolone class. Density function theory (DFT) calculations were applied to evaluate the optimized geometrical structures using the B3LYP method and 6-311G(d,p) basis set. The 3D-QSAR study revealed that there are eight optimum parameters that give the best predictive modulation with good reliability (R² = 0.996, F = 12.004, sigma = 0.426). In silico molecular docking was also performed on the derivatives, and the results revealed the presence of two types of interactions between the Escherichia coli and the derivatives, H-bonding and Van der Waals interactions, and an effective inhibition at the docked site.     

Synthesis and antibacterial activity of new <Emphasis Type="Italic">N</Emphasis>-substituted 7-amino-4-methyl-2<Emphasis Type="Italic">H</Emphasis>-chromen-2-ones

N-Substituted 7-amino-4-methyl-2H-chromen-2-ones containing one or two functionalized azole or azine moieties were synthesized. The structures of all synthesized compounds were confirmed by IR, ¹H NMR, and ¹³C NMR spectroscopy. Some of the synthesized compounds exhibited weak antibacterial activity against Rhizobium radiobacter, Escherichia coli, and Xanthomonas campestris.     

人宫颈癌细胞(Hela)内的31P核磁共振研究

建立了无损伤性³¹P NMR研究细胞内物质的实验方法, 并对人宫颈癌细胞(Hela)的³¹P NMR谱中含磷小分子代谢物的谱峰进行了分析; 细胞内无机磷(Pi)的化学位移对pH非常敏感, 通过测定其化学位移可间接确定细胞内的pH, Hela细胞内Pi峰的化学位移为5.88±0.01 (n＝3), 计算得到细胞内 pH值为7.05±0.01; 通过测量Hela细胞的³¹P NMR谱中ATP的α磷和β磷及γ磷的化学位移差值, 得出Hela细胞内Mg^2＋与ATP结合的复合物MgATP和整个ATP量的比值, 计算得到Hela细胞内游离Mg^2＋浓度为(253.3±0.13) mmol/L (n＝3), 与其它分析方法相比, ³¹P NMR测定细胞内游离Mg^2＋浓度具有对细胞样品无损伤的优点.