Inclusion complex of benzocaine and β-cyclodextrin: 1H NMR and isothermal titration calorimetry studies

NASA Astrophysics Data System (ADS)

Mic, Mihaela; Pırnǎu, Adrian; Bogdan, Mircea; Turcu, Ioan

2013-11-01

The supramolecular structure of the inclusion complex of β-cyclodextrin with benzocaine in aqueous solution has been investigated by 1H NMR spectroscopy and isothermal titration nanocalorimetry (ITC). Analysis of 1H NMR data by continuous variation method indicates that the benzocaine: β-cyclodextrin inclusion complex occurs and has a 1:1 stoichiometry. Rotating frame NOE spectroscopy (ROESY) was used to ascertain the solution geometry of the host-guest complex which indicates that the benzocaine molecule was included with the aromatic ring into the cyclodextrin cavity. Although the affinity of benzocaine for cyclodextrin is relatively high, the association constant cannot be measured using ITC due to the low solubility of benzocaine in water.

Racial differences in the relationship between rate of nicotine metabolism and nicotine intake from cigarette smoking

PubMed Central

Ross, Kathryn C.; Gubner, Noah R.; Tyndale, Rachel F.; Hawk, Larry W.; Lerman, Caryn; George, Tony P.; Cinciripini, Paul; Schnoll, Robert A.; Benowitz, Neal L.

2016-01-01

Rate of nicotine metabolism has been identified as an important factor influencing nicotine intake and can be estimated using the nicotine metabolite ratio (NMR), a validated biomarker of CYP2A6 enzyme activity. Individuals who metabolize nicotine faster (higher NMR) may alter their smoking behavior to titrate their nicotine intake in order to maintain similar levels of nicotine in the body compared to slower nicotine metabolizers. There are known racial differences in the rate of nicotine metabolism with African Americans on average having a slower rate of nicotine metabolism compared to Whites. The goal of this study was to determine if there are racial differences in the relationship between rate of nicotine metabolism and measures of nicotine intake assessed using multiple biomarkers of nicotine and tobacco smoke exposure. Using secondary analyses of the screening data collected in a recently completed clinical trial, treatment-seeking African American and White daily smokers (10 or more cigarettes per day) were grouped into NMR quartiles so that the races could be compared at the same NMR, even though the distribution of NMR within race differed. The results indicated that rate of nicotine metabolism is a more important factor influencing nicotine intake in White smokers. Specifically, Whites were more likely to titrate their nicotine intake based on the rate at which they metabolize nicotine. However, this relationship was not found in African Americans. Overall there was a greater step down, linear type relationship between NMR groups and cotinine or cotinine/cigarette in African Americans, which is consistent with the idea that differences in blood cotinine levels between the African American NMR groups were primarily due to differences in CYP2A6 enzyme activity without titration of nicotine intake among faster nicotine metabolizers. PMID:27180107

NMR and MD Investigations of Human Galectin-1/Oligosaccharide Complexes

PubMed Central

Meynier, Christophe; Feracci, Mikael; Espeli, Marion; Chaspoul, Florence; Gallice, Philippe; Schiff, Claudine; Guerlesquin, Françoise; Roche, Philippe

2009-01-01

Abstract The specific recognition of carbohydrates by lectins plays a major role in many cellular processes. Galectin-1 belongs to a family of 15 structurally related β-galactoside binding proteins that are able to control a variety of cellular events, including cell cycle regulation, adhesion, proliferation, and apoptosis. The three-dimensional structure of galectin-1 has been solved by x-ray crystallography in the free form and in complex with various carbohydrate ligands. In this work, we used a combination of two-dimensional NMR titration experiments and molecular-dynamics simulations with explicit solvent to study the mode of interaction between human galectin-1 and five galactose-containing ligands. Isothermal titration calorimetry measurements were performed to determine their affinities for galectin-1. The contribution of the different hexopyranose units in the protein-carbohydrate interaction was given particular consideration. Although the galactose moiety of each oligosaccharide is necessary for binding, it is not sufficient by itself. The nature of both the reducing sugar in the disaccharide and the interglycosidic linkage play essential roles in the binding to human galectin-1. PMID:20006954

Spectroscopic study on variations in illite surface properties after acid-base titration.

PubMed

Liu, Wen-xin; Coveney, R M; Tang, Hong-xiao

2003-07-01

FT-IR, Raman microscopy, XRD, 29Si and 27Al MAS NMR, were used to investigate changes in surface properties of a natural illite sample after acid-base potentiometric titration. The characteristic XRD lines indicated the presence of surface Al-Si complexes, preferable to Al(OH)3 precipitates. In the microscopic Raman spectra, the vibration peaks of Si-O and Al-O bonds diminished as a result of treatment with acid, then increased after hydroxide back titration. The varied ratio of signal intensity between (IV)Al and (VI)Al species in 27Al MAS NMR spectra, together with the stable BET surface area after acidimetric titration, suggested that edge faces and basal planes in the layer structure of illite participated in dissolution of structural components. The combined spectroscopic evidence demonstrated that the reactions between illite surfaces and acid-leaching silicic acid and aluminum ions should be considered in the model description of surface acid-base properties of the aqueous illite.

Gravity-driven pH adjustment for site-specific protein pKa measurement by solution-state NMR

NASA Astrophysics Data System (ADS)

Li, Wei

2017-12-01

To automate pH adjustment in site-specific protein pKa measurement by solution-state NMR, I present a funnel with two caps for the standard 5 mm NMR tube. The novelty of this simple-to-build and inexpensive apparatus is that it allows automatic gravity-driven pH adjustment within the magnet, and consequently results in a fully automated NMR-monitored pH titration without any hardware modification on the NMR spectrometer.

Characterization of KCNE1 inside Lipodisq Nanoparticles for EPR Spectroscopic Studies of Membrane Proteins.

PubMed

Sahu, Indra D; Zhang, Rongfu; Dunagan, Megan M; Craig, Andrew F; Lorigan, Gary A

2017-06-01

EPR spectroscopic studies of membrane proteins in a physiologically relevant native membrane-bound state are extremely challenging due to the complexity observed in inhomogeneity sample preparation and dynamic motion of the spin-label. Traditionally, detergent micelles are the most widely used membrane mimetics for membrane proteins due to their smaller size and homogeneity, providing high-resolution structure analysis by solution NMR spectroscopy. However, it is often difficult to examine whether the protein structure in a micelle environment is the same as that of the respective membrane-bound state. Recently, lipodisq nanoparticles have been introduced as a potentially good membrane mimetic system for structural studies of membrane proteins. However, a detailed characterization of a spin-labeled membrane protein incorporated into lipodisq nanoparticles is still lacking. In this work, lipodisq nanoparticles were used as a membrane mimic system for probing the structural and dynamic properties of the integral membrane protein KCNE1 using site-directed spin labeling EPR spectroscopy. The characterization of spin-labeled KCNE1 incorporated into lipodisq nanoparticles was carried out using CW-EPR titration experiments for the EPR spectral line shape analysis and pulsed EPR titration experiment for the phase memory time (T m ) measurements. The CW-EPR titration experiment indicated an increase in spectral line broadening with the addition of the SMA polymer which approaches close to the rigid limit at a lipid to polymer weight ratio of 1:1, providing a clear solubilization of the protein-lipid complex. Similarly, the T m titration experiment indicated an increase in T m values with the addition of SMA polymer and approaches ∼2 μs at a lipid to polymer weight ratio of 1:2. Additionally, CW-EPR spectral line shape analysis was performed on six inside and six outside the membrane spin-label probes of KCNE1 in lipodisq nanoparticles. The results indicated significant differences in EPR spectral line broadening and a corresponding inverse central line width between spin-labeled KCNE1 residues located inside and outside of the membrane for lipodisq nanoparticle samples when compared to lipid vesicle samples. These results are consistent with the solution NMR structure of KCNE1. This study will be beneficial for researchers working on studying the structural and dynamic properties of membrane proteins.

Multi-site binding of epigallocatechin gallate to human serum albumin measured by NMR and isothermal titration calorimetry

PubMed Central

Eaton, Joshua D.

2017-01-01

The affinity of epigallocatechin gallate (EGCG) for human serum albumin (HSA) was measured in physiological conditions using NMR and isothermal titration calorimetry (ITC). NMR estimated the Ka (self-dissociation constant) of EGCG as 50 mM. NMR showed two binding events: strong (n1=1.8 ± 0.2; Kd1 =19 ± 12 μM) and weak (n2∼20; Kd2 =40 ± 20 mM). ITC also showed two binding events: strong (n1=2.5 ± 0.03; Kd1 =21.6 ± 4.0 μM) and weak (n2=9 ± 1; Kd2 =22 ± 4 mM). The two techniques are consistent, with an unexpectedly high number of bound EGCG. The strong binding is consistent with binding in the two Sudlow pockets. These results imply that almost all EGCG is transported in the blood bound to albumin and explains the wide tissue distribution and chemical stability of EGCG in vivo. PMID:28424370

Highly sensitive and selective detection of Al(III) ions in aqueous buffered solution with fluorescent peptide-based sensor.

PubMed

In, Byunggyu; Hwang, Gi Won; Lee, Keun-Hyeung

2016-09-15

A fluorescent sensor based on a tripeptide (SerGluGlu) with a dansyl fluorophore detected selectively Al(III) among 16 metal ions in aqueous buffered solutions without any organic cosolvent. The peptide-based sensor showed a highly sensitive turn on response to aluminium ion with high binding affinity (1.84×10(4)M(-1)) in aqueous buffered solutions. The detection limit (230nM, 5.98ppb) of the peptide-based sensor was much lower than the maximum allowable level (7.41μM) of aluminium ions in drinking water demanded by EPA. The binding mode of the peptide sensor with aluminium ions was characterized using ESI mass spectrometry, NMR titration, and pH titration experiments. Copyright © 2016 Elsevier Ltd. All rights reserved.

Blocking the Interactions between Calcium-Bound S100A12 Protein and the V Domain of RAGE Using Tranilast

PubMed Central

Chiou, Jian Wei; Fu, Brian

2016-01-01

The receptor for advanced glycation end products (RAGE), a transmembrane receptor in the immunoglobulin superfamily, is involved in several inflammatory processes. RAGE induces cellular signaling pathways upon binding with various ligands, such as advanced glycation end products (AGEs), β-amyloids, and S100 proteins. The solution structure of S100A12 and the V ligand-binding region of RAGE have been reported previously. Using heteronuclear NMR spectroscopy to conduct 1H–15N heteronuclear single quantum coherence (HSQC) titration experiments, we identified and mapped the binding interface between S100A12 and the V domain of RAGE. The NMR chemical shift data were used as the constraints for the High Ambiguity Driven biomolecular DOCKing (HADDOCK) calculation to generate a structural model of the S100A12–V domain complex. In addition, tranilast (an anti-allergic drug) showed strong interaction with S100A12 in the 1H–15N HSQC titration, fluorescence experiments, and WST-1 assay. The results also indicated that tranilast was located at the binding site between S100A12 and the V domain, blocking interaction between these two proteins. Our results provide the mechanistic details for a structural model and reveal a potential precursor for an inhibitor for pro-inflammatory diseases, which could be useful for the development of new drugs. PMID:27598566

Manipulating Protein-Protein Interactions in Nonribosomal Peptide Synthetase Type II Peptidyl Carrier Proteins.

PubMed

Jaremko, Matt J; Lee, D John; Patel, Ashay; Winslow, Victoria; Opella, Stanley J; McCammon, J Andrew; Burkart, Michael D

2017-10-10

In an effort to elucidate and engineer interactions in type II nonribosomal peptide synthetases, we analyzed biomolecular recognition between the essential peptidyl carrier proteins and adenylation domains using nuclear magnetic resonance (NMR) spectroscopy, molecular dynamics, and mutational studies. Three peptidyl carrier proteins, PigG, PltL, and RedO, in addition to their cognate adenylation domains, PigI, PltF, and RedM, were investigated for their cross-species activity. Of the three peptidyl carrier proteins, only PigG showed substantial cross-pathway activity. Characterization of the novel NMR solution structure of holo-PigG and molecular dynamics simulations of holo-PltL and holo-PigG revealed differences in structures and dynamics of these carrier proteins. NMR titration experiments revealed perturbations of the chemical shifts of the loop 1 residues of these peptidyl carrier proteins upon their interaction with the adenylation domain. These experiments revealed a key region for the protein-protein interaction. Mutational studies supported the role of loop 1 in molecular recognition, as mutations to this region of the peptidyl carrier proteins significantly modulated their activities.

Phosphorus solubility of agricultural soils: a surface charge and phosphorus-31 NMR speciation study

USDA-ARS?s Scientific Manuscript database

We investigated ten soils from six states in United States to determine the relationship between potentiometric titration derived soil surface charge and Phosphorus-31 (P) nuclear magnetic resonance (NMR) speciation with the concentration of water-extractable P (WEP). The surface charge value at the...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Topping, R.J.; Stone, M.P.; Brush, C.K.

The {sup 1}H NMR spectrum of the tetradeoxynucleotide d(TpCpGpA) was examined as a function of temperature, pH, and concentration. At pH 7 and above the solution conformation for this oligodeoxynucleotide appears to be a mixture of random coil and Watson-Crick duplex. At 25{degree}C, a pH titration of d(TpCpGaA) shown that distinct conformational changes occur as the pH is lowered below 7.0. These conformational changes are reversible upon readjusting the pH to neutrality, indicating the presence of a pH-dependent set of conformational equilibria. At 25{degree}C, the various conformational state in the mixture are in rapid exchange on the NMR time scale.more » Examination of the titration curve shown the presence of distinct conformational states at pH greater than 7, and between pH 4 and pH 5. When the pH titration is repeated at 5{degree}C, the conformational equilibria are in slow exchange on the NMR time scale; distinct signals from each conformational state are observable. The stable conformational state present between pH 4 and pH 5 represents an ordered conformation of d(TpCpGpA) which dissociates to a less ordered structure upon raising the temperature. The ordered conformation differs from the Watson-Crick helix, as is shown from nuclear Overhauser enhancement experiments, as well as chemical shift data. These results indicate that their ordered conformation is similar to the conformation of d(TpCpGpA) observed between pH 4 and pH 5. In the present case it is likely that stabilization of an ordered duplex conformation for d(TpCpGpA) is achieved by protonation of cytosine. A possible model which could explain the data involves formation of Hoogsteen C{sup +}:G base pairs.« less

A Colorimetric and Luminescent Dual-Modal Assay for Cu(II) Ion Detection Using an Iridium(III) Complex

PubMed Central

Ma, Dik-Lung; He, Hong-Zhang; Chan, Daniel Shiu-Hin; Wong, Chun-Yuen; Leung, Chung-Hang

2014-01-01

A novel iridium(III) complex-based chemosensor bearing the 5,6-bis(salicylideneimino)-1,10-phenanthroline ligand receptor was developed, which exhibited a highly sensitive and selective color change from colorless to yellow and a visible turn-off luminescence response upon the addition of Cu(II) ions. The interactions of this iridium(III) complex with Cu2+ ions and thirteen other cations have been investigated by UV-Vis absorption titration, emission titration, and 1H NMR titration. PMID:24927177

Entire-Dataset Analysis of NMR Fast-Exchange Titration Spectra: A Mg2+ Titration Analysis for HIV-1 Ribonuclease H Domain.

PubMed

Karki, Ichhuk; Christen, Martin T; Spiriti, Justin; Slack, Ryan L; Oda, Masayuki; Kanaori, Kenji; Zuckerman, Daniel M; Ishima, Rieko

2016-12-15

This article communicates our study to elucidate the molecular determinants of weak Mg 2+ interaction with the ribonuclease H (RNH) domain of HIV-1 reverse transcriptase in solution. As the interaction is weak (a ligand-dissociation constant >1 mM), nonspecific Mg 2+ interaction with the protein or interaction of the protein with other solutes that are present in the buffer solution can confound the observed Mg 2+ -titration data. To investigate these indirect effects, we monitored changes in the chemical shifts of backbone amides of RNH by recording NMR 1 H- 15 N heteronuclear single-quantum coherence spectra upon titration of Mg 2+ into an RNH solution. We performed the titration under three different conditions: (1) in the absence of NaCl, (2) in the presence of 50 mM NaCl, and (3) at a constant 160 mM Cl - concentration. Careful analysis of these three sets of titration data, along with molecular dynamics simulation data of RNH with Na + and Cl - ions, demonstrates two characteristic phenomena distinct from the specific Mg 2+ interaction with the active site: (1) weak interaction of Mg 2+ , as a salt, with the substrate-handle region of the protein and (2) overall apparent lower Mg 2+ affinity in the absence of NaCl compared to that in the presence of 50 mM NaCl. A possible explanation may be that the titrated MgCl 2 is consumed as a salt and interacts with RNH in the absence of NaCl. In addition, our data suggest that Na + increases the kinetic rate of the specific Mg 2+ interaction at the active site of RNH. Taken together, our study provides biophysical insight into the mechanism of weak metal interaction on a protein.

Chemical Characterization and Water Content Determination of Bio-Oils Obtained from Various Biomass Species using 31P NMR Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

David, K.; Ben, H.; Muzzy, J.

2012-03-01

Pyrolysis is a promising approach to utilize biomass for biofuels. One of the key challenges for this conversion is how to analyze complicated components in the pyrolysis oils. Water contents of pyrolysis oils are normally analyzed by Karl Fischer titration. The use of 2-chloro-4,4,5,5,-tetramethyl-1,3,2-dioxaphospholane followed by {sup 31}P NMR analysis has been used to quantitatively analyze the structure of hydroxyl groups in lignin and whole biomass. Results: {sup 31}P NMR analysis of pyrolysis oils is a novel technique to simultaneously characterize components and analyze water contents in pyrolysis oils produced from various biomasses. The water contents of various pyrolysis oilsmore » range from 16 to 40 wt%. The pyrolysis oils obtained from Loblolly pine had higher guaiacyl content, while that from oak had a higher syringyl content. Conclusion: The comparison with Karl Fischer titration shows that {sup 31}P NMR could also reliably be used to measure the water content of pyrolysis oils. Simultaneously with analysis of water content, quantitative characterization of hydroxyl groups, including aliphatic, C-5 substituted/syringyl, guaiacyl, p-hydroxyl phenyl and carboxylic hydroxyl groups, could also be provided by {sup 31}P NMR analysis.« less

Thermodynamics of Host–Guest Interactions between Fullerenes and a Buckycatcher

PubMed Central

2015-01-01

1H NMR and isothermal titration calorimetry (ITC) experiments were employed to obtain reliable thermodynamic data for the formation of the 1:1 inclusion complexes of fullerenes C60 and C70 with the buckycatcher (C60H28). NMR measurements were done in toluene-d8 and chlorobenzene-d5 at 288, 298, and 308 K, while the ITC titrations were performed in toluene, chlorobenzene, o-dichlorobenzene, anisole, and 1,1,2,2-tetrachloroethane at temperatures from 278 to 323 K. The association constants, Ka, obtained with both techniques are in very good agreement. The thermodynamic data obtained by ITC indicate that generally the host–guest association is enthalpy-driven. Interestingly, the entropy contributions are, with rare exceptions, slightly stabilizing or close to zero. Neither ΔH nor ΔS is constant over the temperature range studied, and these thermodynamic functions exhibit classical enthalpy/entropy compensation. The ΔCp values calculated from the temperature dependence of the calorimetric ΔH values are negative for the association of both fullerenes with the buckycatcher in toluene. The negative ΔCp values are consistent with some desolvation of the host-cavity and the guest in the inclusion complexes, C60@C60H28 and C70@C60H28. PMID:25248285

Exploring the palladium- and platinum-bis(pyridine) complex motif by NMR spectroscopy, X-ray crystallography, (tandem) mass spectrometry, and isothermal titration calorimetry: do substituent effects follow chemical intuition?

PubMed

Weilandt, Torsten; Löw, Nora L; Schnakenburg, Gregor; Daniels, Jörg; Nieger, Martin; Schalley, Christoph A; Lützen, Arne

2012-12-21

A series of ten palladium-bis(pyridine) complexes, as well as their corresponding platinum complexes, have been synthesized. The pyridine ligands in each series carried different σ-donor and/or π-acceptor/donor substituents at the para-position of their pyridine rings. These complexes were analysed by NMR spectroscopy, X-ray crystallography, (tandem) MS, and isothermal titration calorimetry (ITC) to validate whether these methods allowed us to obtain a concise and systematic picture of the relative and absolute thermodynamic stabilities of the complexes, as determined by the electronic effects of the substituents. Interestingly, the NMR spectroscopic data hardly correlated with the expected substituent effects but the heteronuclear platinum-phosphorus coupling constants did. Crystallographic data were found to be blurred by packing effects. Instead, tandem MS and ITC data were in line with each other and followed the expected trends. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Thermodynamic and NMR Studies of Solvent Effect on Enantiomeric Recognition for a Chiral Organiz Ammonium Cation by Chiral Diketopyridino-18- Crown-6 Type Ligands at 25.0 deg C.

DTIC Science & Technology

1994-05-11

analyses, 1H NM&, and JR specPit oscopy. The purities were also determined quantitatively by a thermometric titration technique. 19 By titrting...enantiomers of NapEt with 18- crown-6 (SIGMA Chemical Company, its purity was 99.5% as determined by therm--ometric titration agtains a standard NaBr...isoperibol titration calorimetry at 25.0 - 0.1oC in CACi6CHOH solvent mixtures. The initial solution volume in the dewar was 20 mL Tne calorimeter (wac

Binding Isotherms and Time Courses Readily from Magnetic Resonance.

PubMed

Xu, Jia; Van Doren, Steven R

2016-08-16

Evidence is presented that binding isotherms, simple or biphasic, can be extracted directly from noninterpreted, complex 2D NMR spectra using principal component analysis (PCA) to reveal the largest trend(s) across the series. This approach renders peak picking unnecessary for tracking population changes. In 1:1 binding, the first principal component captures the binding isotherm from NMR-detected titrations in fast, slow, and even intermediate and mixed exchange regimes, as illustrated for phospholigand associations with proteins. Although the sigmoidal shifts and line broadening of intermediate exchange distorts binding isotherms constructed conventionally, applying PCA directly to these spectra along with Pareto scaling overcomes the distortion. Applying PCA to time-domain NMR data also yields binding isotherms from titrations in fast or slow exchange. The algorithm readily extracts from magnetic resonance imaging movie time courses such as breathing and heart rate in chest imaging. Similarly, two-step binding processes detected by NMR are easily captured by principal components 1 and 2. PCA obviates the customary focus on specific peaks or regions of images. Applying it directly to a series of complex data will easily delineate binding isotherms, equilibrium shifts, and time courses of reactions or fluctuations.

Conformational heterogeneity in the Hsp70 chaperone-substrate ensemble identified from analysis of NMR-detected titration data.

PubMed

Sekhar, Ashok; Nagesh, Jayashree; Rosenzweig, Rina; Kay, Lewis E

2017-11-01

The Hsp70 chaperone system plays a critical role in cellular homeostasis by binding to client protein molecules. We have recently shown by methyl-TROSY NMR methods that the Escherichia coli Hsp70, DnaK, can form multiple bound complexes with a small client protein, hTRF1. In an effort to characterize the interactions further we report here the results of an NMR-based titration study of hTRF1 and DnaK, where both molecular components are monitored simultaneously, leading to a binding model. A central finding is the formation of a previously undetected 3:1 hTRF1-DnaK complex, suggesting that under heat shock conditions, DnaK might be able to protect cytosolic proteins whose net concentrations would exceed that of the chaperone. Moreover, these results provide new insight into the heterogeneous ensemble of complexes formed by DnaK chaperones and further emphasize the unique role of NMR spectroscopy in obtaining information about individual events in a complex binding scheme by exploiting a large number of probes that report uniquely on distinct binding processes. © 2017 The Protein Society.

Measuring molecular parity nonconservation using nuclear-magnetic-resonance spectroscopy

DOE PAGES

Eills, J.; Blanchard, J. W.; Bougas, L.; ...

2017-10-30

Here, the weak interaction does not conserve parity and therefore induces energy shifts in chiral enantiomers that should in principle be detectable in molecular spectra. Unfortunately, the magnitude of the expected shifts are small and in spectra of a mixture of enantiomers, the energy shifts are not resolvable. We propose a nuclear-magnetic-resonance (NMR) experiment in which we titrate the chirality (enantiomeric excess) of a solvent and measure the diasteriomeric splitting in the spectra of a chiral solute in order to search for an anomalous offset due to parity nonconservation (PNC). We present a proof-of-principle experiment in which we search formore » PNC in the 13C resonances of small molecules, and use the 1H resonances, which are insensitive to PNC, as an internal reference. We set a constraint on molecular PNC in 13C chemical shifts at a level of 10 –5 ppm, and provide a discussion of important considerations in the search for molecular PNC using NMR spectroscopy.« less

Measuring molecular parity nonconservation using nuclear-magnetic-resonance spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eills, J.; Blanchard, J. W.; Bougas, L.

Here, the weak interaction does not conserve parity and therefore induces energy shifts in chiral enantiomers that should in principle be detectable in molecular spectra. Unfortunately, the magnitude of the expected shifts are small and in spectra of a mixture of enantiomers, the energy shifts are not resolvable. We propose a nuclear-magnetic-resonance (NMR) experiment in which we titrate the chirality (enantiomeric excess) of a solvent and measure the diasteriomeric splitting in the spectra of a chiral solute in order to search for an anomalous offset due to parity nonconservation (PNC). We present a proof-of-principle experiment in which we search formore » PNC in the 13C resonances of small molecules, and use the 1H resonances, which are insensitive to PNC, as an internal reference. We set a constraint on molecular PNC in 13C chemical shifts at a level of 10 –5 ppm, and provide a discussion of important considerations in the search for molecular PNC using NMR spectroscopy.« less

Flow-through lipid nanotube arrays for structure-function studies of membrane proteins by solid-state NMR spectroscopy.

PubMed

Chekmenev, Eduard Y; Gor'kov, Peter L; Cross, Timothy A; Alaouie, Ali M; Smirnov, Alex I

2006-10-15

A novel method for studying membrane proteins in a native lipid bilayer environment by solid-state NMR spectroscopy is described and tested. Anodic aluminum oxide (AAO) substrates with flow-through 175 nm wide and 60-mum-long nanopores were employed to form macroscopically aligned peptide-containing lipid bilayers that are fluid and highly hydrated. We demonstrate that the surfaces of both leaflets of such bilayers are fully accessible to aqueous solutes. Thus, high hydration levels as well as pH and desirable ion and/or drug concentrations could be easily maintained and modified as desired in a series of experiments with the same sample. The method allows for membrane protein NMR experiments in a broad pH range that could be extended to as low as 1 and as high as 12 units for a period of up to a few hours and temperatures as high as 70 degrees C without losing the lipid alignment or bilayers from the nanopores. We demonstrate the utility of this method by a solid-state 19.6 T (17)O NMR study of reversible binding effects of mono- and divalent ions on the chemical shift properties of the Leu(10) carbonyl oxygen of transmembrane pore-forming peptide gramicidin A (gA). We further compare the (17)O shifts induced by binding metal ions to the binding of protons in the pH range from 1 to 12 and find a significant difference. This unexpected result points to a difference in mechanisms for ion and proton conduction by the gA pore. We believe that a large number of solid-state NMR-based studies, including structure-function, drug screening, proton exchange, pH, and other titration experiments, will benefit significantly from the method described here.

Characterization and quantification of N-(3-aminopropyl)-N-dodecyl-1,3-propanediamine biocide by NMR, HPLC/MS and titration techniques.

PubMed

Mondin, Andrea; Bogialli, Sara; Venzo, Alfonso; Favaro, Gabriella; Badocco, Denis; Pastore, Paolo

2014-01-01

The present paper reports the determination of the tri-amine N-(3-aminopropyl)-N-dodecyl-1,3-propanediamine (TA) present in a raw material called LONZABAC used to formulate various, widely used commercial biocides. The active principle, TA, is present in LONZABAC together with other molecules at lower concentration levels. Three independent analytical approaches, namely solution NMR spectroscopy, liquid chromatography coupled to high resolution mass spectrometry (LC/HRMS) and acid-base titration in mixed solvent, were used to overcome the problem of the non-availability of the active principle as high purity standard. NMR analysis of raw material, using a suitable internal standard, evidenced in all analyzed lots the presence of the active principle, the N-dodecyl-1,3-propanediamine (DA) and the n-dodecylamine (MA) and the absence of non-organic, NMR-inactive species. NMR peak integration led to a rough composition of the MA:DA:TA as 1:9:90. The LC/HRMS analysis allowed the accurate determination of DA and MA and confirmed in all samples the presence of the TA, which was estimated by difference: MA=1.4±0.3%, DA=11.1±0.7%, TA=87.5±1.3%. The obtained results were used to setup an easy, rapid and cheap acid-base titration method able to furnish a sufficiently accurate evaluation of the active principle both in the raw material and in diluted commercial products. For the raw material the results were: TA+MA=91.1±0.8% and DA-MA=8.9±0.8%, statistically coherent with LC/MS ones. The LC/MS approach demonstrated also its great potentialities to recognize trace of the biocide components both in environmental samples and in the formulated commercial products. Copyright © 2013 Elsevier Ltd. All rights reserved.

Resorcarene-based receptor: versatile behavior in its interaction with heavy and soft metal cations.

PubMed

Danil de Namor, Angela F; Chaaban, Jinane K; Piro, Oscar E; Castellano, Eduardo E

2006-02-09

Standard solution Gibbs energies, DeltasG degrees, of the resorcarene-based receptor 5,11,17,23-ethylthiomethylated calix[4]resorcarene, (characterized by 1H NMR and X-ray diffraction studies) in its monomeric state (established through partition experiments) in various solvents are for the first time reported in the area of resorcarene chemistry. Transfer Gibbs energies of from hexane (reference solvent) to other medium are calculated. Agreement between DeltatG degrees (referred to the pure solvents) and standard partition Gibbs energies, DeltapG degrees (solvent mutually saturated) is found. Cation-ligand interactions were investigated through 1H NMR (CD3CN and CD3OD) and conductometric titrations in acetonitrile and methanol. 1H NMR data revealed the sites of interaction of with the metal cation. The composition of the metal-ion complexes (Ag+ and Pb2+ in acetonitrile and Ag+ and Cu2+ in methanol) was established through conductometric titrations. Thus, complexes of 1:1 stoichiometry were formed between and Ag+ and Pb2+ in acetonitrile and Cu2+ in methanol. However, in moving from acetonitrile to methanol, the composition of the silver complex was altered. Thus, two metal cations are hosted by a unit of the ligand. As far as Cu2+ and in acetonitrile is concerned, conductance data suggest that metalates are formed in which up to four units of Cu2+ are taken up per unit of resorcarene. The contrasting behavior of with Cu2+ in acetonitrile relative to methanol is discussed. As far as mercury (II) is concerned, the unusual jump in conductance observed in the titration of Hg2+ with in acetonitrile and methanol after the formation of a multicharged complex (undefined composition) is attributed to the presence of highly charged smaller units (higher mobility) resulting from the departure of pendant arms from the resorcarene backbone. Isolation of these species followed by X-ray diffraction studies corroborated this statement. The thermodynamic characterization of metal-ion complexes of Ag+ and Pb2+ in acetonitrile and Cu2+ and Ag+ in methanol is reported. Final conclusions are given.

Identification of critical residues of subunit H in its interaction with subunit E of the A-ATP synthase from Methanocaldococcus jannaschii.

PubMed

Gayen, Shovanlal; Balakrishna, Asha M; Biuković, Goran; Yulei, Wu; Hunke, Cornelia; Grüber, Gerhard

2008-04-01

The boomerang-like H subunit of A(1)A(0) ATP synthase forms one of the peripheral stalks connecting the A(1) and A(0) sections. Structural analyses of the N-terminal part (H1-47) of subunit H of the A(1)A(0) ATP synthase from Methanocaldococcus jannaschii have been performed by NMR spectroscopy. Our initial NMR structural calculations for H1-47 indicate that amino acid residues 7-44 fold into a single alpha-helical structure. Using the purified N- (E1-100) and C-terminal domains (E101-206) of subunit E, NMR titration experiments revealed that the N-terminal residues Met1-6, Lys10, Glu11, Ala15, Val20 and Glu24 of H1-47 interact specifically with the N-terminal domain E1-100 of subunit E. A more detailed picture regarding the residues of E1-100 involved in this association was obtained by titration studies using the N-terminal peptides E1-20, E21-40 and E41-60. These data indicate that the N-terminal tail E41-60 interacts with the N-terminal amino acids of H1-47, and this has been confirmed by fluorescence correlation spectroscopy results. Analysis of (1)H-(15)N heteronuclear single quantum coherence (HSQC) spectra of the central stalk subunit F in the presence and absence of E101-206 show no obvious interaction between the C-terminal domain of E and subunit F. The data presented provide, for the first time, structural insights into the interaction of subunits E and H, and their arrangement within A(1)A(0) ATP synthase.

The interaction of ammonia and xenon with the imidazole glycerol phosphate synthase from Thermotoga maritima as detected by NMR spectroscopy

PubMed Central

Liebold, Christoph; List, Felix; Kalbitzer, Hans Robert; Sterner, Reinhard; Brunner, Eike

2010-01-01

The imidazole glycerol phosphate (ImGP) synthase from the hyperthermophilic bacterium Thermotoga maritima is a 1:1 complex of the glutaminase subunit HisH and the cyclase subunit HisF. It has been proposed that ammonia generated by HisH is transported through a channel to the active site of HisF, which generates intermediates of histidine (ImGP) and de novo biosynthesis of 5-aminoimidazole-4-carboxamideribotide. Solution NMR spectroscopy of ammonium chloride-titrated samples was used to study the interaction of NH3 with amino acids inside this channel. Although numerous residues showed 15N chemical shift changes, most of these changes were caused by nonspecific ionic strength effects. However, several interactions appeared to be specific. Remarkably, the amino acid residue Thr 78—which is located in the central channel—shows a large chemical shift change upon titration with ammonium chloride. This result and the reduced catalytic activity of the Thr78Met mutant indicate a special role of this residue in ammonia channeling. To detect and further characterize internal cavities in HisF, which might for example contribute to ammonia channeling, the interaction of HisF with the noble gas xenon was analyzed by solution NMR spectroscopy using 1H-15N HSQC experiments. The results indicate that HisF contains three distinct internal cavities, which could be identified by xenon-induced chemical shift changes of the neighboring amino acid residues. Two of these cavities are located at the active site at opposite ends of the substrate N′-[(5′-phosphoribulosyl)formimino]-5-aminoimidazole-4-carboxamide-ribonucleotide (PRFAR) binding groove. The third cavity is located in the interior of the central β-barrel of HisF and overlaps with the putative ammonia transport channel. PMID:20665694

Synthesis and binding properties of arylethyne-linked porphyrin-zinc complexes for organic electronics applications.

PubMed

Reainthippayasakul, W; Paosawatyanyong, B; Bhanthumnavin, W

2013-05-01

Conjugated meso-alkynyl 5,15-dimesitylporphyrin metal complexes have been synthesized by Sonogashira coupling reaction in good yields. Alkynyl groups were chosen as a link at the meso positions in order to extend the pi-conjugated length of porphyrin rings. These synthesized porphyrin derivatives were characterized by 1H NMR spectroscopy and MALDI-TOF mass spectrometry. Moreover, UV-visible spectroscopy and fluorescence spectroscopy were also used to investigate their photophysical properties. It has been demonstrated that central metal ions as well as meso substituents on porphyrin rings affected the electronic absorption and emission spectra of the compounds. Spectroscopic results revealed that alkyne-linked porphyrin metal complexes showed higher pi-conjugation compared with porphyrin building blocks resulting in red shifts in both absorption and emission spectra. Coordination properties of synthesized porphyrins were preliminarily investigated by UV-visible absorption and fluorescence emission spectroscopic titration with pyridine as axial ligand. The formation of porphyrin-pyridine complexes resulted in significant red shifts in absorption spectra and decrease of fluorescence intensity in emission spectra. Moreover, the 1H NMR titration experiments suggested that central metal ions play an important role to coordinate with pyridine and the coordination of porphyrin zinc(II) complex with pyridine occur in a 1:1 ratio. From these spectroscopic results, alkyne-linked porphyrin metal complexes offer potential applications as materials for optical organic nanosensors.

Triprotic site-specific acid-base equilibria and related properties of fluoroquinolone antibacterials.

PubMed

Rusu, Aura; Tóth, Gergő; Szőcs, Levente; Kökösi, József; Kraszni, Márta; Gyéresi, Árpád; Noszál, Béla

2012-07-01

The complete macro- and microequilibrium analyses of six fluoroquinolone drugs - ciprofloxacin, enrofloxacin, norfloxacin, pefloxacin, ofloxacin and moxifloxacin - are presented. Previous controversial literature data are straightened up, the protonation centers are unambiguously identified, and the protonation macro- and microconstant values are reported. The macroconstants were determined by (1)H NMR-pH titrations while the microconstants were determined by a multi-modal spectroscopic-deductive methodology, in which methyl ester derivatives were synthesized and their NMR-pH titration data contributed to the evaluation of all the microconstants. The full (1)H, (13)C and (15)N NMR assignments, NMR-pH profiles, macro- and microprotonation schemes and species-specific diagrams are included. Our studies show that the fluoroquinolones have three protonation centers: the carboxylate group, the N-1' and N-4' piperazine nitrogens and concentration of the uncharged microspecies is way below the values published earlier. The results could be well interpreted in terms of structural properties. The protonation macro- and microconstant values allow the pre-planned method development in techniques such as capillary zone electrophoresis and also, the interpretation of fluoroquinolone mechanism of biological action, including the pharmacokinetic properties, and antibacterial activities that are all heavily influenced by the states of protonation. Copyright © 2012 Elsevier B.V. All rights reserved.

Selective Nitrate Recognition by a Halogen‐Bonding Four‐Station [3]Rotaxane Molecular Shuttle

PubMed Central

Barendt, Timothy A.; Docker, Andrew; Marques, Igor; Félix, Vítor

2016-01-01

Abstract The synthesis of the first halogen bonding [3]rotaxane host system containing a bis‐iodo triazolium‐bis‐naphthalene diimide four station axle component is reported. Proton NMR anion binding titration experiments revealed the halogen bonding rotaxane is selective for nitrate over the more basic acetate, hydrogen carbonate and dihydrogen phosphate oxoanions and chloride, and exhibits enhanced recognition of anions relative to a hydrogen bonding analogue. This elaborate interlocked anion receptor functions via a novel dynamic pincer mechanism where upon nitrate anion binding, both macrocycles shuttle from the naphthalene diimide stations at the periphery of the axle to the central halogen bonding iodo‐triazolium station anion recognition sites to form a unique 1:1 stoichiometric nitrate anion–rotaxane sandwich complex. Molecular dynamics simulations carried out on the nitrate and chloride halogen bonding [3]rotaxane complexes corroborate the 1H NMR anion binding results. PMID:27436297

A colorimetric and ratiometric fluorescent chemosensor for fluoride based on proton transfer.

PubMed

Jia, Chuandong; Wu, Biao; Liang, Jianjun; Huang, Xiaojuan; Yang, Xiao-Juan

2010-01-01

N-Phenyl-N'-(3-quinolinyl)urea (1) has been developed as a highly selective colorimetric and ratiometric fluorescent chemosensor for fluoride ion based on a proton transfer mechanism. Evidences for the mechanism were provided by UV-vis and fluorescence titration and especially (1)H and (19)F NMR experiments. The sensor gave the largest ratiometric fluorescent response reported so far (R(max)/R(min) = 2620) to fluoride. Taking H(+) as the "recovering reagent", the sensor can be reversibly "used" and "recovered" for several cycles with only a slight decay of the response ability.

A highly selective and sensitive fluorescent chemosensor and its application for rapid on-site detection of Al3 +

NASA Astrophysics Data System (ADS)

Yue, Xiao-li; Wang, Zhao-qing; Li, Chao-rui; Yang, Zheng-yin

2018-03-01

In this paper, a simple naphthalene-based derivative (HL) has been designed and synthesized as a Al3 +-selective fluorescent chemosensor based on the PET mechanism. HL exhibited high selectivity and sensitivity towards Al3 + over other commonly coexisting metal ions in ethanol with a detection limit of 2.72 nM. The 1:1 binding stoichiometry of the complex (HL-Al3 +) was determined from the Job's plot based on fluorescence titrations and the ESI-MS spectrum data. Moreover, the binding site of HL with Al3 + was assured by the 1H NMR titration experiment. The binding constant (Ka) of the complex (HL-Al3 +) was calculated to be 5.06 × 104 M- 1 according to the Benesi-Hildebrand equation. In addition, the recognizing process of HL towards Al3 + was chemically reversible by adding Na2EDTA. Importantly, HL could directly and rapidly detect aluminum ion through the filter paper without resorting to additional instrumental analysis.

Novel water soluble morpholine substituted Zn(II) phthalocyanine: Synthesis, characterization, DNA/BSA binding, DNA photocleavage and topoisomerase I inhibition.

PubMed

Barut, Burak; Demirbaş, Ümit; Özel, Arzu; Kantekin, Halit

2017-12-01

In this study, novel peripherally tetra 3-morpholinophenol substituted zinc(II) phthalocyanine (4) and its water soluble form quaternized zinc(II) phthalocyanine (ZnQ) were synthesized for the first time. These novel compounds were characterized by a combination of different spectroscopic techniques such as FT-IR, 1 H NMR, 13 C NMR, UV-vis and mass. The DNA binding of ZnQ was investigated using UV-vis absorption titration, competitive ethidium bromide, thermal denaturation and viscosity experiments that the ZnQ bound to CT-DNA via intercalation mode. ZnQ indicated photocleavage activity on supercoiled pBR322 plasmid DNA via formation of singlet oxygen under irradiation at 700nm. Besides, the topoisomerase I inhibitory effect experiments showed that ZnQ inhibited topoisomerase I enzyme in a concentration-dependent manner. The bovine serum albumin (BSA) binding experiments indicated that ZnQ bound to proteins through a static quenching mechanism. All of these results claim that ZnQ has potential agent for photodynamic therapy owing to its nucleic acid interactions and photobiological or photochemical properties. Copyright © 2017 Elsevier B.V. All rights reserved.

Structural basis of sodium–potassium exchange of a human telomeric DNA quadruplex without topological conversion

PubMed Central

Wang, Zi-Fu; Li, Ming-Hao; Hsu, Shang-Te Danny; Chang, Ta-Chau

2014-01-01

Understanding the mechanism of Na+/K+-dependent spectral conversion of human telomeric G-quadruplex (G4) sequences has been limited not only because of the structural polymorphism but also the lack of sufficient structural information at different stages along the conversion process for one given oligonucleotide. In this work, we have determined the topology of the Na+ form of Tel23 G4, which is the same hybrid form as the K+ form of Tel23 G4 despite the distinct spectral patterns in their respective nuclear magnetic resonance (NMR) and circular dichroism spectra. The spectral difference, particularly the well-resolved imino proton NMR signals, allows us to monitor the structural conversion from Na+ form to K+ form during Na+/K+ exchange. Time-resolved NMR experiments of hydrogen–deuterium exchange and hybridization clearly exclude involvement of the global unfolding for the fast Na+/K+ spectral conversion. In addition, the K+ titration monitored by NMR reveals that the Na+/K+ exchange in Tel23 G4 is a two-step process. The addition of K+ significantly stabilizes the unfolding kinetics of Tel23 G4. These results offer a possible explanation of rapid spectral conversion of Na+/K+ exchange and insight into the mechanism of Na+/K+ structural conversion in human telomeric G4s. PMID:24476914

Syntheses of amide based anion receptors and investigation of their associations with anions and their molecular structures using proton NMR titration and DFT methods

NASA Astrophysics Data System (ADS)

Navakhun, Korakot; Sawangsri, Ranu; Ruangpornvisuti, Vithaya

2014-03-01

The synthesized disubstituted isophthalamide and pyridine-2,6dicarboxamide derivatives of nine compounds were prepared. Their association constants with tetrabutylammonium fluoride (TBA·F), tetrabutylammonium chloride (TBA·Cl), tetrabutylammonium bromide (TBA·Br), tetrabutylammonium dihydrogenphosphate (TBA·H2PO4), tetrabutylammonium hydrogensulphate (TBA·HSO4) and tetrabutylammonium nitrate (TBA·NO3) were obtained by 1H NMR titration technique. The optimized structures of compounds 1-9 and their association with F-, Cl-, Br-, HPO4-, HSO4- and NO3- were obtained using the B3LYP/6-31+G(d) method. The most favorable complex of compound 3 with Br- was found. The high association constants of complexes 1-6 with F- are expected. Associations of all receptors with anions are exothermic and spontaneous reactions. Thermodynamic properties of all associations obtained using B3LYP/6-31+G(d) method are reported.

Tracking Equilibrium and Nonequilibrium Shifts in Data with TREND.

PubMed

Xu, Jia; Van Doren, Steven R

2017-01-24

Principal component analysis (PCA) discovers patterns in multivariate data that include spectra, microscopy, and other biophysical measurements. Direct application of PCA to crowded spectra, images, and movies (without selecting peaks or features) was shown recently to identify their equilibrium or temporal changes. To enable the community to utilize these capabilities with a wide range of measurements, we have developed multiplatform software named TREND to Track Equilibrium and Nonequilibrium population shifts among two-dimensional Data frames. TREND can also carry this out by independent component analysis. We highlight a few examples of finding concurrent processes. TREND extracts dual phases of binding to two sites directly from the NMR spectra of the titrations. In a cardiac movie from magnetic resonance imaging, TREND resolves principal components (PCs) representing breathing and the cardiac cycle. TREND can also reconstruct the series of measurements from selected PCs, as illustrated for a biphasic, NMR-detected titration and the cardiac MRI movie. Fidelity of reconstruction of series of NMR spectra or images requires more PCs than needed to plot the largest population shifts. TREND reads spectra from many spectroscopies in the most common formats (JCAMP-DX and NMR) and multiple movie formats. The TREND package thus provides convenient tools to resolve the processes recorded by diverse biophysical methods. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Characterization of aspartame-cyclodextrin complexation.

PubMed

Sohajda, Tamás; Béni, Szabolcs; Varga, Erzsébet; Iványi, Róbert; Rácz, Akos; Szente, Lajos; Noszál, Béla

2009-12-05

The inclusion complex formation of aspartame (guest) and various cyclodextrins (host) were examined using 1H NMR titration and capillary electrophoresis. Initially the protonation constants of aspartame were determined by NMR-pH titration with in situ pH measurement to yield log K1=7.83 and log K2=2.96. Based on these values the stability of the complexes formed by aspartame and 21 different cyclodextrins (CDs) were studied at pH 2.5, pH 5.2 and pH 9.0 values where aspartame exists predominantly in monocationic, zwitterionic and monoanionic form, respectively. The host cyclodextrin derivatives differed in various sidechains, degree of substitution, charge and purity so that the effect of these properties could be examined systematically. Concerning size, the seven-membered beta-cyclodextrin and its derivatives have been found to be the most suitable host molecules for complexation. Highest stability was observed for the acetylated derivative with a degree of substitution of 7. The purity of the CD enhanced the complexation while the degree of substitution did not provide obvious consequences. Finally, geometric aspects of the inclusion complex were assessed by 2D ROESY NMR and molecular modelling which proved that the guest's aromatic ring enters the wider end of the host cavity.

Solution structures and backbone dynamics of Escherichia coli rhodanese PspE in its sulfur-free and persulfide-intermediate forms: implications for the catalytic mechanism of rhodanese.

PubMed

Li, Hongwei; Yang, Fan; Kang, Xue; Xia, Bin; Jin, Changwen

2008-04-15

Rhodanese catalyzes the sulfur-transfer reaction that transfers sulfur from thiosulfate to cyanide by a double-displacement mechanism, in which an active cysteine residue plays a central role. Previous studies indicated that the phage-shock protein E (PspE) from Escherichia coli is a rhodanese composed of a single active domain and is the only accessible rhodanese among the three single-domain rhodaneses in E. coli. To understand the catalytic mechanism of rhodanese at the molecular level, we determined the solution structures of the sulfur-free and persulfide-intermediate forms of PspE by nuclear magnetic resonance (NMR) spectroscopy and identified the active site by NMR titration experiments. To obtain further insights into the catalytic mechanism, we studied backbone dynamics by NMR relaxation experiments. Our results demonstrated that the overall structures in both sulfur-free and persulfide-intermediate forms are highly similar, suggesting that no significant conformational changes occurred during the catalytic reaction. However, the backbone dynamics revealed that the motional properties of PspE in its sulfur-free form are different from the persulfide-intermediate state. The conformational exchanges are largely enhanced in the persulfide-intermediate form of PspE, especially around the active site. The present structural and biochemical studies in combination with backbone dynamics provide further insights in understanding the catalytic mechanism of rhodanese.

Ligand binding to 2΄-deoxyguanosine sensing riboswitch in metabolic context

PubMed Central

Kim, Yong-Boum; Wacker, Anna; von Laer, Karl; Rogov, Vladimir V.; Suess, Beatrix

2017-01-01

Abstract The mfl-riboswitch is a transcriptional off-switch, which down-regulates expression of subunit β of ribonucleotide reductase in Mesoplasma florum upon 2΄-deoxyguanosine binding. We characterized binding of 2΄-deoxyguanosine to the mfl-aptamer domain (WT aptamer) and a sequence-stabilized aptamer (MT aptamer) under in vitro and ‘in-cell-like’ conditions by isothermal titration calorimetry (ITC) and nuclear magnetic resonance (NMR) spectroscopy. ‘In-cell-like’ environment was simulated by Bacillus subtilis cell extract, in which both aptamers remained sufficiently stable to detect the resonances of structural elements and ligand binding in 2D NMR experiments. Under ‘in-cell-like’-environment, (i) the WT aptamer bound the endogenous metabolite guanosine and (ii) 2΄-deoxyguanosine efficiently displaced guanosine from the WT aptamer. In contrast, MT aptamer exhibited moderate binding to 2΄-deoxyguanosine and weak binding to guanosine. NMR experiments indicated that binding of guanosine was not limited to the aptamer domain of the riboswitch but also the full-length mfl-riboswitch bound guanosine, impacting on the regulation efficiency of the riboswitch and hinting that, in addition to 2΄-deoxyguanosine, guanosine plays a role in riboswitch function in vivo. Reporter gene assays in B. subtilis demonstrated the regulation capacity of the WT aptamer, whereas the MT aptamer with lower affinity to 2΄-deoxyguanosine was not able to regulate gene expression. PMID:28115631

Two classes of cholesterol binding sites for the β2AR revealed by thermostability and NMR.

PubMed

Gater, Deborah L; Saurel, Olivier; Iordanov, Iordan; Liu, Wei; Cherezov, Vadim; Milon, Alain

2014-11-18

Cholesterol binding to G protein-coupled receptors (GPCRs) and modulation of their activities in membranes is a fundamental issue for understanding their function. Despite the identification of cholesterol binding sites in high-resolution x-ray structures of the ?2 adrenergic receptor (β2AR) and other GPCRs, the binding affinity of cholesterol for this receptor and exchange rates between the free and bound cholesterol remain unknown. In this study we report the existence of two classes of cholesterol binding sites in β2AR. By analyzing the β2AR unfolding temperature in lipidic cubic phase (LCP) as a function of cholesterol concentration we observed high-affinity cooperative binding of cholesterol with sub-nM affinity constant. In contrast, saturation transfer difference (STD) NMR experiments revealed the existence of a second class of cholesterol binding sites, in fast exchange on the STD NMR timescale. Titration of the STD signal as a function of cholesterol concentration provided a lower limit of 100 mM for their dissociation constant. However, these binding sites are specific for both cholesterol and β2AR, as shown with control experiments using ergosterol and a control membrane protein (KpOmpA). We postulate that this specificity is mediated by the high-affinity bound cholesterol molecules and propose the formation of transient cholesterol clusters around the high-affinity binding sites.

Biorelevant physicochemical profiling of (E)- and (Z)-resveratrol determined from isomeric mixtures.

PubMed

Orgován, Gábor; Gonda, Imre; Noszál, Béla

2017-05-10

Biorelevant, isomer-specific physicochemical parameters of resveratrol, a multifunctional component in red wines, with cardioprotective, anti-Alzheimer and several other pharmacologic activities were determined. The parameters include site-specific basicities, lipophilicities, solubilities and diffusion constants for the two geometric isomers. The protonation equilibria of (E)- and (Z)-resveratrol were monitored by 1 H NMR-pH titrations. Five closely related auxiliary compounds ((E)-pinostilbene, (Z)-pinostilbene, (E)-pterostilbene, (Z)-pterostilbene and resorcinol) were also studied. Combining the datasets, the group-specific protonation constants of resveratrol isomers were determined. The results show that (Z)-resveratrol is more basic at every protonation site than the (E)-isomer. Lipophilicities are quantified in terms of logP values and were determined by octanol/water partition experiments and quantitative NMR spectroscopy: (E)-resveratrol was found to be more lipophilic. Since the molecular geometries of the isomers differ, diffusion ordered NMR spectroscopy (DOSY) experiments were also carried out to quantify the diffusion capabilities of the isomers: (Z)-resveratrol of bent shape has a slightly higher diffusion coefficient than its extended (E) counterpart. A striking 10-fold difference of water solubility was found in favor of the (Z) isomer, due obviously to the reduced water-repellent character in the more compact molecule. This is so far the greatest recorded solubility difference between geometric isomers of any compounds. Copyright © 2016. Published by Elsevier B.V.

A sole multi-analyte receptor responds with three distinct fluorescence signals: traffic signal like sensing of Al(3+), Zn(2+) and F(-).

PubMed

Datta, Barun Kumar; Thiyagarajan, Durairaj; Ramesh, Aiyagari; Das, Gopal

2015-08-07

A dialdehyde-based multi-analyte sensor renders distinctive emission spectra for Al(3+), Zn(2+) and F(-) ions. The ligand exhibited different types of interactions with these three different ions resulting in the enhancement of fluorescence intensity at three different wavelengths. All the sensing processes were studied in detail by absorption spectroscopy, emission spectroscopy and (1)H-NMR titration experiment. The ligand has the working ability in a wide pH range including the physiological pH. The ligand is non-toxic and amicable for sensing intracellular Al(3+) and Zn(2+) in live HeLa cells.

NMR studies reveal the role of biomembranes in modulating ligand binding and release by intracellular bile acid binding proteins.

PubMed

Pedò, Massimo; Löhr, Frank; D'Onofrio, Mariapina; Assfalg, Michael; Dötsch, Volker; Molinari, Henriette

2009-12-18

Bile acid molecules are transferred vectorially between basolateral and apical membranes of hepatocytes and enterocytes in the context of the enterohepatic circulation, a process regulating whole body lipid homeostasis. This work addresses the role of the cytosolic lipid binding proteins in the intracellular transfer of bile acids between different membrane compartments. We present nuclear magnetic resonance (NMR) data describing the ternary system composed of the bile acid binding protein, bile acids, and membrane mimetic systems, such as anionic liposomes. This work provides evidence that the investigated liver bile acid binding protein undergoes association with the anionic membrane and binding-induced partial unfolding. The addition of the physiological ligand to the protein-liposome mixture is capable of modulating this interaction, shifting the equilibrium towards the free folded holo protein. An ensemble of NMR titration experiments, based on nitrogen-15 protein and ligand observation, confirm that the membrane and the ligand establish competing binding equilibria, modulating the cytoplasmic permeability of bile acids. These results support a mechanism of ligand binding and release controlled by the onset of a bile salt concentration gradient within the polarized cell. The location of a specific protein region interacting with liposomes is highlighted.

Selective Nitrate Recognition by a Halogen-Bonding Four-Station [3]Rotaxane Molecular Shuttle.

PubMed

Barendt, Timothy A; Docker, Andrew; Marques, Igor; Félix, Vítor; Beer, Paul D

2016-09-05

The synthesis of the first halogen bonding [3]rotaxane host system containing a bis-iodo triazolium-bis-naphthalene diimide four station axle component is reported. Proton NMR anion binding titration experiments revealed the halogen bonding rotaxane is selective for nitrate over the more basic acetate, hydrogen carbonate and dihydrogen phosphate oxoanions and chloride, and exhibits enhanced recognition of anions relative to a hydrogen bonding analogue. This elaborate interlocked anion receptor functions via a novel dynamic pincer mechanism where upon nitrate anion binding, both macrocycles shuttle from the naphthalene diimide stations at the periphery of the axle to the central halogen bonding iodo-triazolium station anion recognition sites to form a unique 1:1 stoichiometric nitrate anion-rotaxane sandwich complex. Molecular dynamics simulations carried out on the nitrate and chloride halogen bonding [3]rotaxane complexes corroborate the (1) H NMR anion binding results. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Nickel binding and [NiFe]-hydrogenase maturation by the metallochaperone SlyD with a single metal-binding site in Escherichia coli.

PubMed

Kaluarachchi, Harini; Altenstein, Matthias; Sugumar, Sonia R; Balbach, Jochen; Zamble, Deborah B; Haupt, Caroline

2012-03-16

SlyD (sensitive to lysis D) is a nickel metallochaperone involved in the maturation of [NiFe]-hydrogenases in Escherichia coli (E. coli) and specifically contributes to the nickel delivery step during enzyme biosynthesis. This protein contains a C-terminal metal-binding domain that is rich in potential metal-binding residues that enable SlyD to bind multiple nickel ions with high affinity. The SlyD homolog from Thermus thermophilus does not contain the extended cysteine- and histidine-rich C-terminal tail of the E. coli protein, yet it binds a single Ni(II) ion tightly. To investigate whether a single metal-binding motif can functionally replace the full-length domain, we generated a truncation of E. coli SlyD, SlyD155. Ni(II) binding to SlyD155 was investigated by using isothermal titration calorimetry, NMR and electrospray ionization mass spectrometry measurements. This in vitro characterization revealed that SlyD155 contains a single metal-binding motif with high affinity for nickel. Structural characterization by X-ray absorption spectroscopy and NMR indicated that nickel was coordinated in an octahedral geometry with at least two histidines as ligands. Heterodimerization between SlyD and another hydrogenase accessory protein, HypB, is essential for optimal hydrogenase maturation and was confirmed for SlyD155 via cross-linking experiments and NMR titrations, as were conserved chaperone and peptidyl-prolyl isomerase activities. Although these properties of SlyD are preserved in the truncated version, it does not modulate nickel binding to HypB in vitro or contribute to the maturation of [NiFe]-hydrogenases in vivo, unlike the full-length protein. This study highlights the importance of the unusual metal-binding domain of E. coli SlyD in hydrogenase biogenesis. Copyright © 2012 Elsevier Ltd. All rights reserved.

Ozone-induced changes in natural organic matter (NOM) structure

USGS Publications Warehouse

Westerhoff, P.; Debroux, J.; Aiken, G.; Amy, G.

1999-01-01

Hydrophobic organic acids (combined humic and fulvic acids), obtained from an Antarctic Lake with predominantly microbially derived organic carbon sources and two US fiver systems with terrestrial organic carbon sources, were ozonated. Several analyses, including 13C-NMR, UV absorbance, fluorescence, hydrophobic/transphilic classification, and potentiometric titrations, were performed before and after ozonation. Ozonation reduced aromatic carbon content, selectively reducing phenolic carbon content. Ozonation of the samples resulted in increased aliphatic, carboxyl, plus acetal and ketal anomeric carbon content and shifted towards less hydrophobic compounds.Hydrophobic organic acids (combined humic and fulvic acids), obtained from an Antarctic Lake with predominantly microbially derived organic carbon sources and two US river systems with terrestrial organic carbon sources, were ozonated. Several analyses, including 13C-NMR, UV absorbance, fluorescence, hydrophobic/transphilic classification, and potentiometric titrations, were performed before and after ozonation. Ozonation reduced aromatic carbon content, selectively reducing phenolic carbon content. Ozonation of the samples resulted in increased aliphatic, carboxyl, plus acetal and ketal anomeric carbon content and shifted towards less hydrophobic compounds.

Ratiometric sensing of fluoride and acetate anions based on a BODIPY-azaindole platform and its application to living cell imaging.

PubMed

Mahapatra, Ajit Kumar; Maji, Rajkishor; Maiti, Kalipada; Adhikari, Susanta Sekhar; Das Mukhopadhyay, Chitrangada; Mandal, Debasish

2014-01-07

A new BODIPY-azaindole based fluorescent sensor 1 was designed and synthesized as a new colorimetric and ratiometric fluorescent chemosensor for fluoride. The binding and sensing abilities of sensor 1 towards various anions were studied by absorption, emission and (1)H NMR titration spectroscopies. The spectral responses of 1 to fluoride in acetonitrile-water were studied: an approximately 69 nm red shift in absorption and ratiometric fluorescent response was observed. The striking light yellow to deep brown color change in ambient light and green to blue emission color change are thought to be due to the deprotonation of the indole moiety of the azaindole fluorophore. From the changes in the absorption, fluorescence, and (1)H NMR titration spectra, proton-transfer mechanisms were deduced. Density function theory and time-dependent density function theory calculations were conducted to rationalize the optical response of the sensor. Results were supported by confocal fluorescence imaging and MTT assay of live cells.

Chemical modeling of acid-base properties of soluble biopolymers derived from municipal waste treatment materials.

PubMed

Tabasso, Silvia; Berto, Silvia; Rosato, Roberta; Marinos, Janeth Alicia Tafur; Ginepro, Marco; Zelano, Vincenzo; Daniele, Pier Giuseppe; Montoneri, Enzo

2015-02-04

This work reports a study of the proton-binding capacity of biopolymers obtained from different materials supplied by a municipal biowaste treatment plant located in Northern Italy. One material was the anaerobic fermentation digestate of the urban wastes organic humid fraction. The others were the compost of home and public gardening residues and the compost of the mix of the above residues, digestate and sewage sludge. These materials were hydrolyzed under alkaline conditions to yield the biopolymers by saponification. The biopolymers were characterized by 13C NMR spectroscopy, elemental analysis and potentiometric titration. The titration data were elaborated to attain chemical models for interpretation of the proton-binding capacity of the biopolymers obtaining the acidic sites concentrations and their protonation constants. The results obtained with the models and by NMR spectroscopy were elaborated together in order to better characterize the nature of the macromolecules. The chemical nature of the biopolymers was found dependent upon the nature of the sourcing materials.

Chemical Modeling of Acid-Base Properties of Soluble Biopolymers Derived from Municipal Waste Treatment Materials

PubMed Central

Tabasso, Silvia; Berto, Silvia; Rosato, Roberta; Tafur Marinos, Janeth Alicia; Ginepro, Marco; Zelano, Vincenzo; Daniele, Pier Giuseppe; Montoneri, Enzo

2015-01-01

This work reports a study of the proton-binding capacity of biopolymers obtained from different materials supplied by a municipal biowaste treatment plant located in Northern Italy. One material was the anaerobic fermentation digestate of the urban wastes organic humid fraction. The others were the compost of home and public gardening residues and the compost of the mix of the above residues, digestate and sewage sludge. These materials were hydrolyzed under alkaline conditions to yield the biopolymers by saponification. The biopolymers were characterized by 13C NMR spectroscopy, elemental analysis and potentiometric titration. The titration data were elaborated to attain chemical models for interpretation of the proton-binding capacity of the biopolymers obtaining the acidic sites concentrations and their protonation constants. The results obtained with the models and by NMR spectroscopy were elaborated together in order to better characterize the nature of the macromolecules. The chemical nature of the biopolymers was found dependent upon the nature of the sourcing materials. PMID:25658795

Towards the elucidation of molecular determinants of cooperativity in the liver bile acid binding protein.

PubMed

Pedò, Massimo; D'Onofrio, Mariapina; Ferranti, Pasquale; Molinari, Henriette; Assfalg, Michael

2009-11-15

Bile acid binding proteins (BABPs) are cytosolic lipid chaperones contributing to the maintenance of bile acid homeostasis and functional distribution within the cell. Liver BABPs act in parallel with ileal transporters to ensure vectorial transport of bile salts in hepatocytes and enterocytes, respectively. We describe the investigation of ligand binding to liver BABP, an essential step in the understanding of intracellular bile salt transport. Binding site occupancies were monitored in NMR titration experiments using (15)N-labelled ligand, while the relative populations of differently bound BABP forms were assessed by mass spectrometry. This site-specific information allowed the determination of intrinsic thermodynamic parameters and the identification of an extremely high cooperativity between two binding sites. Protein-observed NMR experiments revealed a global structural rearrangement which suggests an allosteric mechanism at the basis of the observed cooperativity. The view of a molecular tool capable of buffering against significant concentrations of free bile salts in a large range of solution conditions emerges from the observed pH-dependence of binding. We set to determine the molecular determinants of cooperativity by analysing the binding properties of a protein containing a mutated internal histidine. Both mass spectrometry and NMR experiments are consistent with an overall decreased binding affinity of the mutant, while the measured diffusion coefficients of ligand species reveal that the affinity loss concerns essentially one of the two binding sites. We therefore identified a mutation able to disrupt energetic communication functional to efficient binding and conclude that the buried histidine establishes contacts that stabilize the ternary complex. 2009 Wiley-Liss, Inc.

A multi writable thiophene-based selective and reversible chromogenic fluoride probe with dual -NH functionality

NASA Astrophysics Data System (ADS)

Vishwakarma, Siddharth; Kumar, Ajit; Pandey, Abha; Upadhyay, K. K.

2017-01-01

A chromogenic fluoride probe bearing bis imine groups having dual -NH functionality (BSB) has been designed, synthesised and structurally characterized by its single crystal X-ray diffraction studies. The BSB could visually and spectroscopically recognise F- with high selectivity over other anions by exhibiting intense chromogenic response (from colourless to red) for F- in acetonitrile solution. The UV-visible titration and 1H NMR titration experiments indicated that the observed changes occur via a combined process including hydrogen bonding and deprotonation between the BSB and F-. Moreover theoretical calculations at the Density Functional Theory (DFT) level shed further light upon probe design strategy and the nature of interactions between BSB and F-. The limit of detection and binding constant of BSB towards F- were found to be 6.9 × 10- 7 M and 1.42 ± 0.069 × 108 M- 2 respectively. Finally, by using F- and H+ as chemical inputs and the absorbance as output, a INHIBIT logic gate was constructed, which exhibits "Multi-write" ability without obvious degradation in its optical output.

Modelling the acid/base 1H NMR chemical shift limits of metabolites in human urine.

PubMed

Tredwell, Gregory D; Bundy, Jacob G; De Iorio, Maria; Ebbels, Timothy M D

2016-01-01

Despite the use of buffering agents the 1 H NMR spectra of biofluid samples in metabolic profiling investigations typically suffer from extensive peak frequency shifting between spectra. These chemical shift changes are mainly due to differences in pH and divalent metal ion concentrations between the samples. This frequency shifting results in a correspondence problem: it can be hard to register the same peak as belonging to the same molecule across multiple samples. The problem is especially acute for urine, which can have a wide range of ionic concentrations between different samples. To investigate the acid, base and metal ion dependent 1 H NMR chemical shift variations and limits of the main metabolites in a complex biological mixture. Urine samples from five different individuals were collected and pooled, and pre-treated with Chelex-100 ion exchange resin. Urine samples were either treated with either HCl or NaOH, or were supplemented with various concentrations of CaCl 2 , MgCl 2 , NaCl or KCl, and their 1 H NMR spectra were acquired. Nonlinear fitting was used to derive acid dissociation constants and acid and base chemical shift limits for peaks from 33 identified metabolites. Peak pH titration curves for a further 65 unidentified peaks were also obtained for future reference. Furthermore, the peak variations induced by the main metal ions present in urine, Na + , K + , Ca 2+ and Mg 2+ , were also measured. These data will be a valuable resource for 1 H NMR metabolite profiling experiments and for the development of automated metabolite alignment and identification algorithms for 1 H NMR spectra.

Alternate binding modes for a ubiquitin-SH3 domain interaction studied by NMR spectroscopy.

PubMed

Korzhnev, Dmitry M; Bezsonova, Irina; Lee, Soyoung; Chalikian, Tigran V; Kay, Lewis E

2009-02-20

Surfaces of many binding domains are plastic, enabling them to interact with multiple targets. An understanding of how they bind and recognize their partners is therefore predicated on characterizing such dynamic interfaces. Yet, these interfaces are difficult to study by standard biophysical techniques that often 'freeze' out conformations or that produce data averaged over an ensemble of conformers. In this study, we used NMR spectroscopy to study the interaction between the C-terminal SH3 domain of CIN85 and ubiquitin that involves the 'classical' binding sites of these proteins. Notably, chemical shift titration data of one target with another and relaxation dispersion data that report on millisecond time scale exchange processes are both well fit to a simple binding model in which free protein is in equilibrium with a single bound conformation. However, dissociation constants and chemical shift differences between free and bound states measured from both classes of experiment are in disagreement. It is shown that the data can be reconciled by considering three-state binding models involving two distinct bound conformations. By combining titration and dispersion data, kinetic and thermodynamic parameters of the three-state binding reaction are obtained along with chemical shifts for each state. A picture emerges in which one bound conformer has increased entropy and enthalpy relative to the second and chemical shifts similar to that of the free state, suggesting a less packed interface. This study provides an example of the interplay between entropy and enthalpy to fine-tune molecular interactions involving the same binding surfaces.

Strength order and nature of the π-hole bond of cyanuric chloride and 1,3,5-triazine with halide.

PubMed

Wang, Hui; Li, Chen; Wang, Weizhou; Jin, Wei Jun

2015-08-28

The (13)C NMR chemical shift moving upfield indicates the main model of π-holeX(-) bond between cyanuric chloride/1,3,5-triazine (3ClN/3N), which possess both the π-hole and σ-hole, and X(-). (13)C NMR and UV absorption titration in acetonitrile confirmed that the bonding abilities of 3ClN/3N with X(-) follow the order I(-) > Br(-) > Cl(-), which is apparently the order of the charge transfer ability of halide to 3ClN/3N. Chemical calculations showed that the bonding abilities in solution were essentially consistent with those obtained by titration experiments. However, the results in the gas phase were the reverse, i.e., π-holeCl(-) > π-holeBr(-) > π-holeI(-) in bonding energy, which obeys the order of electrostatic interaction. In fact, the π-hole bond and σ-hole bond compete with solvation and possible anion-hydrogen bond between a solvent molecule and a halide in solution. An explanation is that the apparent charge transfer order of π-/σ-holeI(-) > π-/σ-holeBr(-) > π-/σ-holeCl(-) occurs for weak π-hole bonds and σ-hole bonds, whereas the order of electrostatic attraction of π-/σ-holeCl(-) > π-/σ-holeBr(-) > π-/σ-holeI(-) is valid for strong bonds. It can be concluded by combining energy decomposition analysis and natural bond orbital analysis that the π-holeX(-) bond and σ-holeX(-) bond are electrostatically attractive in nature regardless of whether the order is I(-) > Br(-) > Cl(-) or the reverse.

8-Hydroxyquinoline based push-pull azo dye: Novel colorimetric chemosensor for anion detection

NASA Astrophysics Data System (ADS)

Arslan, Ömer; Aydıner, Burcu; Yalçın, Ergin; Babür, Banu; Seferoğlu, Nurgül; Seferoğlu, Zeynel

2017-12-01

A novel colorimetric chemosensor based on push-pull dye (8HQA) was synthesized and characterized by using IR, 1H/13C NMR and HRMS for the purpose of recognition of anions and cations in DMSO. The absorption maxima of the chemosensor were determined in different solvents. The selectivity and sensitivity of 8HQA to anions were determined with spectrophotometric and 1H NMR titration techniques. The selectivity of 8HQA for studied anions (CN-, F-, Cl-, I-, AcO-, HSO4- and H2PO4-) was determined in DMSO. There is no selectivity between competing anions such as CN-, F- AcO- and H2PO4- at the stoichiometric ratio of 1:1 in UV-vis titrations experiments however, it was observed different color changes upon addition of CN-, F-, AcO- and H2PO4- to the DMSO solution. In addition, the chemosensor showed no colorimetric response for the following anions; Cl-, I- and HSO4- in DMSO. The colorimetric sensing ability of 8HQA was studied in the presence of chloride salts of different cations such as Ca2+, Mg2+, Cu2+, Co2+, Sn2+, Ni2+, Cd2+ and Hg2+. Upon the addition of 4 equiv of each of the cations showed bathochromic shifts except for Ca2+and Cu2+. Interestingly, no selectivity was observed in interaction with metal cations. In addition, the molecular and electronic structures of 8HQA, as well as the molecular complexes of 8HQA, formed with the anions, were obtained theoretically and confirmed by DFT and TD-DFT calculations.

Gallium(III) chelates of mixed phosphonate-carboxylate triazamacrocyclic ligands relevant to nuclear medicine: Structural, stability and in vivo studies.

PubMed

Prata, Maria I M; André, João P; Kovács, Zoltán; Takács, Anett I; Tircsó, Gyula; Tóth, Imre; Geraldes, Carlos F G C

2017-12-01

Three triaza macrocyclic ligands, H 6 NOTP (1,4,7-triazacyclononane-N,N',N″-trimethylene phosphonic acid), H 4 NO2AP (1,4,7-triazacyclononane-N-methylenephosphonic acid-N',N″-dimethylenecarboxylic acid), and H 5 NOA2P (1,4,7-triazacyclononane-N,N'-bis(methylenephosphonic acid)-N″-methylene carboxylic acid), and their gallium(III) chelates were studied in view of their potential interest as scintigraphic and PET (Positron Emission Tomography) imaging agents. A 1 H, 31 P and 71 Ga multinuclear NMR study gave an insight on the structure, internal dynamics and stability of the chelates in aqueous solution. In particular, the analysis of 71 Ga NMR spectra gave information on the symmetry of the Ga 3+ coordination sphere and the stability of the chelates towards hydrolysis. The 31 P NMR spectra afforded information on the protonation of the non-coordinated oxygen atoms from the pendant phosphonate groups and on the number of species in solution. The 1 H NMR spectra allowed the analysis of the structure and the number of species in solution. 31 P and 1 H NMR titrations combined with potentiometry afforded the measurement of the protonation constants (log K Hi ) and the microscopic protonation scheme of the triaza macrocyclic ligands. The remarkably high thermodynamic stability constant (log K GaL =34.44 (0.04) and stepwise protonation constants of Ga(NOA2P) 2- were determined by potentiometry and 69 Ga and 31 P NMR titrations. Biodistribution and gamma imaging studies have been performed on Wistar rats using the radiolabeled 67 Ga(NO2AP) - and 67 Ga(NOA2P) 2- chelates, having both demonstrated to have renal excretion. The correlation of the molecular properties of the chelates with their pharmacokinetic properties has been analysed. Copyright © 2017 Elsevier Inc. All rights reserved.

Mechanism of Competitive Inhibition and Destabilization of Acidothermus cellulolyticus Endoglucanase 1 by Ionic Liquids.

PubMed

Summers, Samantha R; Sprenger, K G; Pfaendtner, Jim; Marchant, Jan; Summers, Michael F; Kaar, Joel L

2017-12-07

The ability of ionic liquids (ILs) to solubilize cellulose has sparked interest in their use for enzymatic biomass processing. However, this potential is yet to be realized, primarily because ILs inactivate requisite cellulases by mechanisms that are yet to be identified. We used a combination of enzymology, circular dichroism (CD), nuclear magnetic resonance (NMR), and molecular dynamics (MD) methods to investigate the molecular basis for the inactivation of the endocellulase 1 (E1) from Acidothermus cellulolyticus by the imidazolium IL 1-butyl-3-methylimidazolium chloride ([BMIM][Cl]). Enzymatic studies revealed that [BMIM][Cl] inactivates E1 in a biphasic manner that involves rapid, reversible inhibition, followed by slow, irreversible deactivation. Backbone NMR signals of the 40.5 kDa E1 were assigned by triple resonance NMR methods, enabling monitoring of residue-specific perturbations. 1 H- 15 N NMR titration experiments revealed that [BMIM][Cl] binds reversibly to the E1 active site, indicating that reversible deactivation is due to competitive inhibition of substrate binding. Prolonged incubation with [BMIM][Cl] led to substantial global changes in the 1 H- 15 N heteronuclear single quantum coherence NMR and CD spectra of E1 indicative of protein denaturation. Notably, weak interactions between [BMIM][Cl] and residues at the termini of several helices were also observed, which, together with MD simulations, suggest that E1 denaturation is promoted by [BMIM][Cl]-induced destabilization of helix capping structures. In addition to identifying determinants of E1 inactivation, our findings establish a molecular framework for engineering cellulases with improved IL compatibility.

Limitations of pH-potentiometric titration for the determination of the degree of deacetylation of chitosan.

PubMed

Balázs, Nándor; Sipos, Pál

2007-01-15

The degree of deacetylation (DDA) of chitosan determines the biopolymer's physico-chemical properties and technological applications. pH-Potentiometric titration seems to offer a simple and convenient means of determining DDA. However, to obtain accurate pH-potentiometric DDA values, several factors have to be taken into consideration. We found that the moisture content of the air-dry chitosan samples can be as high as 15%, and a reasonable fraction of this humidity cannot be removed by ordinary drying. Corrections have to be made for the ash content, as in some samples it can be as high as 1% by weight. The method of equivalence point determination was also found to cause systematic variations in the results and in some samples extra acid as high as 1 mol% of the free amino content was also identified. To compensate for the latter effect, the second equivalence point of the titration has to be determined separately and the analytical concentration of the acid be corrected for it. All the corrections listed here are necessary to obtain DDA values that are in reasonable agreement with those obtained from (1)H NMR and IR spectroscopic measurements. The need for these corrections severely limits the usefulness of pH-metry for determining accurate DDA values and thus potentiometry is hardly able to compete with other standard spectroscopic procedures, that is, (1)H NMR spectroscopy.

Assessing the acid-base and conformational properties of histidine residues in human prion protein (125-228) by means of pK(a) calculations and molecular dynamics simulations.

PubMed

Langella, Emma; Improta, Roberto; Crescenzi, Orlando; Barone, Vincenzo

2006-07-01

A thorough study of the acid-base behavior of the four histidines and the other titratable residues of the structured domain of human prion protein (125-228) is presented. By using multi-tautomer electrostatic calculations, average titration curves have been built for all titratable residues, using the whole bundles of NMR structures determined at pH 4.5 and 7.0. According to our results, (1) only histidine residues are likely to be involved in the first steps of the pH-driven conformational transition of prion protein; (2) the pK(a)'s of His140 and His177 are approximately 7.0, whereas those of His155 and His187 are < 5.5. 10-ns long molecular dynamics simulations have been performed on five different models, corresponding to the most significant combinations of histidine protonation states. A critical comparison between the available NMR structures and our computational results (1) confirms that His155 and His187 are the residues whose protonation is involved in the conformational rearrangement of huPrP in mildly acidic condition, and (2) shows how their protonation leads to the destructuration of the C-terminal part of HB and to the loss of the last turn of HA that represent the crucial microscopic steps of the rearrangement. (c) 2006 Wiley-Liss, Inc.

Mechanisms of antimony adsorption onto soybean stover-derived biochar in aqueous solutions.

PubMed

Vithanage, Meththika; Rajapaksha, Anushka Upamali; Ahmad, Mahtab; Uchimiya, Minori; Dou, Xiaomin; Alessi, Daniel S; Ok, Yong Sik

2015-03-15

Limited mechanistic knowledge is available on the interaction of biochar with trace elements (Sb and As) that exist predominantly as oxoanions. Soybean stover biochars were produced at 300 °C (SBC300) and 700 °C (SBC700), and characterized by BET, Boehm titration, FT-IR, NMR and Raman spectroscopy. Bound protons were quantified by potentiometric titration, and two acidic sites were used to model biochar by the surface complexation modeling based on Boehm titration and NMR observations. The zero point of charge was observed at pH 7.20 and 7.75 for SBC300 and SBC700, respectively. Neither antimonate (Sb(V)) nor antimonite (Sb(III)) showed ionic strength dependency (0.1, 0.01 and 0.001 M NaNO3), indicating inner sphere complexation. Greater adsorption of Sb(III) and Sb(V) was observed for SBC300 having higher -OH content than SBC700. Sb(III) removal (85%) was greater than Sb(V) removal (68%). Maximum adsorption density for Sb(III) was calculated as 1.88 × 10(-6) mol m(-2). The Triple Layer Model (TLM) successfully described surface complexation of Sb onto soybean stover-derived biochar at pH 4-9, and suggested the formation of monodentate mononuclear and binuclear complexes. Spectroscopic investigations by Raman, FT-IR and XPS further confirmed strong chemisorptive binding of Sb to biochar surfaces. Copyright © 2014 Elsevier Ltd. All rights reserved.

Tautomerism, acid-base equilibria, and H-bonding of the six histidines in subtilisin BPN′ by NMR

PubMed Central

Day, Regina M.; Thalhauser, Craig J.; Sudmeier, James L.; Vincent, Matthew P.; Torchilin, Ekaterina V.; Sanford, David G.; Bachovchin, Christopher W.; Bachovchin, William W.

2003-01-01

We have determined by 15N, 1H, and 13C NMR, the chemical behavior of the six histidines in subtilisin BPN′ and their PMSF and peptide boronic acid complexes in aqueous solution as a function of pH in the range of from 5 to 11, and have assigned every 15N, 1H, Cɛ1, and Cδ2 resonance of all His side chains in resting enzyme. Four of the six histidine residues (17, 39, 67, and 226) are neutrally charged and do not titrate. One histidine (238), located on the protein surface, titrates with pKa = 7.30 ± 0.03 at 25°C, having rapid proton exchange, but restricted mobility. The active site histidine (64) in mutant N155A titrates with a pKa value of 7.9 ± 0.3 and sluggish proton exchange behavior, as shown by two-site exchange computer lineshape simulation. His 64 in resting enzyme contains an extremely high Cɛ1-H proton chemical shift of 9.30 parts per million (ppm) owing to a conserved Cɛ1-H. . .O=C H-bond from the active site imidazole to a backbone carbonyl group, which is found in all known serine proteases representing all four superfamilies. Only His 226, and His 64 at high pH, exist as the rare Nδ1-H tautomer, exhibiting 13Cδ1 chemical shifts ~9 ppm higher than those for Nɛ2-H tautomers. His 64 in the PMSF complex, unlike that in the resting enzyme, is highly mobile in its low pH form, as shown by 15N-1H NOE effects, and titrates with rapid proton exchange kinetics linked to a pKa value of 7.47 ± 0.02. PMID:12649438

α, α', α", α'"- meso-tetrahexyltetramethyl-calix[4]pyrrole: An easy-to-prepare, isomerically pure anion extractant with enhanced solubility in organic solvents

DOE PAGES

Williams, Neil J.; Bryantsev, Vyacheslav S.; Custelcean, Radu; ...

2016-01-29

α, α', α", α'"- meso-Tetrahexyltetramethyl-calix[4]pyrrole is easily obtained as a single diastereomer in a one-pot reaction. It exhibits enhanced solubility in organic solvents, including aliphatic solvents, relative to its parent meso-octamethylcalix[4]pyrrole (1). Somewhat surprisingly, the tetrahexyl derivative 2 complexes with tributylmethylammonium chloride in chloroform more strongly than does 1 as shown by NMR titrations. However, 1 and 2 exhibit comparable complexation strength in extraction experiments, the difference between the NMR and extraction results being attributed to the effect of organic-phase water in the extraction systems. Mass-action analysis indicates the formation of the predominant complex TBMA +(1 or 2)Cl – inmore » both NMR and extraction systems, and equilibrium constants are reported. x-Ray crystal structures were obtained for the free ligand 2 and its complex with tetramethylammonium chloride. In addition, the free ligand crystallises in the 1,3-alt conformation with equatorial hexyl arms. In the chloride complex with 2 in its cone conformation, the hexyl arms adopt an axial orientation, enveloping the anion. DFT calculations show this binding conformation to be the most stable, mostly owing to destabilising steric interactions involving the pyrrole C–H and alkyl C–H groups positioned equatorially.« less

α, α', α", α'"- meso-tetrahexyltetramethyl-calix[4]pyrrole: An easy-to-prepare, isomerically pure anion extractant with enhanced solubility in organic solvents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, Neil J.; Bryantsev, Vyacheslav S.; Custelcean, Radu

α, α', α", α'"- meso-Tetrahexyltetramethyl-calix[4]pyrrole is easily obtained as a single diastereomer in a one-pot reaction. It exhibits enhanced solubility in organic solvents, including aliphatic solvents, relative to its parent meso-octamethylcalix[4]pyrrole (1). Somewhat surprisingly, the tetrahexyl derivative 2 complexes with tributylmethylammonium chloride in chloroform more strongly than does 1 as shown by NMR titrations. However, 1 and 2 exhibit comparable complexation strength in extraction experiments, the difference between the NMR and extraction results being attributed to the effect of organic-phase water in the extraction systems. Mass-action analysis indicates the formation of the predominant complex TBMA +(1 or 2)Cl – inmore » both NMR and extraction systems, and equilibrium constants are reported. x-Ray crystal structures were obtained for the free ligand 2 and its complex with tetramethylammonium chloride. In addition, the free ligand crystallises in the 1,3-alt conformation with equatorial hexyl arms. In the chloride complex with 2 in its cone conformation, the hexyl arms adopt an axial orientation, enveloping the anion. DFT calculations show this binding conformation to be the most stable, mostly owing to destabilising steric interactions involving the pyrrole C–H and alkyl C–H groups positioned equatorially.« less

Secondary Structures in a Freeze-Dried Lignite Humic Acid Fraction Caused by Hydrogen-Bonding of Acidic Protons with Aromatic Rings.

PubMed

Cao, Xiaoyan; Drosos, Marios; Leenheer, Jerry A; Mao, Jingdong

2016-02-16

A lignite humic acid (HA) was separated from inorganic and non-HA impurities (i.e., aluminosilicates, metals) and fractionated by a combination of dialysis and XAD-8 resin. Fractionation revealed a more homogeneous structure of lignite HA. New and more specific structural information on the main lignite HA fraction is obtained by solid-state nuclear magnetic resonance (NMR) spectroscopy. Quantitative (13)C multiple cross-polarization (multiCP) NMR indicated oxidized phenyl propane structures derived from lignin. MultiCP experiments, conducted on potassium HA salts titrated to pH 10 and pH 12, revealed shifts consistent with carboxylate and phenolate formation, but structural changes associated with enolate formation from aromatic beta keto acids were not detected. Two-dimensional (1)H-(13)C heteronuclear correlation (2D HETCOR) NMR indicated aryl-aliphatic ketones, aliphatic and aromatic carboxyl groups, phenol, and methoxy phenyl ethers. Acidic protons from carboxyl groups in both the lignite HA fraction and a synthetic HA-like polycondensate were found to be hydrogen-bonded with electron-rich aromatic rings. Our results coupled with published infrared spectra provide evidence for the preferential hydrogen bonding of acidic hydrogens with electron-rich aromatic rings rather than adjacent carbonyl groups. These hydrogen-bonding interactions likely result from stereochemical arrangements in primary structures and folding.

A simple and highly selective 2,2-diferrocenylpropane-based multi-channel ion pair receptor for Pb(2+) and HSO4(-).

PubMed

Wan, Qian; Zhuo, Ji-Bin; Wang, Xiao-Xue; Lin, Cai-Xia; Yuan, Yao-Feng

2015-03-28

A structurally simple, 2,2-diferrocenylpropane-based ion pair receptor 1 was synthesized and characterized by (1)H NMR, (13)C NMR, HRMS, elemental analyses, and single-crystal X-ray diffraction. The ion pair receptor 1 showed excellent selectivity and sensitivity towards Pb(2+) with multi-channel responses: a fluorescence enhancement (more than 42-fold), a notable color change from yellow to red, redox anodic shift (ΔE1/2 = 151 mV), while HSO4(-) promoted fluorescence enhancement when Pb(2+) or Zn(2+) was bonded to the cation binding-site. (1)H NMR titration and density functional theory were performed to reveal the sensing mechanism based on photo-induced electron transfer (PET).

NMRbot: Python scripts enable high-throughput data collection on current Bruker BioSpin NMR spectrometers.

PubMed

Clos, Lawrence J; Jofre, M Fransisca; Ellinger, James J; Westler, William M; Markley, John L

2013-06-01

To facilitate the high-throughput acquisition of nuclear magnetic resonance (NMR) experimental data on large sets of samples, we have developed a simple and straightforward automated methodology that capitalizes on recent advances in Bruker BioSpin NMR spectrometer hardware and software. Given the daunting challenge for non-NMR experts to collect quality spectra, our goal was to increase user accessibility, provide customized functionality, and improve the consistency and reliability of resultant data. This methodology, NMRbot, is encoded in a set of scripts written in the Python programming language accessible within the Bruker BioSpin TopSpin ™ software. NMRbot improves automated data acquisition and offers novel tools for use in optimizing experimental parameters on the fly. This automated procedure has been successfully implemented for investigations in metabolomics, small-molecule library profiling, and protein-ligand titrations on four Bruker BioSpin NMR spectrometers at the National Magnetic Resonance Facility at Madison. The investigators reported benefits from ease of setup, improved spectral quality, convenient customizations, and overall time savings.

Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex.

PubMed

Ortega-Roldan, Jose Luis; Jensen, Malene Ringkjøbing; Brutscher, Bernhard; Azuaga, Ana I; Blackledge, Martin; van Nuland, Nico A J

2009-05-01

The description of the interactome represents one of key challenges remaining for structural biology. Physiologically important weak interactions, with dissociation constants above 100 muM, are remarkably common, but remain beyond the reach of most of structural biology. NMR spectroscopy, and in particular, residual dipolar couplings (RDCs) provide crucial conformational constraints on intermolecular orientation in molecular complexes, but the combination of free and bound contributions to the measured RDC seriously complicates their exploitation for weakly interacting partners. We develop a robust approach for the determination of weak complexes based on: (i) differential isotopic labeling of the partner proteins facilitating RDC measurement in both partners; (ii) measurement of RDC changes upon titration into different equilibrium mixtures of partially aligned free and complex forms of the proteins; (iii) novel analytical approaches to determine the effective alignment in all equilibrium mixtures; and (iv) extraction of precise RDCs for bound forms of both partner proteins. The approach is demonstrated for the determination of the three-dimensional structure of the weakly interacting CD2AP SH3-C:Ubiquitin complex (K(d) = 132 +/- 13 muM) and is shown, using cross-validation, to be highly precise. We expect this methodology to extend the remarkable and unique ability of NMR to study weak protein-protein complexes.

Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex

PubMed Central

Ortega-Roldan, Jose Luis; Jensen, Malene Ringkjøbing; Brutscher, Bernhard; Azuaga, Ana I.; Blackledge, Martin; van Nuland, Nico A. J.

2009-01-01

The description of the interactome represents one of key challenges remaining for structural biology. Physiologically important weak interactions, with dissociation constants above 100 μM, are remarkably common, but remain beyond the reach of most of structural biology. NMR spectroscopy, and in particular, residual dipolar couplings (RDCs) provide crucial conformational constraints on intermolecular orientation in molecular complexes, but the combination of free and bound contributions to the measured RDC seriously complicates their exploitation for weakly interacting partners. We develop a robust approach for the determination of weak complexes based on: (i) differential isotopic labeling of the partner proteins facilitating RDC measurement in both partners; (ii) measurement of RDC changes upon titration into different equilibrium mixtures of partially aligned free and complex forms of the proteins; (iii) novel analytical approaches to determine the effective alignment in all equilibrium mixtures; and (iv) extraction of precise RDCs for bound forms of both partner proteins. The approach is demonstrated for the determination of the three-dimensional structure of the weakly interacting CD2AP SH3-C:Ubiquitin complex (Kd = 132 ± 13 μM) and is shown, using cross-validation, to be highly precise. We expect this methodology to extend the remarkable and unique ability of NMR to study weak protein–protein complexes. PMID:19359362

Chemical groups and structural characterization of lignin via thiol-mediated demethylation

Treesearch

Lihong Hu; Hui Pan; Yonghong Zhou; Chung-Yun Hse; Chengguo Liu; Baofang Zhang; Bin Xu

2014-01-01

A new approach to increase the reactivity of lignin by thiol-mediated demethylation was investigated in this study. Demethylated lignin was characterized by the changes in its hydroxyl and methoxyl groups, molecular weight, and other properties using titration and spectroscopy methods including FT-IR, 1H NMR, UV,and GPC. The total...

Chelation of heavy group 2 (radio)metals by p-tert-butylcalix[4]arene-1,3-crown-6 and logK determination via NMR

NASA Astrophysics Data System (ADS)

Bauer, David; Gott, Matthew; Steinbach, Jörg; Mamat, Constantin

2018-06-01

A crown-bridged calix[4]arene scaffold was investigated as lead compound for the ligation of heavy alkaline earth metals such as strontium and barium, which appear to be useful for radiopharmaceutical applications in diagnosis as well as in radiotherapy. In particular barium, due to its chemical similarities, could serve as a surrogate for radium, a metal of high radiopharmaceutical interest. The ability of p-tert-butylcalix[4]arene-1,3-crown-6 (1) in particular to chelate cations, such as group 1 and 2 metal ions or ammonium ions is well known. Also, the manifold possibilities of structural modification on the upper- and lower-rim as well as on the crown itself produce properties that may lead to a highly selective and effective chelating agent. In this work, titration experiments of the perchlorate salts of Ba2+, Sr2+ and Pb2+ with ligand 1 were performed to determine their stability constants (logK = 4.7, 4.3, and 3.3, respectively) by 1H NMR measurements in acetonitrile-d3.

Effects of urea on selectivity and protein-ligand interactions in multimodal cation exchange chromatography.

PubMed

Holstein, Melissa A; Parimal, Siddharth; McCallum, Scott A; Cramer, Steven M

2013-01-08

Nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations were employed in concert with chromatography to provide insight into the effect of urea on protein-ligand interactions in multimodal (MM) chromatography. Chromatographic experiments with a protein library in ion exchange (IEX) and MM systems indicated that, while urea had a significant effect on protein retention and selectivity for a range of proteins in MM systems, the effects were much less pronounced in IEX. NMR titration experiments carried out with a multimodal ligand, and isotopically enriched human ubiquitin indicated that, while the ligand binding face of ubiquitin remained largely intact in the presence of urea, the strength of binding was decreased. MD simulations were carried out to provide further insight into the effect of urea on MM ligand binding. These results indicated that, while the overall ligand binding face of ubiquitin remained the same, there was a reduction in the occupancy of the MM ligand interaction region along with subtle changes in the residues involved in these interactions. This work demonstrates the effectiveness of urea in enhancing selectivity in MM chromatographic systems and also provides an in-depth analysis of how MM ligand-protein interactions are altered in the presence of this fluid phase modifier.

Structural properties of the promiscuous VP16 activation domain.

PubMed

Jonker, Hendrik R A; Wechselberger, Rainer W; Boelens, Rolf; Folkers, Gert E; Kaptein, Rob

2005-01-25

Herpes simplex virion protein 16 (VP16) contains two strong activation regions that can independently and cooperatively activate transcription in vivo. We have identified the regions and residues involved in the interaction with the human transcriptional coactivator positive cofactor 4 (PC4) and the general transcription factor TFIIB. NMR and biochemical experiments revealed that both VP16 activation regions are required for the interaction and undergo a conformational transition from random coil to alpha-helix upon binding to its target PC4. The interaction is strongly electrostatically driven and the binding to PC4 is enhanced by the presence of its amino-terminal domain. We propose models for binding of VP16 to the core domains of PC4 and TFIIB that are based on two independent docking approaches using NMR chemical shift changes observed in titration experiments. The models are consistent with results from site-directed mutagenesis and provide an explanation for the contribution of both acidic and hydrophobic residues for transcriptional activation by VP16. Both intrinsically unstructured activation domains are attracted to their interaction partner by electrostatic interactions, and adopt an alpha-helical conformation around the important hydrophobic residues. The models showed multiple distinct binding surfaces upon interaction with various partners, providing an explanation for the promiscuous properties, cooperativity, and the high activity of this activation domain.

Spectrophotometric Titration of a Mixture of Calcium and Magnesium.

ERIC Educational Resources Information Center

Fulton, Robert; And Others

1986-01-01

Describes a spectrophotometric titration experiment which uses a manual titration spectrophotometer and manually operated buret, rather than special instrumentation. Identifies the equipment, materials, and procedures needed for the completion of the experiment. Recommends the use of this experiment in introductory quantitative analysis…

Single-stranded DNA Binding by the Helix-Hairpin-Helix Domain of XPF Protein Contributes to the Substrate Specificity of the ERCC1-XPF Protein Complex*

PubMed Central

Das, Devashish; Faridounnia, Maryam; Kovacic, Lidija; Kaptein, Robert; Boelens, Rolf; Folkers, Gert E.

2017-01-01

The nucleotide excision repair protein complex ERCC1-XPF is required for incision of DNA upstream of DNA damage. Functional studies have provided insights into the binding of ERCC1-XPF to various DNA substrates. However, because no structure for the ERCC1-XPF-DNA complex has been determined, the mechanism of substrate recognition remains elusive. Here we biochemically characterize the substrate preferences of the helix-hairpin-helix (HhH) domains of XPF and ERCC-XPF and show that the binding to single-stranded DNA (ssDNA)/dsDNA junctions is dependent on joint binding to the DNA binding domain of ERCC1 and XPF. We reveal that the homodimeric XPF is able to bind various ssDNA sequences but with a clear preference for guanine-containing substrates. NMR titration experiments and in vitro DNA binding assays also show that, within the heterodimeric ERCC1-XPF complex, XPF specifically recognizes ssDNA. On the other hand, the HhH domain of ERCC1 preferentially binds dsDNA through the hairpin region. The two separate non-overlapping DNA binding domains in the ERCC1-XPF heterodimer jointly bind to an ssDNA/dsDNA substrate and, thereby, at least partially dictate the incision position during damage removal. Based on structural models, NMR titrations, DNA-binding studies, site-directed mutagenesis, charge distribution, and sequence conservation, we propose that the HhH domain of ERCC1 binds to dsDNA upstream of the damage, and XPF binds to the non-damaged strand within a repair bubble. PMID:28028171

Electrostatic Interactions in the Binding Pathway of a Transient Protein Complex Studied by NMR and Isothermal Titration Calorimetry*

PubMed Central

Meneses, Erick; Mittermaier, Anthony

2014-01-01

Much of our knowledge of protein binding pathways is derived from extremely stable complexes that interact very tightly, with lifetimes of hours to days. Much less is known about weaker interactions and transient complexes because these are challenging to characterize experimentally. Nevertheless, these types of interactions are ubiquitous in living systems. The combination of NMR relaxation dispersion Carr–Purcell–Meiboom–Gill (CPMG) experiments and isothermal titration calorimetry allows the quantification of rapid binding kinetics for complexes with submillisecond lifetimes that are difficult to study using conventional techniques. We have used this approach to investigate the binding pathway of the Src homology 3 (SH3) domain from the Fyn tyrosine kinase, which forms complexes with peptide targets whose lifetimes are on the order of about a millisecond. Long range electrostatic interactions have been shown to play a critical role in the binding pathways of tightly binding complexes. The role of electrostatics in the binding pathways of transient complexes is less well understood. Similarly to previously studied tight complexes, we find that SH3 domain association rates are enhanced by long range electrostatics, whereas short range interactions are formed late in the docking process. However, the extent of electrostatic association rate enhancement is several orders of magnitudes less, whereas the electrostatic-free basal association rate is significantly greater. Thus, the SH3 domain is far less reliant on electrostatic enhancement to achieve rapid association kinetics than are previously studied systems. This suggests that there may be overall differences in the role played by electrostatics in the binding pathways of extremely stable versus transient complexes. PMID:25122758

Thermodynamic and spectroscopic study of Al3+ interaction with glycine, l-cysteine and tranexamic acid in aqueous solution.

PubMed

Cardiano, Paola; Giacobello, Fausta; Giuffrè, Ottavia; Sammartano, Silvio

2017-11-01

In this paper a thermodynamic and spectroscopic study on the interaction between Al 3+ and glycine (Gly), l-cysteine (Cys), tranexamic acid (Tranex) is reported. Speciation models have been obtained by processing potentiometric titration data to determine stability constants of the species formed in aqueous solution at T=298.15K, 0.15≤I/molL -1 ≤1 in NaCl. Thermodynamic formation parameters have been obtained from calorimetric titration data, at T=298.15K, I=0.15molL -1 using NaCl as ionic medium. Al 3+ -Cys system was also investigated by spectrophotometric and 1 H NMR measurements. 1 H NMR experiments were performed on Al 3+ -Tranex system as well. Different speciation models have been observed for the three systems. The results showed the formation of MLH, ML and M 2 L 2 (OH) 2 species for Gly, ML, M 2 L and MLOH for Cys, MLH and MLOH for Tranex. The formed species are quite stable, i.e. for ML, logβ=7.18, 11.91 for Gly and Cys, respectively, at I=0.15molL -1 and T=298.15K. For all the systems the dependence of formation constants on ionic strength over the range 0.1-1molL -1 is reported. The sequestering ability of the ligands under study was also evaluated by pL 0.5 empiric parameter. For Gly, Cys and Tranex, pL 0.5 =2.51, 3.74, 3.91 respectively, at pH=5, I=0.15molL -1 and T=298.15K. Copyright © 2017 Elsevier B.V. All rights reserved.

A multi writable thiophene-based selective and reversible chromogenic fluoride probe with dual -NH functionality.

PubMed

Vishwakarma, Siddharth; Kumar, Ajit; Pandey, Abha; Upadhyay, K K

2017-01-05

A chromogenic fluoride probe bearing bis imine groups having dual -NH functionality (BSB) has been designed, synthesised and structurally characterized by its single crystal X-ray diffraction studies. The BSB could visually and spectroscopically recognise F(-) with high selectivity over other anions by exhibiting intense chromogenic response (from colourless to red) for F(-) in acetonitrile solution. The UV-visible titration and (1)H NMR titration experiments indicated that the observed changes occur via a combined process including hydrogen bonding and deprotonation between the BSB and F(-). Moreover theoretical calculations at the Density Functional Theory (DFT) level shed further light upon probe design strategy and the nature of interactions between BSB and F(-). The limit of detection and binding constant of BSB towards F(-) were found to be 6.9×10(-7)M and 1.42±0.069×10(8)M(-2) respectively. Finally, by using F(-)and H(+) as chemical inputs and the absorbance as output, a INHIBIT logic gate was constructed, which exhibits "Multi-write" ability without obvious degradation in its optical output. Copyright © 2016 Elsevier B.V. All rights reserved.

Aggregation Number in Water/n-Hexanol Molecular Clusters Formed in Cyclohexane at Different Water/n-Hexanol/Cyclohexane Compositions Calculated by Titration 1H NMR.

PubMed

Flores, Mario E; Shibue, Toshimichi; Sugimura, Natsuhiko; Nishide, Hiroyuki; Moreno-Villoslada, Ignacio

2017-11-09

Upon titration of n-hexanol/cyclohexane mixtures of different molar compositions with water, water/n-hexanol clusters are formed in cyclohexane. Here, we develop a new method to estimate the water and n-hexanol aggregation numbers in the clusters that combines integration analysis in one-dimensional 1 H NMR spectra, diffusion coefficients calculated by diffusion-ordered NMR spectroscopy, and further application of the Stokes-Einstein equation to calculate the hydrodynamic volume of the clusters. Aggregation numbers of 5-15 molecules of n-hexanol per cluster in the absence of water were observed in the whole range of n-hexanol/cyclohexane molar fractions studied. After saturation with water, aggregation numbers of 6-13 n-hexanol and 0.5-5 water molecules per cluster were found. O-H and O-O atom distances related to hydrogen bonds between donor/acceptor molecules were theoretically calculated using density functional theory. The results show that at low n-hexanol molar fractions, where a robust hydrogen-bond network is held between n-hexanol molecules, addition of water makes the intermolecular O-O atom distance shorter, reinforcing molecular association in the clusters, whereas at high n-hexanol molar fractions, where dipole-dipole interactions dominate, addition of water makes the intermolecular O-O atom distance longer, weakening the cluster structure. This correlates with experimental NMR results, which show an increase in the size and aggregation number in the clusters upon addition of water at low n-hexanol molar fractions, and a decrease of these magnitudes at high n-hexanol molar fractions. In addition, water produces an increase in the proton exchange rate between donor/acceptor molecules at all n-hexanol molar fractions.

Application of Computers for Experiment Design, Data Acquisition, and Analysis in the Chemistry Laboratory

DTIC Science & Technology

1990-05-01

Obtain Thermistor Operating Characteristics ................................. 82 25. Ag+/Ci" Thermometric Titration ........................... 85 26...Experiment Program for Thermometric Titrations ............... 85 27. Appearance of the Spreadsheet in the Analysis Mode ............ 86 28...rate experiments, carbon dioxide exhalation monitoring, stream turbidity measurement, photosynthesis monitoring, pendulum timing, thermometric titrations

Analysis of the (Trimethylsilyl)propionic Acid-β(12-28) Peptide Binding Equilibrium with NMR Spectroscopy.

PubMed

Jayawickrama, D A; Larive, C K

1999-06-01

The binding of a small molecule, (trimethylsilyl)propionic acid (TSP), to a 17-residue peptide, β(12-28), is examined using (1)H NMR spectroscopy. β(12-28) (VHHQKLVFFAEDVGSNK) is a central fragment of the 40-42-residue Alzheimer's-associated Aβ peptide. This peptide has been previously shown to form soluble aggregates in low-pH aqueous solution. The TSP resonance is broadened appreciably in solutions containing relatively high concentrations (∼2 mM) of the peptide. The changes in TSP line width measured by titration of a peptide solution with TSP indicate a 1:1 binding stoichiometry. If the concentrations of both the peptide and TSP are reduced by 1 order of magnitude, the resonances of both species are sharp, suggesting that TSP binds predominately to the aggregated peptide. Nuclear Overhauser effect experiments indicate that the TSP interacts predominately with the side chains of the aliphatic peptide residues Leu(17) and Val(18). Pulsed-field gradient NMR measurements of TSP and peptide diffusion coefficients provide a more quantitative picture of the TSP-peptide binding equilibrium. The measured diffusion coefficients were used to calculate the fractions of the free and bound TSP. These results substantiate the conclusion that the stoichiometry of the TSP-peptide binding equilibrium is essentially 1:1 and further indicate anticooperative behavior in solutions containing an excess of TSP resulting in a dissociation of the peptide aggregates.

Domain-specific interactions between MLN8237 and human serum albumin estimated by STD and WaterLOGSY NMR, ITC, spectroscopic, and docking techniques.

PubMed

Yang, Hongqin; Liu, Jiuyang; Huang, Yanmei; Gao, Rui; Tang, Bin; Li, Shanshan; He, Jiawei; Li, Hui

2017-03-30

Alisertib (MLN8237) is an orally administered inhibitor of Aurora A kinase. This small-molecule inhibitor is under clinical or pre-clinical phase for the treatment of advanced malignancies. The present study provides a detailed characterization of the interaction of MLN8237 with a drug transport protein called human serum albumin (HSA). STD and WaterLOGSY nuclear magnetic resonance (NMR)-binding studies were conducted first to confirm the binding of MLN8237 to HSA. In the ligand orientation assay, the binding sites of MLN8237 were validated through two site-specific spy molecules (warfarin sodium and ibuprofen, which are two known site-selective probes) by using STD and WaterLOGSY NMR competition techniques. These competition experiments demonstrate that both spy molecules do not compete with MLN8237 for the specific binding site. The AutoDock-based blind docking study recognizes the hydrophobic subdomain IB of the protein as the probable binding site for MLN8237. Thermodynamic investigations by isothermal titration calorimetry (ITC) reveal that the non-covalent interaction between MLN8237 and HSA (binding constant was approximately 10 5  M -1 ) is driven mainly by favorable entropy and unfavorable enthalpy. In addition, synchronous fluorescence, circular dichroism (CD), and 3D fluorescence spectroscopy suggest that MLN8237 may induce conformational changes in HSA.

Domain-specific interactions between MLN8237 and human serum albumin estimated by STD and WaterLOGSY NMR, ITC, spectroscopic, and docking techniques

PubMed Central

Yang, Hongqin; Liu, Jiuyang; Huang, Yanmei; Gao, Rui; Tang, Bin; Li, Shanshan; He, Jiawei; Li, Hui

2017-01-01

Alisertib (MLN8237) is an orally administered inhibitor of Aurora A kinase. This small-molecule inhibitor is under clinical or pre-clinical phase for the treatment of advanced malignancies. The present study provides a detailed characterization of the interaction of MLN8237 with a drug transport protein called human serum albumin (HSA). STD and WaterLOGSY nuclear magnetic resonance (NMR)-binding studies were conducted first to confirm the binding of MLN8237 to HSA. In the ligand orientation assay, the binding sites of MLN8237 were validated through two site-specific spy molecules (warfarin sodium and ibuprofen, which are two known site-selective probes) by using STD and WaterLOGSY NMR competition techniques. These competition experiments demonstrate that both spy molecules do not compete with MLN8237 for the specific binding site. The AutoDock-based blind docking study recognizes the hydrophobic subdomain IB of the protein as the probable binding site for MLN8237. Thermodynamic investigations by isothermal titration calorimetry (ITC) reveal that the non-covalent interaction between MLN8237 and HSA (binding constant was approximately 105 M−1) is driven mainly by favorable entropy and unfavorable enthalpy. In addition, synchronous fluorescence, circular dichroism (CD), and 3D fluorescence spectroscopy suggest that MLN8237 may induce conformational changes in HSA. PMID:28358124

Domain-specific interactions between MLN8237 and human serum albumin estimated by STD and WaterLOGSY NMR, ITC, spectroscopic, and docking techniques

NASA Astrophysics Data System (ADS)

Yang, Hongqin; Liu, Jiuyang; Huang, Yanmei; Gao, Rui; Tang, Bin; Li, Shanshan; He, Jiawei; Li, Hui

2017-03-01

Alisertib (MLN8237) is an orally administered inhibitor of Aurora A kinase. This small-molecule inhibitor is under clinical or pre-clinical phase for the treatment of advanced malignancies. The present study provides a detailed characterization of the interaction of MLN8237 with a drug transport protein called human serum albumin (HSA). STD and WaterLOGSY nuclear magnetic resonance (NMR)-binding studies were conducted first to confirm the binding of MLN8237 to HSA. In the ligand orientation assay, the binding sites of MLN8237 were validated through two site-specific spy molecules (warfarin sodium and ibuprofen, which are two known site-selective probes) by using STD and WaterLOGSY NMR competition techniques. These competition experiments demonstrate that both spy molecules do not compete with MLN8237 for the specific binding site. The AutoDock-based blind docking study recognizes the hydrophobic subdomain IB of the protein as the probable binding site for MLN8237. Thermodynamic investigations by isothermal titration calorimetry (ITC) reveal that the non-covalent interaction between MLN8237 and HSA (binding constant was approximately 105 M-1) is driven mainly by favorable entropy and unfavorable enthalpy. In addition, synchronous fluorescence, circular dichroism (CD), and 3D fluorescence spectroscopy suggest that MLN8237 may induce conformational changes in HSA.

A combination of 19F NMR and surface plasmon resonance for site-specific hit selection and validation of fragment molecules that bind to the ATP-binding site of a kinase.

PubMed

Nagatoishi, Satoru; Yamaguchi, Sou; Katoh, Etsuko; Kajita, Keita; Yokotagawa, Takane; Kanai, Satoru; Furuya, Toshio; Tsumoto, Kouhei

2018-05-01

19 F NMR has recently emerged as an efficient, sensitive tool for analyzing protein binding to small molecules, and surface plasmon resonance (SPR) is also a popular tool for this purpose. Herein a combination of 19 F NMR and SPR was used to find novel binders to the ATP-binding pocket of MAP kinase extracellular regulated kinase 2 (ERK2) by fragment screening with an original fluorinated-fragment library. The 19 F NMR screening yielded a high primary hit rate of binders to the ERK2 ATP-binding pocket compared with the rate for the SPR screening. Hit compounds were evaluated and categorized according to their ability to bind to different binding sites in the ATP-binding pocket. The binding manner was characterized by using isothermal titration calorimetry and docking simulation. Combining 19 F NMR with other biophysical methods allows the identification of multiple types of hit compounds, thereby increasing opportunities for drug design using preferred fragments. Copyright © 2018 Elsevier Ltd. All rights reserved.

Chemical characterization of a prominent phosphomonoester resonance from mammalian brain. 31P and 1H NMR analysis at 4.7 and 14.1 tesla

NASA Astrophysics Data System (ADS)

Pettegrew, J. W.; Kopp, S. J.; Dadok, J.; Minshew, N. J.; Feliksik, J. M.; Glonek, T.; Cohen, M. M.

A prominent 31P NMR resonance at 3.84 ppm in mammalian brain has been identified as ethanolamine phosphate. The identification was based on 1H and 31P NMR findings (including pH titrations) at 4.7 and 14.1 T, as well as thin-layer chromatography studies. We previously incorrectly assigned the 3.84 ppm resonance to ribose-5-phosphate. The incorrect assignment occurred because the two compounds have very similar 31P chemical shifts, and because we did not carefully consider the effects of counter ions and ionic strengths when interpreting the 31P chemical shifts. In separate preliminary studies we have demonstrated ethanolamine phosphate to be high in immature developing brain and in the degenerating brain of Alzheimer's and Huntington's disease patients. Ethanolamine phosphate may therefore serve as a sensitive marker of membrane phospholipid turnover for both in vitro and in vivo31P NMR studies.

Naphthaldimine-based simple glucose derivative as a highly selective sensor for colorimetric detection of Cu2+ ion in aqueous media

NASA Astrophysics Data System (ADS)

Dolai, Bholanath; Bhaumik, Atanu; Pramanik, Nabakumar; Ghosh, Kalyan Sundar; Atta, Ananta Kumar

2018-07-01

Naphthaldimine-based glucose derivatives 1 and 3 have been designed, synthesized and characterized. In aqueous media, glucose derivative 1, exhibited high selectivity and sensitivity towards Cu2+ ion in comparison with various cations and anions. In presence of Cu2+, sensor 1 has provided significant naked-eye detectable color change. The formation of 1-Cu2+ complex has been analyzed by UV-vis spectroscopy, 1H NMR titration experiments, mass spectrometry and DFT (density functional theory) calculations. Limit of detection of 1 as a colorimetric sensor for Cu2+ ion is found to be 0.23 μM, much lower than recommended value of World Health Organization (WHO), which makes to Cu2+ sensor 1 more effective and useful.

A highly selective colorimetric and fluorescent chemosensor for Al(III) based-on simple naphthol in aqueous solution

NASA Astrophysics Data System (ADS)

Liu, Zhaodi; Xu, Huajie; Sheng, Liangquan; Chen, Shuisheng; Huang, Deqian; Liu, Jie

2016-03-01

A colorimetric and fluorescent chemosensor (L) for Al(III) was synthesized and fully characterized. L could be both used as a colorimetric and fluorescent chemosensor for the detection of Al3 + ions with low detection limit (8.87 × 10- 7 M) in CH3CN-H2O (1:1, v/v) solution. The binding ratio of L-Al3 + was determined from the Job plot (absorption and fluorescence spectra) and MALDI-TOF MS data to be 1:1. The binding constant (Ka) of Al3 + binding to L was calculated to be 4.8 × 105 M- 1 from a Benesi-Hildebrand plot. Moreover, the binding site of L with Al3 + was determined by 1H NMR titration experiment.

FecB, a periplasmic ferric-citrate transporter from E. coli, can bind different forms of ferric-citrate as well as a wide variety of metal-free and metal-loaded tricarboxylic acids.

PubMed

Banerjee, Sambuddha; Paul, Subrata; Nguyen, Leonard T; Chu, Byron C H; Vogel, Hans J

2016-01-01

The Escherichia coli Fec system, consisting of an outer membrane receptor (FecA), a periplasmic substrate binding protein (FecB) and an inner membrane permease-ATPase type transporter (FecC/D), plays an important role in the uptake and transport of Fe(3+)-citrate. Although several FecB sequences from various organisms have been reported, there are no biophysical or structural data available for this protein to date. In this work, using isothermal titration calorimetry (ITC), we report for the first time the ability of FecB to bind different species of Fe(3+)-citrate as well as other citrate complexes with trivalent (Ga(3+), Al(3+), Sc(3+) and In(3+)) and a representative divalent metal ion (Mg(2+)) with low μM affinity. Interestingly, ITC experiments with various iron-free di- and tricarboxylic acids show that FecB can bind tricarboxylates with μM affinity but not biologically relevant dicarboxylates. The ability of FecB to bind with metal-free citrate is also observed in (1)H,(15)N HSQC-NMR titration experiments reported here at two different pH values. Further, differential scanning calorimetry (DSC) experiments indicate that the ligand-bound form of FecB has greater thermal stability than ligand-free FecB under all pH and ligand conditions tested, which is consistent with the idea of domain closure subsequent to ligand binding for this type of periplasmic binding proteins.

Potentiometric and Conductometric Study of Aqueous Solutions of Lithium and Sodium Salts of Poly(thiophen-3-ylacetic acid).

PubMed

Hostnik, Gregor; Vlachy, Vojko; Bondarev, Dmitrij; Jiří, Vohlídal; Cerar, Janez

2012-09-01

The title polymer, PTAA, practically free of ester groups was obtained by oxidative polymerization of methyl thiophen-3-ylacetate and subsequent basic hydrolysis of primary polymer. Poly(thiophen-3-ylacetic acid) has been thoroughly characterized by NMR, IR, Raman, and UV/Vis spectroscopy. The polyacid behavior during neutralization titrations with lithium and sodium hydroxides, carried out under nitrogen atmosphere, has been studied by conductometry and potentiometry. Henderson-Hasselbach plots of potentiometric titration curves show a break point at pH around 6, where the curve slope drops from 1.8 (at lower pH) to a value from 1.05 to 1.3 (at higher pH values). The UV/Vis spectra monitored during back titration show: (i) monotonous decrease of both λmax and εmax as pH decreases, (ii) the presence of the isosbestic point at 401 nm that can be ascribed to conformational transition of PTAA chains, and (iii) absence of the isosbestic point at 392 nm reported previously by other authors.

Calix[4]pyrrole as a Chloride Anion Receptor: Solvent and Counter-Cation Effects

PubMed Central

Sessler, Jonathan L.; Gross, Dustin E.; Cho, Won-Seob; Lynch, Vincent M.; Schmidtchen, Franz P.; Bates, Gareth W.; Light, Mark E.; Gale, Philip A.

2008-01-01

The interaction of calixpyrrole with several chloride salts has been studied in the solid state by X-ray crystallography as well as in solution by isothermal titration calorimetry (ITC) and 1H NMR spectroscopic titrations. The titration results in dimethylsulfoxide, acetonitrile, nitromethane, 1,2-dichloroethane and dichloromethane, carried out using various chloride salts, specifically tetraethylammonium (TEA), tetrapropylammonium (TPA), tetrabutylammonium (TBA), tetraethylphosphonium (TEP), tetrabutylphosphonium (TBP), and tetraphenylphosphonium (TPhP) showed no dependence on method of measurement. The resulting affinity constants (Ka's), on the other hand, were found to be highly dependent on the choice of solvent with Ka's ranging from 102−105 being recorded in the test solvents used for this study. In dichloromethane a strong dependence on the counter-cation was also seen, with the Ka's for the interaction with chloride ranging from 102−104. In the case of TPA, TBA and TBP the ITC data could not be fit to a 1:1 binding profile. PMID:16967979

Protein NMR Studies of Substrate Binding to Human Blood Group A and B Glycosyltransferases.

PubMed

Grimm, Lena Lisbeth; Weissbach, Sophie; Flügge, Friedemann; Begemann, Nora; Palcic, Monica M; Peters, Thomas

2017-07-04

Donor and acceptor substrate binding to human blood group A and B glycosyltransferases (GTA, GTB) has been studied by a variety of protein NMR experiments. Prior crystallographic studies had shown these enzymes to adopt an open conformation in the absence of substrates. Binding either of the donor substrate UDP-Gal or of UDP induces a semiclosed conformation. In the presence of both donor and acceptor substrates, the enzymes shift towards a closed conformation with ordering of an internal loop and the C-terminal residues, which then completely cover the donor-binding pocket. Chemical-shift titrations of uniformly 2 H, 15 N-labeled GTA or GTB with UDP affected about 20 % of all crosspeaks in 1 H, 15 N TROSY-HSQC spectra, reflecting substantial plasticity of the enzymes. On the other hand, it is this conformational flexibility that impedes NH backbone assignments. Chemical-shift-perturbation experiments with δ1-[ 13 C]methyl-Ile-labeled samples revealed two Ile residues-Ile123 at the bottom of the UDP binding pocket, and Ile192 as part of the internal loop-that were significantly disturbed upon stepwise addition of UDP and H-disaccharide, also revealing long-range perturbations. Finally, methyl TROSY-based relaxation dispersion experiments do not reveal micro- to millisecond timescale motions. Although this study reveals substantial conformational plasticity of GTA and GTB, the matter of how binding of substrates shifts the enzymes into catalytically competent states remains enigmatic. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sukri, Shahratul Ain Mohd; Heng, Lee Yook; Karim, Nurul Huda Abd

A platinum (II) salphen complex was synthesised by condensation reaction of 2,4-dihydroxylbenzaldehyde and o-phenylenediamine with potassium tetrachloroplatinate to obtain N,N′-Bis-4-(hydroxysalicylidene)-phenylenediamine-platinum (II). The structure of the complex was confirmed by {sup 1}H and {sup 13}C NMR spectroscopy, FTIR spectroscopy, CHN elemental analyses and ESI-MS spectrometry. The platinum (II) salphen complex with four donor atoms N{sub 2}O{sub 2} from its salphen ligand coordinated to platinum (II) metal centre were determined. The binding mode and interaction of this complex with calf thymus DNA was determined by UV/Vis DNA titration and emission titration. The intercalation between the DNA bases by π-π stacking due tomore » its square planar geometry and aromatic rings structures was proposed.« less

Conformational instability of the MARK3 UBA domain compromises ubiquitin recognition and promotes interaction with the adjacent kinase domain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murphy, James M.; Korzhnev, Dmitry M.; Ceccarelli, Derek F.

2012-10-23

The Par-1/MARK protein kinases play a pivotal role in establishing cellular polarity. This family of kinases contains a unique domain architecture, in which a ubiquitin-associated (UBA) domain is located C-terminal to the kinase domain. We have used a combination of x-ray crystallography and NMR dynamics experiments to understand the interaction of the human (h) MARK3 UBA domain with the adjacent kinase domain as compared with ubiquitin. The x-ray crystal structure of the linked hMARK3 kinase and UBA domains establishes that the UBA domain forms a stable intramolecular interaction with the N-terminal lobe of the kinase domain. However, solution-state NMR studiesmore » of the isolated UBA domain indicate that it is highly dynamic, undergoing conformational transitions that can be explained by a folding-unfolding equilibrium. NMR titration experiments indicated that the hMARK3 UBA domain has a detectable but extremely weak affinity for mono ubiquitin, which suggests that conformational instability of the isolated hMARK3 UBA domain attenuates binding to ubiquitin despite the presence of residues typically involved in ubiquitin recognition. Our data identify a molecular mechanism through which the hMARK3 UBA domain has evolved to bind the kinase domain, in a fashion that stabilizes an open conformation of the N- and C-terminal lobes, at the expense of its capacity to engage ubiquitin. These results may be relevant more generally to the 30% of UBA domains that lack significant ubiquitin-binding activity, and they suggest a unique mechanism by which interaction domains may evolve new binding properties.« less

Substituent Effects on the Coordination Chemistry of Metal-Binding Pharmacophores

DOE Office of Scientific and Technical Information (OSTI.GOV)

Craig, Whitney R.; Baker, Tessa W.; Marts, Amy R.

2017-09-12

A combination of XAS, UV–vis, NMR, and EPR was used to examine the binding of a series of α-hydroxythiones to CoCA. All three appear to bind preferentially in their neutral, protonated forms. Two of the three clearly bind in a monodentate fashion, through the thione sulfur alone. Thiomaltol (TM) appears to show some orientational preference, on the basis of the NMR, while it appears that thiopyromeconic acid (TPMA) retains rotational freedom. In contrast, allothiomaltol (ATM), after initially binding in its neutral form, presumably through the thione sulfur, forms a final complex that is five-coordinate via bidentate coordination of ATM. Onmore » the basis of optical titrations, we speculate that this may be due to the lower initial pKa of ATM (8.3) relative to those of TM (9.0) and TPMA (9.5). Binding through the thione is shown to reduce the hydroxyl pKa by ~0.7 pH unit on metal binding, bringing only ATM’s pKa close to the pH of the experiment, facilitating deprotonation and subsequent coordination of the hydroxyl. The data predict the presence of a solvent-exchangeable proton on TM and TPMA, and Q-band 2-pulse ESEEM experiments on CoCA + TM suggest that the proton is present. ESE-detected EPR also showed a surprising frequency dependence, giving only a subset of the expected resonances at X-band.« less

Solution structure of the C-terminal X domain of the measles virus phosphoprotein and interaction with the intrinsically disordered C-terminal domain of the nucleoprotein.

PubMed

Gely, Stéphane; Lowry, David F; Bernard, Cédric; Jensen, Malene R; Blackledge, Martin; Costanzo, Stéphanie; Bourhis, Jean-Marie; Darbon, Hervé; Daughdrill, Gary; Longhi, Sonia

2010-01-01

In this report, the solution structure of the nucleocapsid-binding domain of the measles virus phosphoprotein (XD, aa 459-507) is described. A dynamic description of the interaction between XD and the disordered C-terminal domain of the nucleocapsid protein, (N(TAIL), aa 401-525), is also presented. XD is an all alpha protein consisting of a three-helix bundle with an up-down-up arrangement of the helices. The solution structure of XD is very similar to the crystal structures of both the free and bound form of XD. One exception is the presence of a highly dynamic loop encompassing XD residues 489-491, which is involved in the embedding of the alpha-helical XD-binding region of N(TAIL). Secondary chemical shift values for full-length N(TAIL) were used to define the precise boundaries of a transient helical segment that coincides with the XD-binding domain, thus shedding light on the pre-recognition state of N(TAIL). Titration experiments with unlabeled XD showed that the transient alpha-helical conformation of N(TAIL) is stabilized upon binding. Lineshape analysis of NMR resonances revealed that residues 483-506 of N(TAIL) are in intermediate exchange with XD, while the 475-482 and 507-525 regions are in fast exchange. The N(TAIL) resonance behavior in the titration experiments is consistent with a complex binding model with more than two states.

Integration and global analysis of isothermal titration calorimetry data for studying macromolecular interactions.

PubMed

Brautigam, Chad A; Zhao, Huaying; Vargas, Carolyn; Keller, Sandro; Schuck, Peter

2016-05-01

Isothermal titration calorimetry (ITC) is a powerful and widely used method to measure the energetics of macromolecular interactions by recording a thermogram of differential heating power during a titration. However, traditional ITC analysis is limited by stochastic thermogram noise and by the limited information content of a single titration experiment. Here we present a protocol for bias-free thermogram integration based on automated shape analysis of the injection peaks, followed by combination of isotherms from different calorimetric titration experiments into a global analysis, statistical analysis of binding parameters and graphical presentation of the results. This is performed using the integrated public-domain software packages NITPIC, SEDPHAT and GUSSI. The recently developed low-noise thermogram integration approach and global analysis allow for more precise parameter estimates and more reliable quantification of multisite and multicomponent cooperative and competitive interactions. Titration experiments typically take 1-2.5 h each, and global analysis usually takes 10-20 min.

The N-terminal Region of the Ubiquitin Regulatory X (UBX) Domain-containing Protein 1 (UBXD1) Modulates Interdomain Communication within the Valosin-containing Protein p97*

PubMed Central

Trusch, Franziska; Matena, Anja; Vuk, Maja; Koerver, Lisa; Knævelsrud, Helene; Freemont, Paul S.; Meyer, Hemmo; Bayer, Peter

2015-01-01

Valosin-containing protein/p97 is an ATP-driven protein segregase that cooperates with distinct protein cofactors to control various aspects of cellular homeostasis. Mutations at the interface between the regulatory N-domain and the first of two ATPase domains (D1 and D2) deregulate the ATPase activity and cause a multisystem degenerative disorder, inclusion body myopathy associated with Paget disease of bone and frontotemporal dementia/amyotrophic lateral sclerosis. Intriguingly, the mutations affect only a subset of p97-mediated pathways correlating with unbalanced cofactor interactions and most prominently compromised binding of the ubiquitin regulatory X domain-containing protein 1 (UBXD1) cofactor during endolysosomal sorting of caveolin-1. However, how the mutations impinge on the p97-cofactor interplay is unclear so far. In cell-based endosomal localization studies, we identified a critical role of the N-terminal region of UBXD1 (UBXD1-N). Biophysical studies using NMR and CD spectroscopy revealed that UBXD1-N can be classified as intrinsically disordered. NMR titration experiments confirmed a valosin-containing protein/p97 interaction motif and identified a second binding site at helices 1 and 2 of UBXD1-N as binding interfaces for p97. In reverse titration experiments, we identified two distant epitopes on the p97 N-domain that include disease-associated residues and an additional interaction between UBXD1-N and the D1D2 barrel of p97 that was confirmed by fluorescence anisotropy. Functionally, binding of UBXD1-N to p97 led to a reduction of ATPase activity and partial protection from proteolysis. These findings indicate that UBXD1-N intercalates into the p97-ND1 interface, thereby modulating interdomain communication of p97 domains and its activity with relevance for disease pathogenesis. We propose that the polyvalent binding mode characterized for UBXD1-N is a more general principle that defines a subset of p97 cofactors. PMID:26475856

Origin and Correction of Magnetic Field Inhomogeneity at the Interface in Biphasic NMR Samples

PubMed Central

Martin, Bryan T.; Chingas, G. C.

2012-01-01

The use of susceptibility matching to minimize spectral distortion of biphasic samples layered in a standard 5 mm NMR tube is described. The approach uses magic angle spinning (MAS) to first extract chemical shift differences by suppressing bulk magnetization. Then, using biphasic coaxial samples, magnetic susceptibilities are matched by titration with a paramagnetic salt. The matched phases are then layered in a standard NMR tube where they can be shimmed and examined. Line widths of two distinct spectral lines, selected to characterize homogeneity in each phase, are simultaneously optimized. Two-dimensional distortion-free, slice-resolved spectra of an octanol/water system illustrate the method. These data are obtained using a 2D stepped-gradient pulse sequence devised for this application. Advantages of this sequence over slice-selective methods are that acquisition efficiency is increased and processing requires only conventional software. PMID:22459062

Molecular Basis of Chemokine CXCL5-Glycosaminoglycan Interactions*

PubMed Central

2016-01-01

Chemokines, a large family of highly versatile small soluble proteins, play crucial roles in defining innate and adaptive immune responses by regulating the trafficking of leukocytes, and also play a key role in various aspects of human physiology. Chemokines share the characteristic feature of reversibly existing as monomers and dimers, and their functional response is intimately coupled to interaction with glycosaminoglycans (GAGs). Currently, nothing is known regarding the structural basis or molecular mechanisms underlying CXCL5-GAG interactions. To address this missing knowledge, we characterized the interaction of a panel of heparin oligosaccharides to CXCL5 using solution NMR, isothermal titration calorimetry, and molecular dynamics simulations. NMR studies indicated that the dimer is the high-affinity GAG binding ligand and that lysine residues from the N-loop, 40s turn, β3 strand, and C-terminal helix mediate binding. Isothermal titration calorimetry indicated a stoichiometry of two oligosaccharides per CXCL5 dimer. NMR-based structural models reveal that these residues form a contiguous surface within a monomer and, interestingly, that the GAG-binding domain overlaps with the receptor-binding domain, indicating that a GAG-bound chemokine cannot activate the receptor. Molecular dynamics simulations indicate that the roles of the individual lysines are not equivalent and that helical lysines play a more prominent role in determining binding geometry and affinity. Further, binding interactions and GAG geometry in CXCL5 are novel and distinctly different compared with the related chemokines CXCL1 and CXCL8. We conclude that a finely tuned balance between the GAG-bound dimer and free soluble monomer regulates CXCL5-mediated receptor signaling and function. PMID:27471273

The site-specific basicity of thyroid hormones and their precursors as regulators of their biological functions.

PubMed

Tóth, Gergo; Hosztafi, Sándor; Kovács, Zsuzsanna; Noszál, Béla

2012-03-05

The complete macro- and microequilibrium analyses of thyroxine, liothyronine, reverse liothyronine and their biological precursors--diiodotyrosine, monoiodotyrosine and tyrosine are presented. Their biosyntheses, receptor- and transport protein-binding are shown to be distinctively dependent on the phenolate basicity. The protonation macroconstants were determined by (1)H NMR-pH and/or UV-pH titrations. Microconstants of the minor microspecies were determined by deductive methods, in which O-methylated and carboxymethylated derivatives were synthesized, and the combination of their NMR-pH and UV-pH titration provided the experimental base to evaluate all the microconstants. NMR-pH profiles, macro-, and microscopic protonation schemes, and species-specific diagrams are included. Biosyntheses of the thyroid hormones take place by oxidative coupling of two iodotyrosine residues catalyzed by thyreoperoxidase in thyreoglobulin. On the grounds of our phenolate microconstants of precursors the thyroxine over liothyronine ratio needs to be 9:1 after their biosynthesis in thyroid gland, which is in good agreement with biochemical data. The microconstants show that the phenolates are in proton donor (-OH) form in liothyronine whereas they occur in proton acceptor (-O(-)) form in thyroxine at the pH of blood. These facts explain several facts that have previously been empirically known: the affinity of liothyronine for the receptor is higher than that of thyroxine, the affinity of thyroxine for the transport proteins is higher than that of liothyronine and the selectivity of thyroxine for the OATP1C1 organic anion transporter is higher than that of liothyronine. Copyright © 2011 Elsevier B.V. All rights reserved.

Structural and dynamic characterization of eukaryotic gene regulatory protein domains in solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Andrew Loyd

Solution NMR was primarily used to characterize structure and dynamics in two different eukaryotic protein systems: the δ-Al-ε activation domain from c-jun and the Drosophila RNA-binding protein Sex-lethal. The second system is the Drosophila Sex-lethal (Sxl) protein, an RNA-binding protein which is the ``master switch`` in sex determination. Sxl contains two adjacent RNA-binding domains (RBDs) of the RNP consensus-type. The NMR spectrum of the second RBD (Sxl-RBD2) was assigned using multidimensional heteronuclear NMR, and an intermediate-resolution family of structures was calculated from primarily NOE distance restraints. The overall fold was determined to be similar to other RBDs: a βαβ-βαβ patternmore » of secondary structure, with the two helices packed against a 4-stranded anti-parallel β-sheet. In addition 15N T 1, T 2, and 15N/ 1H NOE relaxation measurements were carried out to characterize the backbone dynamics of Sxl-RBD2 in solution. RNA corresponding to the polypyrimidine tract of transformer pre-mRNA was generated and titrated into 3 different Sxl-RBD protein constructs. Combining Sxl-RBD1+2 (bht RBDs) with this RNA formed a specific, high affinity protein/RNA complex that is amenable to further NMR characterization. The backbone 1H, 13C, and 15N resonances of Sxl-RBD1+2 were assigned using a triple-resonance approach, and 15N relaxation experiments were carried out to characterize the backbone dynamics of this complex. The changes in chemical shift in Sxl-RBD1+2 upon binding RNA are observed using Sxl-RBD2 as a substitute for unbound Sxl-RBD1+2. This allowed the binding interface to be qualitatively mapped for the second domain.« less

Ascorbic Acid as a Standard for Iodometric Titrations. An Analytical Experiment for General Chemistry

NASA Astrophysics Data System (ADS)

Silva, Cesar R.; Simoni, Jose A.; Collins, Carol H.; Volpe, Pedro L. O.

1999-10-01

Ascorbic acid is suggested as the weighable compound for the standardization of iodine solutions in an analytical experiment in general chemistry. The experiment involves an iodometric titration in which iodine reacts with ascorbic acid, oxidizing it to dehydroascorbic acid. The redox titration endpoint is determined by the first iodine excess that is complexed with starch, giving a deep blue-violet color. The results of the titration of iodine solution using ascorbic acid as a calibration standard were compared with the results acquired by the classic method using a standardized solution of sodium thiosulfate. The standardization of the iodine solution using ascorbic acid was accurate and precise, with the advantages of saving time and avoiding mistakes due to solution preparation. The colorless ascorbic acid solution gives a very clear and sharp titration end point with starch. It was shown by thermogravimetric analysis that ascorbic acid can be dried at 393 K for 2 h without decomposition. This experiment allows general chemistry students to perform an iodometric titration during a single laboratory period, determining with precision the content of vitamin C in pharmaceutical formulations.

Identification and characterization of small molecule inhibitors of the calcium-dependent S100B-p53 tumor suppressor interaction.

PubMed

Markowitz, Joseph; Chen, Ijen; Gitti, Rossi; Baldisseri, Donna M; Pan, Yongping; Udan, Ryan; Carrier, France; MacKerell, Alexander D; Weber, David J

2004-10-07

The binding of S100B to p53 down-regulates wild-type p53 tumor suppressor activity in cancer cells such as malignant melanoma, so a search for small molecules that bind S100B and prevent S100B-p53 complex formation was undertaken. Chemical databases were computationally searched for potential inhibitors of S100B, and 60 compounds were selected for testing on the basis of energy scoring, commercial availability, and chemical similarity clustering. Seven of these compounds bound to S100B as determined by steady state fluorescence spectroscopy (1.0 microM < or = K(D) < or = 120 microM) and five inhibited the growth of primary malignant melanoma cells (C8146A) at comparable concentrations (1.0 microM < or = IC(50) < or = 50 microM). Additionally, saturation transfer difference (STD) NMR experiments confirmed binding and qualitatively identified protons from the small molecule at the small molecule-S100B interface. Heteronuclear single quantum coherence (HSQC) NMR titrations indicate that these compounds interact with the p53 binding site on S100B. An NMR-docked model of one such inhibitor, pentamidine, bound to Ca(2+)-loaded S100B was calculated using intermolecular NOE data between S100B and the drug, and indicates that pentamidine binds into the p53 binding site on S100B defined by helices 3 and 4 and loop 2 (termed the hinge region).

Solution structure of CEH-37 homeodomain of the nematode Caenorhabditis elegans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moon, Sunjin; Lee, Yong Woo; Kim, Woo Taek

Highlights: •We have determined solution structures of CEH-37 homedomain. •CEH-37 HD has a compact α-helical structure with HTH DNA binding motif. •Solution structure of CEH-37 HD shares its molecular topology with that of the homeodomain proteins. •Residues in the N-terminal region and HTH motif are important in binding to Caenorhabditis elegans telomeric DNA. •CEH-37 could play an important role in telomere function via DNA binding. -- Abstract: The nematode Caenorhabditis elegans protein CEH-37 belongs to the paired OTD/OTX family of homeobox-containing homeodomain proteins. CEH-37 shares sequence similarity with homeodomain proteins, although it specifically binds to double-stranded C. elegans telomeric DNA,more » which is unusual to homeodomain proteins. Here, we report the solution structure of CEH-37 homeodomain and molecular interaction with double-stranded C. elegans telomeric DNA using nuclear magnetic resonance (NMR) spectroscopy. NMR structure shows that CEH-37 homeodomain is composed of a flexible N-terminal region and three α-helices with a helix-turn-helix (HTH) DNA binding motif. Data from size-exclusion chromatography and fluorescence spectroscopy reveal that CEH-37 homeodomain interacts strongly with double-stranded C. elegans telomeric DNA. NMR titration experiments identified residues responsible for specific binding to nematode double-stranded telomeric DNA. These results suggest that C. elegans homeodomain protein, CEH-37 could play an important role in telomere function via DNA binding.« less

Development and Validation of 2D Difference Intensity Analysis for Chemical Library Screening by Protein-Detected NMR Spectroscopy.

PubMed

Egner, John M; Jensen, Davin R; Olp, Michael D; Kennedy, Nolan W; Volkman, Brian F; Peterson, Francis C; Smith, Brian C; Hill, R Blake

2018-03-02

An academic chemical screening approach was developed by using 2D protein-detected NMR, and a 352-chemical fragment library was screened against three different protein targets. The approach was optimized against two protein targets with known ligands: CXCL12 and BRD4. Principal component analysis reliably identified compounds that induced nonspecific NMR crosspeak broadening but did not unambiguously identify ligands with specific affinity (hits). For improved hit detection, a novel scoring metric-difference intensity analysis (DIA)-was devised that sums all positive and negative intensities from 2D difference spectra. Applying DIA quickly discriminated potential ligands from compounds inducing nonspecific NMR crosspeak broadening and other nonspecific effects. Subsequent NMR titrations validated chemotypes important for binding to CXCL12 and BRD4. A novel target, mitochondrial fission protein Fis1, was screened, and six hits were identified by using DIA. Screening these diverse protein targets identified quinones and catechols that induced nonspecific NMR crosspeak broadening, hampering NMR analyses, but are currently not computationally identified as pan-assay interference compounds. The results established a streamlined screening workflow that can easily be scaled and adapted as part of a larger screening pipeline to identify fragment hits and assess relative binding affinities in the range of 0.3-1.6 mm. DIA could prove useful in library screening and other applications in which NMR chemical shift perturbations are measured. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis of Novel Thiazole Based Carbaldehyde as Potential Sensor for Fluoride Anion and their Spectroscopic Properties.

PubMed

Tayade, Rajratna P; Sekar, Nagaiyan

2017-05-01

A novel thiazole based carbaldehyde bearing benzimidazole fluorophore as the receptor unit for F - anion was prepared by multi steps synthesis. Density functional theory was used to understand the structural and electronic properties the receptor. The anion sensing activities of receptor 4 were studied for various anions in acetonitrile solvent. The receptor showed fluorescence enhancement in the presence of fluoride anion due to intramolecular charge transfer (ICT) mechanism. No significant changes were observed upon addition of less basic anions such as OAc - , Cl - , Br - , I - , HSO 4 - . After the interaction of fluoride anion with the receptor 4 leads to an 88 nm red shift in emission maxima. [TBA]OH and 1 H NMR titration experiments indicated that deprotonation of N-H in the benzimidazole due to interaction with fluoride anions.

Supramolecular luminescence from oligofluorenol-based supramolecular polymer semiconductors.

PubMed

Zhang, Guang-Wei; Wang, Long; Xie, Ling-Hai; Lin, Jin-Yi; Huang, Wei

2013-11-13

Supramolecular luminescence stems from non-covalent exciton behaviors of active π-segments in supramolecular entities or aggregates via intermolecular forces. Herein, a π-conjugated oligofluorenol, containing self-complementary double hydrogen bonds, was synthesized using Suzuki coupling as a supramolecular semiconductor. Terfluorenol-based random supramolecular polymers were confirmed via concentration-dependent nuclear magnetic resonance (NMR) and dynamic light scattering (DLS). The photoluminescent spectra of the TFOH-1 solution exhibit a green emission band (g-band) at approximately ~520 nm with reversible features, as confirmed through titration experiments. Supramolecular luminescence of TFOH-1 thin films serves as robust evidence for the aggregates of g-band. Our results suggest that the presence of polyfluorene ketone defects is a sufficient condition, rather than a sufficient-necessary condition for the g-band. Supramolecular electroluminescence will push organic devices into the fields of supramolecular optoelectronics, spintronics, and mechatronics.

3-[(E)-(acridin-9‧-ylmethylidene)amino]-1-substituted thioureas and their biological activity

NASA Astrophysics Data System (ADS)

Bečka, Michal; Vilková, Mária; Salem, Othman; Kašpárková, Jana; Brabec, Viktor; Kožurková, Mária

2017-06-01

This paper describes the synthesis of a novel series of acridine thiosemicarbazones through a two-step reaction between various isothiocyanates and hydrazine followed by treatment with acridin-9-carbaldehyde. The properties of this series of seven new derivatives are studied using NMR and biochemical techniques, and the DNA-binding properties of the compounds are determined using spectrophotometric studies (UV-vis absorption, fluorescence, and circular/linear dichroism) and viscometry. The binding constants K are estimated as being in the range of 2.2 to 7.8 × 104 M- 1 and the percentage of hypochromism was found to be 22.11-49.75% (from UV-vis spectral titration). Electrophoretic experiments prove that the novel compounds demonstrate moderate inhibitory effects against Topo I activity at a concentration of 60 × 10- 6 M.

Employing a hydrazine linked asymmetric double naphthalene hybrid for efficient naked eye detection of F-: Crystal structure with real application for F-

NASA Astrophysics Data System (ADS)

Bhattacharyya, Arghyadeep; Makhal, Subhash Chandra; Ghosh, Soumen; Guchhait, Nikhil

2018-06-01

An asymmetric hydrazide, (12E, 13E)-2-((naphthalen-1-yl) methylene)-1-(1-(2-hydroxynaphthalen-6-yl) ethylidene) hydrazine (abbreviated as AH) is synthesized and characterized by standard techniques and crystal structure of AH has been obtained. The naked eye detection of F- in aqueous acetonitrile (acetonitrile: water = 7:3/v:v) by AH has been investigated by UV-Visible titration and in presence of other anions, the limit of detection being 1.31 × 10-6(M). The mechanism of F- sensing has been explored by 1H NMR titration. AH undergoes hydrogen bonding with F- followed by deprotonation. The practical utility of AH has been explored by successful test kit response and color change in toothpaste solution.

A supramolecular miktoarm star polymer based on porphyrin metal complexation in water.

PubMed

Hou, Zhanyao; Dehaen, Wim; Lyskawa, Joël; Woisel, Patrice; Hoogenboom, Richard

2017-07-25

A novel supramolecular miktoarm star polymer was successfully constructed in water from a pyridine end-decorated polymer (Py-PmDEGA) and a metalloporphyrin based star polymer (ZnTPP-(PEG) 4 ) via metal-ligand coordination. The Py-PmDEGA moiety was prepared via a combination of reversible addition-fragmentation chain transfer polymerization (RAFT) and subsequent aminolysis and Michael addition reactions to introduce the pyridine end-group. The ZnTPP(PEG) 4 star-polymer was synthesized by the reaction between tetrakis(p-hydroxyphenyl)porphyrin and toluenesulfonyl-PEG, followed by insertion of a zinc ion into the porphyrin core. The formation of a well-defined supramolecular AB 4 -type miktoarm star polymer was unambiguously demonstrated via UV-Vis spectroscopic titration, isothermal titration calorimetry (ITC) and diffusion ordered NMR spectroscopy (DOSY).

The Quantitative Resolution of a Mixture of Group II Metal Ions by Thermometric Titration with EDTA. An Analytical Chemistry Experiment.

ERIC Educational Resources Information Center

Smith, Robert L.; Popham, Ronald E.

1983-01-01

Presents an experiment in thermometric titration used in an analytic chemistry-chemical instrumentation course, consisting of two titrations, one a mixture of calcium and magnesium, the other of calcium, magnesium, and barium ions. Provides equipment and solutions list/specifications, graphs, and discussion of results. (JM)

Bis-ureidoquinoline as a selective fluoride anion sensor through hydrogen-bond interactions.

PubMed

Jo, Yunhee; Chidalla, Nagesh; Cho, Dong-Gyu

2014-10-03

Bis-ureidoquinoline shows a characteristic UV-vis absorbance and turn-on fluorescence changes in the presence of the fluoride anion. Such selective changes probably originate from the hydrogen-bond interactions, as shown by the (1)H NMR titration and DFT calculations. Bis-ureidoquinoline can be used as a fluoride-selective sensor for the detection of fluoride anions under illumination from a laboratory hand-held UV lamp.

Thermodynamic aspects of dicarboxylate recognition by simple artificial receptors.

PubMed

Linton, B R; Goodman, M S; Fan, E; van Arman, S A; Hamilton, A D

2001-11-02

Recognition of dicarboxylates by bis-functional hydrogen-bonding receptors displays divergent thermodynamics in different solvent systems. NMR titration and isothermal titration calorimetry indicated that neutral bis-urea and bis-thiourea receptors form exothermic complexes with dicarboxylates in DMSO, with a near zero entropic contribution to binding. The increased binding strength of bis-guanidinium receptors precluded quantitative measurement of binding constants in DMSO, but titration calorimetry offered a qualitative picture of the association. Formation of these 1:1 complexes was also exothermic, but additional endothermic events occurred at both lower and higher host-guest ratios. These events indicated multiple binding equilibria but did not always occur at a discrete 2:1 or 1:2 host-guest molar ratio, suggesting higher aggregates. With increasing amounts of methanol as solvent, bis-guanidinium receptors form more endothermic complexes with dicarboxylates, with a favorable entropy of association. This switch from association driven by enthalpy to one driven by entropy may reflect a change from complexation involving the formation of hydrogen bonds to that promoted by solvent liberation from binding sites.

Direct synthesis of acid-base bifunctionalized hexagonal mesoporous silica and its catalytic activity in cascade reactions.

PubMed

Shang, Fanpeng; Sun, Jianrui; Wu, Shujie; Liu, Heng; Guan, Jingqi; Kan, Qiubin

2011-03-01

A series of efficient acid-base bifunctionalized hexagonal mesoporous silica (HMS) catalysts contained aminopropyl and propanesulfonic acid have been synthesized through a simple co-condensation by protection of amino group. The results of small-angle XRD, TEM, and N(2) adsorption-desorption measurements show that the resultant materials have mesoscopic structures. X-ray photoelectron spectroscopies, elemental analysis (EA), back titration, (29)Si NMR and (13)C NMR confirm that the organosiloxanes were condensed as a part of the silica framework. The resultant catalysts exhibit excellent acid-basic properties, which make them possess high activity for one-pot deacetalization-Knoevenagel and deacetalization-nitroaldol (Henry) reactions. Copyright © 2010 Elsevier Inc. All rights reserved.

Characterization of Protein-Carbohydrate Interactions by NMR Spectroscopy.

PubMed

Grondin, Julie M; Langelaan, David N; Smith, Steven P

2017-01-01

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

Simple and Automated Coulometric Titration of Acid Using Nonisolated Electrodes

ERIC Educational Resources Information Center

Kuntzleman, Thomas S.; Kenney, Joshua B.; Hasbrouck, Scott; Collins, Michael J.; Amend, John R.

2011-01-01

Coulometric titrations involve the quantification of analyte by measurements of current and time. In most coulometric titrations, the anode and cathode are placed in isolated cells that are connected by a salt bridge. By contrast, the experiments described here involve coulometric titrations (of acidic protons in solution) using a silver anode and…

Ligand-receptor binding affinities from saturation transfer difference (STD) NMR spectroscopy: the binding isotherm of STD initial growth rates.

PubMed

Angulo, Jesús; Enríquez-Navas, Pedro M; Nieto, Pedro M

2010-07-12

The direct evaluation of dissociation constants (K(D)) from the variation of saturation transfer difference (STD) NMR spectroscopy values with the receptor-ligand ratio is not feasible due to the complex dependence of STD intensities on the spectral properties of the observed signals. Indirect evaluation, by competition experiments, allows the determination of K(D), as long as a ligand of known affinity is available for the protein under study. Herein, we present a novel protocol based on STD NMR spectroscopy for the direct measurements of receptor-ligand dissociation constants (K(D)) from single-ligand titration experiments. The influence of several experimental factors on STD values has been studied in detail, confirming the marked impact on standard determinations of protein-ligand affinities by STD NMR spectroscopy. These factors, namely, STD saturation time, ligand residence time in the complex, and the intensity of the signal, affect the accumulation of saturation in the free ligand by processes closely related to fast protein-ligand rebinding and longitudinal relaxation of the ligand signals. The proposed method avoids the dependence of the magnitudes of ligand STD signals at a given saturation time on spurious factors by constructing the binding isotherms using the initial growth rates of the STD amplification factors, in a similar way to the use of NOE growing rates to estimate cross relaxation rates for distance evaluations. Herein, it is demonstrated that the effects of these factors are cancelled out by analyzing the protein-ligand association curve using STD values at the limit of zero saturation time, when virtually no ligand rebinding or relaxation takes place. The approach is validated for two well-studied protein-ligand systems: the binding of the saccharides GlcNAc and GlcNAcbeta1,4GlcNAc (chitobiose) to the wheat germ agglutinin (WGA) lectin, and the interaction of the amino acid L-tryptophan to bovine serum albumin (BSA). In all cases, the experimental K(D) measured under different experimental conditions converged to the thermodynamic values. The proposed protocol allows accurate determinations of protein-ligand dissociation constants, extending the applicability of the STD NMR spectroscopy for affinity measurements, which is of particular relevance for those proteins for which a ligand of known affinity is not available.

The binding of manganese(II) and zinc(II) to the synthetic oligonucleotide d(C-G-C-G-A-A-T-T-C-G-C-G)2. A 1H NMR study.

PubMed

Frøystein, N A; Sletten, E

1991-03-01

The interaction of the synthetic oligonucleotide d(C-G-C-G-A-A-T-T-C-G-C-G)2 with two different transition-metal ions has been investigated in aqueous solution by means of 1H NMR spectroscopy. The effects on the DNA due to the presence of manganese(II) or zinc(II) have been monitored by observing the paramagnetic broadening and diamagnetic shifts of the non-exchangeable proton resonance lines, respectively. The 1H NMR spectra acquired during the course of the manganese(II) titration show very distinct broadening effects on certain DNA resonance lines. Primarily, the H8 resonance of G4 is affected, but also the H5 and H6 resonances of C3 are clearly affected by the metal. The results imply that the binding of manganese(II) to DNA is sequence specific. The 1H spectra obtained during the zinc(II) titration reveal diamagnetic shift effects which largely conform with the paramagnetic broadening effects due to the presence of manganese(II), although this picture is somewhat more complex. The H8 resonance of G4 displays a clearly visible high-field shift, while for the other guanosine H8 protons this effect is absent. The H1' and H2' protons of C3 show an effect of similar strength, although in the opposite direction, while H5 and H6 of C3 are only slightly affected. Local differences in the structure of the DNA and the basicities of potential binding sites on different base steps in the sequence might account for the observed sequence selectivity.

An NMR-Based Structural Rationale for Contrasting Stoichiometry and Ligand Binding Site(s) in Fatty Acid-binding Proteins†

PubMed Central

He, Yan; Estephan, Rima; Yang, Xiaomin; Vela, Adriana; Wang, Hsin; Bernard, Cédric; Stark, Ruth E.

2011-01-01

Liver fatty acid-binding protein (LFABP) is a 14-kDa cytosolic polypeptide, differing from other family members in number of ligand binding sites, diversity of bound ligands, and transfer of fatty acid(s) to membranes primarily via aqueous diffusion rather than direct collisional interactions. Distinct two-dimensional 1H-15N NMR signals indicative of slowly exchanging LFABP assemblies formed during stepwise ligand titration were exploited, without solving the protein-ligand complex structures, to yield the stoichiometries for the bound ligands, their locations within the protein binding cavity, the sequence of ligand occupation, and the corresponding protein structural accommodations. Chemical shifts were monitored for wild-type LFABP and a R122L/S124A mutant in which electrostatic interactions viewed as essential to fatty acid binding were removed. For wild-type LFABP the results compared favorably with previous tertiary structures of oleate-bound wild-type LFABP in crystals and in solution: there are two oleates, one U-shaped ligand that positions the long hydrophobic chain deep within the cavity and another extended structure with the hydrophobic chain facing the cavity and the carboxylate group lying close to the protein surface. The NMR titration validated a prior hypothesis that the first oleate to enter the cavity occupies the internal protein site. In contrast, 1H/15N chemical shift changes supported only one liganded oleate for R122L/S124A LFABP, at an intermediate location within the protein cavity. A rationale based on protein sequence and electrostatics was developed to explain the stoichiometry and binding site trends for LFABPs and to put these findings into context within the larger protein family. PMID:21226535

Interaction of the S100A6 mutant (C3S) with the V domain of the receptor for advanced glycation end products (RAGE)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mohan, Sepuru K., E-mail: mohansepuri@gmail.com; Gupta, Arun A., E-mail: ninja14gupta@gmail.com; Yu, Chin, E-mail: cyu.nthu@gmail.com

2013-05-03

Highlights: •The halo human S100A6 (C3S) NMR chemical shifts were assigned. •The interactions between S100A6m and RAGE V domain was investigated by ITC. •The residues involved in the S100A6m–RAGE V domain binding were mapped by {sup 1}H–{sup 15}N HSQC titration. •S100A6–RAGE V domain tetrameric complex model was generated from NMR studies. •The S100A6–RAGE V domain interface regions were elucidated based on HADDOCK model. -- Abstract: S100A6 is involved in several vital biological functions, such as calcium sensing and cell proliferation. It is a homodimeric protein that belongs to the S100 protein family. The receptor for advanced glycation end products (RAGE)more » has been shown to play a role in the progression of various disease conditions, such as diabetes and immune/inflammatory disorders. Information regarding the association of RAGE with S100 proteins at a molecular level is useful to understand the diversity of the RAGE signaling pathways. In this report, biomolecular NMR techniques were utilized for the resonance assignment of the C3S mutation in human S100A6 and characterizing its interaction with the RAGE V domain. Further binding affinity between S100A6m and the RAGE V domain was determined by isothermal titration calorimetric studies. HADDOCK was used to generate a heterotetramer model of the S100A6m–RAGE V domain complex. This model provides an important insights into the S100–RAGE cellular signaling pathway.« less

Label-free quantitative 1H NMR spectroscopy to study low-affinity ligand–protein interactions in solution: A contribution to the mechanism of polyphenol-mediated astringency

PubMed Central

Delius, Judith; Frank, Oliver

2017-01-01

Nuclear magnetic resonance (NMR) spectroscopy is well-established in assessing the binding affinity between low molecular weight ligands and proteins. However, conventional NMR-based binding assays are often limited to small proteins of high purity and may require elaborate isotopic labeling of one of the potential binding partners. As protein–polyphenol complexation is assumed to be a key event in polyphenol-mediated oral astringency, here we introduce a label-free, ligand-focused 1H NMR titration assay to estimate binding affinities and characterize soluble complex formation between proteins and low molecular weight polyphenols. The method makes use of the effects of NMR line broadening due to protein–ligand interactions and quantitation of the non-bound ligand at varying protein concentrations by quantitative 1H NMR spectroscopy (qHNMR) using electronic reference to access in vivo concentration (ERETIC 2). This technique is applied to assess the interaction kinetics of selected astringent tasting polyphenols and purified mucin, a major lubricating glycoprotein of human saliva, as well as human whole saliva. The protein affinity values (BC50) obtained are subsequently correlated with the intrinsic mouth-puckering, astringent oral sensation imparted by these compounds. The quantitative NMR method is further exploited to study the effect of carboxymethyl cellulose, a candidate “anti-astringent” protein binding antagonist, on the polyphenol–protein interaction. Consequently, the NMR approach presented here proves to be a versatile tool to study the interactions between proteins and low-affinity ligands in solution and may find promising applications in the discovery of bioactives. PMID:28886151

The influence of mechanochemical modification on prevention of toxic ability of humic acids towards phenanthrene in aquatic environment

NASA Astrophysics Data System (ADS)

Shekhovtsova, N. S.; Maltseva, E. V.; Glyzina, T. S.; Ovchinnikova, I. S.

2015-11-01

The aim of the research work is to quantify interaction between phenanthrene with modified humic acids in aquatic environment. The changes in the structure and properties of humic acids after modifications were studied with 1H NMR spectroscopy and potentiometric titration methods. Our research demonstrates that the application of thiourea as a modified agent increases the binding capacity of humic acids towards phenanthrene.

Host-Guest Interaction of Cucurbit[8]uril with N-(3-Aminopropyl)cyclohexylamine: Cyclohexyl Encapsulation Triggered Ternary Complex.

PubMed

Xia, Yu; Wang, Chuan-Zeng; Tian, Mengkui; Tao, Zhu; Ni, Xin-Long; Prior, Timothy J; Redshaw, Carl

2018-01-15

The host-guest interaction of a series of cyclohexyl-appended guests with cucurbit[8]uril (Q[8]) was studied by ¹H NMR spectroscopy, isothermal titration calorimetry (ITC), and X-ray crystallography. The X-ray structure revealed that two cycloalkane moieties can be simultaneously encapsulated in the hydrophobic cavity of the Q[8] host to form a ternary complex for the first time.

Agents Within our Midst

DTIC Science & Technology

2012-03-14

agents; and the development of bio -monitoring protocols for civilian and service personnel during a chemical attack. These efforts have resulted in greater...produced by staphylococcal bacteria that is and is classified as a CDC select agent which has the potential to be used as a biological weapon .1...NMR chemical shift perturbation titrations with Fab (fragment, antigen binding regions) domains of 20B1, 14G8, and 6D3 using deuterated (2H) SEB

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kroupa, Daniel M.; Anderson, Nicholas C.; Castaneda, Chloe V.

Here, we employed quantitative NMR spectroscopy and spectrophotometric absorbance titration to study a quantum dot X-type ligand exchange reaction. We find that the exchange is highly cooperative, where at low extents of exchange the change in free energy of the reaction, Δ G XC, is ~11 kJ mol –1 while at higher extents of exchange Δ G XC saturates to ~–4 kJ mol –1. A modified Fowler binding isotherm is developed to describe the reaction.

Reproducibility of NMR Analysis of Urine Samples: Impact of Sample Preparation, Storage Conditions, and Animal Health Status

PubMed Central

Schreier, Christina; Kremer, Werner; Huber, Fritz; Neumann, Sindy; Pagel, Philipp; Lienemann, Kai; Pestel, Sabine

2013-01-01

Introduction. Spectroscopic analysis of urine samples from laboratory animals can be used to predict the efficacy and side effects of drugs. This employs methods combining 1H NMR spectroscopy with quantification of biomarkers or with multivariate data analysis. The most critical steps in data evaluation are analytical reproducibility of NMR data (collection, storage, and processing) and the health status of the animals, which may influence urine pH and osmolarity. Methods. We treated rats with a solvent, a diuretic, or a nephrotoxicant and collected urine samples. Samples were titrated to pH 3 to 9, or salt concentrations increased up to 20-fold. The effects of storage conditions and freeze-thaw cycles were monitored. Selected metabolites and multivariate data analysis were evaluated after 1H NMR spectroscopy. Results. We showed that variation of pH from 3 to 9 and increases in osmolarity up to 6-fold had no effect on the quantification of the metabolites or on multivariate data analysis. Storage led to changes after 14 days at 4°C or after 12 months at −20°C, independent of sample composition. Multiple freeze-thaw cycles did not affect data analysis. Conclusion. Reproducibility of NMR measurements is not dependent on sample composition under physiological or pathological conditions. PMID:23865070

Reproducibility of NMR analysis of urine samples: impact of sample preparation, storage conditions, and animal health status.

PubMed

Schreier, Christina; Kremer, Werner; Huber, Fritz; Neumann, Sindy; Pagel, Philipp; Lienemann, Kai; Pestel, Sabine

2013-01-01

Spectroscopic analysis of urine samples from laboratory animals can be used to predict the efficacy and side effects of drugs. This employs methods combining (1)H NMR spectroscopy with quantification of biomarkers or with multivariate data analysis. The most critical steps in data evaluation are analytical reproducibility of NMR data (collection, storage, and processing) and the health status of the animals, which may influence urine pH and osmolarity. We treated rats with a solvent, a diuretic, or a nephrotoxicant and collected urine samples. Samples were titrated to pH 3 to 9, or salt concentrations increased up to 20-fold. The effects of storage conditions and freeze-thaw cycles were monitored. Selected metabolites and multivariate data analysis were evaluated after (1)H NMR spectroscopy. We showed that variation of pH from 3 to 9 and increases in osmolarity up to 6-fold had no effect on the quantification of the metabolites or on multivariate data analysis. Storage led to changes after 14 days at 4°C or after 12 months at -20°C, independent of sample composition. Multiple freeze-thaw cycles did not affect data analysis. Reproducibility of NMR measurements is not dependent on sample composition under physiological or pathological conditions.

Spectroscopic and calorimetric studies on the interaction between PAMAM G4-OH and 5-fluorouracil in aqueous solutions

NASA Astrophysics Data System (ADS)

Buczkowski, Adam; Urbaniak, Pawel; Piekarski, Henryk; Palecz, Bartlomiej

2017-01-01

The results of spectroscopic measurements (an increase in solubility, equilibrium dialysis, 1H NMR titration) and calorimetric measurements (isothermal titration ITC) indicate spontaneous (ΔG < 0) binding of 5-fluorouracil molecules by PAMAM G4-OH dendrimer with terminal hydroxyl groups in an aqueous solution. PAMAM G4-OH dendrimer bonds about n = 8 ± 1 molecules of the drug with an equilibrium constant of K = 70 ± 10. The process of saturating the dendrimer active sites by the drug molecules is exothermal (ΔH < 0) and is accompanied by an advantageous change in entropy (ΔS > 0). The parameters of binding 5-fluorouracil by PAMAM G4-OH dendrimer were compared with those of binding this drug by the macromolecules of PAMAM G3-OH and G5-OH.

Proton dissociation properties of arylphosphonates: Determination of accurate Hammett equation parameters.

PubMed

Dargó, Gergő; Bölcskei, Adrienn; Grün, Alajos; Béni, Szabolcs; Szántó, Zoltán; Lopata, Antal; Keglevich, György; Balogh, György T

2017-09-05

Determination of the proton dissociation constants of several arylphosphonic acid derivatives was carried out to investigate the accuracy of the Hammett equations available for this family of compounds. For the measurement of the pK a values modern, accurate methods, such as the differential potentiometric titration and NMR-pH titration were used. We found our results significantly different from the pK a values reported before (pK a1 : MAE = 0.16 pK a2 : MAE=0.59). Based on our recently measured pK a values, refined Hammett equations were determined that might be used for predicting highly accurate ionization constants of newly synthesized compounds (pK a1 =1.70-0.894σ, pK a2 =6.92-0.934σ). Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular tweezers with varying anions: a comparative study.

PubMed

Dutt, Som; Wilch, Constanze; Gersthagen, Thomas; Talbiersky, Peter; Bravo-Rodriguez, Kenny; Hanni, Matti; Sánchez-García, Elsa; Ochsenfeld, Christian; Klärner, Frank-Gerrit; Schrader, Thomas

2013-07-05

Selective binding of the phosphate-substituted molecular tweezer 1a to protein lysine residues was suggested to explain the inhibition of certain enzymes and the aberrant aggregation of amyloid petide Aβ42 or α-synuclein, which are assumed to be responsible for Alzheimer's and Parkinson's disease, respectively. In this work we systematically investigated the binding of four water-soluble tweezers 1a-d (substituted by phosphate, methanephosphonate, sulfate, or O-methylenecarboxylate groups) to amino acids and peptides containing lysine or arginine residues by using fluorescence spectroscopy, NMR spectroscopy, and isothermal titration calorimetry (ITC). The comparison of the experimental results with theoretical data obtained by a combination of QM/MM and ab initio(1)H NMR shift calculations provides clear evidence that the tweezers 1a-c bind the amino acid or peptide guest molecules by threading the lysine or arginine side chain through the tweezers' cavity, whereas in the case of 1d the guest molecule is preferentially positioned outside the tweezer's cavity. Attractive ionic, CH-π, and hydrophobic interactions are here the major binding forces. The combination of experiment and theory provides deep insight into the host-guest binding modes, a prerequisite to understanding the exciting influence of these tweezers on the aggregation of proteins and the activity of enzymes.

Supramolecular Luminescence from Oligofluorenol-Based Supramolecular Polymer Semiconductors

PubMed Central

Zhang, Guang-Wei; Wang, Long; Xie, Ling-Hai; Lin, Jin-Yi; Huang, Wei

2013-01-01

Supramolecular luminescence stems from non-covalent exciton behaviors of active π-segments in supramolecular entities or aggregates via intermolecular forces. Herein, a π-conjugated oligofluorenol, containing self-complementary double hydrogen bonds, was synthesized using Suzuki coupling as a supramolecular semiconductor. Terfluorenol-based random supramolecular polymers were confirmed via concentration-dependent nuclear magnetic resonance (NMR) and dynamic light scattering (DLS). The photoluminescent spectra of the TFOH-1 solution exhibit a green emission band (g-band) at approximately ~520 nm with reversible features, as confirmed through titration experiments. Supramolecular luminescence of TFOH-1 thin films serves as robust evidence for the aggregates of g-band. Our results suggest that the presence of polyfluorene ketone defects is a sufficient condition, rather than a sufficient-necessary condition for the g-band. Supramolecular electroluminescence will push organic devices into the fields of supramolecular optoelectronics, spintronics, and mechatronics. PMID:24232455

Reversible sol-to-gel transformation of uracil gelators: specific colorimetric and fluorimetric sensor for fluoride ions.

PubMed

Xing, Ling-Bao; Yang, Bing; Wang, Xiao-Jun; Wang, Jiu-Ju; Chen, Bin; Wu, Qianhong; Peng, Hui-Xing; Zhang, Li-Ping; Tung, Chen-Ho; Wu, Li-Zhu

2013-03-05

A new type of anthracene organogelator based on uracil was obtained using organic aromatic solvents, cyclohexane, DMSO, ethanol, and ethyl acetate. It was further characterized by field-emission scanning electron microscopy and transmission electron microscopy. Specifically, the resulting organogels were demonstrated to be promising colorimetric and fluorescent sensors toward fluoride ions with high sensitivity and selectivity, accompanying the disruption of the gelators. Spectroscopic study and (1)H NMR titration experiment revealed that the deprotonation of the hydrogen atom on the N position of uracil moiety by fluoride ions is responsible for the recognition events, evidenced by immediate transformation from the sol phase to the gel state upon adding a small amount of a proton solvent, methanol. The process is reversible, with zero loss in sensing activity and sol-to-gel transformation ability even after five runs.

A high selective anion colorimetric sensor based on salicylaldehyde for fluoride in aqueous media.

PubMed

Li, Jianwei; Lin, Hai; Cai, Zunsheng; Lin, Huakuan

2009-06-01

A new and simple salicylaldehyde-based sensor 1 designed for fluoride sensing has been investigated in DMSO and even in the 9/1 DMSO/H(2)O (v/v) mixtures. The affinity constants of receptor 1 for anionic species in the 9/1 DMSO/H(2)O (v/v) reveal that it is sensitive to F. Also, the color changes induced by anions can provide a way of detection by 'naked-eye'. These result can be substantiated by the spectrum changes upon the addition of 25equiv. anions to 1 in the 9/1 DMSO/H(2)O solution. The further insights to the nature of interactions between the sensor 1 and F(-) were investigated by (1)H NMR titration experiments in 9/1 DMSO-d(6)/H(2)O (v/v). In addition, the proposed binding mode between 1 and F(-) was suggested.

A Series of Fluorescent and Colorimetric Chemodosimeters for Selective Recognition of Cyanide Based on the FRET Mechanism.

PubMed

Hua, Ying-Xi; Shao, Yongliang; Wang, Ya-Wen; Peng, Yu

2017-06-16

A series of fluorescence "turn-on" probes (PY, AN, NA, B1, and B2) have been developed and successfully applied to detect cyanide anions based on the Michael addition reaction and FRET mechanism. These probes demonstrated good selectivity, high sensitivity, and very fast recognition for CN - . In particular, the fluorescence response of probe NA finished within 3 s. Low limits of detection (down to 63 nM) are also obtained in these probes with remarkable fluorescence enhancement factors. In addition, fluorescence colors of these probes turned to blue, yellow, or orange upon sensing CN - . In UV-vis mode, all of them showed ratiometric response for CN - . 1 H NMR titration experiments and TDDFT calculations were taken to verify the mechanism of the specific reaction and fluorescence properties of the corresponding compounds. Moreover, silica gel plates with these probes were also fabricated and utilized to detect cyanide.

Atomic Resolution Description of the Interaction between the Nucleoprotein and Phosphoprotein of Hendra Virus

PubMed Central

Yabukarski, Filip; Blocquel, David; Schneider, Robert; Tarbouriech, Nicolas; Papageorgiou, Nicolas; Ruigrok, Rob W. H.; Jamin, Marc; Jensen, Malene Ringkjøbing; Longhi, Sonia; Blackledge, Martin

2013-01-01

Hendra virus (HeV) is a recently emerged severe human pathogen that belongs to the Henipavirus genus within the Paramyxoviridae family. The HeV genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid. Recruitment of the viral polymerase onto the nucleocapsid template relies on the interaction between the C-terminal domain, NTAIL, of N and the C-terminal X domain, XD, of the polymerase co-factor phosphoprotein (P). Here, we provide an atomic resolution description of the intrinsically disordered NTAIL domain in its isolated state and in intact nucleocapsids using nuclear magnetic resonance (NMR) spectroscopy. Using electron microscopy, we show that HeV nucleocapsids form herringbone-like structures typical of paramyxoviruses. We also report the crystal structure of XD of P that consists of a three-helix bundle. We study the interaction between NTAIL and XD using NMR titration experiments and provide a detailed mapping of the reciprocal binding sites. We show that the interaction is accompanied by α-helical folding of the molecular recognition element of NTAIL upon binding to a hydrophobic patch on the surface of XD. Finally, using solution NMR, we investigate the interaction between intact nucleocapsids and XD. Our results indicate that monomeric XD binds to NTAIL without triggering an additional unwinding of the nucleocapsid template. The present results provide a structural description at the atomic level of the protein-protein interactions required for transcription and replication of HeV, and the first direct observation of the interaction between the X domain of P and intact nucleocapsids in Paramyxoviridae. PMID:24086133

Atomic resolution description of the interaction between the nucleoprotein and phosphoprotein of Hendra virus.

PubMed

Communie, Guillaume; Habchi, Johnny; Yabukarski, Filip; Blocquel, David; Schneider, Robert; Tarbouriech, Nicolas; Papageorgiou, Nicolas; Ruigrok, Rob W H; Jamin, Marc; Jensen, Malene Ringkjøbing; Longhi, Sonia; Blackledge, Martin

2013-01-01

Hendra virus (HeV) is a recently emerged severe human pathogen that belongs to the Henipavirus genus within the Paramyxoviridae family. The HeV genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid. Recruitment of the viral polymerase onto the nucleocapsid template relies on the interaction between the C-terminal domain, N(TAIL), of N and the C-terminal X domain, XD, of the polymerase co-factor phosphoprotein (P). Here, we provide an atomic resolution description of the intrinsically disordered N(TAIL) domain in its isolated state and in intact nucleocapsids using nuclear magnetic resonance (NMR) spectroscopy. Using electron microscopy, we show that HeV nucleocapsids form herringbone-like structures typical of paramyxoviruses. We also report the crystal structure of XD of P that consists of a three-helix bundle. We study the interaction between N(TAIL) and XD using NMR titration experiments and provide a detailed mapping of the reciprocal binding sites. We show that the interaction is accompanied by α-helical folding of the molecular recognition element of N(TAIL) upon binding to a hydrophobic patch on the surface of XD. Finally, using solution NMR, we investigate the interaction between intact nucleocapsids and XD. Our results indicate that monomeric XD binds to N(TAIL) without triggering an additional unwinding of the nucleocapsid template. The present results provide a structural description at the atomic level of the protein-protein interactions required for transcription and replication of HeV, and the first direct observation of the interaction between the X domain of P and intact nucleocapsids in Paramyxoviridae.

The Acid-Base Titration of a Very Weak Acid: Boric Acid

ERIC Educational Resources Information Center

Celeste, M.; Azevedo, C.; Cavaleiro, Ana M. V.

2012-01-01

A laboratory experiment based on the titration of boric acid with strong base in the presence of d-mannitol is described. Boric acid is a very weak acid and direct titration with NaOH is not possible. An auxiliary reagent that contributes to the release of protons in a known stoichiometry facilitates the acid-base titration. Students obtain the…

Analysis of monoglycerides, diglycerides, sterols, and free fatty acids in coconut (Cocos nucifera L.) oil by 31P NMR spectroscopy.

PubMed

Dayrit, Fabian M; Buenafe, Olivia Erin M; Chainani, Edward T; de Vera, Ian Mitchelle S

2008-07-23

Phosphorus-31 nuclear magnetic resonance spectroscopy ( (31)P NMR) was used to differentiate virgin coconut oil (VCO) from refined, bleached, deodorized coconut oil (RCO). Monoglycerides (MGs), diglycerides (DGs), sterols, and free fatty acids (FFAs) in VCO and RCO were converted into dioxaphospholane derivatives and analyzed by (31)P NMR. On the average, 1-MG was found to be higher in VCO (0.027%) than RCO (0.019%). 2-MG was not detected in any of the samples down to a detection limit of 0.014%. On the average, total DGs were lower in VCO (1.55%) than RCO (4.10%). When plotted in terms of the ratio [1,2-DG/total DGs] versus total DGs, VCO and RCO samples grouped separately. Total sterols were higher in VCO (0.096%) compared with RCO (0.032%), and the FFA content was 8 times higher in VCO than RCO (0.127% vs 0.015%). FFA determination by (31)P NMR and titration gave comparable results. Principal components analysis shows that the 1,2-DG, 1,3-DG, and FFAs are the most important parameters for differentiating VCO from RCO.

Mass spectrometry for fragment screening.

PubMed

Chan, Daniel Shiu-Hin; Whitehouse, Andrew J; Coyne, Anthony G; Abell, Chris

2017-11-08

Fragment-based approaches in chemical biology and drug discovery have been widely adopted worldwide in both academia and industry. Fragment hits tend to interact weakly with their targets, necessitating the use of sensitive biophysical techniques to detect their binding. Common fragment screening techniques include differential scanning fluorimetry (DSF) and ligand-observed NMR. Validation and characterization of hits is usually performed using a combination of protein-observed NMR, isothermal titration calorimetry (ITC) and X-ray crystallography. In this context, MS is a relatively underutilized technique in fragment screening for drug discovery. MS-based techniques have the advantage of high sensitivity, low sample consumption and being label-free. This review highlights recent examples of the emerging use of MS-based techniques in fragment screening. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

A newly synthesized thiazole derivative as a fluoride ion chemosensor: naked-eye, spectroscopic, electrochemical and NMR studies.

PubMed

Sarıgüney, Ahmet Burak; Saf, Ahmet Özgür; Coşkun, Ahmet

2014-07-15

2,3-Indoledione 3-thiosemicarbazone (TSCI) and a novel compound 3-(2-(4-(4-phenoxyphenyl)thiazol-2-yl)hydrazono)indolin-2-one (FTHI) were synthesized with high yield and characterized by spectroscopic techniques. The complexation behaviors of TSCI and FTHI for various anionic species (F(-), Cl(-), Br(-), I(-), NO2(-), NO3(-), BzO(-), HSO4(-), ClO4(-)) in CH3CN were investigated and compared by UV-vis spectroscopy, cyclic voltammetry and (1)H NMR titration techniques. FTHI showed high degree of selectivity for fluoride over other anions. This selectivity could be easily observed by the naked eye, indicating that FTHI is potential colorimetric sensor for fluoride anion. Copyright © 2014 Elsevier B.V. All rights reserved.

Host-guest inclusion system of ferulic acid with p-Sulfonatocalix[n]arenes: Preparation, characterization and antioxidant activity

NASA Astrophysics Data System (ADS)

Chao, Jianbin; Wang, Huijuan; Song, Kailun; Wang, Yongzhao; Zuo, Ying; Zhang, Liwei; Zhang, Bingtai

2017-02-01

The inclusion complexes of ferulic acid (FA) with p-Sulfonatocalix[n]arenes (SCXn, n = 4, 6, 8) were prepared and characterized both in the solid state and in solution using fluorescence spectroscopy, 1H nuclear magnetic resonance (1H NMR), attenuated total reflectance-fourier transform infrared spectroscopy (ATR-FTIR), atomic force microscopy (AFM) and differential scanning calorimetry (DSC). The results show that FA is able to form inclusion complexes with SCXn in a molar ratio of 1:1, causing a significant decrease in the fluorescence intensity of FA. The association constant of the inclusion complexes was calculated from the fluorescence titration data. 1H NMR spectroscopy analysis demonstrates that the aromatic ring and methoxy group of FA are partially covered by SCXn.

Caffeine and Sugars Interact in Aqueous Solutions: A Simulation and NMR Study

PubMed Central

Tavagnacco, Letizia; Engström, Olof; Schnupf, Udo; Saboungi, Marie-Louise; Himmel, Michael; Widmalm, Göran; Cesàro, Attilio; Brady, John W.

2012-01-01

Molecular dynamics simulations were carried out on several systems of caffeine interacting with simple sugars. These included a single caffeine molecule in a 3 molal solution of α-D-glucopyranose, at a caffeine concentration of 0.083 molal; a single caffeine in a 3 molal solution of β-D-glucopyranose, and a single caffeine molecule in a 1.08 molal solution of sucrose (table sugar). Parallel Nuclear Magnetic Resonance titration experiments were carried out on the same solutions under similar conditions. Consistent with previous thermodynamic experiments, the sugars were found to have an affinity for the caffeine molecules in both the simulations and experiments, and that the binding in these complexes occurs by face-to-face stacking of the hydrophobic triad of protons of the pyranose rings against the caffeine face, rather than by hydrogen bonding. For the disaccharide, the binding occurs via stacking of the glucose ring against the caffeine, with a lesser affinity for the fructose observed. These findings are consistent with the association being driven by hydrophobic hydration, and are similar to the previously observed binding of glucose rings to various other planar molecules, including indole, serotonin, and phenol. PMID:22897449

Caffeine and sugars interact in aqueous solutions: a simulation and NMR study.

PubMed

Tavagnacco, Letizia; Engström, Olof; Schnupf, Udo; Saboungi, Marie-Louise; Himmel, Michael; Widmalm, Göran; Cesàro, Attilio; Brady, John W

2012-09-27

Molecular dynamics simulations were carried out on several systems of caffeine interacting with simple sugars. These included a single caffeine molecule in a 3 m solution of α-D-glucopyranose, at a caffeine concentration of 0.083 m, a single caffeine in a 3 m solution of β-D-glucopyranose, and a single caffeine molecule in a 1.08 m solution of sucrose (table sugar). Parallel nuclear magnetic resonance titration experiments were carried out on the same solutions under similar conditions. Consistent with previous thermodynamic experiments, the sugars were found to have an affinity for the caffeine molecules in both the simulations and experiments, and the binding in these complexes occurs by face-to-face stacking of the hydrophobic triad of protons of the pyranose rings against the caffeine face, rather than by hydrogen bonding. For the disaccharide, the binding occurs via stacking of the glucose ring against the caffeine, with a lesser affinity for the fructose observed. These findings are consistent with the association being driven by hydrophobic hydration and are similar to the previously observed binding of glucose rings to various other planar molecules, including indole, serotonin, and phenol.

Phosphorus-31, sup 15 N, and sup 13 C NMR of glyphosate: Comparison of pH titrations to the herbicidal dead-end complex with 5-enolpyruvoylshikimate-3-phosphate synthase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castellino, S.; Leo, G.C.; Sammons, R.D.

1989-05-02

The herbicidal dead-end ternary complex (E{sup S3P}{sub Glyph}) of glyphosate (N-(phosphonomethyl)glycine) with 5-enolpyruvoylshikimate-3-phosphate synthase (EPSPS) and the substrate shikimate 3-phosphate (S3P) has been characterized by {sup 31}P, {sup 15}N, and {sup 13}C NMR. The NMR spectra of EPSPS-bound glyphosate show unique chemical shifts ({delta}) for each of the three nuclei. By {sup 31}P NMR, glyphosate in the dead-end complex is a distinct species 3.5 ppm downfield from free glyphosate. The {sup 13}C signal of glyphosate in the dead-end complex is shifted 4 ppm downfield from that of free glyphosate. The {sup 15}N signal for glyphosate (99%) in the dead-end complexmore » is 5 ppm further downfield than that of any free zwitterionic species and 10 ppm downfield from that of the average free species at pH 10.1. The structures of each ionic state of glyphosate are modeled with force field calculations by using MacroModel. A correlation is made for the {sup 31}P {delta} and the C-P-O bond angle, and the {sup 13}C and {sup 15}N {delta} values are postulated to be related to C-C-O and C-N-C bond angles, respectively. The downfield {sup 31}P chemical shift perturbation for S3P in the EPSPS binary complex is consistent with ionization of the 3-phosphate of S3P upon binding. Comparison with the S3P {sup 31}P {delta} vs pH titration curve specifies predominantly the dianion of the 3-phosphate in the E{sup S3P} binary complex, while the E{sup S3P}{sub Glyph} complex indicates net protonation at the 3-phosphate. Chemical shift perturbations of this latter type may be explained by changes in the O-P-O bond angle.« less

Nanodisc-Targeted STD NMR Spectroscopy Reveals Atomic Details of Ligand Binding to Lipid Environments.

PubMed

Muñoz-García, Juan C; Inacio Dos Reis, Rosana; Taylor, Richard J; Henry, Alistair J; Watts, Anthony

2018-05-18

Saturation transfer difference (STD) NMR spectroscopy is one of the most popular ligand-based NMR techniques for the study of protein-ligand interactions. This is due to its robustness and the fact that it is focused on the signals of the ligand, without any need for NMR information on the macromolecular target. This technique is most commonly applied to systems involving different types of ligands (e.g., small organic molecules, carbohydrates or lipids) and a protein as the target, in which the latter is selectively saturated. However, only a few examples have been reported where membrane mimetics are the macromolecular binding partners. Here, we have employed STD NMR spectroscopy to investigate the interactions of the neurotransmitter dopamine with mimetics of lipid bilayers, such as nanodiscs, by saturation of the latter. In particular, the interactions between dopamine and model lipid nanodiscs formed either from charged or zwitterionic lipids have been resolved at the atomic level. The results, in agreement with previous isothermal titration calorimetry studies, show that dopamine preferentially binds to negatively charged model membranes, but also provide detailed atomic insights into the mode of interaction of dopamine with membrane mimetics. Our findings provide relevant structural information for the design of lipid-based drug carriers of dopamine and its structural analogues and are of general applicability to other systems. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Side chain-side chain interactions of arginine with tyrosine and aspartic acid in Arg/Gly/Tyr-rich domains within plant glycine-rich RNA binding proteins.

PubMed

Kumaki, Yasuhiro; Nitta, Katsutoshi; Hikichi, Kunio; Matsumoto, Takeshi; Matsushima, Norio

2004-07-01

Plant glycine-rich RNA-binding proteins (GRRBPs) contain a glycine-rich region at the C-terminus whose structure is quite unknown. The C-terminal glycine-rich part is interposed with arginine and tyrosine (arginine/glycine/tyrosine (RGY)-rich domain). Comparative sequence analysis of forty-one GRRBPs revealed that the RGY-rich domain contains multiple repeats of Tyr-(Xaa)h-(Arg)k-(Xaa)l, where Xaa is mainly Gly, "k" is 1 or 2, and "h" and "l" range from 0 to 10. Two peptides, 1 (G1G2Y3G4G5G6R7R8D9G10) and 2 (G1G2R3R4D5G6G7Y8G9G10), corresponding to sections of the RGY-rich domain in Zea mays RAB15, were selected for CD and NMR experiments. The CD spectra indicate a unique, positive band near 228 nm in both peptides that has been ascribed to tyrosine residues in ordered structures. The pH titration by NMR revealed that a side chain-side chain interaction, presumably an H-Nepsilon...O=Cgamma hydrogen bonding interaction in the salt bridge, occurs between Arg (i) and Asp (i + 2). 1D GOESY experiments indicated the presence of NOE between the aromatic side chain proton and the arginine side chain proton in the two peptides suggesting strongly that the Arg (i) aromatic side chain interacts directly with the Tyr (i +/- 4 or i +/- 5) side chain.

Tetraalkylammonium Salts as Hydrogen-Bonding Catalysts.

PubMed

Shirakawa, Seiji; Liu, Shiyao; Kaneko, Shiho; Kumatabara, Yusuke; Fukuda, Airi; Omagari, Yumi; Maruoka, Keiji

2015-12-21

Although the hydrogen-bonding ability of the α hydrogen atoms on tetraalkylammonium salts is often discussed with respect to phase-transfer catalysts, catalysis that utilizes the hydrogen-bond-donor properties of tetraalkylammonium salts remains unknown. Herein, we demonstrate hydrogen-bonding catalysis with newly designed tetraalkylammonium salt catalysts in Mannich-type reactions. The structure and the hydrogen-bonding ability of the new ammonium salts were investigated by X-ray diffraction analysis and NMR titration studies. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Adsorption interactions of humic acids with biocides

NASA Astrophysics Data System (ADS)

Mal'Tseva, E. V.; Ivanov, A. A.; Yudina, N. V.

2009-11-01

The chemical composition of humic acids from brown coal (Aldrich) was determined by element analysis, 13C NMR spectroscopy, and potentiometric titration. The adsorption ability of humic acids with different biocides (cyproconasol, propiconasol, tebuconasol, irgarol 1051, and DCOIT) was studied. The adsorption ability of a mixture of biocides in aqueous solutions was higher than that of the individual components. The limiting concentration of humic acids at which adsorption of biocides was maximum was determined. Adsorption constants were calculated by the Freundlich equation for each biocide in aqueous solution.

Electrophoretic separation of alginic sodium diester and sodium hexametaphosphate in chondroitin sulfate that interfere with the cetylpyridinium chloride titration assay.

PubMed

Weiguo, Zhang; Giancaspro, Gabriel; Adams, Kristie M; Neal-Kababick, James; Hildreth, Jana; Li, Aishan; Roman, Mark C; Betz, Joseph M

2014-01-01

The most commonly used chondroitin sulfate (CS) assay method is cetylpyridinium chloride (CPC) titration. Cellulose acetate membrane electrophoresis (CAME) is the technique used for detection of impurities in the U.S. Pharmacopeia's CS monograph. Because CPC titration is a relatively nonspecific quantitative technique, the apparent amount of CS as determined by CPC titration alone may not reflect the true amount of CS due to possible interference with the CPC assay by impurities that contain CPC titratable functional groups. When CAME is used in conjunction with CPC titration, certain non-CS and adulterants can be visualized and estimated, and a true value for CS can be assigned once the presence of these non-CS impurities has been ruled out. This study examines conjunct application of CPC and CAME in ascertaining CS assay and purity in the presence of certain adulterants. These include propylene glycol alginate sulfate sodium, known in commerce as alginic sodium diester (ASD), and Zero One (Z1), a water-soluble agent newly reported in the CS marketplace and subsequently identified as sodium hexametaphosphate. ASD, Z1, and CS are similar in physical appearance and solubility in water and ethanol. They are also titratable anions and form ionic pairs with CPC, therefore interfering with the CPC titration assay for CS CAME separates these adulterants from each other and from CS by differences in their electrophoretic mobility. CAME is able to detect these impurities in CS at levels as low as 0.66% by weight. Although it is recommended that a method for detecting impurities (e.g., CAME) be used in cormbination with relatively nonspecific assay methods such as CPC titration, this is seldom done in practice. Assay results for CS derived fromn CPC titration may, therefore, be misleading, leaving the CS supply chain vulnerable to adulteration. In this study, the authors investigated ASD and Z1 adulteration of CS and developed an electrophoretic separation of these adulterants in CS and procedures to isolate ASD from CS matrixes containing these adulterants. The authors describe in this paper utilization of an orthogonal approach to establish the identity of Z1 as sodium hexametaphosphate and to confirm the identity of ASD, including ethanol fractionation, FTIR spectroscopy, differential scanning calorimetry, and NMR spectroscopy. The authors suggest that CAME is a cost-effective and easy to use methodfor detecting certain impurities in CS raw ingredients and recommend that CPC and CAME be used in combination by QC laboratories as a means of effectively deterring the practice of adulterating CS raw materials with the known adulterants ASD and Z1 and/or other non-chondroitin substances that can be separated from CSby CAME and that exhibit CPC titration behavior similar to CS.

A coumarin-pyrazolone based fluorescent probe for selective colorimetric and fluorimetric fluoride detection: Synthesis, spectroscopic properties and DFT calculations

NASA Astrophysics Data System (ADS)

Babür, Banu; Seferoğlu, Nurgül; Seferoğlu, Zeynel

2018-06-01

A novel coumarin based fluorescence anion chemosensor (P-1) bearing pyrazolone as a receptoric part was synthesized and characterized by using FT-IR, 1H/13C NMR and HRMS for the purpose of recognition of anions in DMSO. P-1 has four tautomeric structures and the most stable tautomeric form of P-1 was determined experimentally and theoretically. The chemosensor P-1 consists two receptoric parts as free amide Nsbnd H and enamine Nsbnd H which is stabilized intramolecular H-bonding with coumarin carbonyl oxygen. P-1 interacts selectively with fluoride anion via amide Nsbnd H. The selectivity and sensitivity of probe to various anions were determined with spectrophotometric and 1H NMR titration techniques as experimentally and all results were also explained by theoretical calculations.

Study on the inclusion behavior of p-sulfonatocalix[6]arene with propranolol by spectrofluorometry

NASA Astrophysics Data System (ADS)

Li, Hui; Song, Jin-Ping; Chao, Jian-Bin; Shuang, Shao-Min; Dong, Chuan

2012-11-01

The inclusion interaction between propranolol (PPL) and p-sulfonatocalix[6]arene (SCX6) was investigated by fluorescence and 1H NMR spectroscopy. Influences of pH, temperature, ionic strength and the concentration of SCX6 were examined in detail. In phosphate buffer solution with pH 7.5, the fluorescence of PPL dramatically quenched upon addition of SCX6 revealing the formation of inclusion complexes between PPL and SCX6. The stoichiometric ratio was verified to be 1:1 by the continuous variation method. The inclusion constant of PPL-SCX6 complexes was calculated as 2.2 × 104 L/mol by the nonlinear curve fitting method. 1H NMR titration spectra testified that the aliphatic chain of PPL may be partially penetrated into the hydrophobic cavity of SCX6. This was confirmed by molecular dynamics calculations.

Students' integration of multiple representations in a titration experiment

NASA Astrophysics Data System (ADS)

Kunze, Nicole M.

A complete understanding of a chemical concept is dependent upon a student's ability to understand the microscopic or particulate nature of the phenomenon and integrate the microscopic, symbolic, and macroscopic representations of the phenomenon. Acid-base chemistry is a general chemistry topic requiring students to understand the topics of chemical reactions, solutions, and equilibrium presented earlier in the course. In this study, twenty-five student volunteers from a second semester general chemistry course completed two interviews. The first interview was completed prior to any classroom instruction on acids and bases. The second interview took place after classroom instruction, a prelab activity consisting of a titration calculation worksheet, a titration computer simulation, or a microscopic level animation of a titration, and two microcomputer-based laboratory (MBL) titration experiments. During the interviews, participants were asked to define and describe acid-base concepts and in the second interview they also drew the microscopic representations of four stages in an acid-base titration. An analysis of the data showed that participants had integrated the three representations of an acid-base titration to varying degrees. While some participants showed complete understanding of acids, bases, titrations, and solution chemistry, other participants showed several alternative conceptions concerning strong acid and base dissociation, the formation of titration products, and the dissociation of soluble salts. Before instruction, participants' definitions of acid, base, and pH were brief and consisted of descriptive terms. After instruction, the definitions were more scientific and reflected the definitions presented during classroom instruction.

Self-assembly behavior of tail-to-tail superstructure formed by mono-6-O-(4-carbamoylmethoxy-benzoyl)-β-cyclodextrin in solution and the solid state.

PubMed

Xu, Zhe; Chen, Xin; Liu, Jing; Yan, Dong-Qing; Diao, Chun-Hua; Guo, Min-Jie; Fan, Zhi

2014-07-01

A novel mono-modified β-cyclodextrin (β-CD) consisting of 4-carbamoylmethoxy-benzoyl unit at the primary side was synthesized and its self-assembly behavior was determined by X-ray crystallography and NMR spectroscopy. The crystal structure shows a 'Yin-Yang'-like packing mode, in which the modified β-CD exhibits a channel superstructure formed by a tail-to-tail dimer as the repeating motif with the substituted group embedded within the hydrophobic cavity of the facing β-CD. The geometry of the substituted group is determined by the inclusion of the cavity and is further stabilized by two intermolecular hydrogen bonds between the carbonyl O atom and phenyl group. Furthermore, NMR ROESY investigation indicates that the self-assembly behavior of the substituted group within the β-CD cavity is retained in aqueous solution, and the effective binding constant Ka was calculated to be 1330 M(-1) by means of (1)H NMR titration according to iterative determination. Copyright © 2014 Elsevier Ltd. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stepanyuk, Galina A.; Serrano, Pedro; Peralta, Eigen

RNA-binding protein 39 (RBM39) is a splicing factor and a transcriptional co-activator of estrogen receptors and Jun/AP-1, and its function has been associated with malignant progression in a number of cancers. The C-terminal RRM domain of RBM39 belongs to the U2AF homology motif family (UHM), which mediate protein–protein interactions through a short tryptophan-containing peptide known as the UHM-ligand motif (ULM). Here, crystal and solution NMR structures of the RBM39-UHM domain, and the crystal structure of its complex with U2AF65-ULM, are reported. The RBM39–U2AF65 interaction was confirmed by co-immunoprecipitation from human cell extracts, by isothermal titration calorimetry and by NMR chemicalmore » shift perturbation experiments with the purified proteins. When compared with related complexes, such as U2AF35–U2AF65 and RBM39–SF3b155, the RBM39-UHM–U2AF65-ULM complex reveals both common and discriminating recognition elements in the UHM–ULM binding interface, providing a rationale for the known specificity of UHM–ULM interactions. This study therefore establishes a structural basis for specific UHM–ULM interactions by splicing factors such as U2AF35, U2AF65, RBM39 and SF3b155, and a platform for continued studies of intermolecular interactions governing disease-related alternative splicing in eukaryotic cells.« less

Development of a Platform to Enable Fully Automated Cross-Titration Experiments.

PubMed

Cassaday, Jason; Finley, Michael; Squadroni, Brian; Jezequel-Sur, Sylvie; Rauch, Albert; Gajera, Bharti; Uebele, Victor; Hermes, Jeffrey; Zuck, Paul

2017-04-01

In the triage of hits from a high-throughput screening campaign or during the optimization of a lead compound, it is relatively routine to test compounds at multiple concentrations to determine potency and maximal effect. Additional follow-up experiments, such as agonist shift, can be quite valuable in ascertaining compound mechanism of action (MOA). However, these experiments require cross-titration of a test compound with the activating ligand of the receptor requiring 100-200 data points, severely limiting the number tested in MOA assays in a screening triage. We describe a process to enhance the throughput of such cross-titration experiments through the integration of Hewlett Packard's D300 digital dispenser onto one of our robotics platforms to enable on-the-fly cross-titration of compounds in a 1536-well plate format. The process handles all the compound management and data tracking, as well as the biological assay. The process relies heavily on in-house-built software and hardware, and uses our proprietary control software for the platform. Using this system, we were able to automate the cross-titration of compounds for both positive and negative allosteric modulators of two different G protein-coupled receptors (GPCRs) using two distinct assay detection formats, IP1 and Ca 2+ detection, on nearly 100 compounds for each target.

Fluorinated tripodal receptors for potentiometric chloride detection in biological fluids.

PubMed

Pankratova, Nadezda; Cuartero, Maria; Jowett, Laura A; Howe, Ethan N W; Gale, Philip A; Bakker, Eric; Crespo, Gastón A

2018-01-15

Fluorinated tripodal compounds were recently reported to be efficient transmembrane transporters for a series of inorganic anions. In particular, this class of receptors has been shown to be suitable for the effective complexation of chloride, nitrate, bicarbonate and sulfate anions via hydrogen bonding. The potentiometric properties of urea and thiourea-based fluorinated tripodal receptors are explored here for the first time, in light of the need for reliable sensors for chloride monitoring in undiluted biological fluids. The ion selective electrode (ISE) membranes with tren-based tris-urea bis(CF 3 ) tripodal compound (ionophore I) were found to exhibit the best selectivity for chloride over major lipophilic anions such as salicylate ( [Formula: see text] ) and thiocyanate ( [Formula: see text] ). Ionophore I-based ISEs were successfully applied for chloride determination in undiluted human serum as well as artificial serum sample, the slope of the linear calibration at the relevant background of interfering ions being close to Nernstian (49.8±1.7mV). The results of potentiometric measurements were confirmed by argentometric titration. Moreover, the ionophore I-based ISE membrane was shown to exhibit a very good long-term stability of potentiometric performance over the period of 10 weeks. Nuclear magnetic resonance (NMR) titrations, potentiometric sandwich membrane experiments and density functional theory (DFT) computational studies were performed to determine the binding constants and suggest 1:1 complexation stoichiometry for the ionophore I with chloride as well as salicylate. Copyright © 2017 Elsevier B.V. All rights reserved.

Coulometric Titration of Ethylenediaminetetraacetate (EDTA) with Spectrophotometric Endpoint Detection: An Experiment for the Instrumental Analysis Laboratory

ERIC Educational Resources Information Center

Williams, Kathryn R.; Young, Vaneica Y.; Killian, Benjamin J.

2011-01-01

Ethylenediaminetetraacetate (EDTA) is commonly used as an anticoagulant in blood-collection procedures. In this experiment for the instrumental analysis laboratory, students determine the quantity of EDTA in commercial collection tubes by coulometric titration with electrolytically generated Cu[superscript 2+]. The endpoint is detected…

Mixed ligand complexes of Cu(II)/Zn(II) ions containing (m-)/(p-) carboxylato phenyl azo pentane 2,4-dione and 2,2‧-bipyridine/1,10 phenanthroline: Synthesis, characterization, DNA binding, nuclease and topoisomerase I inhibitory activity

NASA Astrophysics Data System (ADS)

Hasan, Md. Amin; Kumari, Niraj; Singh, Kanhaiya; Singh, Kiran; Mishra, Lallan

2016-01-01

Metal complexes of type [Cu(L1H)2(bpy)] (1), [Zn(L1H)2(bpy)] (2), [Cu(L2H)2(bpy)] (3) and [Cu(L2H)2(Phen)] (4) (L1H2 = 3-[N‧-(1-acetyl-2-oxo-propylidene)-hydrazino]-benzoic acid, L2H2 = 4-[N‧-(1-acetyl-2-oxo-propylidene)-hydrazino]-benzoic acid, bpy = 2,2‧-bipyridine, Phen = 1,10 phenanthroline) are synthesized and characterized using spectroscopic techniques (FT-IR, 1H NMR, 13C NMR, electronic absorption and emission) and elemental analysis data. The assembly of the complexes involving intramolecular H-bonding is displayed using corresponding crystal structure. Binding of the complexes separately with Calf Thymus DNA is monitored using UV-vis spectral titrations. The displacement of ethidium bromide (EB) bound to DNA by the complexes, in phosphate buffer solution (pH ∼ 7.2) is monitored using fluorescence spectral titrations. Nuclease activity of the complexes follow the order 4 > 3 > 1 > 2. The gel electrophoretic mobility assay measurement in presence of minor groove binder 4‧,6-diamidino-2-phenylindole (DAPI), suggests that complexes preferably bind with the minor groove of DNA. Topoisomerase I inhibitory activity of the complexes 3 and 4 inhibit topoisomerase I activity with IC50 values of 112 and 87 μM respectively.

A Microscale Spectrophotometric Determination of Water Hardness

NASA Astrophysics Data System (ADS)

Gordon, James S.

2001-08-01

A spectrophotometric titration was performed to determine water hardness. The titration incorporated the traditional titration method employing EDTA as the titrant and calmagite as the indicator. The microscale experiment was carried out in a spectrometer cuvette and made use of a Texas Instruments (TI-83) calculator interfaced through a TI Calculator-Based Laboratory system to a Vernier colorimeter as the detector. Monitoring at 635 nm, one of the colorimeter's fixed wavelengths, was well suited for this analysis. Agreement was found with results from traditional titrations.

Quantitative Analysis of Sulfate in Water by Indirect EDTA Titration

ERIC Educational Resources Information Center

Belle-Oudry, Deirdre

2008-01-01

The determination of sulfate concentration in water by indirect EDTA titration is an instructive experiment that is easily implemented in an analytical chemistry laboratory course. A water sample is treated with excess barium chloride to precipitate sulfate ions as BaSO[subscript 4](s). The unprecipitated barium ions are then titrated with EDTA.…

Determination of Titratable Acidity in Wine Using Potentiometric, Conductometric, and Photometric Methods

ERIC Educational Resources Information Center

Volmer, Dietrich A.; Curbani, Luana; Parker, Timothy A.; Garcia, Jennifer; Schultz, Linda D.; Borges, Endler Marcel

2017-01-01

This experiment describes a simple protocol for teaching acid-base titrations using potentiometry, conductivity, and/or photometry to determine end points without an added indicator. The chosen example examines the titratable acidity of a red wine with NaOH. Wines contain anthocyanins, the colors of which change with pH. Importantly, at the…

Intracellular segment between transmembrane helices S0 and S1 of BK channel α subunit contains two amphipathic helices connected by a flexible loop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Pan; High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui, 230031; Li, Dong

2013-08-02

Highlights: •The loop between S0 and S1 of BK channel was overexpressed and purified in DPC. •NMR studies indicated BK-IS1 contained two helices connected by a flexible loop. •Mg{sup 2+} titration of BK-IS1 indicated two possible binding sites of divalent ions. -- Abstract: The BK channel, a tetrameric potassium channel with very high conductance, has a central role in numerous physiological functions. The BK channel can be activated by intracellular Ca{sup 2+} and Mg{sup 2+}, as well as by membrane depolarization. Unlike other tetrameric potassium channels, the BK channel has seven transmembrane helices (S0–S6) including an extra helix S0. Themore » intracellular segment between S0 and S1 (BK-IS1) is essential to BK channel functions and Asp99 in BK-IS1 is reported to be responsible for Mg{sup 2+} coordination. In this study, BK-IS1 (44–113) was over-expressed using a bacterial system and purified in the presence of detergent micelles for multidimensional heteronuclear nuclear magnetic resonance (NMR) structural studies. Backbone resonance assignment and secondary structure analysis showed that BK-IS1 contains two amphipathic helices connected by a 36-residue loop. Amide {sup 1}H–{sup 15}N heteronuclear NOE analysis indicated that the loop is very flexible, while the two amphipathic helices are possibly stabilized through interaction with the membrane. A solution NMR-based titration assay of BK-IS1 was performed with various concentrations of Mg{sup 2+}. Two residues (Thr45 and Leu46) with chemical shift changes were observed but no, or very minor, chemical shift difference was observed for Asp99, indicating a possible site for binding divalent ions or other modulation partners.« less

Charge Effect on the Formation of Polyoxometalate-Based Supramolecular Polygons Driven by Metal Coordination.

PubMed

Piot, Madeleine; Hupin, Sébastien; Lavanant, Hélène; Afonso, Carlos; Bouteiller, Laurent; Proust, Anna; Izzet, Guillaume

2017-07-17

The metal-driven self-assembly of a Keggin-based hybrid bearing two remote pyridine units was investigated. The resulting supramolecular species were identified by combination of 2D diffusion NMR spectroscopy (DOSY) and electrospray ionization mass spectrometry (ESI-MS) as a mixture of molecular triangles and squares. This behavior is different from that of the structural analogue Dawson-based hybrid displaying a higher charge, which only led to the formation of molecular triangles. This study highlights the decisive effect of the charge of the POMs in their self-assembly processes that disfavors the formation of large assemblies. An isothermal titration calorimetry (ITC) experiment confirmed the stronger binding in the case of the Keggin hybrids. A correlation between the diffusion coefficient D and the molecular mass M of the POM-based building block and its coordination oligomers was also observed. We show that the diffusion coefficient of these compounds is mainly determined by their occupied volume rather than by their shape.

New water soluble Hg2 + selective fluorescent calix[4]arenes: Synthesis and application in living cells imaging

NASA Astrophysics Data System (ADS)

Oguz, Mehmet; Bhatti, Asif Ali; Karakurt, Serdar; Aktas, Mehmet; Yilmaz, Mustafa

2017-01-01

The present study demonstrates the synthesis of water-soluble fluorescent calix[4]arenes (6 and 7) and its application in living cell imaging for Hg2 + detection at a low level. The synthesized fluorescent ligands 6 and 7 were characterized by 1H NMR technique. The fluorescent study showed both water soluble ligands were Hg2 + selective and follow photo-induced electron transfer (PET) process. From the fluorimeter titration experiment detection limit was calculated as 1.14 × 10- 5 and 3.42 × 10- 5 for ligand 6 and 7, respectively. From the Benesi-Hildebrand plot binding constant values were evaluated as 666.7 and 733.3 M- 1 for 6 and 7, respectively. The interactions between ligands 6 and 7 and Hg2 + were also demonstrated in living cells, SW-620, using Fluorescent Cell Imager. While ligands 6 and 7 alone show fluorescent properties, they loss their action with the presence of Hg2 + in SW-620 cells.

Pullulan-protamine as efficient haemocompatible gene delivery vector: synthesis and in vitro characterization.

PubMed

Priya, S S; Rekha, M R; Sharma, Chandra P

2014-02-15

Biodegradable non-viral vectors with good transfection efficiency is essential for successful gene delivery. The purpose of this study was to design a non-viral vector by conjugating protamine to pullulan and elucidate the potential use of pullulan protamine conjugate (PPA) as an effective, non toxic and haemocompatible gene delivery system. The particle size and surface charge were measured using Nanosizer. Derivatization was confirmed by NMR, FTIR and DSC analyses. Acid base titration revealed the buffering behaviour of the conjugate. The protection of DNA from nuclease enzyme and interaction of plasma components on the stability of nanoplexes were also analysed. The uptake studies confirmed the plasmid delivery into the nucleus and the inhibitor studies determined the uptake mechanism. Transfection experiments revealed the capability of PPA to cellular uptake in C6 cells and facilitate high gene expression. Thus, PPA proves to be a promising non-viral vector. Copyright © 2013 Elsevier Ltd. All rights reserved.

A light-up probe targeting for Bcl-2 2345 G-quadruplex DNA with carbazole TO

NASA Astrophysics Data System (ADS)

Gu, Yingchun; Lin, Dayong; Tang, Yalin; Fei, Xuening; Wang, Cuihong; Zhang, Baolian; Zhou, Jianguo

2018-02-01

As its significant role, the selective recognition of G-quadruplex with specific structures and functions is important in biological and medicinal chemistry. Carbazole derivatives have been reported as a kind of fluorescent probe with many excellent optical properties. In the present study, the fluorescence of the dye (carbazole TO) increased almost 70 fold in the presence of bcl-2 2345 G4 compared to that alone in aqueous buffer condition with almost no fluorescence and 10-30 fold than those in the presence of other DNAs. The binding study results by activity inhibition of G4/Hemin peroxidase experiment, NMR titration and molecular docking simulation showed the high affinity and selectivity to bcl-2 2345 G4 arises from its end-stacking interaction with G-quartet. It is said that a facile approach with excellent sensitive, good selectivity and quick response for bcl-2 2345 G-quadruplex was developed and may be used for antitumor recognition or antitumor agents.

A novel coumarin-pyrazole-triazine based fluorescence chemosensor for fluoride detection via deprotonation process: Experimental and theoretical studies

NASA Astrophysics Data System (ADS)

Yalçın, Ergin; Alkış, Meltem; Seferoğlu, Nurgül; Seferoğlu, Zeynel

2018-03-01

A novel fluorescence coumarin-pyrazole-triazine based chemosensor (CPT) bearing 5-hydroxypyrazole as a receptoric part was synthesized and characterized by using IR, 1H/13C NMR and HRMS for the purpose of recognition of anions in DMSO. The most stable tautomeric form of CPT was determined by experimental techniques and theoretical calculations. The selectivity and sensitivity of CPT towards anions (CN-, F-, Cl-, Br-, I-, AcO-, HSO4-, H2PO4- and ClO4-) were determined using spectrophotometric and 1H NMR titration techniques as the experimental approach, and the results were explained by employing theoretical calculations. It was found to be suitable for the selective detection of F- in the presence of CN- and AcO- as competing anions. In addition, CPT exhibits significant "light-up" effect after interaction with TFA in CH2Cl2.

Triprotic acid-base microequilibria and pharmacokinetic sequelae of cetirizine.

PubMed

Marosi, Attila; Kovács, Zsuzsanna; Béni, Szabolcs; Kökösi, József; Noszál, Béla

2009-06-28

(1)H NMR-pH titrations of cetirizine, the widely used antihistamine and four related compounds were carried out and the related 11 macroscopic protonation constants were determined. The interactivity parameter between the two piperazine amine groups was obtained from two symmetric piperazine derivatives. Combining these two types of datasets, all the 12 microconstants and derived tautomeric constants of cetirizine were calculated. Upon this basis, the conflicting literature data of cetirizine microspeciation were clarified, and the pharmacokinetic absorption-distribution properties could be interpreted. The pH-dependent distribution of the microspecies is provided.

In situ spectroscopic characterization of a solution-phase X-type ligand exchange at colloidal lead sulphide quantum dot surfaces

DOE PAGES

Kroupa, Daniel M.; Anderson, Nicholas C.; Castaneda, Chloe V.; ...

2016-11-07

Here, we employed quantitative NMR spectroscopy and spectrophotometric absorbance titration to study a quantum dot X-type ligand exchange reaction. We find that the exchange is highly cooperative, where at low extents of exchange the change in free energy of the reaction, Δ G XC, is ~11 kJ mol –1 while at higher extents of exchange Δ G XC saturates to ~–4 kJ mol –1. A modified Fowler binding isotherm is developed to describe the reaction.

Collaborative development for setup, execution, sharing and analytics of complex NMR experiments.

PubMed

Irvine, Alistair G; Slynko, Vadim; Nikolaev, Yaroslav; Senthamarai, Russell R P; Pervushin, Konstantin

2014-02-01

Factory settings of NMR pulse sequences are rarely ideal for every scenario in which they are utilised. The optimisation of NMR experiments has for many years been performed locally, with implementations often specific to an individual spectrometer. Furthermore, these optimised experiments are normally retained solely for the use of an individual laboratory, spectrometer or even single user. Here we introduce a web-based service that provides a database for the deposition, annotation and optimisation of NMR experiments. The application uses a Wiki environment to enable the collaborative development of pulse sequences. It also provides a flexible mechanism to automatically generate NMR experiments from deposited sequences. Multidimensional NMR experiments of proteins and other macromolecules consume significant resources, in terms of both spectrometer time and effort required to analyse the results. Systematic analysis of simulated experiments can enable optimal allocation of NMR resources for structural analysis of proteins. Our web-based application (http://nmrplus.org) provides all the necessary information, includes the auxiliaries (waveforms, decoupling sequences etc.), for analysis of experiments by accurate numerical simulation of multidimensional NMR experiments. The online database of the NMR experiments, together with a systematic evaluation of their sensitivity, provides a framework for selection of the most efficient pulse sequences. The development of such a framework provides a basis for the collaborative optimisation of pulse sequences by the NMR community, with the benefits of this collective effort being available to the whole community. Copyright © 2013 Elsevier Inc. All rights reserved.

Comparison of methods for accurate end-point detection of potentiometric titrations

NASA Astrophysics Data System (ADS)

Villela, R. L. A.; Borges, P. P.; Vyskočil, L.

2015-01-01

Detection of the end point in potentiometric titrations has wide application on experiments that demand very low measurement uncertainties mainly for certifying reference materials. Simulations of experimental coulometric titration data and consequential error analysis of the end-point values were conducted using a programming code. These simulations revealed that the Levenberg-Marquardt method is in general more accurate than the traditional second derivative technique used currently as end-point detection for potentiometric titrations. Performance of the methods will be compared and presented in this paper.

Design and synthesis of a new organic receptor and evaluation of colorimetric anion sensing ability in organo-aqueous medium

NASA Astrophysics Data System (ADS)

Srikala, P.; Tarafder, Kartick; Trivedi, Darshak R.

2017-01-01

A new organic receptor has been designed and synthesized by the combination of aromatic dialdehyde with nitro-substituted aminophenol resulting in a Schiff base compound. The receptor exhibited a colorimetric response for F- and AcO- ion with a distinct color change from pale yellow to red and pink respectively in dry DMSO solvent and yellow to pale greenish yellow in DMSO:H2O (9:1, v/v). UV-Vis titration studies displayed a significant shift in absorption maxima in comparison with the free receptor. The shift could be attributed to the hydrogen bonding interactions between the active anions and the hydroxyl functionality aided by the electron withdrawing nitro substituent on the receptor. 1H NMR titration and density functionality studies have been performed to understand the nature of interaction of receptor and anions. The lower detection limit of 1.12 ppm was obtained in organic media for F- ion confirming the real time application of the receptor.

Tested Demonstrations: Buffer Capacity of Various Acetic Acid-Sodium Acetate Systems: A Lecture Experiment.

ERIC Educational Resources Information Center

Donahue, Craig J.; Panek, Mary G.

1985-01-01

Background information and procedures are provided for a lecture experiment which uses indicators to illustrate the concept of differing buffer capacities by titrating acetic acid/sodium acetate buffers with 1.0 molar hydrochloric acid and 1.0 molar sodium hydroxide. A table with data used to plot the titration curve is included. (JN)

Using Conductivity Measurements to Determine the Identities and Concentrations of Unknown Acids: An Inquiry Laboratory Experiment

ERIC Educational Resources Information Center

Smith, K. Christopher; Garza, Ariana

2015-01-01

This paper describes a student designed experiment using titrations involving conductivity measurements to identify unknown acids as being either HCl or H[subscript 2]SO[subscript 4], and to determine the concentrations of the acids, thereby improving the utility of standard acid-base titrations. Using an inquiry context, students gain experience…

Titration of a Solid Acid Monitored by X-Ray Diffraction

ERIC Educational Resources Information Center

Dungey, Keenan E.; Epstein, Paul

2007-01-01

An experiment is described to introduce students to an important class of solid-state reactions while reinforcing concepts of titration by using a pH meter and a powder X-ray diffractometer. The experiment was successful in teaching students the abstract concepts of solid-state structure and diffraction by applying the diffraction concepts learned…

NMR-monitored titration of acid-stress bacterial chaperone HdeA reveals that Asp and Glu charge neutralization produces a loosened dimer structure in preparation for protein unfolding and chaperone activation

PubMed Central

Garrison, McKinzie A; Crowhurst, Karin A

2014-01-01

HdeA is a periplasmic chaperone found in several gram-negative pathogenic bacteria that are linked to millions of cases of dysentery per year worldwide. After the protein becomes activated at low pH, it can bind to other periplasmic proteins, protecting them from aggregation when the bacteria travel through the stomach on their way to colonize the intestines. It has been argued that one of the major driving forces for HdeA activation is the protonation of aspartate and glutamate side chains. The goal for this study, therefore, was to investigate, at the atomic level, the structural impact of this charge neutralization on HdeA during the transition from near-neutral conditions to pH 3.0, in preparation for unfolding and activation of its chaperone capabilities. NMR spectroscopy was used to measure pKa values of Asp and Glu residues and monitor chemical shift changes. Measurements of R2/R1 ratios from relaxation experiments confirm that the protein maintains its dimer structure between pH 6.0 and 3.0. However, calculated correlation times and changes in amide protection from hydrogen/deuterium exchange experiments provide evidence for a loosening of the tertiary and quaternary structures of HdeA; in particular, the data indicate that the dimer structure becomes progressively weakened as the pH decreases. Taken together, these results provide insight into the process by which HdeA is primed to unfold and carry out its chaperone duties below pH 3.0, and it also demonstrates that neutralization of aspartate and glutamate residues is not likely to be the sole trigger for HdeA dissociation and unfolding. PMID:24375557

Interaction between S100P and the anti-allergy drug cromolyn

DOE Office of Scientific and Technical Information (OSTI.GOV)

Penumutchu, Srinivasa R.; Chou, Ruey-Hwang; Department of Biotechnology, Asia University, Taichung 413, Taiwan

2014-11-21

Highlights: • The interaction between S100P–cromolyn was investigated by fluorescence spectroscopy. • The interfacial residues on S100P and cromolyn contact surface were mapped by {sup 1}H-{sup 15}N HSQC experiments. • S100P–cromolyn complex model was generated from NMR restraints using HADDOCK program. • The stability of the S100P–cromolyn complex was studied using molecular dynamics simulations. - Abstract: The S100P protein has been known to mediate cell proliferation by binding the receptor for advanced glycation end products (RAGE) to activate signaling pathways, such as the extracellular regulated kinase (ERK) and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathways. S100P/RAGE signaling ismore » involved in a variety of diseases, such as cancer, metastasis, and diabetes. Cromolyn is an anti-allergy drug that binds S100P to block the interaction between S100P and RAGE. In the present study, we characterized the properties of the binding between cromolyn and calcium-bound S100P using various biophysical techniques. The binding affinity for S100P and cromolyn was measured to be in the millimolar range by fluorescence spectroscopy. NMR-HSQC titration experiments and HADDOCK modeling was employed to determine the spatial structure of the proposed heterotetramer model of the S100P–cromolyn complex. Additional MD simulation results revealed the important properties in the complex stability and conformational flexibility of the S100P–cromolyn complex. This proposed model has provided an understanding of the molecular level interactions of S100P–cromolyn complex.« less

The crystal structure of the AgamOBP1•Icaridin complex reveals alternative binding modes and stereo-selective repellent recognition.

PubMed

Drakou, Christina E; Tsitsanou, Katerina E; Potamitis, Constantinos; Fessas, Dimitrios; Zervou, Maria; Zographos, Spyros E

2017-01-01

Anopheles gambiae Odorant Binding Protein 1 in complex with the most widely used insect repellent DEET, was the first reported crystal structure of an olfactory macromolecule with a repellent, and paved the way for OBP1-structure-based approaches for discovery of new host-seeking disruptors. In this work, we performed STD-NMR experiments to directly monitor and verify the formation of a complex between AgamOBP1 and Icaridin, an efficient DEET alternative. Furthermore, Isothermal Titration Calorimetry experiments provided evidence for two Icaridin-binding sites with different affinities (Kd = 0.034 and 0.714 mM) and thermodynamic profiles of ligand binding. To elucidate the binding mode of Icaridin, the crystal structure of AgamOBP1•Icaridin complex was determined at 1.75 Å resolution. We found that Icaridin binds to the DEET-binding site in two distinct orientations and also to a novel binding site located at the C-terminal region. Importantly, only the most active 1R,2S-isomer of Icaridin's equimolar diastereoisomeric mixture binds to the AgamOBP1 crystal, providing structural evidence for the possible contribution of OBP1 to the stereoselectivity of Icaridin perception in mosquitoes. Structural analysis revealed two ensembles of conformations differing mainly in spatial arrangement of their sec-butyl moieties. Moreover, structural comparison with DEET indicates a common recognition mechanism for these structurally related repellents. Ligand interactions with both sites and binding modes were further confirmed by 2D 1 H- 15 N HSQC NMR spectroscopy. The identification of a novel repellent-binding site in AgamOBP1 and the observed structural conservation and stereoselectivity of its DEET/Icaridin-binding sites open new perspectives for the OBP1-structure-based discovery of next-generation insect repellents.

Evolution of Functional Groups during Pyrolysis Oil Upgrading

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stankovikj, Filip; Tran, Chi-Cong; Kaliaguine, Serge

In this paper, we examine the evolution of functional groups (carbonyl, carboxyl, phenol, and hydroxyl) during stabilization at 100–200 °C of two typical wood derived pyrolysis oils from BTG and Amaron in a batch reactor over Ru/C catalyst for 4h. An aqueous and an oily phase were obtained. The content of functional groups in both phases were analyzed by GC/MS, 31P-NMR, 1H-NMR, elemental analysis, KF titration, carbonyl groups by Faix, Folin – Ciocalteu method and UV-Fluorescence. The consumption of hydrogen was between 0.007 and 0.016 g/g oil, and 0.001-0.020 g of CH4/g of oil, 0.005-0.016 g of CO2/g oil andmore » 0.03-0.10 g H2O/g oil were formed. The content of carbonyl, hydroxyl, and carboxyl groups in the volatile GC-MS detectable fraction decreased (80, 65, and ~70% respectively), while their behavior in the total oil and hence in the non-volatile fraction was more complex. The carbonyl groups initially decreased having minimum at ~125-150°C and then increased, while the hydroxyl groups had reversed trend. This might be explained by initial hydrogenation of the carbonyl groups to form hydroxyls, followed by continued dehydration reactions at higher temperatures that may increase their content. The 31P-NMR was on the limit of its sensitivity for the carboxylic groups to precisely detect changes in the non-volatile fraction, however the more precise titration method showed that the concentration of carboxylic groups in the non-volatile fraction remains constant with increased stabilization temperature. The UV-Fluorescence results show that repolymerization increases with temperature. ATR-FTIR method coupled with deconvolution of the region between 1490 and 1850 cm-1 showed to be a good tool for following the changes in carbonyl groups and phenols of the stabilized pyrolysis oils. The deconvolution of the IR bands around 1050 and 1260 cm-1 correlated very well with the changes in the 31P-NMR silent O groups (likely ethers). Most of the H2O formation could be explained from the significant reduction of these silent O groups (from 12% in the fresh oils, to 6 to 2% in the stabilized oils) most probably belonging to ethers.« less

Structural and functional characterization of the NHR1 domain of the Drosophila neuralized E3 ligase in the notch signaling pathway.

PubMed

He, Fahu; Saito, Kohei; Kobayashi, Naohiro; Harada, Takushi; Watanabe, Satoru; Kigawa, Takanori; Güntert, Peter; Ohara, Osamu; Tanaka, Akiko; Unzai, Satoru; Muto, Yutaka; Yokoyama, Shigeyuki

2009-10-23

The Notch signaling pathway is critical for many developmental processes and requires complex trafficking of both Notch receptor and its ligands, Delta and Serrate. In Drosophila melanogaster, the endocytosis of Delta in the signal-sending cell is essential for Notch receptor activation. The Neuralized protein from D. melanogaster (Neur) is a ubiquitin E3 ligase, which binds to Delta through its first neuralized homology repeat 1 (NHR1) domain and mediates the ubiquitination of Delta for endocytosis. Tom, a Bearded protein family member, inhibits the Neur-mediated endocytosis through interactions with the NHR1 domain. We have identified the domain boundaries of the novel NHR1 domain, using a screening system based on our cell-free protein synthesis method, and demonstrated that the identified Neur NHR1 domain had binding activity to the 20-residue peptide corresponding to motif 2 of Tom by isothermal titration calorimetry experiments. We also determined the solution structure of the Neur NHR1 domain by heteronuclear NMR methods, using a (15)N/(13)C-labeled sample. The Neur NHR1 domain adopts a characteristic beta-sandwich fold, consisting of a concave five-stranded antiparallel beta-sheet and a convex seven-stranded antiparallel beta-sheet. The long loop (L6) between the beta6 and beta7 strands covers the hydrophobic patch on the concave beta-sheet surface, and the Neur NHR1 domain forms a compact globular fold. Intriguingly, in spite of the slight, but distinct, differences in the topology of the secondary structure elements, the structure of the Neur NHR1 domain is quite similar to those of the B30.2/SPRY domains, which are known to mediate specific protein-protein interactions. Further NMR titration experiments of the Neur NHR1 domain with the 20-residue Tom peptide revealed that the resonances originating from the bottom area of the beta-sandwich (the L3, L5, and L11 loops, as well as the tip of the L6 loop) were affected. In addition, a structural comparison of the Neur NHR1 domain with the first NHR domain of the human KIAA1787 protein, which is from another NHR subfamily and does not bind to the 20-residue Tom peptide, suggested the critical amino acid residues for the interactions between the Neur NHR1 domain and the Tom peptide. The present structural study will shed light on the role of the Neur NHR1 domain in the Notch signaling pathway.

Volumetric Titrations Using Electrolytically Generated Reagents for the Determination of Ascorbic Acid and Iron in Dietary Supplement Tablets: An Undergraduate Laboratory Experiment

ERIC Educational Resources Information Center

Scanlon, Christopher; Gebeyehu, Zewdu; Griffin, Kameron; Dabke, Rajeev B.

2014-01-01

An undergraduate laboratory experiment for the volumetric quantitative analysis of ascorbic acid and iron in dietary supplement tablets is presented. Powdered samples of the dietary supplement tablets were volumetrically titrated against electrolytically generated reagents, and the mass of dietary reagent in the tablet was determined from the…

Complexation Effect on Redox Potential of Iron(III)-Iron(II) Couple: A Simple Potentiometric Experiment

ERIC Educational Resources Information Center

Rizvi, Masood Ahmad; Syed, Raashid Maqsood; Khan, Badruddin

2011-01-01

A titration curve with multiple inflection points results when a mixture of two or more reducing agents with sufficiently different reduction potentials are titrated. In this experiment iron(II) complexes are combined into a mixture of reducing agents and are oxidized to the corresponding iron(III) complexes. As all of the complexes involve the…

Solution NMR structure and functional analysis of the integral membrane protein YgaP from Escherichia coli.

PubMed

Eichmann, Cédric; Tzitzilonis, Christos; Bordignon, Enrica; Maslennikov, Innokentiy; Choe, Senyon; Riek, Roland

2014-08-22

The solution NMR structure of the α-helical integral membrane protein YgaP from Escherichia coli in mixed 1,2-diheptanoyl-sn-glycerol-3-phosphocholine/1-myristoyl-2-hydroxy-sn-glycero-3-phospho-(1'-rac-glycerol) micelles is presented. In these micelles, YgaP forms a homodimer with the two transmembrane helices being the dimer interface, whereas the N-terminal cytoplasmic domain includes a rhodanese-fold in accordance to its sequence homology to the rhodanese family of sulfurtransferases. The enzymatic sulfur transfer activity of full-length YgaP as well as of the N-terminal rhodanese domain only was investigated performing a series of titrations with sodium thiosulfate and potassium cyanide monitored by NMR and EPR. The data indicate the thiosulfate concentration-dependent addition of several sulfur atoms to the catalytic Cys-63, which process can be reversed by the addition of potassium cyanide. The catalytic reaction induces thereby conformational changes within the rhodanese domain, as well as on the transmembrane α-helices of YgaP. These results provide insights into a potential mechanism of YgaP during the catalytic thiosulfate activity in vivo. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Protonation linked equilibria and apparent affinity constants: the thermodynamic profile of the alpha-chymotrypsin-proflavin interaction.

PubMed

Bruylants, Gilles; Wintjens, René; Looze, Yvan; Redfield, Christina; Bartik, Kristin

2007-12-01

Protonation/deprotonation equilibria are frequently linked to binding processes involving proteins. The presence of these thermodynamically linked equilibria affects the observable thermodynamic parameters of the interaction (K(obs), DeltaH(obs)(0) ). In order to try and elucidate the energetic factors that govern these binding processes, a complete thermodynamic characterisation of each intrinsic equilibrium linked to the complexation event is needed and should furthermore be correlated to structural information. We present here a detailed study, using NMR and ITC, of the interaction between alpha-chymotrypsin and one of its competitive inhibitors, proflavin. By performing proflavin titrations of the enzyme, at different pH values, we were able to highlight by NMR the effect of the complexation of the inhibitor on the ionisable residues of the catalytic triad of the enzyme. Using ITC we determined the intrinsic thermodynamic parameters of the different equilibria linked to the binding process. The possible driving forces of the interaction between alpha-chymotrypsin and proflavin are discussed in the light of the experimental data and on the basis of a model of the complex. This study emphasises the complementarities between ITC and NMR for the study of binding processes involving protonation/deprotonation equilibria.

Joint neutron crystallographic and NMR solution studies of Tyr residue ionization and hydrogen bonding: Implications for enzyme-mediated proton transfer

PubMed Central

Michalczyk, Ryszard; Unkefer, Clifford J.; Bacik, John-Paul; Schrader, Tobias E.; Ostermann, Andreas; Kovalevsky, Andrey Y.; McKenna, Robert; Fisher, Suzanne Zoë

2015-01-01

Human carbonic anhydrase II (HCA II) uses a Zn-bound OH−/H2O mechanism to catalyze the reversible hydration of CO2. This catalysis also involves a separate proton transfer step, mediated by an ordered solvent network coordinated by hydrophilic residues. One of these residues, Tyr7, was previously shown to be deprotonated in the neutron crystal structure at pH 10. This observation indicated that Tyr7 has a perturbed pKa compared with free tyrosine. To further probe the pKa of this residue, NMR spectroscopic measurements of [13C]Tyr-labeled holo HCA II (with active-site Zn present) were preformed to titrate all Tyr residues between pH 5.4–11.0. In addition, neutron studies of apo HCA II (with Zn removed from the active site) at pH 7.5 and holo HCA II at pH 6 were conducted. This detailed interrogation of tyrosines in HCA II by NMR and neutron crystallography revealed a significantly lowered pKa of Tyr7 and how pH and Tyr proximity to Zn affect hydrogen-bonding interactions. PMID:25902526

Standardization of chemical analytical techniques for pyrolysis bio-oil: history, challenges, and current status of methods

DOE PAGES

Ferrell, Jack R.; Olarte, Mariefel V.; Christensen, Earl D.; ...

2016-07-05

Here, we discuss the standardization of analytical techniques for pyrolysis bio-oils, including the current status of methods, and our opinions on future directions. First, the history of past standardization efforts is summarized, and both successful and unsuccessful validation of analytical techniques highlighted. The majority of analytical standardization studies to-date has tested only physical characterization techniques. In this paper, we present results from an international round robin on the validation of chemical characterization techniques for bio-oils. Techniques tested included acid number, carbonyl titrations using two different methods (one at room temperature and one at 80 °C), 31P NMR for determination ofmore » hydroxyl groups, and a quantitative gas chromatography–mass spectrometry (GC-MS) method. Both carbonyl titration and acid number methods have yielded acceptable inter-laboratory variabilities. 31P NMR produced acceptable results for aliphatic and phenolic hydroxyl groups, but not for carboxylic hydroxyl groups. As shown in previous round robins, GC-MS results were more variable. Reliable chemical characterization of bio-oils will enable upgrading research and allow for detailed comparisons of bio-oils produced at different facilities. Reliable analytics are also needed to enable an emerging bioenergy industry, as processing facilities often have different analytical needs and capabilities than research facilities. We feel that correlations in reliable characterizations of bio-oils will help strike a balance between research and industry, and will ultimately help to -determine metrics for bio-oil quality. Lastly, the standardization of additional analytical methods is needed, particularly for upgraded bio-oils.« less

Standardization of chemical analytical techniques for pyrolysis bio-oil: history, challenges, and current status of methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ferrell, Jack R.; Olarte, Mariefel V.; Christensen, Earl D.

Here, we discuss the standardization of analytical techniques for pyrolysis bio-oils, including the current status of methods, and our opinions on future directions. First, the history of past standardization efforts is summarized, and both successful and unsuccessful validation of analytical techniques highlighted. The majority of analytical standardization studies to-date has tested only physical characterization techniques. In this paper, we present results from an international round robin on the validation of chemical characterization techniques for bio-oils. Techniques tested included acid number, carbonyl titrations using two different methods (one at room temperature and one at 80 °C), 31P NMR for determination ofmore » hydroxyl groups, and a quantitative gas chromatography–mass spectrometry (GC-MS) method. Both carbonyl titration and acid number methods have yielded acceptable inter-laboratory variabilities. 31P NMR produced acceptable results for aliphatic and phenolic hydroxyl groups, but not for carboxylic hydroxyl groups. As shown in previous round robins, GC-MS results were more variable. Reliable chemical characterization of bio-oils will enable upgrading research and allow for detailed comparisons of bio-oils produced at different facilities. Reliable analytics are also needed to enable an emerging bioenergy industry, as processing facilities often have different analytical needs and capabilities than research facilities. We feel that correlations in reliable characterizations of bio-oils will help strike a balance between research and industry, and will ultimately help to -determine metrics for bio-oil quality. Lastly, the standardization of additional analytical methods is needed, particularly for upgraded bio-oils.« less

Competitive counterion complexation allows the true host : guest binding constants from a single titration by ionic receptors.

PubMed

Pessêgo, Márcia; Basílio, Nuno; Muñiz, M Carmen; García-Río, Luis

2016-07-06

Counterion competitive complexation is a background process currently ignored by using ionic hosts. Consequently, guest binding constants are strongly affected by the design of the titration experiments in such a way that the results are dependent on the guest concentration and on the presence of added salts, usually buffers. In the present manuscript we show that these experimental difficulties can be overcome by just considering the counterion competitive complexation. Moreover a single titration allows us to obtain not only the true binding constants but also the stoichiometry of the complex showing the formation of 1 : 1 : 1 (host : guest : counterion) complexes. The detection of high stoichiometry complexes is not restricted to a single titration experiment but also to a displacement assay where both competitive and competitive-cooperative complexation models are taken into consideration.

The n-propyl 3-azido-2,3-dideoxy-β-D-arabino-hexopyranoside: Syntheses, crystal structure, physical properties and stability constants of their complexes with Cu(II), Ni(II) and VO(II)

NASA Astrophysics Data System (ADS)

Barabaś, Anna; Madura, Izabela D.; Marek, Paulina H.; Dąbrowska, Aleksandra M.

2017-11-01

The structure, conformation and configuration of the n-propyl 3-azido-2,3-dideoxy-β-D-arabino-hexopyranoside (BAra-nPr) were determined by 1H NMR, 13C NMR, and IR spectroscopy, as well as by optical rotation. The crystal structure was confirmed by single-crystal X-ray diffraction studies at room temperature. The compound crystallizes in P21 space group symmetry of the monoclinic system. The molecule has a 4C1 chair conformation with azide group in the equatorial position both in a solution as well as in the crystal. The spatial arrangement of azide group is compared to other previously determined azidosugars. The hydrogen bonds between the hydroxyl group of sugar molecules lead to a ribbon structure observed also for the ethyl homolog. The packing of ribbons is dependent on the alkyl substituent length and with the elongation changes from pseudohexagonal to lamellar. Acidity constants for the n-propyl 3-azido-2,3-dideoxy-β-D-arabino-hexopyranoside (BAra-nPr) in an aqueous solution were evaluated by the spectrophotometric and potentiometric titrations methods. Title compound exhibit blue absorption with the maximum wavelengths in the range of 266 nm and 306 nm. Based on these measurements we showed equilibria existing in a particular solution and a distribution of species which have formed during the titration. We also investigated interactions between Cu(II), Ni(II) and VO(II) and title compound (as ligand L) during complexometric titration. On these bases we identified that in [CuII-BAra-nPr]2+ the ratio of the ligand L to metal ion M(II) was 3:1, while in [NiII-BAra-nPr]2+ and [VOII-BAra-nPr]2+ complexes 2:1 ratios were found. The cumulative stability constants (as log β) occurring in an aqueous solution for the complexes of BAra-nPr with Cu(II), Ni(II) and VO(IV) were 14.57; 11.71 and 4.20, respectively.

Ras signaling requires dynamic properties of Ets1 for phosphorylation-enhanced binding to coactivator CBP.

PubMed

Nelson, Mary L; Kang, Hyun-Seo; Lee, Gregory M; Blaszczak, Adam G; Lau, Desmond K W; McIntosh, Lawrence P; Graves, Barbara J

2010-06-01

Ras/MAPK signaling is often aberrantly activated in human cancers. The downstream effectors are transcription factors, including those encoded by the ETS gene family. Using cell-based assays and biophysical measurements, we have determined the mechanism by which Ras/MAPK signaling affects the function of Ets1 via phosphorylation of Thr38 and Ser41. These ERK2 phosphoacceptors lie within the unstructured N-terminal region of Ets1, immediately adjacent to the PNT domain. NMR spectroscopic analyses demonstrated that the PNT domain is a four-helix bundle (H2-H5), resembling the SAM domain, appended with two additional helices (H0-H1). Phosphorylation shifted a conformational equilibrium, displacing the dynamic helix H0 from the core bundle. The affinity of Ets1 for the TAZ1 (or CH1) domain of the coactivator CBP was enhanced 34-fold by phosphorylation, and this binding was sensitive to ionic strength. NMR-monitored titration experiments mapped the interaction surfaces of the TAZ1 domain and Ets1, the latter encompassing both the phosphoacceptors and PNT domain. Charge complementarity of these surfaces indicate that electrostatic forces act in concert with a conformational equilibrium to mediate phosphorylation effects. We conclude that the dynamic helical elements of Ets1, appended to a conserved structural core, constitute a phospho-switch that directs Ras/MAPK signaling to downstream changes in gene expression. This detailed structural and mechanistic information will guide strategies for targeting ETS proteins in human disease.

Cancer-Associated Mutants of RNA Helicase DDX3X Are Defective in RNA-Stimulated ATP Hydrolysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Epling, Leslie B.; Grace, Christy R.; Lowe, Brandon R.

The DEAD-box RNA helicase DDX3X is frequently mutated in pediatric medulloblastoma. We dissect how these mutants affect DDX3X function with structural, biochemical, and genetic experiments. We identify an N-terminal extension (“ATP-binding loop”, ABL) that is critical for the stimulation of ATP hydrolysis by RNA. We present crystal structures suggesting that the ABL interacts dynamically with ATP and confirming that the interaction occurs in solution by NMR chemical shift perturbation and isothermal titration calorimetry. DEAD-box helicases require interaction between two conserved RecA-like helicase domains, D1 and D2 for function. We use NMR chemical shift perturbation to show that DDX3X interacts specificallymore » with double-stranded RNA through its D1 domain, with contact mediated by residues G302 and G325. Mutants of these residues, G302V and G325E, are associated with pediatric medulloblastoma. These mutants are defective in RNA-stimulated ATP hydrolysis. We show that DDX3X complements the growth defect in a ded1 temperature-sensitive strain of Schizosaccharomyces pombe, but the cancer-associated mutants G302V and G325E do not complement and exhibit protein expression defects. In conclusion, taken together, our results suggest that impaired translation of important mRNA targets by mutant DDX3X represents a key step in the development of medulloblastoma.« less

Cancer-Associated Mutants of RNA Helicase DDX3X Are Defective in RNA-Stimulated ATP Hydrolysis

DOE PAGES

Epling, Leslie B.; Grace, Christy R.; Lowe, Brandon R.; ...

2015-02-25

The DEAD-box RNA helicase DDX3X is frequently mutated in pediatric medulloblastoma. We dissect how these mutants affect DDX3X function with structural, biochemical, and genetic experiments. We identify an N-terminal extension (“ATP-binding loop”, ABL) that is critical for the stimulation of ATP hydrolysis by RNA. We present crystal structures suggesting that the ABL interacts dynamically with ATP and confirming that the interaction occurs in solution by NMR chemical shift perturbation and isothermal titration calorimetry. DEAD-box helicases require interaction between two conserved RecA-like helicase domains, D1 and D2 for function. We use NMR chemical shift perturbation to show that DDX3X interacts specificallymore » with double-stranded RNA through its D1 domain, with contact mediated by residues G302 and G325. Mutants of these residues, G302V and G325E, are associated with pediatric medulloblastoma. These mutants are defective in RNA-stimulated ATP hydrolysis. We show that DDX3X complements the growth defect in a ded1 temperature-sensitive strain of Schizosaccharomyces pombe, but the cancer-associated mutants G302V and G325E do not complement and exhibit protein expression defects. In conclusion, taken together, our results suggest that impaired translation of important mRNA targets by mutant DDX3X represents a key step in the development of medulloblastoma.« less

A Computer-Based Simulation of an Acid-Base Titration

ERIC Educational Resources Information Center

Boblick, John M.

1971-01-01

Reviews the advantages of computer simulated environments for experiments, referring in particular to acid-base titrations. Includes pre-lab instructions and a sample computer printout of a student's use of an acid-base simulation. Ten references. (PR)

Interactions and encapsulation of vitamins C, B3, and B6 with dendrimers in water.

PubMed

Boisselier, Elodie; Liang, Liyuan; Dalko-Csiba, Maria; Ruiz, Jaime; Astruc, Didier

2010-05-25

Titrations of commercial diaminobutane (DAB) and polyamidoamine (PAMAM) dendrimers by vitamins C (ascorbic acid, AA), B(3) (nicotinic acid), and B(6) (pyridoxine) were monitored by (1)H NMR spectroscopy using the chemical shifts of both dendrimer and vitamin protons and analyzed by comparison with the titration of propylamine. Quaternarizations of the terminal primary amino groups and intradendritic tertiary amino groups, which are nearly quantitative with vitamin C, were characterized by more or less sharp variations (Deltadelta) of the (1)H chemical shift (delta) at the equivalence points. The peripheral primary amino groups of the DAB dendrimers were quaternarized first, but not selectively, whereas a sharp chemical-shift variation was recorded for the inner methylene protons near the tertiary amines, thereby indicating encapsulation, when all the dendritic amines were quaternarized. With DAB-G5-64-NH(2), some excess acid is required to protonate the inner amino groups, presumably because of basicity decrease due to excess charge repulsion. On the other hand, this selectivity was not observed with PAMAM dendrimers. The special case of the titration of the dendrimers by vitamin B(6) indicates only dominant supramolecular hydrogen-bonding interactions and no quaternarization, with core amino groups being privileged, which indicates the strong tendency to encapsulate vitamins. With vitamin B(3), a carboxylic acid, titration of DAB-G3-16-NH(2) shows that only six peripheral amino groups are protonated on average, even with excess vitamin B(3), because protonation is all the more difficult due to increased charge repulsion, as positive charges accumulate around the dendrimer. Inner amino groups interact with this vitamin, however, thus indicating encapsulation presumably with supramolecular hydrogen bonding without much charge transfer.

Kinetics of bacterial potentiometric titrations: the effect of equilibration time on buffering capacity of Pantoea agglomerans suspensions.

PubMed

Kapetas, Leon; Ngwenya, Bryne T; Macdonald, Alan M; Elphick, Stephen C

2011-07-15

Several recent studies have made use of continuous acid-base titration data to describe the surface chemistry of bacterial cells as a basis for accurately modelling metal adsorption to bacteria and other biomaterials of potential industrial importance. These studies do not share a common protocol; rather they titrate in different pH ranges and they use different stability criteria to define equilibration time during titration. In the present study we investigate the kinetics of bacterial titrations and test the effect they have on the derivation of functional group concentrations and acidity constants. We titrated suspensions of Pantoea agglomerans by varying the equilibration time between successive titrant additions until stability of 0.1 or 0.001 mV s(-1) was attained. We show that under longer equilibration times, titration results are less reproducible and suspensions exhibit marginally higher buffering. Fluorescence images suggest that cell lysis is not responsible for these effects. Rather, high DOC values and titration reversibility hysterisis after long equilibration times suggest that variability in buffering is due to the presence of bacterial exudates, as demonstrated by titrating supernatants separated from suspensions of different equilibration times. It is recommended that an optimal equilibration time is always determined with variable stability control and preliminary reversibility titration experiments. Copyright © 2011 Elsevier Inc. All rights reserved.

Spectroscopic studies on the interactions of 5-ethyl-6-phenyl-3,8-bis((3-aminoalkyl)propanamido)phenanthridin-5-ium derivatives with G-quadruplex DNA

NASA Astrophysics Data System (ADS)

Yalçın, Ergin; Duyar, Halil; Ihmels, Heiko; Seferoğlu, Zeynel

2018-05-01

An improved microwave-induced synthesis of five ethidium derivatives (Ethidium derivatives, 2a-d) is presented. As the derivatives 2a-d have been proposed previously to be telomerase inhibitors, the binding interactions of these ethidium derivatives with G-quadruplex DNA were evaluated by means of photometric and fluorimetric titration, thermal DNA denaturation, CD and 1H NMR spectroscopy. In particular, the compound bearing 3,8-bis(pyrrolidin-1-yl)propanamido substituent 2a exhibits high selectivity for G-quadruplex DNA relative to duplex DNA.

Selective conversion of {Mo132} Keplerate ion into 4-electron reduced crown-capped Keggin derivative [Te5Mo15O57](8-). A key intermediate to single-phase M1 multielement MoVTeO light-alkanes oxidation catalyst.

PubMed

Canioni, Romain; Marchal-Roch, Catherine; Leclerc-Laronze, Nathalie; Haouas, Mohamed; Taulèlle, Francis; Marrot, Jérôme; Paul, Sebastien; Lamonier, Carole; Paul, Jean-François; Loridant, Stéphane; Millet, Jean-Marc M; Cadot, Emmanuel

2011-06-14

{Mo(132)} Keplerate anion reacts with tellurites to give a soluble precursor to produce in hydrothermal conditions single-phase M1 MoVTeO light-alkanes oxidation catalyst. Characterization of this Te-containing intermediate by single-crystal X-ray diffraction, (125)Te NMR, UV-visible and redox titration reveals a molybdotellurite anion as a crown-capped Keggin derivative. This journal is © The Royal Society of Chemistry 2011

Ion-selective electrodes in potentiometric titrations; a new method for processing and evaluating titration data.

PubMed

Granholm, Kim; Sokalski, Tomasz; Lewenstam, Andrzej; Ivaska, Ari

2015-08-12

A new method to convert the potential of an ion-selective electrode to concentration or activity in potentiometric titration is proposed. The advantage of this method is that the electrode standard potential and the slope of the calibration curve do not have to be known. Instead two activities on the titration curve have to be estimated e.g. the starting activity before the titration begins and the activity at the end of the titration in the presence of large excess of titrant. This new method is beneficial when the analyte is in a complexed matrix or in a harsh environment which affects the properties of the electrode and the traditional calibration procedure with standard solutions cannot be used. The new method was implemented both in a method of linearization based on the Grans's plot and in determination of the stability constant of a complex and the concentration of the complexing ligand in the sample. The new method gave accurate results when using titrations data from experiments with samples of known composition and with real industrial harsh black liquor sample. A complexometric titration model was also developed. Copyright © 2015 Elsevier B.V. All rights reserved.

Fourier Analysis and Structure Determination. Part II: Pulse NMR and NMR Imaging.

ERIC Educational Resources Information Center

Chesick, John P.

1989-01-01

Uses simple pulse NMR experiments to discuss Fourier transforms. Studies the generation of spin echoes used in the imaging procedure. Shows that pulse NMR experiments give signals that are additions of sinusoids of differing amplitudes, frequencies, and phases. (MVL)

Experimental Aspects of Polarization Optimized Experiments (POE) for Magic Angle Spinning Solid-State NMR of Microcrystalline and Membrane-Bound Proteins.

PubMed

Gopinath, T; Veglia, Gianluigi

2018-01-01

Conventional NMR pulse sequences record one spectrum per experiment, while spending most of the time waiting for the spin system to return to the equilibrium. As a result, a full set of multidimensional NMR experiments for biological macromolecules may take up to several months to complete. Here, we present a practical guide for setting up a new class of MAS solid-state NMR experiments (POE or polarization optimized experiments) that enable the simultaneous acquisition of multiple spectra of proteins, accelerating data acquisition. POE exploit the long-lived 15 N polarization of isotopically labeled proteins and enable one to obtain up to eight spectra, by concatenating classical NMR pulse sequences. This new strategy propels data throughput of solid-state NMR spectroscopy of fibers, microcrystalline preparations, as well as membrane proteins.

Filtrates & Residues: Olfactory Titration.

ERIC Educational Resources Information Center

Wood, John T.; Eddy, Roberta M.

1996-01-01

Presents an experiment that uses a unique acid-base indicator--the odor of raw onion--to indicate the end point of the titration of sodium hydroxide with hydrochloric acid. Allows the student to detect the completion of the neutralization reaction by olfaction rather than sight. (JRH)

A novel fluorescence probe based on triphenylamine Schiff base for bioimaging and responding to pH and Fe3.

PubMed

Wang, Lei; Yang, Xiaodong; Chen, Xiuli; Zhou, Yuping; Lu, Xiaodan; Yan, Chenggong; Xu, Yikai; Liu, Ruiyuan; Qu, Jinqing

2017-03-01

A novel fluorescence probe 1 based on triphenylamine was synthesized and characterized by NMR, IR, high resolution mass spectrometry and elemental analysis. Its fluorescence was quenched when pH below 2. There was a linear relationship between the fluorescence intensity and pH value ranged from 2 to 7. And its fluorescence emission was reversibility in acidic and alkaline solution. Furthermore, it exhibited remarkable selectivity and high sensitivity to Fe 3+ and was able to detect Fe 3+ in aqueous solution with low detection limit of 0.511μM. Job plot showed that the binding stoichiometry of 1 with Fe 3+ was 1:1. Further observations of 1 H NMR titration suggested that coordination interaction between Fe 3+ and nitrogen atom on CN bond promoted the intramolecular charge transfer (ICT) or energy transfer process causing fluorescence quenching. Additionally, 1 was also able to be applied for detecting Fe 3+ in living cell and bioimaging. Copyright © 2016. Published by Elsevier B.V.

Second-generation supramolecular dendrimer with a defined structure due to orthogonal binding.

PubMed

Eckelmann, Jens; Dethlefs, Christiane; Brammer, Stefan; Doğan, Ahmet; Uphoff, Andreas; Lüning, Ulrich

2012-07-02

A second-generation supramolecular dendrimer has been prepared by orthogonal multiple hydrogen bonding. In the first (inner) recognition domain, the interaction of one bis-isocyanuric acid (25) with two branching units (21) that carry complementary Hamilton receptors has been exploited. In the second (outer) generation, the two ADDA (A=hydrogen-bond acceptor, D=donor) receptors of each branching unit (21) have bound complementary DAAD units (4). The problem of limited solubility of the building blocks has been overcome by the introduction of branched ethylhexyl residues and by the use of flexible alkylene or oligo(ethylene glycol) linking chains. The orthogonal binding of the two hydrogen-bonding pairs was elucidated by chemical induced shift NMR titrations, which proved that the two pairs, isocyanuric acid with the Hamilton receptor and ADDA with DAAD, bind preferentially. The formation of the supramolecular self-assembled 1:2:4 dendrimer with a molecular weight of 5065 g mol(-1) was investigated by diffusion NMR spectroscopy. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular Docking and NMR Binding Studies to Identify Novel Inhibitors of Human Phosphomevalonate Kinase

PubMed Central

Boonsri, Pornthip; Neumann, Terrence S.; Olson, Andrew L.; Cai, Sheng; Herdendorf, Timothy J.; Miziorko, Henry M.; Hannongbua, Supa; Sem, Daniel S.

2012-01-01

Phosphomevalonate kinase (PMK) phosphorylates mevalonate-5-phosphate (M5P) in the mevalonate pathway, which is the sole source of isoprenoids and steroids in humans. We have identified new PMK inhibitors with virtual screening, using Autodock. Promising hits were verified and their affinity measured using NMR-based 1H-15N Heteronuclear Single Quantum Coherence (HSQC) chemical shift perturbation and fluorescence titrations. Chemical shift changes were monitored, plotted, and fitted to obtain dissociation constants (Kd). Tight binding compounds with Kd’s ranging from 6–60 µM were identified. These compounds tended to have significant polarity and negative charge, similar to the natural substrates (M5P and ATP). HSQC crosspeak changes suggest that binding induces a global conformational change, such as domain closure. Compounds identified in this study serve as chemical genetic probes of human PMK, to explore pharmacology of the mevalonate pathway, as well as starting points for further drug development. PMID:23146631

Calorimetric and spectroscopic studies of the interaction between zidovudine and human serum albumin

NASA Astrophysics Data System (ADS)

Pîrnău, Adrian; Mic, Mihaela; Neamţu, Silvia; Floare, Călin G.; Bogdan, Mircea

2018-02-01

A quantitative analysis of the interaction between zidovudine (AZT) and human serum albumin (HSA) was achieved using Isothermal titration calorimetry (ITC) in combination with fluorescence and 1H NMR spectroscopy. ITC directly measure the heat during a biomolecular binding event and gave us thermodynamic parameters and the characteristic association constant. By fluorescence quenching, the binding parameters of AZT-HSA interaction was determined and location to binding site I of HSA was confirmed. Via T1 NMR selective relaxation time measurements the drug-protein binding extent was evaluated as dissociation constants Kd and the involvement of azido moiety of zidovudine in molecular complex formation was put in evidence. All three methods indicated a very weak binding interaction. The association constant determined by ITC (3.58 × 102 M- 1) is supported by fluorescence quenching data (2.74 × 102 M- 1). The thermodynamic signature indicates that at least hydrophobic and electrostatic type interactions played a main role in the binding process.

Aluminum(III) speciation with acetate and oxalate. A potentiometric and sup 27 Al NMR study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thomas, F.; Rouiller, J.; Genevrier, F.

1991-09-01

Aluminum (III) hydrolysis and precipitation in the presence of acetic acid and oxalic acid have been studied by combining potentiometric titration and liquid-state {sup 27}Al NMR. The main aluminum species have thus been identified and quantified: unreacted hydrolyzed, complexed monomers, and the Al{sub 13} tridecamer. A solid species appeared when precipitation occurred and was quantified by difference with the other species. The quantitative evolution of these species was followed for pH values up to 5. Acetate forms weak complexes with aluminum. The precipitated phase was hypothesized to be aggregated Al{sub 13}. Oxalate forms strong multiligand complexes to form Al{sub 13}more » requires higher hydroxyl content. High oxalate contents (L/M > 1) inhibit tridecamer formation and precipitation occurs only at high pH values. With oxalate the precipitated phase seems to be devoid of Al{sub 13} and of a more condensed nature than it is with acetate.« less

Heteroleptic metallosupramolecular racks, rectangles, and trigonal prisms: stoichiometry-controlled reversible interconversion.

PubMed

Neogi, Subhadip; Lorenz, Yvonne; Engeser, Marianne; Samanta, Debabrata; Schmittel, Michael

2013-06-17

A simple approach toward preparation of heteroleptic two-dimensional (2D) rectangles and three-dimensional (3D) triangular prisms is described utilizing the HETPYP (HETeroleptic PYridyl and Phenanthroline metal complexes) concept. By mixing metal-loaded linear bisphenanthrolines of varying lengths with diverse (multi)pyridine (py) ligands in a proper ratio, six different self-assembled architectures arise cleanly and spontaneously in the absence of any template. They are characterized by (1)H and DOSY NMR, ESI-FT-ICR mass spectrometry as well as by Job plots and UV-vis titrations. Density functional theory (DFT) computations provide information about each structure. A stoichiometry-controlled supramolecule-to-supramolecule interconversion based on the relative amounts of metal bisphenanthroline and bipyridine forces the rectangular assembly to reorganize to a rack architecture and back to the rectangle, as clearly supported by variable temperature and DOSY NMR as well as dynamic light scattering data. The highly dynamic nature of the assemblies represents a promising starting point for constitutional dynamic materials.

Determination of the equilibrium constant of C60 fullerene binding with drug molecules.

PubMed

Mosunov, Andrei A; Pashkova, Irina S; Sidorova, Maria; Pronozin, Artem; Lantushenko, Anastasia O; Prylutskyy, Yuriy I; Parkinson, John A; Evstigneev, Maxim P

2017-03-01

We report a new analytical method that allows the determination of the magnitude of the equilibrium constant of complexation, K h , of small molecules to C 60 fullerene in aqueous solution. The developed method is based on the up-scaled model of C 60 fullerene-ligand complexation and contains the full set of equations needed to fit titration datasets arising from different experimental methods (UV-Vis spectroscopy, 1 H NMR spectroscopy, diffusion ordered NMR spectroscopy, DLS). The up-scaled model takes into consideration the specificity of C 60 fullerene aggregation in aqueous solution and allows the highly dispersed nature of C 60 fullerene cluster distribution to be accounted for. It also takes into consideration the complexity of fullerene-ligand dynamic equilibrium in solution, formed by various types of self- and hetero-complexes. These features make the suggested method superior to standard Langmuir-type analysis, the approach used to date for obtaining quantitative information on ligand binding with different nanoparticles.

NMR Fragment Screening Hit Induces Plasticity of BRD7/9 Bromodomains.

PubMed

Wang, Na; Li, Fudong; Bao, Hongyu; Li, Jie; Wu, Jihui; Ruan, Ke

2016-08-03

The complex biology associated with inhibition of bromodomain and extra-terminal (BET) domains by chemical probes has attracted increasing attention, and there is a need to identify non-BET bromodomain (BD) inhibitors. Several potent inhibitors of the BRD9 BD have recently been discovered, with anticancer and anti-inflammation activity. However, its paralogue, BRD7 BD, remains unexploited. Here, we identified new chemotypes targeting BRD7 BD by using NMR fragment-based screening. BRD7/9 BDs exhibit similar patterns of chemical-shift perturbation upon the titration of hit compound 1. The crystal structure revealed that 1 repels the Y222 group of BRD9 BD in a similar way to that for butyryllysine, but not acetyllysine and known inhibitors. Hit 1 induced less rearrangement of residue F161 of BRD9 BD than acetyllysine, butyryllysine, and crotonyllysine. Our study provides structural insight into a new generation of butyryllysine mimics for probing the function of BRD7/9 BD. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Functional roles of H98 and W99 and β2α2 loop dynamics in the α-l-arabinofuranosidase from Thermobacillus xylanilyticus.

PubMed

Arab-Jaziri, Faten; Bissaro, Bastien; Barbe, Sophie; Saurel, Olivier; Débat, Hélène; Dumon, Claire; Gervais, Virginie; Milon, Alain; André, Isabelle; Fauré, Régis; O'Donohue, Michael J

2012-10-01

This study is focused on the elucidation of the functional role of the mobile β2α2 loop in the α-L-arabinofuranosidase from Thermobacillus xylanilyticus, and particularly on the roles of loop residues H98 and W99. Using site-directed mutagenesis, coupled to characterization methods including isothermal titration calorimetry (ITC) and saturation transfer difference nuclear magnetic resonance (STD-NMR) spectroscopy, and molecular dynamics simulations, it has been possible to provide a molecular level view of interactions and the consequences of mutations. Binding of para-nitrophenyl α-L-arabinofuranoside (pNP-α-l-Araf) to the wild-type arabinofuranosidase was characterized by K(d) values (0.32 and 0.16 mm, from ITC and STD-NMR respectively) that highly resembled that of the arabinoxylo-oligosaccharide XA(3)XX (0.21 mm), and determination of the thermodynamic parameters of enzyme : pNP-α-L-Araf binding revealed that this process is driven by favourable entropy, which is linked to the movement of the β2α2 loop. Loop closure relocates the solvent-exposed W99 into a buried location, allowing its involvement in substrate binding and in the formation of a functional active site. Similarly, the data underline the role of H98 in the ‘dynamic’ formation and definition of a catalytically operational active site, which may be a specific feature of a subset of GH51 arabinofuranosidases. Substitution of H98 and W99 by alanine or phenylalanine revealed that mutations affected K(M) and/or k(cat). Molecular dynamics performed on W99A implied that this mutation causes the loss of a hydrogen bond and leads to an alternative binding mode that is detrimental for catalysis. STD-NMR experiments revealed altered binding of the aglycon motif in the active site, combined with reduced STD intensities of the α-L-arabinofuranosyl moiety for W99 substitutions. © 2012 The Authors Journal compilation © 2012 FEBS.

Backbone dynamics of a model membrane protein: assignment of the carbonyl carbon /sup 13/C NMR resonances in detergent-solubilized M13 coat protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Henry, G.D.; Weiner, J.H.; Sykes, B.D.

The major coat protein of the filamentous bacteriophage M13 is a 50-residue amphiphilic polypeptide which is inserted, as an integral membrane-spanning protein, in the inner membrane of the Escherichia coli host during infection. /sup 13/C was incorporated biosynthetically into a total of 23 of the peptide carbonyls using labeled amino acids (alanine, glycine, lysine, phenylalanine, and proline). The structure and dynamics of carbonyl-labeled M13 coat protein were monitored by /sup 13/C nuclear magnetic resonance (NMR) spectroscopy. Assignment of many resonances was achieved by using protease digestion, pH titration, or labeling of the peptide bond with both /sup 13/C and /supmore » 15/N. The carbonyl region of the natural-abundance /sup 13/C NMR spectrum of M13 coat protein in sodium dodecyl sulfate solution shows approximately eight backbone carbonyl resonances with line widths much narrower than the rest. Three of these more mobile residues correspond to assigned peaks (glycine-3, lysine-48, and alanine-49) in the individual amino acid spectra, and another almost certainly arises from glutamic acid-2. A ninth residue, alanine-1, also gives rise to a very narrow carbonyl resonance if the pH is well above or below the pK/sub a/ of the terminal amino group. These data suggest that only about four residues at either end of the protein experience large-amplitude spatial fluctuations; the rest of the molecule is essentially rigid on the time scale of the overall rotational tumbling of the protein-detergent complex. The relative exposure of different regions of detergent-bound protein was monitored by limited digestion with proteinase K. Comparable spectra and digestion patterns were obtained when the protein was solubilized in sodium deoxycholate, suggesting that the coat protein binds both amphiphiles in a similar fashion.« less

Accessible NMR Experiments Studying the Hydrodynamics of [subscript 15]N-Enriched Ubiquitin at Low Fields

ERIC Educational Resources Information Center

Thompson, Laura E.; Rovnyak, David

2007-01-01

We have recently developed and implemented two experiments in biomolecular NMR for an undergraduate-level biophysical chemistry laboratory with commercially available [subscript 15]N-enriched human ubiquitin. These experiments take advantage of [subscript 15]N direct detection of the NMR signal. The first experiment develops skills in acquiring…

Accessible NMR Experiments Studying the Hydrodynamics of [superscript 15]N-Enriched Ubiquitin at Low Fields

ERIC Educational Resources Information Center

Thompson, Laura E.; Rovnyak, David

2007-01-01

We have recently developed and implemented two experiments in biomolecular NMR for an undergraduate-level biophysical chemistry laboratory with commercially available [superscript 15]N-enriched human ubiquitin. These experiments take advantage of [superscript 15]N direct detection of the NMR signal. The first experiment develops skills in…

Structure and DNA-binding of meiosis-specific protein Hop2

NASA Astrophysics Data System (ADS)

Zhou, Donghua; Moktan, Hem; Pezza, Roberto

2014-03-01

Here we report structure elucidation of the DNA binding domain of homologous pairing protein 2 (Hop2), which is important to gene diversity when sperms and eggs are produced. Together with another protein Mnd1, Hop2 enhances the strand invasion activity of recombinase Dmc1 by over 30 times, facilitating proper synapsis of homologous chromosomes. However, the structural and biochemical bases for the function of Hop2 and Mnd1 have not been well understood. As a first step toward such understanding, we recently solved the structure for the N-terminus of Hop2 (1-84) using solution NMR. This fragment shows a typical winged-head conformation with recognized DNA binding activity. DNA interacting sites were then investigated by chemical shift perturbations in a titration experiment. Information of these sites was used to guide protein-DNA docking with MD simulation, revealing that helix 3 is stably lodged in the DNA major groove and that wing 1 (connecting strands 2 and 3) transiently comes in contact with the minor groove in nanosecond time scale. Mutagenesis analysis further confirmed the DNA binding sites in this fragment of the protein.

Binding behaviors of p-sulfonatocalix[4]arene with gemini guests.

PubMed

Zhao, Hong-Xia; Guo, Dong-Sheng; Liu, Yu

2013-02-14

A dozen of homoditopic cations, possessing different spacer lengths and rigidities, as well as sizes, shapes, and charges of terminal groups, were synthesized as candidate gemini guests for the complexation of p-sulfonatocalix[4]arenes (SC4A). The 12 gemini guests are divided into five species according to the different terminal groups: imidazolium (G1-G3), pyridinium (G4-G6), quinolinium (G7), viologen (G8-G11), and 1,4-diazabicyclo[2.2.2]octane (DBO, G12). Their binding structures and stoichiometries with SC4A were examined by NMR spectroscopy, which is helpful to construct diverse highly ordered assemblies. The obtained results show that the length of the linkers, as well as the charge numbers on the end groups have a pronounced effect on the binding stoichiometry, whereas the size and shape of the terminal groups have no significant influence. Furthermore, both the stability constants and thermodynamic parameters of SC4A with the terminal subunits were determined by the isothermal titration calorimetry experiments, which are valuable to understand the binding behavior, giving quantitatively deep insight.

The Effects of Extended Release Niacin on Lipoprotein Sub-Particle Concentrations in HIV-Infected Patients

PubMed Central

Lin, Chunrong; Grandinetti, Andrew; Shikuma, Cecilia; Souza, Scott; Parikh, Nisha; Nakamoto, Beau; Kallianpur, Kalpana J

2013-01-01

With the advent of highly active antiretroviral therapy (HAART), Cardiovascular Disease (CVD) has emerged as the leading cause of death in Human Immunodeficiency Virus (HIV) infected patients. An atherogenic lipoprotein phenotype has been described in HIV- infected patients with a predominance of small, low density lipoprotein (SLDL) particles with accompanying elevated triglycerides and reduced high density lipoprotein cholesterol. This randomized controlled pilot study was conducted to evaluate the efficacy of Extended Release Niacin (ERN) in improving the lipid profile in HIV patients. A total of 17 HIV positive subjects on HAART therapy with High Density Lipoprotein Cholesterol (HDL) levels below 40mg/dl and Low Density Lipoprotein Cholesterol (LDL) below 130mg/dl were enrolled. Nine were randomized to be treated with ERN titrated from a starting level of 500mg/night and titrated to a level of 1500mg/night. Eight patients were assigned to the control arm. No placebo was used. Lipoprotein profiles of the subjects were analyzed at baseline and at the end of 12 weeks using Nuclear Magnetic Resonance (NMR) spectroscopy. At the end of 12 weeks, NMR spectroscopic analysis revealed a significant increase in overall LDL size (1.2% in ERN treated subjects vs 2.0% decrease in control patients, P=.04) and a decrease in small LDL particle concentration (17.0% in ERN treated subjects vs 21.4% increase in control patients, P=.03) in subjects receiving ERN as compared to those in the control group. Only 1 subject receiving ERN developed serious flushing which was attributed to an accidental overdose of the drug. This pilot study demonstrates that ERN therapy in HIV-infected patients with low HDL is safe and effective in improving the lipoprotein profile in these patients. PMID:23795312

Does aluminium bind to histidine? An NMR investigation of amyloid β12 and amyloid β16 fragments.

PubMed

Narayan, Priya; Krishnarjuna, Bankala; Vishwanathan, Vinaya; Jagadeesh Kumar, Dasappa; Babu, Sudhir; Ramanathan, Krishna Venkatachala; Easwaran, Kalpathy Ramaier Katchap; Nagendra, Holenarasipur Gundurao; Raghothama, Srinivasarao

2013-07-01

Aluminium and zinc are known to be the major triggering agents for aggregation of amyloid peptides leading to plaque formation in Alzheimer's disease. While zinc binding to histidine in Aβ (amyloid β) fragments has been implicated as responsible for aggregation, not much information is available on the interaction of aluminium with histidine. In the NMR study of the N-terminal Aβ fragments, DAEFRHDSGYEV (Aβ12) and DAEFRHDSGYEVHHQK (Aβ16) presented here, the interactions of the fragments with aluminium have been investigated. Significant chemical shifts were observed for few residues near the C-terminus when aluminium chloride was titrated with Aβ12 and Aβ16 peptides. Surprisingly, it is nonhistidine residues which seem to be involved in aluminium binding. Based on NMR constrained structure obtained by molecular modelling, aluminium-binding pockets in Aβ12 were around charged residues such as Asp, Glu. The results are discussed in terms of native structure propagation, and the relevance of histidine residues in the sequences for metal-binding interactions. We expect that the study of such short amyloid peptide fragments will not only provide clues for plaque formation in aggregated conditions but also facilitate design of potential drugs for these targets. © 2013 John Wiley & Sons A/S.

Molecular docking and NMR binding studies to identify novel inhibitors of human phosphomevalonate kinase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boonsri, Pornthip; Department of Chemistry, NANOTEC Center of Nanotechnology, National Nanotechnology Center, Faculty of Science, Kasetsart University, Bangkok 10900; Neumann, Terrence S.

2013-01-04

Highlights: Black-Right-Pointing-Pointer Natural and synthetic inhibitors of human phosphomevalonate kinase identified. Black-Right-Pointing-Pointer Virtual screening yielded a hit rate of 15%, with inhibitor K{sub d}'s of 10-60 {mu}M. Black-Right-Pointing-Pointer NMR studies indicate significant protein conformational changes upon binding. -- Abstract: Phosphomevalonate kinase (PMK) phosphorylates mevalonate-5-phosphate (M5P) in the mevalonate pathway, which is the sole source of isoprenoids and steroids in humans. We have identified new PMK inhibitors with virtual screening, using autodock. Promising hits were verified and their affinity measured using NMR-based {sup 1}H-{sup 15}N heteronuclear single quantum coherence (HSQC) chemical shift perturbation and fluorescence titrations. Chemical shift changes were monitored,more » plotted, and fitted to obtain dissociation constants (K{sub d}). Tight binding compounds with K{sub d}'s ranging from 6-60 {mu}M were identified. These compounds tended to have significant polarity and negative charge, similar to the natural substrates (M5P and ATP). HSQC cross peak changes suggest that binding induces a global conformational change, such as domain closure. Compounds identified in this study serve as chemical genetic probes of human PMK, to explore pharmacology of the mevalonate pathway, as well as starting points for further drug development.« less

Determination of Structural Topology of a Membrane Protein in Lipid -Bilayers using Polarization Optimized Experiments (POE) for Static and MAS Solid State NMR Spectroscopy

PubMed Central

Mote, Kaustubh R.; Gopinath, T.; Veglia, Gianluigi

2013-01-01

The low sensitivity inherent to both the static and magic angle spinning techniques of solid-state NMR (ssNMR) spectroscopy has thus far limited the routine application of multidimensional experiments to determine the structure of membrane proteins in lipid bilayers. Here, we demonstrate the advantage of using a recently developed class of experiments, polarization optimized experiments (POE), for both static and MAS spectroscopy to achieve higher sensitivity and substantial time-savings for 2D and 3D experiments. We used sarcolipin, a single pass membrane protein, reconstituted in oriented bicelles (for oriented ssNMR) and multilamellar vesicles (for MAS ssNMR) as a benchmark. The restraints derived by these experiments are then combined into a hybrid energy function to allow simultaneous determination of structure and topology. The resulting structural ensemble converged to a helical conformation with a backbone RMSD ∼ 0.44 Å, a tilt angle of 24° ± 1°, and an azimuthal angle of 55° ± 6°. This work represents a crucial first step toward obtaining high-resolution structures of large membrane proteins using combined multidimensional O-ssNMR and MAS-ssNMR. PMID:23963722

Native ESI Mass Spectrometry Can Help to Avoid Wrong Interpretations from Isothermal Titration Calorimetry in Difficult Situations

NASA Astrophysics Data System (ADS)

Wolff, Philippe; Da Veiga, Cyrielle; Ennifar, Eric; Bec, Guillaume; Guichard, Gilles; Burnouf, Dominique; Dumas, Philippe

2017-02-01

We studied by native ESI-MS the binding of various DNA-polymerase-derived peptides onto DNA-polymerase processivity rings from Escherichia coli, Pseudomonas aeruginosa, and Mycobacterium tuberculosis. These homodimeric rings present two equivalent specific binding sites, which leads to successive formation during a titration experiment of singly- and doubly occupied rings. By using the ESI-MS free-ring spectrum as a ruler, we derived by robust linear regression the fractions of the different ring species at each step of a titration experiment. These results led to accurate Kd values (from 0.03 to 0.5 μM) along with the probability of peptide loss due to gas phase dissociation (GPD). We show that this good quality is due to the increased information content of a titration experiment with a homodimer. Isothermal titration calorimetry (ITC) led with the same binding model to Kd(ITC) values systematically higher than their ESI-MS counterparts and, often, to poor fit of the ITC curves. A processing with two competing modes of binding on the same site requiring determination of two (Kd, ΔH) pairs greatly improved the fits and yielded a second Kd(ITC) close to Kd(ESI-MS). The striking features are: (1) ITC detected a minor binding mode ( 20%) of `low-affinity' that did not appear with ESI-MS; (2) the simplest processing of ITC data with only one (Kd, ΔH) pair led wrongly to the Kd of the low-affinity binding mode but to the ΔH of the high-affinity binding mode. Analogous misleading results might well exist in published data based on ITC experiments.

Native ESI Mass Spectrometry Can Help to Avoid Wrong Interpretations from Isothermal Titration Calorimetry in Difficult Situations.

PubMed

Wolff, Philippe; Da Veiga, Cyrielle; Ennifar, Eric; Bec, Guillaume; Guichard, Gilles; Burnouf, Dominique; Dumas, Philippe

2017-02-01

We studied by native ESI-MS the binding of various DNA-polymerase-derived peptides onto DNA-polymerase processivity rings from Escherichia coli, Pseudomonas aeruginosa, and Mycobacterium tuberculosis. These homodimeric rings present two equivalent specific binding sites, which leads to successive formation during a titration experiment of singly- and doubly occupied rings. By using the ESI-MS free-ring spectrum as a ruler, we derived by robust linear regression the fractions of the different ring species at each step of a titration experiment. These results led to accurate K d values (from 0.03 to 0.5 μM) along with the probability of peptide loss due to gas phase dissociation (GPD). We show that this good quality is due to the increased information content of a titration experiment with a homodimer. Isothermal titration calorimetry (ITC) led with the same binding model to K d (ITC) values systematically higher than their ESI-MS counterparts and, often, to poor fit of the ITC curves. A processing with two competing modes of binding on the same site requiring determination of two (K d , ΔH) pairs greatly improved the fits and yielded a second K d (ITC) close to K d (ESI-MS). The striking features are: (1) ITC detected a minor binding mode (~20%) of 'low-affinity' that did not appear with ESI-MS; (2) the simplest processing of ITC data with only one (K d , ΔH) pair led wrongly to the Kd of the low-affinity binding mode but to the ΔH of the high-affinity binding mode. Analogous misleading results might well exist in published data based on ITC experiments. Graphical Abstract ᅟ.

The Effect of Salts in Promoting Specific and Competitive Interactions between Zinc Finger Proteins and Metals

NASA Astrophysics Data System (ADS)

Li, Gongyu; Yuan, Siming; Zheng, Shihui; Chen, Yuting; Zheng, Zhen; Liu, Yangzhong; Huang, Guangming

2017-12-01

Specific protein-metal interactions (PMIs) fulfill essential functions in cells and organic bodies, and activation of these functions in vivo are mostly modulated by the complex environmental factors, including pH value, small biomolecules, and salts. Specifically, the role of salts in promoting specific PMIs and their competition among various metals has remained untapped mainly due to the difficulty to distinguish nonspecific PMIs from specific PMIs by classic spectroscopic techniques. Herein, we report Hofmeister salts differentially promote the specific PMIs by combining nanoelectrospray ionization mass spectrometry and spectroscopic techniques (fluorescence measurement and circular dichroism). Furthermore, to explore the influence of salts in competitive binding between metalloproteins and various metals, we designed a series of competitive experiments and applied to a well-defined model system, the competitive binding of zinc (II) and arsenic (III) to holo-promyelocytic leukemia protein (PML). These experiments not only provided new insights at the molecular scale as complementary to previous NMR and spectroscopic results, but also deduced the relative binding ability between zinc finger proteins and metals at the molecular scale, which avoids the mass spectrometric titration-based determination of binding constants that is frequently affected and often degraded by variable solution conditions including salt contents. [Figure not available: see fulltext.

Cooperativity and tunable excited state deactivation: modular self-assembly of depsipeptide dendrons on a Hamilton receptor modified porphyrin platform.

PubMed

Gnichwitz, Jan-Frederik; Wielopolski, Mateusz; Hartnagel, Kristine; Hartnagel, Uwe; Guldi, Dirk M; Hirsch, Andreas

2008-07-02

A series of novel supramolecular architectures were built around a tin tetraphenyl porphyrin platform 6--functionalized by a 2-fold 1-ethyl-3-3-(3-dimethylaminopropyl)carbodiimide (EDC) promoted condensation reaction--and chiral depsipeptide dendrons of different generations 1-4. Here, implementation of a Hamilton receptor provided the necessary means to keep the constituents together via strong hydrogen bonding. Characterization of all architectures has been performed, including 4 which is the fourth generation, on the basis of NMR and photophysical methods. In particular, several titration experiments were conducted suggesting positive cooperativity, an assessment that is based on association constants that tend to be higher for the second binding step than for the first step. Importantly, molecular modeling calculations reveal a significant deaggregation of the intermolecular network of 6 during the course of the first binding step. As a consequence, an improved accessibility of the second Hamilton receptor unit in 6 emerges and, in turn, facilitates the higher association constants. The features of the equilibrium, that is, the dynamic exchange of depsipeptide dendrons 1-4 with fullerene 5, was tested in photophysical reference experiments. These steady-state and time-resolved measurements showed the tunable excited-state deactivations of these complexes upon photoexcitation.

The crystal structure of ribonuclease A in complex with thymidine-3'-monophosphate provides further insight into ligand binding.

PubMed

Doucet, Nicolas; Jayasundera, Thusitha B; Simonović, Miljan; Loria, J Patrick

2010-08-15

Thymidine-3'-monophosphate (3'-TMP) is a competitive inhibitor analogue of the 3'-CMP and 3'-UMP natural product inhibitors of bovine pancreatic ribonuclease A (RNase A). Isothermal titration calorimetry experiments show that 3'-TMP binds the enzyme with a dissociation constant (K(d)) of 15 microM making it one of the strongest binding members of the five natural bases found in nucleic acids (A, C, G, T, and U). To further investigate the molecular properties of this potent natural affinity, we have determined the crystal structure of bovine pancreatic RNase A in complex with 3'-TMP at 1.55 A resolution and we have performed NMR binding experiments with 3'-CMP and 3'-TMP. Our results show that binding of 3'-TMP is very similar to other natural and non-natural pyrimidine ligands, demonstrating that single nucleotide affinity is independent of the presence or absence of a 2'-hydroxyl on the ribose moiety of pyrimidines and suggesting that the pyrimidine binding subsite of RNase A is not a significant contributor of inhibitor discrimination. Accumulating evidence suggests that very subtle structural, chemical, and potentially motional variations contribute to ligand discrimination in this enzyme. 2010 Wiley-Liss, Inc.

Principal component analysis of chemical shift perturbation data of a multiple-ligand-binding system for elucidation of respective binding mechanism.

PubMed

Konuma, Tsuyoshi; Lee, Young-Ho; Goto, Yuji; Sakurai, Kazumasa

2013-01-01

Chemical shift perturbations (CSPs) in NMR spectra provide useful information about the interaction of a protein with its ligands. However, in a multiple-ligand-binding system, determining quantitative parameters such as a dissociation constant (K(d) ) is difficult. Here, we used a method we named CS-PCA, a principal component analysis (PCA) of chemical shift (CS) data, to analyze the interaction between bovine β-lactoglobulin (βLG) and 1-anilinonaphthalene-8-sulfonate (ANS), which is a multiple-ligand-binding system. The CSP on the binding of ANS involved contributions from two distinct binding sites. PCA of the titration data successfully separated the CSP pattern into contributions from each site. Docking simulations based on the separated CSP patterns provided the structures of βLG-ANS complexes for each binding site. In addition, we determined the K(d) values as 3.42 × 10⁻⁴ M² and 2.51 × 10⁻³ M for Sites 1 and 2, respectively. In contrast, it was difficult to obtain reliable K(d) values for respective sites from the isothermal titration calorimetry experiments. Two ANS molecules were found to bind at Site 1 simultaneously, suggesting that the binding occurs cooperatively with a partial unfolding of the βLG structure. On the other hand, the binding of ANS to Site 2 was a simple attachment without a significant conformational change. From the present results, CS-PCA was confirmed to provide not only the positions and the K(d) values of binding sites but also information about the binding mechanism. Thus, it is anticipated to be a general method to investigate protein-ligand interactions. Copyright © 2012 Wiley Periodicals, Inc.

Acidic-basic properties of three alanine-based peptides containing acidic and basic side chains: comparison between theory and experiment.

PubMed

Makowska, Joanna; Bagińska, Katarzyna; Liwo, Adam; Chmurzyński, Lech; Scheraga, Harold A

2008-01-01

The purpose of this work was to evaluate the effect of the nature of the ionizable end groups, and the solvent, on their acid-base properties in alanine-based peptides. Hence, the acid-base properties of three alanine-based peptides: Ac-KK-(A)(7)-KK-NH(2) (KAK), Ac-OO-(A)(7)-DD-NH(2) (OAD), Ac-KK-(A)(7)-EE-NH(2) (KAE), where A, D, E, K, and O denote alanine, aspartic acid, glutamic acid, lysine, and ornithine, respectively, were determined in water and in methanol by potentiometry. With the availability of these data, the ability of two theoretical methods to simulate pH-metric titration of those peptides was assessed: (i) the electrostatically driven Monte Carlo method with the ECEPP/3 force field and the Poisson-Boltzmann approach to compute solvation energy (EDMC/PB/pH), and (ii) the molecular dynamics method with the AMBER force field and the Generalized Born model (MD/GB/pH). For OAD and KAE, pK(a1) and pK(a2) correspond to the acidic side chains. For all three compounds in both solvents, the pK(a1) value is remarkably lower than the pK(a) of a compound modeling the respective isolated side chain, which can be explained by the influence of the electrostatic field from positively charged ornithine or lysine side chains. The experimental titration curves are reproduced well by the MD/GB/pH approach, the agreement being better if restraints derived from NMR measurements are incorporated in the conformational search. Poorer agreement is achieved by the EDMC/PB/pH method.

Determination of Acidity Constants by Gradient Flow-Injection Titration

ERIC Educational Resources Information Center

Conceicao, Antonio C. L.; Minas da Piedade, Manuel E.

2006-01-01

A three-hour laboratory experiment, designed for an advanced undergraduate course in instrumental analysis that illustrates the application of the gradient chamber flow-injection titration (GCFIT) method with spectrophotometric detection to determine acidity constants is presented. The procedure involves the use of an acid-base indicator to obtain…

Acid-base properties of the alumina surface: influence of the titration procedures on the microcalorimetric results.

PubMed

Morel, Jean-Pierre; Marmier, Nicolas; Hurel, Charlotte; Morel-Desrosiers, Nicole

2009-10-01

The enthalpy changes associated with the protonation and deprotonation of an alumina surface have been determined on the basis of microcalorimetry experiments and acid-base potentiometric titrations at 25 degrees C. It has been shown that the results may vary significantly according to the experimental procedure. In order to do so, the potentiometric and microcalorimetric titrations have been carried out first from an acidic pH to basic pH and second from a pH near the pH(zpc) of alumina to acidic or basic pH. It has been demonstrated that the pK(a) values deduced from the potentiometric titrations are the same whatever the experimental protocol whereas the only way to obtain meaningful enthalpies of proton exchange is to carry out microcalorimetric titrations by starting around the point of zero charge.

Assessment of residual active chlorine in sodium hypochlorite solutions after dissolution of porcine incisor pulpal tissue.

PubMed

Clarkson, R M; Smith, T K; Kidd, B A; Evans, G E; Moule, A J

2013-12-01

In previous studies, surfactant-containing Hypochlor brands of sodium hypochlorite showed better tissue solubilizing abilities than Milton; differences not explained by original active chlorine content or presence of surfactant. It was postulated that exhaustion of active chlorine content could explain differences. This study aimed to assess whether Milton's poorer performance was due to exhaustion of active chlorine. Parallel experiments assessed the influence of titration methods, and the presence of chlorates, on active chlorine measurements. Time required to dissolve one or groups of 10 samples of porcine incisor pulp samples in Milton was determined. Residual active chlorine was assessed by thermometric titration. Iodometric and thermometric titration was carried out on samples of Milton. Chlorate content was also measured. Dissolution of single and 10 pulp samples caused a mean loss of 1% and 3% respectively of active chlorine, not being proportional to tissue dissolved. Thermometric ammonium ion titration resulted in 10% lower values than iodometric titration. Chlorate accounted for much of this difference. Depletion of active chlorine is not the reason for differences in tissue dissolving capabilities of Milton. Thermometric ammonium ion titration gives more accurate measurement of active chlorine content than iodometric titration. © 2013 Australian Dental Association.

Insights into eukaryotic DNA priming from the structure and functional interactions of the 4Fe-4S cluster domain of human DNA primase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vaithiyalingam, Sivaraja; Warren, Eric M.; Eichman, Brandt F.

2010-10-19

DNA replication requires priming of DNA templates by enzymes known as primases. Although DNA primase structures are available from archaea and bacteria, the mechanism of DNA priming in higher eukaryotes remains poorly understood in large part due to the absence of the structure of the unique, highly conserved C-terminal regulatory domain of the large subunit (p58C). Here, we present the structure of this domain determined to 1.7-{angstrom} resolution by X-ray crystallography. The p58C structure reveals a novel arrangement of an evolutionarily conserved 4Fe-4S cluster buried deeply within the protein core and is not similar to any known protein structure. Analysismore » of the binding of DNA to p58C by fluorescence anisotropy measurements revealed a strong preference for ss/dsDNA junction substrates. This approach was combined with site-directed mutagenesis to confirm that the binding of DNA occurs to a distinctively basic surface on p58C. A specific interaction of p58C with the C-terminal domain of the intermediate subunit of replication protein A (RPA32C) was identified and characterized by isothermal titration calorimetry and NMR. Restraints from NMR experiments were used to drive computational docking of the two domains and generate a model of the p58C-RPA32C complex. Together, our results explain functional defects in human DNA primase mutants and provide insights into primosome loading on RPA-coated ssDNA and regulation of primase activity.« less

Rapid Inpatient Titration of Intravenous Treprostinil for Pulmonary Arterial Hypertension: Safe and Tolerable.

PubMed

El-Kersh, Karim; Ruf, Kathryn M; Smith, J Shaun

There is no standard protocol for intravenous treprostinil dose escalation. In most cases, slow up-titration is performed in the outpatient setting. However, rapid up-titration in an inpatient setting is an alternative that provides opportunity for aggressive treatment of common side effects experienced during dose escalation. In this study, we describe our experience with inpatient rapid up-titration of intravenous treprostinil. This was a single-center, retrospective study in which we reviewed the data of subjects with pulmonary arterial hypertension treated at our center who underwent inpatient rapid up-titration of intravenous treprostinil. Our treprostinil dose escalation protocol included initiation at 2 ng·kg·min with subsequent up-titration by 1 ng·kg·min every 6 to 8 hours as tolerated by side effects. A total of 16 subjects were identified. Thirteen subjects were treprostinil naive (naive group), and 3 subjects were receiving subcutaneous treprostinil but were hospitalized for further intravenous up-titration of treprostinil dose (nonnaive group). In the naive group, the median maximum dose achieved was 20 ng·kg·min with an interquartile range (IQR) of 20-23 ng·kg·min. The median up-titration interval was 6 days (IQR: 4-9). In the nonnaive group, the median maximum dose achieved was 20 ng·kg·min (range: 17-30). The median up-titration interval was 8.5 days (range: 1.5-11). Overall, the median maximum dose achieved was 20 ng·kg·min (IQR: 20-23.5), and the median up-titration interval was 6 days (IQR: 4.6-9.25), with no reported significant adverse hemodynamic events. In patients with pulmonary arterial hypertension, rapid inpatient titration of intravenous treprostinil is safe and tolerable.

An Inversion Recovery NMR Kinetics Experiment

ERIC Educational Resources Information Center

Williams, Travis J.; Kershaw, Allan D.; Li, Vincent; Wu, Xinping

2011-01-01

A convenient laboratory experiment is described in which NMR magnetization transfer by inversion recovery is used to measure the kinetics and thermochemistry of amide bond rotation. The experiment utilizes Varian spectrometers with the VNMRJ 2.3 software, but can be easily adapted to any NMR platform. The procedures and sample data sets in this…

Differential Binding Models for Direct and Reverse Isothermal Titration Calorimetry.

PubMed

Herrera, Isaac; Winnik, Mitchell A

2016-03-10

Isothermal titration calorimetry (ITC) is a technique to measure the stoichiometry and thermodynamics from binding experiments. Identifying an appropriate mathematical model to evaluate titration curves of receptors with multiple sites is challenging, particularly when the stoichiometry or binding mechanism is not available. In a recent theoretical study, we presented a differential binding model (DBM) to study calorimetry titrations independently of the interaction among the binding sites (Herrera, I.; Winnik, M. A. J. Phys. Chem. B 2013, 117, 8659-8672). Here, we build upon our DBM and show its practical application to evaluate calorimetry titrations of receptors with multiple sites independently of the titration direction. Specifically, we present a set of ordinary differential equations (ODEs) with the general form d[S]/dV that can be integrated numerically to calculate the equilibrium concentrations of free and bound species S at every injection step and, subsequently, to evaluate the volume-normalized heat signal (δQ(V) = δq/dV) of direct and reverse calorimetry titrations. Additionally, we identify factors that influence the shape of the titration curve and can be used to optimize the initial concentrations of titrant and analyte. We demonstrate the flexibility of our updated DBM by applying these differentials and a global regression analysis to direct and reverse calorimetric titrations of gadolinium ions with multidentate ligands of increasing denticity, namely, diglycolic acid (DGA), citric acid (CIT), and nitrilotriacetic acid (NTA), and use statistical tests to validate the stoichiometries for the metal-ligand pairs studied.

Binding of group 15 and group 16 oxides by a concave host containing an isophthalamide unit.

PubMed

Eckelmann, Jens; Saggiomo, Vittorio; Fischmann, Svenja; Lüning, Ulrich

2012-01-01

A bi-macrocycle with an incorporated isophthalamide substructure was synthesized by double amide formation between an isophthaloyl dichloride and two equivalents of a bis(alkenyloxy)aniline, followed by ring-closing metathesis and hydrogenation. In contrast to many related isophthalamides, the concave host exhibits a better binding for oxides, such as DMSO or pyridine-N-oxide, than for halide anions. A general method for a quick estimation of the strength of binding derived from only a few data points is presented and gives an estimated K(ass) of pyridine-N-oxide of ca. 40 M(-1), NMR titration confirms 25 M(-1).

Designing of a fluoride selective receptor through molecular orbital engineering

NASA Astrophysics Data System (ADS)

Mishra, Rakesh K.; Kumar, Virendra; Diwan, Uzra; Upadhyay, K. K.; Roy Chowdhury, P. K.

2012-11-01

The stepwise substitution of appropriate groups over the 3-[(2,4-dinitro-phenyl)-hydrazono]-butyric acid ethyl ester (R3) lead receptor R1 which showed selectivity towards fluoride in DMSO. The UV-vis and 1H NMR titration studies revealed the details of the binding between receptor R1 and fluoride. The receptor R1 also recognized fluoride in a toothpaste solution to as low as 50 ppm. The theoretical simulations of recognition event at Density Functional Theory (DFT) level using B3LYP/6-31G** basis set and polarizable continuum model (PCM) approach lead a semi-quantitative match with the experimental results.

Pyrrole-pyridine and pyrrole-naphthyridine hosts for anion recognition.

PubMed

García, M Angeles; Farrán, M Angeles; María, Dolores Santa; Claramunt, Rosa M; Torralba, M Carmen; Torres, M Rosario; Jaime, Carlos; Elguero, José

2015-05-27

The association constants of the complexes formed by two hosts containing pyrrole, amide and azine (pyridine and 1,8-naphthyridine) groups and six guests, all monoanions (Cl-, CH3CO2-, NO3-, H2PO4-, BF4-, PF6-), have been determined using NMR titrations. The X-ray crystal structure of the host N2,N5-bis(6-methylpyridin-2-yl)-3,4-diphenyl-1H-pyrrole- 2,5-dicarboxamide (1) has been solved (P21/c monoclinic space group). B3LYP/6-31G(d,p) and calculations were carried out in an attempt to rationalize the trends observed in the experimental association constants.

Highly selective fluorescence turn-on sensor for fluoride detection.

PubMed

Sui, Binglin; Kim, Bosung; Zhang, Yuanwei; Frazer, Andrew; Belfield, Kevin D

2013-04-24

Through click chemistry, triazole and triazolium groups have been explored to recognize anions through C-H···A(-) hydrogen-bonding complexion. Herein, we demonstrate evidence of fluoride-induced deprotonation of a C-H bond and its application in fluoride detection. The combination of fluorene and triazolium units produced a highly selective fluorescence turn-on prototype sensor for fluoride. The interactions between the C-H bond and F(-) were studied by fluorescence spectroscopy and (1)H NMR titrations. Test papers were prepared to detect fluoride in aqueous media at concentrations down to 1.9 ppm, important for estimating whether the fluoride concentration in drinking water is at a safe level.

Synthesis, characterization, crystal structure and DNA-binding studies of transition metal hydrazone complexes

NASA Astrophysics Data System (ADS)

Kanchanadevi, S.; Parveen, S.; Mahalingam, V.

2018-04-01

Three new complexes containing salicylaldazine (HL) ligand were synthesised by reacting suitable precursor complex [MCl2(PPh3)2] with the ligand (where M = Cu(II) or Ni(II) or Co(II)). The new complexes were characterised by various spectral studies such as IR, UV-Vis,1H NMR,EPR,fluorescence and elemental analyses. The binding modes of the complexes with HS-DNA have been studied by UV-Vis absorption titration. Binding of the complexes with bovine serum albumin (BSA) protein has been investigated using UV-visible, fluorescence and synchronous fluorescence spectroscopic methods. Redox behaviour of the complexes has been investigated by cyclic voltammetry.

Equilibrium Speciation of Select Lanthanides in the Presence of Acidic Ligands in Homo- and Heterogeneous Solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robinson, Troy A

2011-08-01

This dissertation explores lanthanide speciation in liquid solution systems related to separation schemes involving the acidic ligands: bis(2-ethylhexyl) phosphoric acid (HDEHP), lactate, and 8-hydroxyquinoline. Equilibrium speciation of neodymium (Nd 3+), sodium (Na+), HDEHP, water, and lactate in the TALSPEAK liquid-liquid extraction system was explored under varied Nd 3+ loading of HDEHP in the organic phase and through extraction from aqueous HCl and lactate media. System speciation was probed through vapor pressure osmometry, visible and Fourier Transform Infrared (FTIR) spectroscopy, 22Na and 13C labeled lactate radiotracer distribution measurements, Karl Fischer titrations, and equilibrium pH measurements. Distribution of Nd 3+, Na +,more » lactate, and equilibrium pH were modeled using the SXLSQI software to obtain logKNd and logKNa extraction constants under selected conditions. Results showed that high Nd 3+ loading of the HDEHP led to Nd 3+ speciation that departs from the ion exchange mechanism and includes formation of highly aggregated, polynuclear [NdLactate(DEHP) 2] x; (with x > 1). By substituting lanthanum (La 3+) for Nd 3+ in this system, NMR scoping experiments using 23Na, 31P nuclei and 13C labeled lactate were performed. Results indicated that this technique is sensitive to changes in system speciation, and that further experiments are warranted. In a homogeneous system representing the TALSPEAK aqueous phase, Lactate protonation behavior at various temperatures was characterized using a combination of potentiometric titration and modeling with the Hyperquad computer program. The temperature dependent deprotonation behavior of lactate showed little change with temperature at 2.0 M NaCl ionic strength. Cloud point extraction is a non-traditional separation technique that starts with a homogeneous phase that becomes heterogeneous by the micellization of surfactants through the increase of temperature. To better understand the behavior of europium (Eu 3+) and 8-hydroxyquinoline under cloud point extraction conditions, potentiometric and spectrophotometric titrations coupled with modeling with Hyperquad and SQUAD computer programs were performed to assess europium (Eu 3+) and 8-hydroxyquinoline speciation. Experiments in both water and a 1wt% Triton X-114/water mixed solvent were compared to understand the effect of Triton X-114 on the system speciation. Results indicated that increased solvation of 8-hydroxyquinoline by the mixed solvent lead to more stable complexes involving 8-hydroxyquinoline than in water, whereas competition between hydroxide and Triton X-114 for Eu 3+ led to lower stability hydrolysis complexes in the mixed solvent than in water. Lanthanide speciation is challenging due to the trivalent oxidation state that leads to multiple ligand complexes, including some mixed complexes. The complexity of the system demands well-designed and precise experiments that capture the nuances of the chemistry. This work increased the understanding of lanthanide speciation in the explored systems, but more work is required to produce a comprehensive understanding of the speciation involved.« less

Titration and HPLC Characterization of Kombucha Fermentation: A Laboratory Experiment in Food Analysis

ERIC Educational Resources Information Center

Miranda, Breanna; Lawton, Nicole M.; Tachibana, Sean R.; Swartz, Natasja A.; Hall, W. Paige

2016-01-01

Quantification of the many constituents that make up our food, whether they are desirable (vitamins, antioxidants, nutrients) or undesirable (pesticides, toxins), is one of the most practical applications of chemistry. In this study, kombucha, a popular fermented tea beverage, was analyzed using acid-base titration and high-performance liquid…

Synthesis and Resolution of the Atropisomeric 1,1'-Bi-2-Naphthol: An Experiment in Organic Synthesis and 2-D NMR Spectroscopy

ERIC Educational Resources Information Center

Mak, Kendrew K. W.

2004-01-01

NMR spectroscopy is presented. It is seen that the experiment regarding the synthesis and resolution of 1,1'-Bi-2-naphtol presents a good experiment for teaching organic synthesis and NMR spectroscopy and provides a strategy for obtaining enantiopure compounds from achiral starting materials.

Using an NMR Spectrometer to Do Magnetic Resonance Imaging: An Undergraduate Physical Chemistry Laboratory Experiment

ERIC Educational Resources Information Center

Steinmetz, Wayne E.; Maher, M. Cyrus

2007-01-01

A conventional Fourier-transform NMR spectrometer with a triple-axis gradient probe can function as a MRI imager. In this experiment students gain hands-on experience with MRI while they learn about important principles underlying the practice of NMR, such as gradients, multi-dimensional spectroscopy, and relaxation. Students image a biological…

Enhancing the resolution of 1H and 13C solid-state NMR spectra by reduction of anisotropic bulk magnetic susceptibility broadening.

PubMed

Hanrahan, Michael P; Venkatesh, Amrit; Carnahan, Scott L; Calahan, Julie L; Lubach, Joseph W; Munson, Eric J; Rossini, Aaron J

2017-10-25

We demonstrate that natural isotopic abundance 2D heteronuclear correlation (HETCOR) solid-state NMR spectra can be used to significantly reduce or eliminate the broadening of 1 H and 13 C solid-state NMR spectra of organic solids due to anisotropic bulk magnetic susceptibility (ABMS). ABMS often manifests in solids with aromatic groups, such as active pharmaceutical ingredients (APIs), and inhomogeneously broadens the NMR peaks of all nuclei in the sample. Inhomogeneous peaks with full widths at half maximum (FWHM) of ∼1 ppm typically result from ABMS broadening and the low spectral resolution impedes the analysis of solid-state NMR spectra. ABMS broadening of solid-state NMR spectra has previously been eliminated using 2D multiple-quantum correlation experiments, or by performing NMR experiments on diluted materials or single crystals. However, these experiments are often infeasible due to their poor sensitivity and/or provide limited gains in resolution. 2D 1 H- 13 C HETCOR experiments have previously been applied to reduce susceptibility broadening in paramagnetic solids and we show that this strategy can significantly reduce ABMS broadening in diamagnetic organic solids. Comparisons of 1D solid-state NMR spectra and 1 H and 13 C solid-state NMR spectra obtained from 2D 1 H- 13 C HETCOR NMR spectra show that the HETCOR spectrum directly increases resolution by a factor of 1.5 to 8. The direct gain in resolution is determined by the ratio of the inhomogeneous 13 C/ 1 H linewidth to the homogeneous 1 H linewidth, with the former depending on the magnitude of the ABMS broadening and the strength of the applied field and the latter on the efficiency of homonuclear decoupling. The direct gains in resolution obtained using the 2D HETCOR experiments are better than that obtained by dilution. For solids with long proton longitudinal relaxation times, dynamic nuclear polarization (DNP) was applied to enhance sensitivity and enable the acquisition of 2D 1 H- 13 C HETCOR NMR spectra. 2D 1 H- 13 C HETCOR experiments were applied to resolve and partially assign the NMR signals of the form I and form II polymorphs of aspirin in a sample containing both forms. These findings have important implications for ultra-high field NMR experiments, optimization of decoupling schemes and assessment of the fundamental limits on the resolution of solid-state NMR spectra.

Using NMR chemical shift imaging to monitor swelling and molecular transport in drug-loaded tablets of hydrophobically modified poly(acrylic acid): methodology and effects of polymer (in)solubility.

PubMed

Knöös, Patrik; Topgaard, Daniel; Wahlgren, Marie; Ulvenlund, Stefan; Piculell, Lennart

2013-11-12

A new technique has been developed using NMR chemical shift imaging (CSI) to monitor water penetration and molecular transport in initially dry polymer tablets that also contain small low-molecular weight compounds to be released from the tablets. Concentration profiles of components contained in the swelling tablets could be extracted via the intensities and chemical shift changes of peaks corresponding to protons of the components. The studied tablets contained hydrophobically modified poly(acrylic acid) (HMPAA) as the polymer component and griseofulvin and ethanol as hydrophobic and hydrophilic, respectively, low-molecular weight model compounds. The water solubility of HMPAA could be altered by titration with NaOH. In the pure acid form, HMPAA tablets only underwent a finite swelling until the maximum water content of the polymer-rich phase, as confirmed by independent phase studies, had been reached. By contrast, after partial neutralization with NaOH, the polyacid became fully miscible with water. The solubility of the polymer affected the water penetration, the polymer release, and the releases of both ethanol and griseofulvin. The detailed NMR CSI concentration profiles obtained highlighted the clear differences in the disintegration/dissolution/release behavior for the two types of tablet and provided insights into their molecular origin. The study illustrates the potential of the NMR CSI technique to give information of importance for the development of pharmaceutical tablets and, more broadly, for the general understanding of any operation that involves the immersion and ultimate disintegration of a dry polymer matrix in a solvent.

Optimizing Glycemic Control Through Titration of Insulin Glargine 100 U/mL: A Review of Current and Future Approaches with a Focus on Asian Populations.

PubMed

Deerochanawong, Chaicharn; Bajpai, Shailendra; Dwipayana, I Made Pande; Hussein, Zanariah; Mabunay, Maria Aileen; Rosales, Reynaldo; Tsai, Shih-Tzer; Tsang, Man Wo

2017-12-01

Various data have demonstrated inadequate glycemic control amongst Asians with type 2 diabetes mellitus (T2DM), possibly on account of suboptimal titration of basal insulin-an issue which needs to be further examined. Here we review the available global and Asia-specific data on titration of basal insulin, with a focus on the use of insulin glargine 100 U/mL (Gla-100). We also discuss clinical evidence on the efficacy and safety of titrating Gla-100, different approaches to titration, including some of the latest technological advancements, and guidance on the titration of basal insulin from international and local Asian guidelines. The authors also provide their recommendations for the initiation and titration of basal insulin for Asian populations. Discussion of the data included in this review and in relation to the authors' clinical experience with treating T2DM in Asian patients is also included. Briefly, clinical studies demonstrate the achievement of adequate glycemic control in adults with T2DM through titration of Gla-100. However, studies investigating approaches to titration, specifically in Asian populations, are lacking and need to be conducted. Given that the management of insulin therapy is a multidisciplinary team effort involving endocrinologists, primary care physicians, nurse educators, and patients, greater resources and education targeted at these groups are needed regarding the optimal titration of basal insulin. Technological advancements in the form of mobile or web-based applications for automated dose adjustment can aid different stakeholders in optimizing the dose of basal insulin, enabling a larger number of patients in Asia to reach their target glycemic goals with improved outcomes.

Parametric changes in response equilibrium during an intra-cranial self stimulation (ICSS) task: can reward value be assessed independently of absolute threshold?

PubMed

Easterling, K W; Holtzman, S G

1997-01-01

Traditional ICSS methodologies have attempted to evaluate changes in the rewarding value of brain stimulation by assessing the lowest value of the stimulation that will support responding. However, orderly changes in suprathreshold indicants of hedonic magnitude such as titration point have been shown. In the present experiments, rats were trained to respond on two ICSS autotitration schedules in which every response on one lever produced stimulation of the medial forebrain bundle, and every Xth response decreased either the stimulation current or the stimulation frequency. At any time, a response on a second "reset" lever restored the stimulation current or frequency available on the stimulation lever to its starting level and operationally defined changes in "reward value". In order to study this titration point measure, two response requirements (responses/stepdown; step size) and two stimulation parameters (initial stimulation level; train duration) were systematically varied. Under both current and frequency titration schedules, data indicated that response rate and titration point remained stable over repeated trials and multiple testing days--parameters being constant. Across all conditions, compared to the frequency titration schedule, subjects responding under the current titration schedule showed significantly higher titration points and lower rates of responding. Indicating the independence of rate and titration point data, parametric manipulations did not affect titration point and rate data concurrently. Results support the conclusion that titration point is a relative measure of "reward value" that is generally independent of response rate, but that is affected by manipulations that alter the amount of stimulation available between "resets". Additional work is needed in order to determine the relationship between the magnitude of stimulation needed to maintain minimal responding and that needed to maintain response equilibrium in an autotitration task.

A Solid-State NMR Experiment: Analysis of Local Structural Environments in Phosphate Glasses

ERIC Educational Resources Information Center

Anderson, Stanley E.; Saiki, David; Eckert, Hellmut; Meise-Gresch, Karin

2004-01-01

An experiment that can be used to directly study the local chemical environments of phosphorus in solid amorphous materials is demonstrated. The experiment aims at familiarizing the students of chemistry with the principles of solid-state NMR, by having them synthesize a simple phosphate glass, and making them observe the (super 31)P NMR spectrum,…

U.S. EPA High-Field NMR Facility with Remote Accessibility

EPA Science Inventory

EPA’s High-Field Nuclear Magnetic Resonance Research Facility housed in Athens, GA has two Varian 600 MHz NMR spectrometers used for conducting sophisticated experiments in environmental science. Off-site users can ship their samples and perform their NMR experiments remotely fr...

Charge Density Quantification of Polyelectrolyte Polysaccharides by Conductometric Titration: An Analytical Chemistry Experiment

ERIC Educational Resources Information Center

Farris, Stefano; Mora, Luigi; Capretti, Giorgio; Piergiovanni, Luciano

2012-01-01

An easy analytical method for determination of the charge density of polyelectrolytes, including polysaccharides and other biopolymers, is presented. The basic principles of conductometric titration, which is used in the pulp and paper industry as well as in colloid and interface science, were adapted to quantify the charge densities of a…

Isothermal Titration Calorimetry and Macromolecular Visualization for the Interaction of Lysozyme and Its Inhibitors

ERIC Educational Resources Information Center

Wei, Chin-Chuan; Jensen, Drake; Boyle, Tiffany; O'Brien, Leah C.; De Meo, Cristina; Shabestary, Nahid; Eder, Douglas J.

2015-01-01

To provide a research-like experience to upper-division undergraduate students in a biochemistry teaching laboratory, isothermal titration calorimetry (ITC) is employed to determine the binding constants of lysozyme and its inhibitors, N-acetyl glucosamine trimer (NAG[subscript 3]) and monomer (NAG). The extremely weak binding of lysozyme/NAG is…

Novel dimeric metabolites from Alternaria tagetica.

PubMed

Gamboa-Angulo, M M; Alejos-González, F; Escalante-Erosa, F; García-Sosa, K; Delgado-Lamas, G; Peña-Rodríguez, L M

2000-08-01

Two novel polyketides, bis-7-O-8' '.8-O-7' '- and bis-7-O-7' '. 8-O-8' '-zinniol (2 and 3, respectively) were isolated from the organic crude extract of culture filtrates from Alternaria tagetica. Both structures were determined on the basis of their spectroscopic data (IR, MS, (1)H NMR, (13)C NMR, and 2D NMR experiments) and confirmed by chemical synthesis. Zinniol (1) was isolated as a major component, and its (13)C NMR data was correctly assigned after careful analysis of data from its 2D NMR experiments (HMQC and HMBC).

Interaction of lafutidine in binding to human serum albumin in gastric ulcer therapy: STD-NMR, WaterLOGSY-NMR, NMR relaxation times, Tr-NOESY, molecule docking, and spectroscopic studies.

PubMed

Yang, Hongqin; Huang, Yanmei; He, Jiawei; Li, Shanshan; Tang, Bin; Li, Hui

2016-09-15

In this study, lafutidine (LAF) was used as a model compound to investigate the binding mechanism between antiulcer drugs and human serum albumin (HSA) through various techniques, including STD-NMR, WaterLOGSY-NMR, (1)H NMR relaxation times, tr-NOESY, molecule docking calculation, FT-IR spectroscopy, and CD spectroscopy. The analyses of STD-NMR, which derived relative STD (%) intensities, and WaterLOGSY-NMR, determined that LAF bound to HSA. In particular, the pyridyl group of LAF was in close contact with HSA binding pocket, whereas furyl group had a secondary binding. Competitive STD-NMR and WaterLOGSY-NMR experiments, with warifarin and ibuprofen as site-selective probes, indicated that LAF preferentially bound to site II in the hydrophobic subdomains IIIA of HSA. The bound conformation of LAF at the HSA binding site was further elucidated by transferred NOE effect (tr-NOESY) experiment. Relaxation experiments provided quantitative information about the relationship between the affinity and structure of LAF. The molecule docking simulations conducted with AutoDock and the restraints derived from STD results led to three-dimensional models that were consistent with the NMR spectroscopic data. The presence of hydrophobic forces and hydrogen interactions was also determined. Additionally, FT-IR and CD spectroscopies showed that LAF induced secondary structure changes of HSA. Copyright © 2016 Elsevier Inc. All rights reserved.

Light-triggered self-assembly of triarylamine-based nanospheres

NASA Astrophysics Data System (ADS)

Moulin, Emilie; Niess, Frédéric; Fuks, Gad; Jouault, Nicolas; Buhler, Eric; Giuseppone, Nicolas

2012-10-01

Tailored triarylamine units modified with terpyridine ligands were coordinated to Zn2+ ions and characterized as discrete dimeric entities. Interestingly, when these complexes were subsequently irradiated with simple visible light in chloroform, they readily self-assembled into monodisperse spheres with a mean diameter of 160 nm.Tailored triarylamine units modified with terpyridine ligands were coordinated to Zn2+ ions and characterized as discrete dimeric entities. Interestingly, when these complexes were subsequently irradiated with simple visible light in chloroform, they readily self-assembled into monodisperse spheres with a mean diameter of 160 nm. Electronic supplementary information (ESI) available: Synthetic procedures and products' characterization (2-4 and 6-9). 1H NMR titration of compound 6 by Zn(OTf)2 to form complex 7. Kinetic measurements by UV-Vis-NIR spectroscopy. Transmission electron microscopy imaging for complexes 8 and 9. UV-Vis-NIR for an Fe2+ analogue of complex 7. Dynamic light scattering and time autocorrelation function for self-assembly of complexes 7-9. Copies of 1H and 13C NMR spectra for compounds 2-4 and 6. See DOI: 10.1039/c2nr32168h

Targeting SDF-1/CXCL12 with a ligand that prevents activation of CXCR4 through structure based drug design

PubMed Central

Veldkamp, Christopher T.; Ziarek, Joshua J.; Peterson, Francis C.; Chen, Yu; Volkman, Brian F.

2010-01-01

CXCL12 is an attractive target for clinical therapy because of its involvement in autoimmune diseases, cancer growth, metastasis, and neovascularization. Tyrosine sulfation at three positions in the CXCR4 N-terminus is crucial for specific, high-affinity CXCL12 binding. An NMR structure of the complex between the CXCL12 dimer and a sulfotyrosine-containing CXCR4 fragment enabled high-throughput in silico screening for inhibitors of the chemokine-receptor interface. A total of 1.4 million compounds from the ZINC database were docked into a cleft on the CXCL12 surface normally occupied by sulfotyrosine 21 (sY21), and five were selected for experimental screening. NMR titrations with CXCL12 revealed that four compounds occupy the sY21 site, one of which binds with a Kd of 64 µM. This compound selectively inhibits SDF1-induced CXCR4 signaling in THP1 cells. Our results suggest that sulfotyrosine recognition sites can be targeted for the development of novel chemokine inhibitors. PMID:20459090

Bidentate urea derivatives of p-tert-butyldihomooxacalix[4]arene: neutral receptors for anion complexation.

PubMed

Marcos, Paula M; Teixeira, Filipa A; Segurado, Manuel A P; Ascenso, José R; Bernardino, Raul J; Michel, Sylvia; Hubscher-Bruder, Véronique

2014-01-17

Three new bidentate ureidodihomooxacalix[4]arene derivatives (phenyl 5a, n-propyl 5b, and tert-butyl 5c) were synthesized in four steps from the parent compound p-tert-butyldihomooxacalix[4]arene and obtained in the cone conformation, as shown by NMR studies. The binding ability of these neutral receptors toward spherical, linear, trigonal planar, and tetrahedrical anions was assessed by (1)H NMR and UV-vis titrations. The structures and complexation energies of some complexes were also studied by DFT methods. The data showed that the association constants are strongly dependent on the nature of the substituent (aryl/alkyl) at the urea moiety. In general, for all the receptors, the association constants decrease with decrease of anion basicity. Ph-urea 5a is the best anion receptor, showing the strongest complexation for F(-) (log K(assoc) = 3.10 in CDCl3) and also high binding affinity for the carboxylates AcO(-) and BzO(-). Similar results were obtained by UV-vis studies and were also corroborated by DFT calculations.

Butyrylation of Maize and Potato Starches and Characterization of the Products by Nuclear Magnetic Resonance and In Vitro Fermentation.

PubMed

Nielsen, Tina Skau; Canibe, Nuria; Larsen, Flemming Hofmann

2018-05-18

Intake of butyrylated starches may increase colonic butyrate supply, which can be of public health and clinical benefit by maintaining colonic health. The objective was to investigate if an organocatalytic method with tartaric acid as a catalyst could be applied to produce butyrylated products from different starch sources and to characterize their chemical structure and fermentation capability by using solid-state 13 C MAS NMR (magic angle spinning nuclear magnetic resonance) spectroscopy and an in vitro fermentation model, respectively. Low-amylose and high-amylose potato starch (LAPS and HAPS) and low-amylose and high-amylose maize starch (LAMS and HAMS) were subjected to organocatalytic butyrylation. This resulted in products with an increasing degree of substitution (DS) measured by heterogenous saponification and back titration with the HCl (chemical method) depending on reaction time. NMR analysis, however, showed that the major part of the acylation was induced by tartarate (75⁻89%) and only a minor part (11⁻25%) by butyrate. Generally, the chemical method overestimated the DS by 38% to 91% compared with the DS determination by NMR. Increasing the DS appeared to lower the in vitro fermentation capability of starches independent of the starch source and, therefore, do not seem to present a feasible method to deliver more butyrate to the colon than lower DS products.

Physicochemical perspectives (aggregation, structure and dynamics) of interaction between pluronic (L31) and surfactant (SDS).

PubMed

Prameela, G K S; Phani Kumar, B V N; Pan, A; Aswal, V K; Subramanian, J; Mandal, A B; Moulik, S P

2015-11-11

The influence of the water soluble non-ionic tri-block copolymer PEO-PPO-PEO [poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide)] i.e., E2P16E2 (L31) on the microstructure and self-aggregation dynamics of the anionic surfactant sodium dodecylsulfate (SDS) in aqueous solution was investigated using cloud point (CP), isothermal titration calorimetry (ITC), high resolution nuclear magnetic resonance (NMR), electron paramagnetic resonance (EPR), and small-angle neutron scattering (SANS) measurements. CP provided the thermodynamic information on the Gibbs free energy, enthalpy, entropy and heat capacity changes pertaining to the phase separation of the system at elevated temperature. The ITC and NMR self-diffusion measurements helped to understand the nature of the binding isotherms of SDS in the presence of L31 in terms of the formation of mixed aggregates and free SDS micelles in solution. EPR analysis provided the micro-viscosity of the spin probe 5-DSA in terms of rotational correlation time. The SANS study indicated the presence of prolate ellipsoidal mixed aggregates, whose size increased with the increasing addition of L31. At a large [L31], SANS also revealed the progressive decreasing size of the ellipsoidal mixed aggregates of SDS-L31 into nearly globular forms with the increasing SDS addition. Wrapping of the spherical SDS micelles by L31 was also corroborated from (13)C NMR and SANS measurements.

Host-guest complexes between cucurbit[n]urils and acetanilides having aminopropyl units.

PubMed

Buaki-Sogo, Mireia; Montes-Navajas, Pedro; Alvaro, Mercedes; Garcia, Hermenegildo

2013-06-01

2-(Propylamino)acetamide of aniline (1a), and bis-2-(propylamino)acetamide of ortho- (1b) and para-(1c) phenylenediamine form host-guest complexes with CB[6], CB[7] and CB[8] as evidenced by the variations in the (1)H NMR spectroscopy chemical shifts and observation in MALDI-TOF-MS and ESI-MS of ions at the corresponding mass. Binding constants for the 1:1 complexes were estimated from fluorescence titrations and were in the range 10(5)-10(6)M(-1). Models based on molecular mechanics for these supramolecular complexes are provided. In spite of the different geometries arising from the ortho- or para-substitution, phenylenediamides form complexes of similar strength in which the hydrophobic alkyl chains are accommodated inside the host cavity. Formation of these host-guest complexes in the solid state was also achieved by modifying an aminopropyl silica with chloroacetanilides and preparing three silica having analogues of compounds 1a-c anchored to the solid particles. Titrations showed, however, that these solids can adsorb a large percentage of CBs by unselective interactions that are not related to the formation of inclusion complexes. Copyright © 2013 Elsevier Inc. All rights reserved.

Equivalence-point electromigration acid-base titration via moving neutralization boundary electrophoresis.

PubMed

Yang, Qing; Fan, Liu-Yin; Huang, Shan-Sheng; Zhang, Wei; Cao, Cheng-Xi

2011-04-01

In this paper, we developed a novel method of acid-base titration, viz. the electromigration acid-base titration (EABT), via a moving neutralization boundary (MNR). With HCl and NaOH as the model strong acid and base, respectively, we conducted the experiments on the EABT via the method of moving neutralization boundary for the first time. The experiments revealed that (i) the concentration of agarose gel, the voltage used and the content of background electrolyte (KCl) had evident influence on the boundary movement; (ii) the movement length was a function of the running time under the constant acid and base concentrations; and (iii) there was a good linearity between the length and natural logarithmic concentration of HCl under the optimized conditions, and the linearity could be used to detect the concentration of acid. The experiments further manifested that (i) the RSD values of intra-day and inter-day runs were less than 1.59 and 3.76%, respectively, indicating similar precision and stability in capillary electrophoresis or HPLC; (ii) the indicators with different pK(a) values had no obvious effect on EABT, distinguishing strong influence on the judgment of equivalence-point titration in the classic one; and (iii) the constant equivalence-point titration always existed in the EABT, rather than the classic volumetric analysis. Additionally, the EABT could be put to good use for the determination of actual acid concentrations. The experimental results achieved herein showed a new general guidance for the development of classic volumetric analysis and element (e.g. nitrogen) content analysis in protein chemistry. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Automatic Tuning Matching Cycler (ATMC) in situ NMR spectroscopy as a novel approach for real-time investigations of Li- and Na-ion batteries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pecher, Oliver; Bayley, Paul M.; Liu, Hao

We have developed and explored the use of a new Automatic Tuning Matching Cycler (ATMC) in situ NMR probe system to track the formation of intermediate phases and investigate electrolyte decomposition during electrochemical cycling of Li- and Na-ion batteries (LIBs and NIBs). The new approach addresses many of the issues arising during in situ NMR, e.g., significantly different shifts of the multi-component samples, changing sample conditions (such as the magnetic susceptibility and conductivity) during cycling, signal broadening due to paramagnetism as well as interferences between the NMR and external cycler circuit that might impair the experiments. We provide practical insightmore » into how to conduct ATMC in situ NMR experiments and discuss applications of the methodology to LiFePO4 (LFP) and Na3V2(PO4)2F3 cathodes as well as Na metal anodes. Automatic frequency sweep 7Li in situ NMR reveals significant changes of the strongly paramagnetic broadened LFP line shape in agreement with the structural changes due to delithiation. Additionally, 31P in situ NMR shows a full separation of the electrolyte and cathode NMR signals and is a key feature for a deeper understanding of the processes occurring during charge/discharge on the local atomic scale of NMR. 31P in situ NMR with “on-the-fly” re-calibrated, varying carrier frequencies on Na3V2(PO4)2F3 as a cathode in a NIB enabled the detection of different P signals within a huge frequency range of 4000 ppm. The experiments show a significant shift and changes in the number as well as intensities of 31P signals during desodiation/sodiation of the cathode. The in situ experiments reveal changes of local P environments that in part have not been seen in ex situ NMR investigations. Furthermore, we applied ATMC 23Na in situ NMR on symmetrical Na–Na cells during galvanostatic plating. An automatic adjustment of the NMR carrier frequency during the in situ experiment ensured on-resonance conditions for the Na metal and electrolyte peak, respectively. Thus, interleaved measurements with different optimal NMR set-ups for the metal and electrolyte, respectively, became possible. This allowed the formation of different Na metal species as well as a quantification of electrolyte consumption during the electrochemical experiment to be monitored. The new approach is likely to benefit a further understanding of Na-ion battery chemistries.« less

Automatic Tuning Matching Cycler (ATMC) in situ NMR spectroscopy as a novel approach for real-time investigations of Li- and Na-ion batteries

NASA Astrophysics Data System (ADS)

Pecher, Oliver; Bayley, Paul M.; Liu, Hao; Liu, Zigeng; Trease, Nicole M.; Grey, Clare P.

2016-04-01

We have developed and explored the use of a new Automatic Tuning Matching Cycler (ATMC) in situ NMR probe system to track the formation of intermediate phases and investigate electrolyte decomposition during electrochemical cycling of Li- and Na-ion batteries (LIBs and NIBs). The new approach addresses many of the issues arising during in situ NMR, e.g., significantly different shifts of the multi-component samples, changing sample conditions (such as the magnetic susceptibility and conductivity) during cycling, signal broadening due to paramagnetism as well as interferences between the NMR and external cycler circuit that might impair the experiments. We provide practical insight into how to conduct ATMC in situ NMR experiments and discuss applications of the methodology to LiFePO4 (LFP) and Na3V2(PO4)2F3 cathodes as well as Na metal anodes. Automatic frequency sweep 7Li in situ NMR reveals significant changes of the strongly paramagnetic broadened LFP line shape in agreement with the structural changes due to delithiation. Additionally, 31P in situ NMR shows a full separation of the electrolyte and cathode NMR signals and is a key feature for a deeper understanding of the processes occurring during charge/discharge on the local atomic scale of NMR. 31P in situ NMR with "on-the-fly" re-calibrated, varying carrier frequencies on Na3V2(PO4)2F3 as a cathode in a NIB enabled the detection of different P signals within a huge frequency range of 4000 ppm. The experiments show a significant shift and changes in the number as well as intensities of 31P signals during desodiation/sodiation of the cathode. The in situ experiments reveal changes of local P environments that in part have not been seen in ex situ NMR investigations. Furthermore, we applied ATMC 23Na in situ NMR on symmetrical Na-Na cells during galvanostatic plating. An automatic adjustment of the NMR carrier frequency during the in situ experiment ensured on-resonance conditions for the Na metal and electrolyte peak, respectively. Thus, interleaved measurements with different optimal NMR set-ups for the metal and electrolyte, respectively, became possible. This allowed the formation of different Na metal species as well as a quantification of electrolyte consumption during the electrochemical experiment to be monitored. The new approach is likely to benefit a further understanding of Na-ion battery chemistries.

Nuclear magnetic resonance studies of quadrupolar nuclei and dipolar field effects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Urban, Jeffry Todd

Experimental and theoretical research conducted in two areas in the field of nuclear magnetic resonance (NMR) spectroscopy is presented: (1) studies of the coherent quantum-mechanical control of the angular momentum dynamics of quadrupolar (spin I > 1/2) nuclei and its application to the determination of molecular structure; and (2) applications of the long-range nuclear dipolar field to novel NMR detection methodologies.The dissertation is organized into six chapters. The first two chapters and associated appendices are intended to be pedagogical and include an introduction to the quantum mechanical theory of pulsed NMR spectroscopy and the time dependent theory of quantum mechanics.more » The third chapter describes investigations of the solid-state multiple-quantum magic angle spinning (MQMAS) NMR experiment applied to I = 5/2 quadrupolar nuclei. This work reports the use of rotary resonance-matched radiofrequency irradiation for sensitivity enhancement of the I = 5/2 MQMAS experiment. These experiments exhibited certain selective line narrowing effects which were investigated theoretically.The fourth chapter extends the discussion of multiple quantum spectroscopy of quadrupolar nuclei to a mostly theoretical study of the feasibility of enhancing the resolution of nitrogen-14 NMR of large biomolecules in solution via double-quantum spectroscopy. The fifth chapter continues to extend the principles of multiple quantum NMR spectroscopy of quadrupolar nuclei to make analogies between experiments in NMR/nuclear quadrupolar resonance (NQR) and experiments in atomic/molecular optics (AMO). These analogies are made through the Hamiltonian and density operator formalism of angular momentum dynamics in the presence of electric and magnetic fields.The sixth chapter investigates the use of the macroscopic nuclear dipolar field to encode the NMR spectrum of an analyte nucleus indirectly in the magnetization of a sensor nucleus. This technique could potentially serve as an encoding module for the recently developed NMR remote detection experiment. The feasibility of using hyperpolarized xenon-129 gas as a sensor is discussed. This work also reports the use of an optical atomic magnetometer to detect the nuclear magnetization of Xe-129 gas, which has potential applicability as a detection module for NMR remote detection experiments.« less

Effect of temperature on the acid-base properties of the alumina surface: microcalorimetry and acid-base titration experiments.

PubMed

Morel, Jean-Pierre; Marmier, Nicolas; Hurel, Charlotte; Morel-Desrosiers, Nicole

2006-06-15

Sorption reactions on natural or synthetic materials that can attenuate the migration of pollutants in the geosphere could be affected by temperature variations. Nevertheless, most of the theoretical models describing sorption reactions are at 25 degrees C. To check these models at different temperatures, experimental data such as the enthalpies of sorption are thus required. Highly sensitive microcalorimeters can now be used to determine the heat effects accompanying the sorption of radionuclides on oxide-water interfaces, but enthalpies of sorption cannot be extracted from microcalorimetric data without a clear knowledge of the thermodynamics of protonation and deprotonation of the oxide surface. However, the values reported in the literature show large discrepancies and one must conclude that, amazingly, this fundamental problem of proton binding is not yet resolved. We have thus undertaken to measure by titration microcalorimetry the heat effects accompanying proton exchange at the alumina-water interface at 25 degrees C. Based on (i) the surface sites speciation provided by a surface complexation model (built from acid-base titrations at 25 degrees C) and (ii) results of the microcalorimetric experiments, calculations have been made to extract the enthalpic variations associated respectively to first and second deprotonation of the alumina surface. Values obtained are deltaH1 = 80+/-10 kJ mol(-1) and deltaH2 = 5+/-3 kJ mol(-1). In a second step, these enthalpy values were used to calculate the alumina surface acidity constants at 50 degrees C via the van't Hoff equation. Then a theoretical titration curve at 50 degrees C was calculated and compared to the experimental alumina surface titration curve. Good agreement between the predicted acid-base titration curve and the experimental one was observed.

Determining the folding and binding free energy of DNA-based nanodevices and nanoswitches using urea titration curves

PubMed Central

Idili, Andrea

2017-01-01

Abstract DNA nanotechnology takes advantage of the predictability of DNA interactions to build complex DNA-based functional nanoscale structures. However, when DNA functional and responsive units that are based on non-canonical DNA interactions are employed it becomes quite challenging to predict, understand and control their thermodynamics. In response to this limitation, here we demonstrate the use of isothermal urea titration experiments to estimate the free energy involved in a set of DNA-based systems ranging from unimolecular DNA-based nanoswitches to more complex DNA folds (e.g. aptamers) and nanodevices. We propose here a set of fitting equations that allow to analyze the urea titration curves of these DNA responsive units based on Watson–Crick and non-canonical interactions (stem-loop, G-quadruplex, triplex structures) and to correctly estimate their relative folding and binding free energy values under different experimental conditions. The results described herein will pave the way toward the use of urea titration experiments in the field of DNA nanotechnology to achieve easier and more reliable thermodynamic characterization of DNA-based functional responsive units. More generally, our results will be of general utility to characterize other complex supramolecular systems based on different biopolymers. PMID:28605461

A generalized approach to automated NMR peak list editing: application to reduced dimensionality triple resonance spectra.

PubMed

Moseley, Hunter N B; Riaz, Nadeem; Aramini, James M; Szyperski, Thomas; Montelione, Gaetano T

2004-10-01

We present an algorithm and program called Pattern Picker that performs editing of raw peak lists derived from multidimensional NMR experiments with characteristic peak patterns. Pattern Picker detects groups of correlated peaks within peak lists from reduced dimensionality triple resonance (RD-TR) NMR spectra, with high fidelity and high yield. With typical quality RD-TR NMR data sets, Pattern Picker performs almost as well as human analysis, and is very robust in discriminating real peak sets from noise and other artifacts in unedited peak lists. The program uses a depth-first search algorithm with short-circuiting to efficiently explore a search tree representing every possible combination of peaks forming a group. The Pattern Picker program is particularly valuable for creating an automated peak picking/editing process. The Pattern Picker algorithm can be applied to a broad range of experiments with distinct peak patterns including RD, G-matrix Fourier transformation (GFT) NMR spectra, and experiments to measure scalar and residual dipolar coupling, thus promoting the use of experiments that are typically harder for a human to analyze. Since the complexity of peak patterns becomes a benefit rather than a drawback, Pattern Picker opens new opportunities in NMR experiment design.

Binding of group 15 and group 16 oxides by a concave host containing an isophthalamide unit

PubMed Central

Eckelmann, Jens; Saggiomo, Vittorio; Fischmann, Svenja

2012-01-01

Summary A bi-macrocycle with an incorporated isophthalamide substructure was synthesized by double amide formation between an isophthaloyl dichloride and two equivalents of a bis(alkenyloxy)aniline, followed by ring-closing metathesis and hydrogenation. In contrast to many related isophthalamides, the concave host exhibits a better binding for oxides, such as DMSO or pyridine-N-oxide, than for halide anions. A general method for a quick estimation of the strength of binding derived from only a few data points is presented and gives an estimated K ass of pyridine-N-oxide of ca. 40 M−1, NMR titration confirms 25 M−1. PMID:22423268

Two-dimensional NMR spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farrar, T.C.

1987-06-01

This article is the second in a two-part series. In part one (ANALYTICAL CHEMISTRY, May 15) the authors discussed one-dimensional nuclear magnetic resonance (NMR) spectra and some relatively advanced nuclear spin gymnastics experiments that provide a capability for selective sensitivity enhancements. In this article and overview and some applications of two-dimensional NMR experiments are presented. These powerful experiments are important complements to the one-dimensional experiments. As in the more sophisticated one-dimensional experiments, the two-dimensional experiments involve three distinct time periods: a preparation period, t/sub 0/; an evolution period, t/sub 1/; and a detection period, t/sub 2/.

Spectroscopic and molecular docking studies on the charge transfer complex of bovine serum albumin with quinone in aqueous medium and its influence on the ligand binding property of the protein.

PubMed

Satheshkumar, Angupillai; Elango, Kuppanagounder P

2014-09-15

The spectral techniques such as UV-Vis, (1)H NMR and fluorescence and electrochemical experiments have been employed to investigate the interaction between 2-methoxy-3,5,6-trichloro-1,4-benzoquinone (MQ; a water soluble quinone) and bovine serum albumin (BSA) in aqueous medium. The fluorescence of BSA was quenched by MQ via formation of a 1:1 BSA-MQ charge transfer adduct with a formation constant of 3.3×10(8) L mol(-1). Based on the Forster's theory the binding distance between them is calculated as 2.65 nm indicating high probability of binding. For the first time, influence of quinone on the binding property of various types of ligands such as aspirin, ascorbic acid, nicotinimide and sodium stearate has also been investigated. The results indicated that the strong and spontaneous binding existing between BSA and MQ, decreased the intensity of binding of these ligands with BSA. Since Tryptophan (Trp) is the basic residue present in BSA, a comparison between binding property of Trp-MQ adduct with that of BSA-MQ with these ligands has also been attempted. 1H NMR titration study indicated that the Trp forms a charge transfer complex with MQ, which reduces the interaction of Trp with the ligands. Molecular docking study supported the fact that the quinone interacts with the Trp212 unit of the BSA and the free energy change of binding (ΔG) for the BSA-MQ complex was found to be -46 kJ mol(-1), which is comparable to our experimental free energy of binding (-49 kJ mol(-1)) obtained from fluorescence study. Copyright © 2014 Elsevier B.V. All rights reserved.

Solution structure of the parvulin-type PPIase domain of Staphylococcus aureus PrsA – Implications for the catalytic mechanism of parvulins

PubMed Central

Heikkinen, Outi; Seppala, Raili; Tossavainen, Helena; Heikkinen, Sami; Koskela, Harri; Permi, Perttu; Kilpeläinen, Ilkka

2009-01-01

Background Staphylococcus aureus is a Gram-positive pathogenic bacterium causing many kinds of infections from mild respiratory tract infections to life-threatening states as sepsis. Recent emergence of S. aureus strains resistant to numerous antibiotics has created a need for new antimicrobial agents and novel drug targets. S. aureus PrsA is a membrane associated extra-cytoplasmic lipoprotein which contains a parvulin-type peptidyl-prolyl cis-trans isomerase domain. PrsA is known to act as an essential folding factor for secreted proteins in Gram-positive bacteria and thus it is a potential target for antimicrobial drugs against S. aureus. Results We have solved a high-resolution solution structure of the parvulin-type peptidyl-prolyl cis-trans isomerase domain of S. aureus PrsA (PrsA-PPIase). The results of substrate peptide titrations pinpoint the active site and demonstrate the substrate preference of the enzyme. With detailed NMR spectroscopic investigation of the orientation and tautomeric state of the active site histidines we are able to give further insight into the structure of the catalytic site. NMR relaxation analysis gives information on the dynamic behaviour of PrsA-PPIase. Conclusion Detailed structural description of the S. aureus PrsA-PPIase lays the foundation for structure-based design of enzyme inhibitors. The structure resembles hPin1-type parvulins both structurally and regarding substrate preference. Even though a wealth of structural data is available on parvulins, the catalytic mechanism has yet to be resolved. The structure of S. aureus PrsA-PPIase and our findings on the role of the conserved active site histidines help in designing further experiments to solve the detailed catalytic mechanism. PMID:19309529

Suramin blocks interaction between human FGF1 and FGFR2 D2 domain and reduces downstream signaling activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Zong-Sian, E-mail: gary810426@hotmail.com; Liu, Che Fu, E-mail: s9823002@m98.nthu.edu.tw; Fu, Brian, E-mail: brianfu9@gmail.com

2016-09-02

The extracellular portion of the human fibroblast growth factor receptor2 D2 domain (FGFR2 D2) interacts with human fibroblast growth factor 1 (hFGF1) to activate a downstream signaling cascade that ultimately affects mitosis and differentiation. Suramin is an antiparasiticdrug and a potent inhibitor of FGF-induced angiogenesis. Suramin has been shown to bind to hFGF1, and might block the interaction between hFGF1 and FGFR2 D2. Here, we titrated hFGF1 with FGFR2 D2 and suramin to elucidate their interactions using the detection of NMR. The docking results of both hFGF1-FGFR2 D2 domain and hFGF1-suramin complex were superimposed. The results indicate that suramin blocksmore » the interaction between hFGF1 and FGFR2 D2. We used the PyMOL software to show the hydrophobic interaction of hFGF1-suramin. In addition, we used a Water-soluble Tetrazolium salts assay (WST1) to assess hFGF1 bioactivity. The results will be useful for the development of new antimitogenic activity drugs. - Highlights: • The interfacial residues on hFGF1-FGFR2 D2 and hFGF1-Suramin contact surface were mapped by {sup 1}H-{sup 15}N HSQC experiments. • hFGF1-FGFR2 D2 and hFGF1-Suramin complex models were generated from NMR restraints by using HADDOCK program. • We analyzed hFGF1-Suramin complex models and found the interaction between hFGF1-Suramin is hydrophobic. • The bioactivity of the hFGF1-FGFR2 D2 and hFGF1-Suramin complex was studied by using WST1 assay.« less

Spectroscopic and molecular docking studies on the charge transfer complex of bovine serum albumin with quinone in aqueous medium and its influence on the ligand binding property of the protein

NASA Astrophysics Data System (ADS)

Satheshkumar, Angupillai; Elango, Kuppanagounder P.

2014-09-01

The spectral techniques such as UV-Vis, 1H NMR and fluorescence and electrochemical experiments have been employed to investigate the interaction between 2-methoxy-3,5,6-trichloro-1,4-benzoquinone (MQ; a water soluble quinone) and bovine serum albumin (BSA) in aqueous medium. The fluorescence of BSA was quenched by MQ via formation of a 1:1 BSA-MQ charge transfer adduct with a formation constant of 3.3 × 108 L mol-1. Based on the Forster’s theory the binding distance between them is calculated as 2.65 nm indicating high probability of binding. For the first time, influence of quinone on the binding property of various types of ligands such as aspirin, ascorbic acid, nicotinimide and sodium stearate has also been investigated. The results indicated that the strong and spontaneous binding existing between BSA and MQ, decreased the intensity of binding of these ligands with BSA. Since Tryptophan (Trp) is the basic residue present in BSA, a comparison between binding property of Trp-MQ adduct with that of BSA-MQ with these ligands has also been attempted. 1H NMR titration study indicated that the Trp forms a charge transfer complex with MQ, which reduces the interaction of Trp with the ligands. Molecular docking study supported the fact that the quinone interacts with the Trp212 unit of the BSA and the free energy change of binding (ΔG) for the BSA-MQ complex was found to be -46 kJ mol-1, which is comparable to our experimental free energy of binding (-49 kJ mol-1) obtained from fluorescence study.

Water absorption of freeze-dried meat at different water activities: a multianalytical approach using sorption isotherm, differential scanning calorimetry, and nuclear magnetic resonance.

PubMed

Venturi, Luca; Rocculi, Pietro; Cavani, Claudio; Placucci, Giuseppe; Dalla Rosa, Marco; Cremonini, Mauro A

2007-12-26

Hydration of freeze-dried chicken breast meat was followed in the water activity range of aw=0.12-0.99 by a multianalytical approach comprising of sorption isotherm, differential scanning calorimetry (DSC), and nuclear magnetic resonance (NMR). The amount of frozen water and the shape of the T2-relaxogram were evaluated at each water content by DSC and NMR, respectively. Data revealed an agreement between sorption isotherm and DSC experiments about the onset of bulk water (aw=0.83-0.86), and NMR detected mobile water starting at aw=0.75. The origin of the short-transverse relaxation time part of the meat NMR signal was also reinvestigated through deuteration experiments and proposed to arise from protons belonging to plasticized matrix structures. It is proved both by D2O experiments and by gravimetry that the extra protons not contributing to the water content in the NMR experiments are about 6.4% of the total proton NMR CPMG signal of meat.

A systematic investigation of aluminium ion speciation at high temperature. Part 1. Solution studies.

PubMed

Shafran, Kirill L; Perry, Carole C

2005-06-21

Speciation diagrams of aluminium ions in aqueous solution (0.2 M) at high temperature (90 degrees C) have been obtained from 48 h time-resolved multi-batch titration experiments monitored by 27Al NMR spectroscopy, potentiometry and dynamic light scattering. The quantitative speciation patterns and kinetic data obtained offer a dynamic picture of the distribution of soluble and insoluble Al species as a function of hydrolysis ratio h(h=[OH-]/[Al3+]) over a very broad range of conditions (-1.0 < or =h < or = 4.0). Monomeric, small oligomeric, tridecameric (the 'Al13-mer') and the recently characterised 30-meric aluminium species (the 'Al30-mer') as well as aluminium hydroxide have been identified and quantified. The Al13-mer species dominates over a relatively broad range of hydrolysis ratios (1.5 < or =h< or = 2.7) during the first 6 h of experiment, but are gradually replaced by Al30-mers at longer reaction times. Kinetic profiles indicate that the formation of the Al30-mer is limited by the disappearance of the Al13 species at mildly acidic conditions. The estimated rate constants of both hydrolytic processes show good internal correlation at h> or = 1.5. The effect of local perturbations leading to the formation of aluminium hydroxide below the electroneutrality point (h= 3.0) has been estimated quantitatively.

H-Bond Self-Assembly: Folding versus Duplex Formation.

PubMed

Núñez-Villanueva, Diego; Iadevaia, Giulia; Stross, Alexander E; Jinks, Michael A; Swain, Jonathan A; Hunter, Christopher A

2017-05-17

Linear oligomers equipped with complementary H-bond donor (D) and acceptor (A) sites can interact via intermolecular H-bonds to form duplexes or fold via intramolecular H-bonds. These competing equilibria have been quantified using NMR titration and dilution experiments for seven systems featuring different recognition sites and backbones. For all seven architectures, duplex formation is observed for homo-sequence 2-mers (AA·DD) where there are no competing folding equilibria. The corresponding hetero-sequence AD 2-mers also form duplexes, but the observed self-association constants are strongly affected by folding equilibria in the monomeric states. When the backbone is flexible (five or more rotatable bonds separating the recognition sites), intramolecular H-bonding is favored, and the folded state is highly populated. For these systems, the stability of the AD·AD duplex is 1-2 orders of magnitude lower than that of the corresponding AA·DD duplex. However, for three architectures which have more rigid backbones (fewer than five rotatable bonds), intramolecular interactions are not observed, and folding does not compete with duplex formation. These systems are promising candidates for the development of longer, mixed-sequence synthetic information molecules that show sequence-selective duplex formation.

NMR structural study of the intracellular loop 3 of the serotonin 5-HT(1A) receptor and its interaction with calmodulin.

PubMed

Chen, Angela Shuyi; Kim, Young Mee; Gayen, Shovanlal; Huang, Qiwei; Raida, Manfred; Kang, Congbao

2011-09-01

The serotonin (5-HT(1A)) receptor, a G-protein-coupled receptor (GPCR), plays important roles in serotonergic signaling in the central nervous system. The third intracellular loop (ICL3) of the 5-HT(1A) receptor has been shown to be important for the regulation of this receptor through interactions with proteins such as G-proteins and calmodulin. In this study, the ICL3 of 5-HT(1A) receptor was expressed in E. coli and purified. Gel filtration and mass spectrometry were used to confirm the molecular weight of the purified ICL3. Secondary structure analysis using circular dichroism (CD) demonstrated the presence of α-helical structures. Backbone assignment of ICL3 was achieved using three-dimensional experiments. A chemical shift index and Talos+ analysis showed that residues E326 to R339 form α-helical structure. Residues G256 to S269 of ICL3 were shown to be a novel region that has a molecular interaction with calmodulin in titration assays. Peptide derived from the ICL3 containing residues from G256 to S269 also showed molecular interaction with calmodulin. Copyright © 2011 Elsevier B.V. All rights reserved.

Isatinphenylsemicarbazones as efficient colorimetric sensors for fluoride and acetate anions - anions induce tautomerism.

PubMed

Jakusová, Klaudia; Donovalová, Jana; Cigáň, Marek; Gáplovský, Martin; Garaj, Vladimír; Gáplovský, Anton

2014-04-05

The anion induced tautomerism of isatin-3-4-phenyl(semicarbazone) derivatives is studied herein. The interaction of F(-), AcO(-), H2PO4(-), Br(-) or HSO4(-) anions with E and Z isomers of isatin-3-4-phenyl(semicarbazone) and N-methylisatin-3-4-phenyl(semicarbazone) as sensors influences the tautomeric equilibrium of these sensors in the liquid phase. This tautomeric equilibrium is affected by (1) the inter- and intra-molecular interactions' modulation of isatinphenylsemicarbazone molecules due to the anion induced change in the solvation shell of receptor molecules and (2) the sensor-anion interaction with the urea hydrogens. The acid-base properties of anions and the difference in sensor structure influence the equilibrium ratio of the individual tautomeric forms. Here, the tautomeric equilibrium changes were indicated by "naked-eye" experiment, UV-VIS spectral and (1)H NMR titration, resulting in confirmation that appropriate selection of experimental conditions leads to a high degree of sensor selectivity for some investigated anions. Sensors' E and Z isomers differ in sensitivity, selectivity and sensing mechanism. Detection of F(-) or CH3COO(-) anions at high weakly basic anions' excess is possible. Copyright © 2014 Elsevier B.V. All rights reserved.

Galectin-1-asialofetuin interaction is inhibited by peptides containing the tyr-xxx-tyr motif acting on the glycoprotein.

PubMed

Wéber, Edit; Hetényi, Anasztázia; Váczi, Balázs; Szolnoki, Eva; Fajka-Boja, Roberta; Tubak, Vilmos; Monostori, Eva; Martinek, Tamás A

2010-01-25

Galectin-1 (Gal-1), a ubiquitous beta-galactoside-binding protein expressed by various normal and pathological tissues, has been implicated in cancer and autoimmune/inflammatory diseases in consequence of its regulatory role in adhesion, cell viability, proliferation, and angiogenesis. The functions of Gal-1 depend on its affinity for beta-galactoside-containing glycoconjugates; accordingly, the inhibition of sugar binding blocks its functions, hence promising potential therapeutic tools. The Tyr-Xxx-Tyr peptide motifs have been reported to be glycomimetic sequences, mainly on the basis of their inhibitory effect on the Gal-1-asialofetuin (ASF) interaction. However, the results regarding the efficacy of the Tyr-Xxx-Tyr motif as a glycomimetic inhibitor are still controversial. The present STD and trNOE NMR experiments reveal that the Tyr-Xxx-Tyr peptides studied do not bind to Gal-1, whereas their binding to ASF is clearly detected. (15)N,(1)H HSQC titrations with (15)N-labeled Gal-1 confirm the absence of any peptide-Gal-1 interaction. These data indicate that the Tyr-Xxx-Tyr peptides tested in this work are not glycomimetics as they interact with ASF via an unrevealed molecular linkage.

Computer Series, 88.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1987-01-01

Describes two experiments in college chemistry which use microcomputers. One experiment deals with chemical oscillations, while the other involves colorimeter titration with laser excitation and computer-interfaced endpoint detection. (TW)

Beyond Fourier

NASA Astrophysics Data System (ADS)

Hoch, Jeffrey C.

2017-10-01

Non-Fourier methods of spectrum analysis are gaining traction in NMR spectroscopy, driven by their utility for processing nonuniformly sampled data. These methods afford new opportunities for optimizing experiment time, resolution, and sensitivity of multidimensional NMR experiments, but they also pose significant challenges not encountered with the discrete Fourier transform. A brief history of non-Fourier methods in NMR serves to place different approaches in context. Non-Fourier methods reflect broader trends in the growing importance of computation in NMR, and offer insights for future software development.

Efficient DNP NMR of Membrane Proteins: Sample Preparation Protocols, Sensitivity, and Radical Location

PubMed Central

Liao, Shu Y.; Lee, Myungwoon; Wang, Tuo; Sergeyev, Ivan V.; Hong, Mei

2016-01-01

Although dynamic nuclear polarization (DNP) has dramatically enhanced solid-state NMR spectral sensitivities of many synthetic materials and some biological macromolecules, recent studies of membrane-protein DNP using exogenously doped paramagnetic radicals as polarizing agents have reported varied and sometimes surprisingly limited enhancement factors. This motivated us to carry out a systematic evaluation of sample preparation protocols for optimizing the sensitivity of DNP NMR spectra of membrane-bound peptides and proteins at cryogenic temperatures of ~110 K. We show that mixing the radical with the membrane by direct titration instead of centrifugation gives a significant boost to DNP enhancement. We quantify the relative sensitivity enhancement between AMUPol and TOTAPOL, two commonly used radicals, and between deuterated and protonated lipid membranes. AMUPol shows ~4 fold higher sensitivity enhancement than TOTAPOL, while deuterated lipid membrane does not give net higher sensitivity for the membrane peptides than protonated membrane. Overall, a ~100 fold enhancement between the microwave-on and microwave-off spectra can be achieved on lipid-rich membranes containing conformationally disordered peptides, and absolute sensitivity gains of 105–160 can be obtained between low-temperature DNP spectra and high-temperature non-DNP spectra. We also measured the paramagnetic relaxation enhancement of lipid signals by TOTAPOL and AMUPol, to determine the depths of these two radicals in the lipid bilayer. Our data indicate a bimodal distribution of both radicals, a surface-bound fraction and a membrane-bound fraction where the nitroxides lie at ~10 Å from the membrane surface. TOTAPOL appears to have a higher membrane-embedded fraction than AMUPol. These results should be useful for membrane-protein solid-state NMR studies under DNP conditions and provide insights into how biradicals interact with phospholipid membranes. PMID:26873390

Dipeptide Structural Analysis Using Two-Dimensional NMR for the Undergraduate Advanced Laboratory

ERIC Educational Resources Information Center

Gonzalez, Elizabeth; Dolino, Drew; Schwartzenburg, Danielle; Steiger, Michelle A.

2015-01-01

A laboratory experiment was developed to introduce students in either an organic chemistry or biochemistry lab course to two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy using simple biomolecules. The goal of this experiment is for students to understand and interpret the information provided by a 2D NMR spectrum. Students are…

A stable and convenient protein electrophoresis titration device with bubble removing system.

PubMed

Zhang, Qiang; Fan, Liu-Yin; Li, Wen-Lin; Cong, Feng-Song; Zhong, Ran; Chen, Jing-Jing; He, Yu-Chen; Xiao, Hua; Cao, Cheng-Xi

2017-07-01

Moving reaction boundary titration (MRBT) has a potential application to immunoassay and protein content analysis with high selectivity. However, air bubbles often impair the accuracy of MRBT, and the leakage of electrolyte greatly decreases the safety and convenience of electrophoretic titration. Addressing these two issues a reliable MRBT device with modified electrolyte chamber of protein titration was designed. Multiphysics computer simulation was conducted for optimization according to two-phase flow. The single chamber was made of two perpendicular cylinders with different diameters. After placing electrophoretic tube, the resident air in the junction next to the gel could be eliminated by a simple fast electrolyte flow. Removing the electrophoretic tube automatically prevented electrolyte leakage at the junction due to the gravity-induced negative pressure within the chamber. Moreover, the numerical simulation and experiments showed that the improved MRBT device has following advantages: (i) easy and rapid setup of electrophoretic tube within 20 s; (ii) simple and quick bubble dissipates from the chamber of titration within 2 s; (iii) no electrolyte leakage from the two chambers: and (iv) accurate protein titration and safe instrumental operation. The developed technique and apparatus greatly improves the performance of the previous MRBT device, and providing a new route toward practical application. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

1H NMR studies of molecular interaction of D-glucosamine and N-acetyl-D-glucosamine with capsaicin in aqueous and non-aqueous media.

PubMed

Higuera-Ciapara, Inocencio; Virués, Claudia; Jiménez-Chávez, Marcela; Martínez-Benavidez, Evelin; Hernández, Javier; Domínguez, Zaira; López-Rendón, Roberto; Velázquez, Enrique F; Inoue, Motomichi

2017-11-27

Complex formation of D-glucosamine (Gl) and N-acetyl-D-glucosamine (AGl) with capsaicin (Cp) were studied by 1 H NMR titrations in H 2 O-d 2 and DMSO-d 6 ; capsaicin is the major bioactive component of chili peppers. Every titration curve has been interpreted by formulating a suitable model for the reaction equilibrium, to elucidate intermolecular interactions. In DMSO, glucosamine cations associate with each other to yield linear aggregates, and undergo pseudo-1:1-complexation with capsaicin, the formation constant being ca. 30 M -1 . N-Acetylglucosamine, without self-association, forms a 2:1-complex AGl 2 Cp with the stability of ca. 70 M -2 . These complexations are achieved by intermolecular hydrogen bonds. In D 2 O, glucosamine undergoes reversible protonation equilibrium between Gl 0 and GlH + with the logarithmic protonation constants log K D  = 8.63 for α-glucosamine and 8.20 for β-isomer. Both anomeric isomers of deprotonated glucosamine form Gl 0 Cp-type complexes of capsaicin, in a competitive manner, with a formation constant of 1040 M -1 for the α-glucosamine complex and 830 M -1 for the β-complex; the anomeric carbons result in the difference in thermodynamic stability. The reactant molecules are closed up by the solvent-exclusion effect and/or the van der Waals interaction; the resulting pair is stabilized by intermolecular hydrogen bonding within a local water-free space between the component molecules. By contrast, neither protonated glucosamine (GlH + ) nor N-acetylglucosamine yields a capsaicin complex with the definite stoichiometry. The monosaccharides recognize capsaicin under only a controlled condition; the same phenomena are predicted for biological systems and nanocarriers based on polysaccharides such as chitosan. Copyright © 2017 Elsevier Ltd. All rights reserved.

On the characterization of dynamic supramolecular systems: a general mathematical association model for linear supramolecular copolymers and application on a complex two-component hydrogen-bonding system.

PubMed

Odille, Fabrice G J; Jónsson, Stefán; Stjernqvist, Susann; Rydén, Tobias; Wärnmark, Kenneth

2007-01-01

A general mathematical model for the characterization of the dynamic (kinetically labile) association of supramolecular assemblies in solution is presented. It is an extension of the equal K (EK) model by the stringent use of linear algebra to allow for the simultaneous presence of an unlimited number of different units in the resulting assemblies. It allows for the analysis of highly complex dynamic equilibrium systems in solution, including both supramolecular homo- and copolymers without the recourse to extensive approximations, in a field in which other analytical methods are difficult. The derived mathematical methodology makes it possible to analyze dynamic systems such as supramolecular copolymers regarding for instance the degree of polymerization, the distribution of a given monomer in different copolymers as well as its position in an aggregate. It is to date the only general means to characterize weak supramolecular systems. The model was fitted to NMR dilution titration data by using the program Matlab, and a detailed algorithm for the optimization of the different parameters has been developed. The methodology is applied to a case study, a hydrogen-bonded supramolecular system, salen 4+porphyrin 5. The system is formally a two-component system but in reality a three-component system. This results in a complex dynamic system in which all monomers are associated to each other by hydrogen bonding with different association constants, resulting in homo- and copolymers 4n5m as well as cyclic structures 6 and 7, in addition to free 4 and 5. The system was analyzed by extensive NMR dilution titrations at variable temperatures. All chemical shifts observed at different temperatures were used in the fitting to obtain the DeltaH degrees and DeltaS degrees values producing the best global fit. From the derived general mathematical expressions, system 4+5 could be characterized with respect to above-mentioned parameters.

Proton NMR studies of functionalized nanoparticles in aqueous environments

NASA Astrophysics Data System (ADS)

Tataurova, Yulia Nikolaevna

Nanoscience is an emerging field that can provide potential routes towards addressing critical issues such as clean and sustainable energy, environmental remediation and human health. Specifically, porous nanomaterials, such as zeolites and mesoporous silica, are found in a wide range of applications including catalysis, drug delivery, imaging, environmental protection, and sensing. The characterization of the physical and chemical properties of nanocrystalline materials is essential to the realization of these innovative applications. The great advantage of porous nanocrystals is their increased external surface area that can control their biological, chemical and catalytic activities. Specific functional groups synthesized on the surface of nanoparticles are able to absorb heavy metals from the solution or target disease cells, such as cancer cells. In these studies, three main issues related to functionalized nanomaterials will be addressed through the application of nuclear magnetic resonance (NMR) techniques including: 1) surface composition and structure of functionalized nanocrystalline particles; 2) chemical properties of the guest molecules on the surface of nanomaterials, and 3) adsorption and reactivity of surface bound functional groups. Nuclear magnetic resonance (NMR) is one of the major spectroscopic techniques available for the characterization of molecular structure and conformational dynamics with atomic level detail. This thesis deals with the application of 1H solution state NMR to porous nanomaterial in an aqueous environment. Understanding the aqueous phase behavior of functionalized nanomaterials is a key factor in the design and development of safe nanomaterials because their interactions with living systems are always mediated through the aqueous phase. This is often due to a lack of fundamental knowledge in interfacial chemical and physical phenomena that occur on the surface of nanoparticles. The use of solution NMR spectroscopy results in high-resolution NMR spectra. This technique is selective for protons on the surface organic functional groups due to their motional averaging in solution. In this study, 1H solution NMR spectroscopy was used to investigate the interface of the organic functional groups in D2O. The pKa for these functional groups covalently bound to the surface of nanoparticles was determined using an NMR-pH titration method based on the variation in the proton chemical shift for the alkyl group protons closest to the amine group with pH. The adsorption of toxic contaminants (chromate and arsenate anions) on the surface of functionalized silicalite-1 and mesoporous silica nanoparticles has been studied by 1H solution NMR spectroscopy. With this method, the surface bound contaminants are detected. The analysis of the intensity and position of these peaks allows quantitative assessment of the relative amounts of functional groups with adsorbed metal ions. These results demonstrate the sensitivity of solution NMR spectroscopy to the electronic environment and structure of the surface functional groups on porous nanomaterials.

Anvil cell gasket design for high pressure nuclear magnetic resonance experiments beyond 30 GPa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meier, Thomas; Haase, Jürgen

2015-12-15

Nuclear magnetic resonance (NMR) experiments are reported at up to 30.5 GPa of pressure using radiofrequency (RF) micro-coils with anvil cell designs. These are the highest pressures ever reported with NMR, and are made possible through an improved gasket design based on nano-crystalline powders embedded in epoxy resin. Cubic boron-nitride (c-BN), corundum (α-Al{sub 2}O{sub 3}), or diamond based composites have been tested, also in NMR experiments. These composite gaskets lose about 1/2 of their initial height up to 30.5 GPa, allowing for larger sample quantities and preventing damages to the RF micro-coils compared to precipitation hardened CuBe gaskets. It ismore » shown that NMR shift and resolution are less affected by the composite gaskets as compared to the more magnetic CuBe. The sensitivity can be as high as at normal pressure. The new, inexpensive, and simple to engineer gaskets are thus superior for NMR experiments at high pressures.« less

nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.

PubMed

Schober, Daniel; Jacob, Daniel; Wilson, Michael; Cruz, Joseph A; Marcu, Ana; Grant, Jason R; Moing, Annick; Deborde, Catherine; de Figueiredo, Luis F; Haug, Kenneth; Rocca-Serra, Philippe; Easton, John; Ebbels, Timothy M D; Hao, Jie; Ludwig, Christian; Günther, Ulrich L; Rosato, Antonio; Klein, Matthias S; Lewis, Ian A; Luchinat, Claudio; Jones, Andrew R; Grauslys, Arturas; Larralde, Martin; Yokochi, Masashi; Kobayashi, Naohiro; Porzel, Andrea; Griffin, Julian L; Viant, Mark R; Wishart, David S; Steinbeck, Christoph; Salek, Reza M; Neumann, Steffen

2018-01-02

NMR is a widely used analytical technique with a growing number of repositories available. As a result, demands for a vendor-agnostic, open data format for long-term archiving of NMR data have emerged with the aim to ease and encourage sharing, comparison, and reuse of NMR data. Here we present nmrML, an open XML-based exchange and storage format for NMR spectral data. The nmrML format is intended to be fully compatible with existing NMR data for chemical, biochemical, and metabolomics experiments. nmrML can capture raw NMR data, spectral data acquisition parameters, and where available spectral metadata, such as chemical structures associated with spectral assignments. The nmrML format is compatible with pure-compound NMR data for reference spectral libraries as well as NMR data from complex biomixtures, i.e., metabolomics experiments. To facilitate format conversions, we provide nmrML converters for Bruker, JEOL and Agilent/Varian vendor formats. In addition, easy-to-use Web-based spectral viewing, processing, and spectral assignment tools that read and write nmrML have been developed. Software libraries and Web services for data validation are available for tool developers and end-users. The nmrML format has already been adopted for capturing and disseminating NMR data for small molecules by several open source data processing tools and metabolomics reference spectral libraries, e.g., serving as storage format for the MetaboLights data repository. The nmrML open access data standard has been endorsed by the Metabolomics Standards Initiative (MSI), and we here encourage user participation and feedback to increase usability and make it a successful standard.

Mini-Column Ion-Exchange Separation and Atomic Absorption Quantitation of Nickel, Cobalt, and Iron: An Undergraduate Quantitative Analysis Experiment.

ERIC Educational Resources Information Center

Anderson, James L.; And Others

1980-01-01

Presents an undergraduate quantitative analysis experiment, describing an atomic absorption quantitation scheme that is fast, sensitive and comparatively simple relative to other titration experiments. (CS)

Hydrolysis Studies and Quantitative Determination of Aluminum Ions Using [superscript 27]Al NMR: An Undergraduate Analytical Chemistry Experiment

ERIC Educational Resources Information Center

Curtin, Maria A.; Ingalls, Laura R.; Campbell, Andrew; James-Pederson, Magdalena

2008-01-01

This article describes a novel experiment focused on metal ion hydrolysis and the equilibria related to metal ions in aqueous systems. Using [superscript 27]Al NMR, the students become familiar with NMR spectroscopy as a quantitative analytical tool for the determination of aluminum by preparing a standard calibration curve using standard aluminum…

Experimental Determination of pK[subscript a] Values by Use of NMR Chemical Shifts, Revisited

ERIC Educational Resources Information Center

Gift, Alan D.; Stewart, Sarah M.; Bokashanga, Patrick Kwete

2012-01-01

This laboratory experiment, using proton NMR spectroscopy to determine the dissociation constant for heterocyclic bases, has been modified from a previously described experiment. A solution of a substituted pyridine is prepared using deuterium oxide (D[subscript 2]O) as the solvent. The pH of the solution is adjusted and proton NMR spectra are…

Beyond Fourier.

PubMed

Hoch, Jeffrey C

2017-10-01

Non-Fourier methods of spectrum analysis are gaining traction in NMR spectroscopy, driven by their utility for processing nonuniformly sampled data. These methods afford new opportunities for optimizing experiment time, resolution, and sensitivity of multidimensional NMR experiments, but they also pose significant challenges not encountered with the discrete Fourier transform. A brief history of non-Fourier methods in NMR serves to place different approaches in context. Non-Fourier methods reflect broader trends in the growing importance of computation in NMR, and offer insights for future software development. Copyright © 2017 Elsevier Inc. All rights reserved.

Substituent effects and pH profiles for stability constants of arylboronic acid diol esters.

PubMed

Martínez-Aguirre, Mayte A; Villamil-Ramos, Raul; Guerrero-Alvarez, Jorge A; Yatsimirsky, Anatoly K

2013-05-17

Stability constants of boronic acid diol esters in aqueous solution have been determined potentiometrically for a series of meta-, para-substituted phenylboronic acids and diols of variable acidity. The constants β(11-1) for reactions between neutral forms of reactants producing the anionic ester plus proton follow the Hammett equation with ρ depending on pKa of diol and varying from 2.0 for glucose to 1.29 for 4-nitrocatechol. Observed stability constants (K(obs)) measured by UV-vis and fluorometric titrations at variable pH for esters of 4,5-dihydroxy-1,3-benzenedisulfonate (Tiron) generally agree with those expected on the basis of β(11-1) values, but the direct fitting of K(obs) vs pH profiles gives shifted pKa values both for boronic acids and diol as a result of significant interdependence of fitting parameters. The subsituent effects on absorption and fluorescence spectra of Tiron arylboronate esters are characterized. The K(obs) for Tiron determined by (11)B NMR titrations are approximately 1 order of magnitude smaller than those determined by UV-vis titrations under identical conditions. A general equation, which makes possible an estimate of β(11-1) for any pair of boronic acid and diol from their pKa values, is proposed on the basis of established Brönsted-type correlation of Hammett parameters for β(11-1) with acidity of diols. The equation allows one to calculate stability constants expected only on basis of acid-base properties of the components, thus permitting more strict evaluation of contributions of additional factors such as steric or charge effects to the ester stability.

Multiple acquisition of magic angle spinning solid-state NMR experiments using one receiver: Application to microcrystalline and membrane protein preparations

NASA Astrophysics Data System (ADS)

Gopinath, T.; Veglia, Gianluigi

2015-04-01

Solid-state NMR spectroscopy of proteins is a notoriously low-throughput technique. Relatively low-sensitivity and poor resolution of protein samples require long acquisition times for multidimensional NMR experiments. To speed up data acquisition, we developed a family of experiments called Polarization Optimized Experiments (POE), in which we utilized the orphan spin operators that are discarded in classical multidimensional NMR experiments, recovering them to allow simultaneous acquisition of multiple 2D and 3D experiments, all while using conventional probes with spectrometers equipped with one receiver. POE allow the concatenation of multiple 2D or 3D pulse sequences into a single experiment, thus potentially combining all of the aforementioned advances, boosting the capability of ssNMR spectrometers at least two-fold without the addition of any hardware. In this perspective, we describe the first generation of POE, such as dual acquisition MAS (or DUMAS) methods, and then illustrate the evolution of these experiments into MEIOSIS, a method that enables the simultaneous acquisition of multiple 2D and 3D spectra. Using these new pulse schemes for the solid-state NMR investigation of biopolymers makes it possible to obtain sequential resonance assignments, as well as distance restraints, in about half the experimental time. While designed for acquisition of heteronuclei, these new experiments can be easily implemented for proton detection and coupled with other recent advancements, such as dynamic nuclear polarization (DNP), to improve signal to noise. Finally, we illustrate the application of these methods to microcrystalline protein preparations as well as single and multi-span membrane proteins reconstituted in lipid membranes.

Multiple acquisition of magic angle spinning solid-state NMR experiments using one receiver: application to microcrystalline and membrane protein preparations.

PubMed

Gopinath, T; Veglia, Gianluigi

2015-04-01

Solid-state NMR spectroscopy of proteins is a notoriously low-throughput technique. Relatively low-sensitivity and poor resolution of protein samples require long acquisition times for multidimensional NMR experiments. To speed up data acquisition, we developed a family of experiments called Polarization Optimized Experiments (POE), in which we utilized the orphan spin operators that are discarded in classical multidimensional NMR experiments, recovering them to allow simultaneous acquisition of multiple 2D and 3D experiments, all while using conventional probes with spectrometers equipped with one receiver. POE allow the concatenation of multiple 2D or 3D pulse sequences into a single experiment, thus potentially combining all of the aforementioned advances, boosting the capability of ssNMR spectrometers at least two-fold without the addition of any hardware. In this perspective, we describe the first generation of POE, such as dual acquisition MAS (or DUMAS) methods, and then illustrate the evolution of these experiments into MEIOSIS, a method that enables the simultaneous acquisition of multiple 2D and 3D spectra. Using these new pulse schemes for the solid-state NMR investigation of biopolymers makes it possible to obtain sequential resonance assignments, as well as distance restraints, in about half the experimental time. While designed for acquisition of heteronuclei, these new experiments can be easily implemented for proton detection and coupled with other recent advancements, such as dynamic nuclear polarization (DNP), to improve signal to noise. Finally, we illustrate the application of these methods to microcrystalline protein preparations as well as single and multi-span membrane proteins reconstituted in lipid membranes. Copyright © 2015 Elsevier Inc. All rights reserved.

Multiple Acquisition of Magic Angle Spinning Solid-State NMR Experiments Using One Receiver: Application to Microcrystalline and Membrane Protein Preparations

PubMed Central

Gopinath, T.; Veglia, Gianluigi

2015-01-01

Solid-State NMR spectroscopy of proteins is a notoriously low-throughput technique. Relatively low-sensitivity and poor resolution of protein samples require long acquisition times for multidimensional NMR experiments. To speed up data acquisition, we developed a family of experiments called Polarization Optimized Experiments (POE), in which we utilized the orphan spin operators that are discarded in classical multidimensional NMR experiments, recovering them to allow simultaneous acquisition of multiple 2D and 3D experiments, all while using conventional probes with spectrometers equipped with one receiver. POEs allow the concatenation of multiple 2D or 3D pulse sequences into a single experiment, thus potentially combining all of the aforementioned advances, boosting the capability of ssNMR spectrometers at least two-fold without the addition of any hardware. In this Perspective, we describe the first generation of POEs, such as dual acquisition MAS (or DUMAS) methods, and then illustrate the evolution of these experiments into MEIOSIS, a method that enables the simultaneous acquisition of multiple 2D and 3D spectra. Using these new pulse schemes for the solid-state NMR investigation of biopolymers makes it possible to obtain sequential resonance assignments, as well as distance restraints, in about half the experimental time. While designed for acquisition of heteronuclei, these new experiments can be easily implemented for proton detection and coupled with other recent advancements, such as dynamic polarization, to improve signal to noise. Finally, we illustrate the application of these methods to microcrystalline protein preparations as well as single and multi-span membrane proteins reconstituted in lipid membranes. PMID:25797011

Simultaneous addition of two ligands: a potential strategy for estimating divalent ion affinities in EF-hand proteins by isothermal titration calorimetry.

PubMed

Henzl, Michael T; Markus, Lindsey A; Davis, Meredith E; McMillan, Andrew T

2013-03-01

Capable of providing a detailed thermodynamic picture of noncovalent association reactions, isothermal titration calorimetry (ITC) has become a popular method for studying protein-ligand interactions. We routinely employ the technique to study divalent ion-binding by two-site EF-hand proteins from the parvalbumin- and polcalcin lineages. The combination of high Ca(2+) affinity and relatively low Mg(2+) affinity, and the attendant complication of parameter correlation, conspire to make the simultaneous extraction of binding constants and -enthalpies for both ions challenging. Although global analysis of multiple ITC experiments can overcome these hurdles, our current experimental protocol includes upwards of 10 titrations - requiring a substantial investment in labor, machine time, and material. This paper explores the potential for using a smaller suite of experiments that includes simultaneous titrations with Ca(2+) and Mg(2+) at different ratios of the two ions. The results obtained for four proteins, differing substantially in their divalent ion-binding properties, suggest that the approach has merit. The Ca(2+)- and Mg(2+)-binding constants afforded by the streamlined analysis are in reasonable agreement with those obtained from the standard analysis protocol. Likewise, the abbreviated analysis provides comparable values for the Ca(2+)-binding enthalpies. However, the streamlined analysis can yield divergent values for the Mg(2+)-binding enthalpies - particularly those for lower affinity sites. This shortcoming can be remedied, in large measure, by including data from a direct Ca(2+) titration in the presence of a high, fixed Mg(2+) concentration. Copyright © 2013. Published by Elsevier Inc.

Structure, dynamics and RNA binding of the multi-domain splicing factor TIA-1

PubMed Central

Wang, Iren; Hennig, Janosch; Jagtap, Pravin Kumar Ankush; Sonntag, Miriam; Valcárcel, Juan; Sattler, Michael

2014-01-01

Alternative pre-messenger ribonucleic acid (pre-mRNA) splicing is an essential process in eukaryotic gene regulation. The T-cell intracellular antigen-1 (TIA-1) is an apoptosis-promoting factor that modulates alternative splicing of transcripts, including the pre-mRNA encoding the membrane receptor Fas. TIA-1 is a multi-domain ribonucleic acid (RNA) binding protein that recognizes poly-uridine tract RNA sequences to facilitate 5′ splice site recognition by the U1 small nuclear ribonucleoprotein (snRNP). Here, we characterize the RNA interaction and conformational dynamics of TIA-1 by nuclear magnetic resonance (NMR), isothermal titration calorimetry (ITC) and small angle X-ray scattering (SAXS). Our NMR-derived solution structure of TIA-1 RRM2–RRM3 (RRM2,3) reveals that RRM2 adopts a canonical RNA recognition motif (RRM) fold, while RRM3 is preceded by an non-canonical helix α0. NMR and SAXS data show that all three RRMs are largely independent structural modules in the absence of RNA, while RNA binding induces a compact arrangement. RRM2,3 binds to pyrimidine-rich FAS pre-mRNA or poly-uridine (U9) RNA with nanomolar affinities. RRM1 has little intrinsic RNA binding affinity and does not strongly contribute to RNA binding in the context of RRM1,2,3. Our data unravel the role of binding avidity and the contributions of the TIA-1 RRMs for recognition of pyrimidine-rich RNAs. PMID:24682828

Metrological approaches to organic chemical purity: primary reference materials for vitamin D metabolites.

PubMed

Nelson, Michael A; Bedner, Mary; Lang, Brian E; Toman, Blaza; Lippa, Katrice A

2015-11-01

Given the critical role of pure, organic compound primary reference standards used to characterize and certify chemical Certified Reference Materials (CRMs), it is essential that associated mass purity assessments be fit-for-purpose, represented by an appropriate uncertainty interval, and metrologically sound. The mass fraction purities (% g/g) of 25-hydroxyvitamin D (25(OH)D) reference standards used to produce and certify values for clinical vitamin D metabolite CRMs were investigated by multiple orthogonal quantitative measurement techniques. Quantitative (1)H-nuclear magnetic resonance spectroscopy (qNMR) was performed to establish traceability of these materials to the International System of Units (SI) and to directly assess the principal analyte species. The 25(OH)D standards contained volatile and water impurities, as well as structurally-related impurities that are difficult to observe by chromatographic methods or to distinguish from the principal 25(OH)D species by one-dimensional NMR. These impurities have the potential to introduce significant biases to purity investigations in which a limited number of measurands are quantified. Combining complementary information from multiple analytical methods, using both direct and indirect measurement techniques, enabled mitigation of these biases. Purities of 25(OH)D reference standards and associated uncertainties were determined using frequentist and Bayesian statistical models to combine data acquired via qNMR, liquid chromatography with UV absorbance and atmospheric pressure-chemical ionization mass spectrometric detection (LC-UV, LC-ACPI-MS), thermogravimetric analysis (TGA), and Karl Fischer (KF) titration.

Microscale Determination of Vitamin C by Weight Titrimetry

NASA Astrophysics Data System (ADS)

East, Gaston A.; Nascimento, Erica C.

2002-01-01

A laboratory experiment involving the quantitative microscale determination of ascorbic acid in pharmaceutical tablets of vitamin C by weight-titrimetry using (diacetoxyiodo)benzene as titrant and differential electrolytic potentiometry to locate the end-point is presented. The experiment affords an opportunity for students to explore nonconventional techniques such as the use of a novel organic oxidimetric titrant, titration in a semiaqueous medium, gravimetric titration, and an electrometric method of end-point detection using polarized electrodes. Synthesis, purification, and purity checking of the titrant may also be included in the project. Some advantages of the method are very low reagent consumption, low-cost equipment, improved sensitivity, and high precision and accuracy. Furthermore, the experiment will help the student to relate chemical analysis to everyday life.

Citrus Quality Control: An NMR/MRI Problem-Based Experiment

ERIC Educational Resources Information Center

Erhart, Sarah E.; McCarrick, Robert M.; Lorigan, Gary A.; Yezierski, Ellen J.

2016-01-01

An experiment seated in an industrial context can provide an engaging framework and unique learning opportunity for an upper-division physical chemistry laboratory. An experiment that teaches NMR/MRI through a problem-based quality control of citrus products was developed. In this experiment, using a problem-based learning (PBL) approach, students…

Chlorination of humic materials: Byproduct formation and chemical interpretations

USGS Publications Warehouse

Reckhow, D.A.; Singer, P.C.; Malcolm, R.L.

1990-01-01

Ten aquatic humic and fulvic acids were isolated and studied with respect to their reaction with chlorine. Yields of TOX, chloroform, trichloroacetic acid, dichloroacetic acid, dichloroacetonitrile, and 1,1,1-trichloropropanone were measured at pH 7 and 12. Humic acids produced higher concentrations than their corresponding fulvic acids of all byproducts except 1,1,1-trichloropropanone. Chlorine consumption and byproduct formation were related to fundamental chemical characteristics of the humic materials. A statistical model was proposed for activated aromatic content based on 13C NMR and base titration data. The values estimated from this model were found to be well correlated with chlorine consumption. Specific byproduct formation was related to UV absorbance, nitrogen content, or the activated aromatic content. ?? 1990 American Chemical Society.

A novel fluoride ion colorimetric chemosensor based on coumarin.

PubMed

Zhuang, Xiaoqing; Liu, Weimin; Wu, Jiasheng; Zhang, Hongyan; Wang, Pengfei

2011-09-01

A novel visible colorimetric sensor (L1) with high selectivity for fluoride ion based on coumarin has been synthesized by a simple modification of our earlier report. The chemosensor L1 shows an obvious color change from yellow to blue upon addition of fluoride ion with a large red shift of 145 nm in acetonitrile, and without interference of other anions such as Cl-, Br-, I-, NO3-, H2PO4-, HSO4-, and AcO-. The investigation of 1H NMR spectrum titration indicates the proposed mechanism is that F- first establishes a hydrogen bonding interaction with L1, and then the formation of [F-H-F]- induces deprotonation. Copyright © 2011 Elsevier B.V. All rights reserved.

NMR study of xenotropic murine leukemia virus-related virus protease in a complex with amprenavir

DOE Office of Scientific and Technical Information (OSTI.GOV)

Furukawa, Ayako; Okamura, Hideyasu; Morishita, Ryo

2012-08-24

Highlights: Black-Right-Pointing-Pointer Protease (PR) of XMR virus (XMRV) was successfully synthesized with cell-free system. Black-Right-Pointing-Pointer Interface of XMRV PR with an inhibitor, amprenavir (APV), was identified with NMR. Black-Right-Pointing-Pointer Structural heterogeneity is induced for two PR protomers in the APV:PR = 1:2 complex. Black-Right-Pointing-Pointer Structural heterogeneity is transmitted even to distant regions from the interface. Black-Right-Pointing-Pointer Long-range transmission of structural change may be utilized for drug discovery. -- Abstract: Xenotropic murine leukemia virus-related virus (XMRV) is a virus created through recombination of two murine leukemia proviruses under artificial conditions during the passage of human prostate cancer cells in athymic nudemore » mice. The homodimeric protease (PR) of XMRV plays a critical role in the production of functional viral proteins and is a prerequisite for viral replication. We synthesized XMRV PR using the wheat germ cell-free expression system and carried out structural analysis of XMRV PR in a complex with an inhibitor, amprenavir (APV), by means of NMR. Five different combinatorially {sup 15}N-labeled samples were prepared and backbone resonance assignments were made by applying Otting's method, with which the amino acid types of the [{sup 1}H, {sup 15}N] HSQC resonances were automatically identified using the five samples (Wu et al., 2006) . A titration experiment involving APV revealed that one APV molecule binds to one XMRV PR dimer. For many residues, two distinct resonances were observed, which is thought to be due to the structural heterogeneity between the two protomers in the APV:XMRV PR = 1:2 complex. PR residues at the interface with APV have been identified on the basis of chemical shift perturbation and identification of the intermolecular NOEs by means of filtered NOE experiments. Interestingly, chemical shift heterogeneity between the two protomers of XMRV PR has been observed not only at the interface with APV but also in regions apart from the interface. This indicates that the structural heterogeneity induced by the asymmetry of the binding of APV to the XMRV PR dimer is transmitted to distant regions. This is in contrast to the case of the APV:HIV-1 PR complex, in which the structural heterogeneity is only localized at the interface. Long-range transmission of the structural change identified for the XMRV PR complex might be utilized for the discovery of a new type of drug.« less

The effects of structural variations of thiophene-containing Ru(II) complexes on the acid-base and DNA binding properties.

PubMed

Yuan, Cui-Li; Zhang, An-Guo; Zheng, Ze-Bo; Wang, Ke-Zhi

2013-03-01

A phenylthiophenyl-bearing Ru(II) complex of [Ru(bpy)₂(Hbptip)](PF₆)₂ {bpy = 2,2'-bipyridine, Hbptip = 2-(4-phenylthiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline} was synthesized and characterized by elemental analysis, ¹H NMR spectroscopy, and electrospray ionization mass spectrometry. The ground- and excited-state acid-base properties of the complex were studied by UV-visible absorption and photoluminescence spectrophotometric pH titrations and the negative logarithm values of the ground-state acid ionization constants were derived to be pK(a1) = 1.31 ± 0.09 and pK(a2) = 5.71 ± 0.11 with the pK(a2) associated deprotonation/protonation process occurring over 3 pK(a) units more acidic than thiophenyl-free parent complex of [Ru(bpy)₂(Hpip)]²⁺ {Hpip = 2-phenyl-1H-imidazo[4,5-f][1,10]phenanthroline}. The calf thymus DNA-binding properties of [Ru(bpy)₂(Hbptip)]²⁺ in Tris-HCl buffer (pH 7.1 and 50 mM NaCl) were investigated by DNA viscosities and density functional theoretical calculations as well as UV-visible and emission spectroscopy techniques of UV-visible and luminescence titrations, steady-state emission quenching by [Fe(CN)₆]⁴⁻, DNA competitive binding with ethidium bromide, DNA melting experiments, and reverse salt effects. The complex was evidenced to bind to the DNA intercalatively with binding affinity being greater than those for previously reported analogs of [Ru(bpy)₂(Hip)]²⁺, [Ru(bpy)₂(Htip)]²⁺, and [Ru(bpy)₂(Haptip)]²⁺ {Hip = 1H-imidazo[4,5-f][1,10]phenanthroline, Htip = 2-thiophenimidazo[4,5-f][1,10]phenanthroline, Haptip = 2-(5-phenylthiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline}.

NMR spectroscopy of single sub-nL ova with inductive ultra-compact single-chip probes

PubMed Central

Grisi, Marco; Vincent, Franck; Volpe, Beatrice; Guidetti, Roberto; Harris, Nicola; Beck, Armin; Boero, Giovanni

2017-01-01

Nuclear magnetic resonance (NMR) spectroscopy enables non-invasive chemical studies of intact living matter. However, the use of NMR at the volume scale typical of microorganisms is hindered by sensitivity limitations, and experiments on single intact organisms have so far been limited to entities having volumes larger than 5 nL. Here we show NMR spectroscopy experiments conducted on single intact ova of 0.1 and 0.5 nL (i.e. 10 to 50 times smaller than previously achieved), thereby reaching the relevant volume scale where life development begins for a broad variety of organisms, humans included. Performing experiments with inductive ultra-compact (1 mm2) single-chip NMR probes, consisting of a low noise transceiver and a multilayer 150 μm planar microcoil, we demonstrate that the achieved limit of detection (about 5 pmol of 1H nuclei) is sufficient to detect endogenous compounds. Our findings suggest that single-chip probes are promising candidates to enable NMR-based study and selection of microscopic entities at biologically relevant volume scales. PMID:28317887

Interactive effects of dietary adaptation period length and titration diet type on apparent ileal phosphorus digestibility and phosphorus retention in growing broilers.

PubMed

Perryman, K R; Cattley, R C; Masey O'Neill, H V; Bedford, M R; Dozier, W A

2016-10-01

Two experiments were conducted to examine the effects of different corn titration diets and dietary adaptation period length (DAPL) on intestinal histology, apparent ileal P digestibility (AIPD), and apparent P retention (APR) in Ross × Ross 708 male broilers from 20 to 24 d of age. It was hypothesized that purified ingredients in nutrient-deficient titration diets may affect P availability with varying DAPL. In experiment 1, 1,152 broilers were utilized in a 3 × 3 factorial treatment structure with 3 diets (control, 25% corn titration diet [25CTD], or 75% corn titration diet [75CTD]) and 3 DAPL (0, 24, or 72 h). Experiment 2 was conducted with 576 broilers as a 4 × 3 factorial arrangement with 4 diets (control, 25CTD, 75CTD, or nitrogen-free diet [NFD]) and 3 DAPL (24, 48, or 72 h). All diets contained purified ingredients except for the control diet, which had the same formulation as the common starter and served as a control for DAPL. The NFD diet was fed as a highly purified protein-free diet. Broilers were fed a common diet until 19 d of age and then transferred to experimental diets at 20 d of age. In experiment 1, diet type did not affect (P > 0.05) intestinal histology. However, diet type and DAPL each influenced (P.≤.0.001) diet AIPD. Higher (P.≤.0.001) AIPD was measured for the control diet compared with the 75CDT, and the 25CTD had the lowest AIPD. Following a 24 h DAPL, AIPD was higher (P.≤.0.001) than after a DAPL of 0 or 72 h. In experiment 2, diet type × DAPL interactions (P.≤.0.001) were observed for APR of the control diet, 75CTD, and NFD, but not the 25CTD. Because APR of the control diet was affected by varying DAPL, factors other than differences in diet type may have been responsible for inconsistencies in the measure of P availability. Furthermore, no clear evidence was observed that broilers were able to adapt to P-deficient diets by increasing APR or AIPD. In conclusion, a standard DAPL should be established as a means to reduce variability associated with measuring of feedstuff P availability. © 2016 Poultry Science Association Inc.

An NMR-Guided Screening Method for Selective Fragment Docking and Synthesis of a Warhead Inhibitor.

PubMed

Khattri, Ram B; Morris, Daniel L; Davis, Caroline M; Bilinovich, Stephanie M; Caras, Andrew J; Panzner, Matthew J; Debord, Michael A; Leeper, Thomas C

2016-07-16

Selective hits for the glutaredoxin ortholog of Brucella melitensis are determined using STD NMR and verified by trNOE and (15)N-HSQC titration. The most promising hit, RK207, was docked into the target molecule using a scoring function to compare simulated poses to experimental data. After elucidating possible poses, the hit was further optimized into the lead compound by extension with an electrophilic acrylamide warhead. We believe that focusing on selectivity in this early stage of drug discovery will limit cross-reactivity that might occur with the human ortholog as the lead compound is optimized. Kinetics studies revealed that lead compound 5 modified with an ester group results in higher reactivity than an acrylamide control; however, after modification this compound shows little selectivity for bacterial protein versus the human ortholog. In contrast, hydrolysis of compound 5 to the acid form results in a decrease in the activity of the compound. Together these results suggest that more optimization is warranted for this simple chemical scaffold, and opens the door for discovery of drugs targeted against glutaredoxin proteins-a heretofore untapped reservoir for antibiotic agents.

Host-guest chemistry of dendrimer-drug complexes. 4. An in-depth look into the binding/encapsulation of guanosine monophosphate by dendrimers.

PubMed

Hu, Jingjing; Fang, Min; Cheng, Yiyun; Zhang, Jiahai; Wu, Qinglin; Xu, Tongwen

2010-06-03

In the present study, we investigated the host-guest chemistry of dendrimer/guanosine monophosphate (GMP) and present an in-depth look into the binding/encapsulation of GMP by dendrimers using NMR studies. (1)H NMR spectra showed a significant downfield shift of methylene protons in the outmost layer of the G5 dendrimer, indicating the formation of ion pairs between cationic amine groups of dendrimer and anionic phosphate groups of GMP. Chemical shift titration results showed that the binding constant between G5 dendrimer and GMP is 17,400 M(-1) and each G5 dendrimer has 107 binding sites. The binding of GMP to dendrimers prevents its aggregation in aqueous solutions and thereby enhances its stability. Nuclear Overhauser effect measurements indicated that a GMP binding and encapsulation balance occurs on the surface and in the interior of dendrimer. The binding/encapsulation transitions can be easily tailored by altering the surface and interior charge densities of the dendrimer. All these findings provide a new insight into the host-guest chemistry of dendrimer/guest complexes and may play important roles in the study of dendrimer/DNA aggregates by a "bottom-up" strategy.

Solution structure of the catalytic domain of RICH protein from goldfish.

PubMed

Kozlov, Guennadi; Denisov, Alexey Y; Pomerantseva, Ekaterina; Gravel, Michel; Braun, Peter E; Gehring, Kalle

2007-03-01

Regeneration-induced CNPase homolog (RICH) is an axonal growth-associated protein, which is induced in teleost fish upon optical nerve injury. RICH consists of a highly acidic N-terminal domain, a catalytic domain with 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) activity and a C-terminal isoprenylation site. In vitro RICH and mammalian brain CNPase specifically catalyze the hydrolysis of 2',3'-cyclic nucleotides to produce 2'-nucleotides, but the physiologically relevant in vivo substrate remains unknown. Here, we report the NMR structure of the catalytic domain of goldfish RICH and describe its binding to CNPase inhibitors. The structure consists of a twisted nine-stranded antiparallel beta-sheet surrounded by alpha-helices on both sides. Despite significant local differences mostly arising from a seven-residue insert in the RICH sequence, the active site region is highly similar to that of human CNPase. Likewise, refinement of the catalytic domain of rat CNPase using residual dipolar couplings gave improved agreement with the published crystal structure. NMR titrations of RICH with inhibitors point to a similar catalytic mechanism for RICH and CNPase. The results suggest a functional importance for the evolutionarily conserved phosphodiesterase activity and hint of a link with pre-tRNA splicing.

Synthesis, characterization, spectroscopic and antioxidation studies of Cu(II)-morin complex

NASA Astrophysics Data System (ADS)

Panhwar, Qadeer Khan; Memon, Shahabuddin; Bhanger, M. I.

2010-04-01

Complex formation between copper (II) sulfate and morin (3,5,7,2',4'-pentahydroxyflavone) have been studied in methanol. Structure of the complex was determined through various analytical techniques including UV-vis, IR, 1H NMR, thermal, gravimetric and elemental analyses. The stoichiometric ratio for the reaction between the flavonoid and the metal ion in methanol has been determined by Job's method and elemental analysis for metal content of complex by titration with EDTA, which confirm that morin forms a 1:1 metal:ligand complex. 1H NMR study reveals that, 3OH and 4CO groups of morin take part in complexation with a copper ion. Individual stress was given to the site of central ion and composition of the complex. Antioxidant activity of the complex was evaluated by using 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging method, which showed that the antioxidant activity of complexed morin has higher value as compared to the free morin. Moreover, it was observed that the metal complex is sufficiently stable as well as the data indicates the spontaneous formation of complex (-Δ G) that is exothermic in nature (-Δ H) and entropically unfavourable (-Δ S).

Thermal aging of electrolytes used in lithium-ion batteries - An investigation of the impact of protic impurities and different housing materials

NASA Astrophysics Data System (ADS)

Handel, Patricia; Fauler, Gisela; Kapper, Katja; Schmuck, Martin; Stangl, Christoph; Fischer, Roland; Uhlig, Frank; Koller, Stefan

2014-12-01

Thermal degradation products in lithium-ion batteries result mainly from hydrolysis sensitivity of lithium hexafluorophosphate (LiPF6). As organic carbonate solvents contain traces of protic impurities, the thermal decomposition of electrolytes is enhanced. Therefore, resulting degradation products are studied with nuclear magnetic resonance spectroscopy (NMR) and gas chromatography mass spectrometry (GC-MS). The electrolyte contains 1 M LiPF6 in a binary mixture of ethylene carbonate (EC) and diethylene carbonate (DEC) in a ratio of 1:2 (v/v) and is aged at ambient and elevated temperature. The impact of protic impurities, either added as deionized water or incorporated in positive electrode material, upon aging is investigated. Further, the influence of different housing materials on the electrolyte degradation is shown. Difluorophosphoric acid is identified as main decomposition product by NMR-spectroscopy. Traces of other decomposition products are determined by headspace GC-MS. Acid-base and coulometric titration are used to determine the total amount of acid and water content upon aging, respectively. The aim of this investigation is to achieve profound understanding about the thermal decomposition of one most common used electrolyte in a battery-like housing material.

Self-sorted photoconductive xerogels† †Electronic supplementary information (ESI) available: Full experimental details, rheological data, pK a titrations, further NMR data, full details of the photoconductivity set-up, further photoconductivity measurements. See DOI: 10.1039/c6sc02644c Click here for additional data file.

PubMed Central

Draper, Emily R.; Lee, Jonathan R.; Wallace, Matthew; Jäckel, Frank; Cowan, Alexander J.

2016-01-01

We show that a perylene bisimide (PBI)-based gelator forms self-sorted mixtures with a stilbene-based gelator. To form the self-sorted gels, we use a slow pH change induced by the hydrolysis of glucono-δ-lactone (GdL) to gluconic acid. We prove that self-sorting occurs using NMR spectroscopy, UV-Vis spectroscopy, rheology, and viscometry. The corresponding xerogels are photoconductive. Importantly, the wavelength dependence of the photoconductive films is different to that of the films formed from the perylene bisimide alone. Transient absorption spectroscopy of the xerogels reveals changes in the spectrum of the PBI on the picosecond timescale in the presence of stilbene with a PBI radical anion being formed within 10 ps when the stilbene is present. The ability to form the PBI radical anion under visible light leads to the enhanced spectral response of the multicomponent gels. These systems therefore have potential as useful visible-active optoelectronics. PMID:28451108

Design of pH-responsive nanoparticles of terpolymer of poly(methacrylic acid), polysorbate 80 and starch for delivery of doxorubicin.

PubMed

Shalviri, Alireza; Chan, Ho Ka; Raval, Gaurav; Abdekhodaie, Mohammad J; Liu, Qiang; Heerklotz, Heiko; Wu, Xiao Yu

2013-01-01

This work focused on the design of new pH-responsive nanoparticles for controlled delivery of anticancer drug doxorubicin (Dox). Nanoparticles of poly(methacrylic acid)-polysorbate 80-grafted starch (PMAA-PS 80-g-St) were synthesized by using a one-pot method that enabled simultaneous grafting of PMAA and PS 80 onto starch and nanoparticle formation in an aqueous medium. The particles were characterized by FTIR, (1)H NMR, TEM, DLS, and potentiometric titration. Dox loading and in vitro release from the nanoparticles were investigated. The FTIR and (1)H NMR confirmed the chemical composition of the graft terpolymer. The nanoparticles were relatively spherical with narrow size distribution and porous morphology. They exhibited pH-dependent swelling in a physiological pH range. The particle size and magnitude of phase transition were dependent on polymer composition and formulation parameters such as concentrations of surfactant and cross-linking agent and total monomer concentration. The nanoparticles with optimized compositions showed high loading capacity for Dox and sustained Dox release. The results suggest that the new pH-responsive terpolymer nanoparticles are useful in controlled drug delivery. Copyright © 2012 Elsevier B.V. All rights reserved.

Insights into the multi-equilibrium, superstructure system based on β-cyclodextrin and a highly water soluble guest.

PubMed

De Paula, Elgte Elmin B; De Sousa, Frederico B; Da Silva, Júlio César C; Fernandes, Flaviana R; Melo, Maria Norma; Frézard, Frédéric; Grazul, Richard M; Sinisterra, Rubén D; Machado, Flávia C

2012-12-15

Pentamidine isethionate (PNT) is an antiprotozoal active in many cases of leishmaniasis, despite the present limitations including high toxicity and parenteral administration. In the present work, a PNT encapsulation strategy into β-cyclodextrin cavity at 1:1 and 2:1 (βCD:PNT) molar ratios was used in order to improve the drug's physical and chemical properties. Combining thermodynamic and structural approaches such as isothermal titration calorimetry (ITC), electrospray ionization mass spectrometry (ESI-MS) and nuclear magnetic resonance ((1)H NMR, and ROESY) the inclusion process and the thermodynamics parameters were identified. ITC and ESI-MS experimental data suggest the simultaneous formation of different supramolecular complexes in solution. Moreover, NMR data are in accordance with these results, suggesting a deep inclusion of PNT into the βCD cavity, through correlations observed in 2D ROESY contour maps. The systems were also characterized by FTIR, TG/DTA and SEM. These techniques indicate the formation of inclusion complex in the solid state. In vivo PNT activity was evaluated orally in mice. The inclusion complex showed a significant reduction of parasite load compared to free PNT. Copyright © 2012 Elsevier B.V. All rights reserved.

Solubilization of ibuprofen with β-cyclodextrin derivatives: energetic and structural studies.

PubMed

di Cagno, Massimiliano; Stein, Paul C; Skalko-Basnet, Nataša; Brandl, Martin; Bauer-Brandl, Annette

2011-06-01

The aim of this work was to investigate the complexation of ibuprofen as model drug with various β-cyclodextrins (native β-cyclodextrin, hydroxypropyl-β-cyclodextrin with two different molar degrees of substitution, and methyl-β-cyclodextrin). Solutions of the commercially available β-cyclodextrins were prepared in phosphate buffer (73mM). The pH value was adjusted to 7.4 and the solutions were isotonized with NaCl. A solution of ibuprofen was prepared in the same way. A thermal activity monitor was used for isothermal titration calorimetry (ITC). (1)H NMR analysis was employed to investigate the structures of the complexes. ITC analysis showed that each type of β-cyclodextrin had its characteristic values of both enthalpy and mass equilibrium constant for the complexation processes with the drug molecules. (1)H NMR spectroscopy of the complexes showed through significant differences in chemical shifts that the physical interaction between the cyclodextrins and ibuprofen molecules were also different, probably due to different three-dimensional arrangements of ibuprofen in the cyclodextrin cavity, induced by the different substituents bonded to the glucose rings. These differences were connected to the thermodynamic parameters of the complexes. Copyright © 2011 Elsevier B.V. All rights reserved.

Intermolecular hydrogen bond complexes by in situ charge transfer complexation of o-tolidine with picric and chloranilic acids

NASA Astrophysics Data System (ADS)

Refat, Moamen S.; Saad, Hosam A.; Adam, Abdel Majid A.

2011-08-01

A two new charge transfer complexes formed from the interactions between o-tolidine (o-TOL) and picric (PA) or chloranilic (CA) acids, with the compositions, [(o-TOL)(PA) 2] and [(o-TOL)(CA) 2] have been prepared. The 13C NMR, 1H NMR, 1H-Cosy, and IR show that the charge-transfer chelation occurs via the formation of chain structures O-H⋯N intermolecular hydrogen bond between 2NH 2 groups of o-TOL molecule and OH group in each PA or CA units. Photometric titration measurements concerning the two reactions in methanol were performed and the measurements show that the donor-acceptor molar ratio was found to be 1:2 using the modified Benesi-Hildebrand equation. The spectroscopic data were discussed in terms of formation constant, molar extinction coefficient, oscillator strength, dipole moment, standard free energy, and ionization potential. Thermal behavior of both charge transfer complexes showed that the complexes were more stable than their parents. The thermodynamic parameters were estimated from the differential thermogravimetric curves. The results indicated that the formation of molecular charge transfer complexes is spontaneous and endothermic.

Intermolecular hydrogen bond complexes by in situ charge transfer complexation of o-tolidine with picric and chloranilic acids.

PubMed

Refat, Moamen S; Saad, Hosam A; Adam, Abdel Majid A

2011-08-01

A two new charge transfer complexes formed from the interactions between o-tolidine (o-TOL) and picric (PA) or chloranilic (CA) acids, with the compositions, [(o-TOL)(PA)(2)] and [(o-TOL)(CA)(2)] have been prepared. The (13)C NMR, (1)H NMR, (1)H-Cosy, and IR show that the charge-transfer chelation occurs via the formation of chain structures O-H⋯N intermolecular hydrogen bond between 2NH(2) groups of o-TOL molecule and OH group in each PA or CA units. Photometric titration measurements concerning the two reactions in methanol were performed and the measurements show that the donor-acceptor molar ratio was found to be 1:2 using the modified Benesi-Hildebrand equation. The spectroscopic data were discussed in terms of formation constant, molar extinction coefficient, oscillator strength, dipole moment, standard free energy, and ionization potential. Thermal behavior of both charge transfer complexes showed that the complexes were more stable than their parents. The thermodynamic parameters were estimated from the differential thermogravimetric curves. The results indicated that the formation of molecular charge transfer complexes is spontaneous and endothermic. Copyright © 2011 Elsevier B.V. All rights reserved.

Development of peptoid-based ligands for the removal of cadmium from biological media

DOE PAGES

Knight, Abigail S.; Zhou, Effie Y.; Francis, Matthew B.

2015-05-14

Cadmium poisoning poses a serious health concern due to cadmium's increasing industrial use, yet there is currently no recommended treatment. The selective coordination of cadmium in a biological environment—i.e. in the presence of serum ions, small molecules, and proteins—is a difficult task. To address this challenge, a combinatorial library of peptoid-based ligands has been evaluated to identify structures that selectively bind to cadmium in human serum with minimal chelation of essential metal ions. Eighteen unique ligands were identified in this screening procedure, and the binding affinity of each was measured using metal titrations monitored by UV-vis spectroscopy. To evaluate themore » significance of each chelating moiety, sequence rearrangements and substitutions were examined. Analysis of a metal–ligand complex by NMR spectroscopy highlighted the importance of particular residues. Depletion experiments were performed in serum mimetics and human serum with exogenously added cadmium. These depletion experiments were used to compare and demonstrate the ability of these peptoids to remove cadmium from blood-like mixtures. In one of these depletion experiments, the peptoid sequence was able to deplete the cadmium to a level comparable to the reported acute toxicity limit. Evaluation of the metal selectivity in buffered solution and in human serum was performed to verify minimal off-target binding. These studies highlight a screening platform for the identification of metal–ligands that are capable of binding in a complex environment. They additionally demonstrate the potential utility of biologically-compatible ligands for the treatment of heavy metal poisoning.« less

Development of peptoid-based ligands for the removal of cadmium from biological media

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knight, Abigail S.; Zhou, Effie Y.; Francis, Matthew B.

Cadmium poisoning poses a serious health concern due to cadmium's increasing industrial use, yet there is currently no recommended treatment. The selective coordination of cadmium in a biological environment—i.e. in the presence of serum ions, small molecules, and proteins—is a difficult task. To address this challenge, a combinatorial library of peptoid-based ligands has been evaluated to identify structures that selectively bind to cadmium in human serum with minimal chelation of essential metal ions. Eighteen unique ligands were identified in this screening procedure, and the binding affinity of each was measured using metal titrations monitored by UV-vis spectroscopy. To evaluate themore » significance of each chelating moiety, sequence rearrangements and substitutions were examined. Analysis of a metal–ligand complex by NMR spectroscopy highlighted the importance of particular residues. Depletion experiments were performed in serum mimetics and human serum with exogenously added cadmium. These depletion experiments were used to compare and demonstrate the ability of these peptoids to remove cadmium from blood-like mixtures. In one of these depletion experiments, the peptoid sequence was able to deplete the cadmium to a level comparable to the reported acute toxicity limit. Evaluation of the metal selectivity in buffered solution and in human serum was performed to verify minimal off-target binding. These studies highlight a screening platform for the identification of metal–ligands that are capable of binding in a complex environment. They additionally demonstrate the potential utility of biologically-compatible ligands for the treatment of heavy metal poisoning.« less

Enhanced efficiency of solid-state NMR investigations of energy materials using an external automatic tuning/matching (eATM) robot.

PubMed

Pecher, Oliver; Halat, David M; Lee, Jeongjae; Liu, Zigeng; Griffith, Kent J; Braun, Marco; Grey, Clare P

2017-02-01

We have developed and explored an external automatic tuning/matching (eATM) robot that can be attached to commercial and/or home-built magic angle spinning (MAS) or static nuclear magnetic resonance (NMR) probeheads. Complete synchronization and automation with Bruker and Tecmag spectrometers is ensured via transistor-transistor-logic (TTL) signals. The eATM robot enables an automated "on-the-fly" re-calibration of the radio frequency (rf) carrier frequency, which is beneficial whenever tuning/matching of the resonance circuit is required, e.g. variable temperature (VT) NMR, spin-echo mapping (variable offset cumulative spectroscopy, VOCS) and/or in situ NMR experiments of batteries. This allows a significant increase in efficiency for NMR experiments outside regular working hours (e.g. overnight) and, furthermore, enables measurements of quadrupolar nuclei which would not be possible in reasonable timeframes due to excessively large spectral widths. Additionally, different tuning/matching capacitor (and/or coil) settings for desired frequencies (e.g. 7 Li and 31 P at 117 and 122MHz, respectively, at 7.05 T) can be saved and made directly accessible before automatic tuning/matching, thus enabling automated measurements of multiple nuclei for one sample with no manual adjustment required by the user. We have applied this new eATM approach in static and MAS spin-echo mapping NMR experiments in different magnetic fields on four energy storage materials, namely: (1) paramagnetic 7 Li and 31 P MAS NMR (without manual recalibration) of the Li-ion battery cathode material LiFePO 4 ; (2) paramagnetic 17 O VT-NMR of the solid oxide fuel cell cathode material La 2 NiO 4+δ ; (3) broadband 93 Nb static NMR of the Li-ion battery material BNb 2 O 5 ; and (4) broadband static 127 I NMR of a potential Li-air battery product LiIO 3 . In each case, insight into local atomic structure and dynamics arises primarily from the highly broadened (1-25MHz) NMR lineshapes that the eATM robot is uniquely suited to collect. These new developments in automation of NMR experiments are likely to advance the application of in and ex situ NMR investigations to an ever-increasing range of energy storage materials and systems. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Enhanced efficiency of solid-state NMR investigations of energy materials using an external automatic tuning/matching (eATM) robot

NASA Astrophysics Data System (ADS)

Pecher, Oliver; Halat, David M.; Lee, Jeongjae; Liu, Zigeng; Griffith, Kent J.; Braun, Marco; Grey, Clare P.

2017-02-01

We have developed and explored an external automatic tuning/matching (eATM) robot that can be attached to commercial and/or home-built magic angle spinning (MAS) or static nuclear magnetic resonance (NMR) probeheads. Complete synchronization and automation with Bruker and Tecmag spectrometers is ensured via transistor-transistor-logic (TTL) signals. The eATM robot enables an automated "on-the-fly" re-calibration of the radio frequency (rf) carrier frequency, which is beneficial whenever tuning/matching of the resonance circuit is required, e.g. variable temperature (VT) NMR, spin-echo mapping (variable offset cumulative spectroscopy, VOCS) and/or in situ NMR experiments of batteries. This allows a significant increase in efficiency for NMR experiments outside regular working hours (e.g. overnight) and, furthermore, enables measurements of quadrupolar nuclei which would not be possible in reasonable timeframes due to excessively large spectral widths. Additionally, different tuning/matching capacitor (and/or coil) settings for desired frequencies (e.g.7Li and 31P at 117 and 122 MHz, respectively, at 7.05 T) can be saved and made directly accessible before automatic tuning/matching, thus enabling automated measurements of multiple nuclei for one sample with no manual adjustment required by the user. We have applied this new eATM approach in static and MAS spin-echo mapping NMR experiments in different magnetic fields on four energy storage materials, namely: (1) paramagnetic 7Li and 31P MAS NMR (without manual recalibration) of the Li-ion battery cathode material LiFePO4; (2) paramagnetic 17O VT-NMR of the solid oxide fuel cell cathode material La2NiO4+δ; (3) broadband 93Nb static NMR of the Li-ion battery material BNb2O5; and (4) broadband static 127I NMR of a potential Li-air battery product LiIO3. In each case, insight into local atomic structure and dynamics arises primarily from the highly broadened (1-25 MHz) NMR lineshapes that the eATM robot is uniquely suited to collect. These new developments in automation of NMR experiments are likely to advance the application of in and ex situ NMR investigations to an ever-increasing range of energy storage materials and systems.

Development and validation of a simplified titration method for monitoring volatile fatty acids in anaerobic digestion.

PubMed

Sun, Hao; Guo, Jianbin; Wu, Shubiao; Liu, Fang; Dong, Renjie

2017-09-01

The volatile fatty acids (VFAs) concentration has been considered as one of the most sensitive process performance indicators in anaerobic digestion (AD) process. However, the accurate determination of VFAs concentration in AD processes normally requires advanced equipment and complex pretreatment procedures. A simplified method with fewer sample pretreatment procedures and improved accuracy is greatly needed, particularly for on-site application. This report outlines improvements to the Nordmann method, one of the most popular titrations used for VFA monitoring. The influence of ion and solid interfering subsystems in titrated samples on results accuracy was discussed. The total solid content in titrated samples was the main factor affecting accuracy in VFA monitoring. Moreover, a high linear correlation was established between the total solids contents and VFA measurement differences between the traditional Nordmann equation and gas chromatography (GC). Accordingly, a simplified titration method was developed and validated using a semi-continuous experiment of chicken manure anaerobic digestion with various organic loading rates. The good fitting of the results obtained by this method in comparison with GC results strongly supported the potential application of this method to VFA monitoring. Copyright © 2017. Published by Elsevier Ltd.

Superoxygenated Water as an Experimental Sample for NMR Relaxometry

ERIC Educational Resources Information Center

Nestle, Nikolaus; Dakkouri, Marwan; Rauscher, Hubert

2004-01-01

The increase in NMR relaxation rates as a result of dissolved paramagnetic species on the sample of superoxygenated drinking water is demonstrated. It is concluded that oxygen content in NMR samples is an important issue and can give rise to various problems in the interpretation of both spectroscopic and NMR imaging or relaxation experiments.

Numerical simulation of NQR/NMR: Applications in quantum computing.

PubMed

Possa, Denimar; Gaudio, Anderson C; Freitas, Jair C C

2011-04-01

A numerical simulation program able to simulate nuclear quadrupole resonance (NQR) as well as nuclear magnetic resonance (NMR) experiments is presented, written using the Mathematica package, aiming especially applications in quantum computing. The program makes use of the interaction picture to compute the effect of the relevant nuclear spin interactions, without any assumption about the relative size of each interaction. This makes the program flexible and versatile, being useful in a wide range of experimental situations, going from NQR (at zero or under small applied magnetic field) to high-field NMR experiments. Some conditions specifically required for quantum computing applications are implemented in the program, such as the possibility of use of elliptically polarized radiofrequency and the inclusion of first- and second-order terms in the average Hamiltonian expansion. A number of examples dealing with simple NQR and quadrupole-perturbed NMR experiments are presented, along with the proposal of experiments to create quantum pseudopure states and logic gates using NQR. The program and the various application examples are freely available through the link http://www.profanderson.net/files/nmr_nqr.php. Copyright © 2011 Elsevier Inc. All rights reserved.

Down-titration of biologics for the treatment of rheumatoid arthritis: a systematic literature review.

PubMed

Lau, Chak Sing; Gibofsky, Allan; Damjanov, Nemanja; Lula, Sadiq; Marshall, Lisa; Jones, Heather; Emery, Paul

2017-11-01

Biologic therapies have improved the management of rheumatoid arthritis (RA) and the treat-to-target approach has resulted in many patients achieving remission. In the current treatment landscape, clinicians have begun considering dose reduction/tapering for their patients. Rheumatology guidelines in Asia, Europe, and the United States include down-titration of biologics but admit that the level of evidence is moderate. We conducted a systematic literature review to assess the published studies that evaluate down-titration of biologics in RA. The published literature was searched for studies that down-titrated the following biologics: abatacept, adalimumab, certolizumab, etanercept, golimumab, infliximab, rituximab, and tocilizumab. Eligible studies included randomized controlled trials (RCTs), non-RCTs, observational, and pharmacoeconomic studies. The outcomes of interest were (1) efficacy and health-related quality of life, (2) disease flares, and (3) impact on cost. Eleven full-text publications were identified; only three were RCTs. Study results suggest that dosing down may be an option in many patients who have achieved remission or low disease activity. However, some patients are likely to experience a disease flare. Across the studies, the definition of disease flare and the down-titration criteria were inconsistent, making it difficult to conclude which patients may be appropriate and when to attempt down-titration. Studies have evaluated the practice of dosing down biologic therapy in patients with RA; however, a relatively small number of RCTs have been published. Although down-titration may be an option for some patients in LDA or remission, additional RCTs are needed to provide guidance on this practice.

High-sensitivity NMR beyond 200,000 atmospheres of pressure

NASA Astrophysics Data System (ADS)

Meier, T.; Reichardt, S.; Haase, J.

2015-08-01

Pressure-induced changes in the chemical or electronic structure of solids require pressures well into the Giga-Pascal (GPa) range due to the strong bonding. Anvil cell designs can reach such pressures, but their small and mostly inaccessible sample chamber has severely hampered NMR experiments in the past. With a new cell design that has a radio frequency (RF) micro-coil in the high pressure chamber, NMR experiments beyond 20 Giga-Pascal are reported for the first time. 1 H NMR of water shows sensitivity and resolution obtained with the cells, and 63 Cu NMR on a cuprate superconductor (YBa2Cu3O7-δ) demonstrates that single-crystals can be investigated, as well. 115 In NMR of the ternary chalcogenide AgInTe2 discovers an insulator-metal transition with shift and relaxation measurements. The pressure cells can be mounted easily on standard NMR probes that fit commercial wide-bore magnets with regular cryostats for field- and temperature-dependent measurements ready for many applications in physics and chemistry.

Multiple acquisitions via sequential transfer of orphan spin polarization (MAeSTOSO): How far can we push residual spin polarization in solid-state NMR?

NASA Astrophysics Data System (ADS)

Gopinath, T.; Veglia, Gianluigi

2016-06-01

Conventional multidimensional magic angle spinning (MAS) solid-state NMR (ssNMR) experiments detect the signal arising from the decay of a single coherence transfer pathway (FID), resulting in one spectrum per acquisition time. Recently, we introduced two new strategies, namely DUMAS (DUal acquisition Magic Angle Spinning) and MEIOSIS (Multiple ExperIments via Orphan SpIn operatorS), that enable the simultaneous acquisitions of multidimensional ssNMR experiments using multiple coherence transfer pathways. Here, we combined the main elements of DUMAS and MEIOSIS to harness both orphan spin operators and residual polarization and increase the number of simultaneous acquisitions. We show that it is possible to acquire up to eight two-dimensional experiments using four acquisition periods per each scan. This new suite of pulse sequences, called MAeSTOSO for Multiple Acquisitions via Sequential Transfer of Orphan Spin pOlarization, relies on residual polarization of both 13C and 15N pathways and combines low- and high-sensitivity experiments into a single pulse sequence using one receiver and commercial ssNMR probes. The acquisition of multiple experiments does not affect the sensitivity of the main experiment; rather it recovers the lost coherences that are discarded, resulting in a significant gain in experimental time. Both merits and limitations of this approach are discussed.

Alternating current circuit theory and pulsed NMR (Nuclear Magnetic Resonance)

NASA Astrophysics Data System (ADS)

Gerstein, B. C.

1987-06-01

Pulsed NMR, by definition, deals with time varying excitations. These excitations, supplied by resonant circuits which provide a pulse of radiofrequency (frequencies in the megahertz region) power to a resonant circuit containing, among other things, a coil of wire, or inductor, in which a sample under investigation is placed for purposes of the nuclear magnetic resonance experiment. There are therefore two features of the pulse NMR experiment. First is the fact that we have available a source of continuous wave (CW) alternating current at some angular frequency, omega, measured in radians per second. This source is generally supplied by an ultrastable device called a frequency synthesizer. The second feature of the pulsed NMR experiment is that the sample is not continuously irradiated, but a pulse of radiofrequency oscillation is applied to the sample. This report discusses alternating current theory, resonant circuits and the equipment used in this experiment.

Nuclear magnetic resonance of laser-polarized noble gases in molecules, materials and organisms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goodson, Boyd McLean

1999-12-01

Conventional nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) are fundamentally challenged by the insensitivity that stems from the ordinarily low spin polarization achievable in even the strongest NMR magnets. However, by transferring angular momentum from laser light to electronic and nuclear spins, optical pumping methods can increase the nuclear spin polarization of noble gases by several orders of magnitude, thereby greatly enhancing their NMR sensitivity. This dissertation is primarily concerned with the principles and practice of optically pumped nuclear magnetic resonance (OPNMR). The enormous sensitivity enhancement afforded by optical pumping noble gases can be exploited to permitmore » a variety of novel NMR experiments across many disciplines. Many such experiments are reviewed, including the void-space imaging of organisms and materials, NMR and MRI of living tissues, probing structure and dynamics of molecules in solution and on surfaces, and zero-field NMR and MRI.« less

A fast field-cycling device for high-resolution NMR: Design and application to spin relaxation and hyperpolarization experiments

NASA Astrophysics Data System (ADS)

Kiryutin, Alexey S.; Pravdivtsev, Andrey N.; Ivanov, Konstantin L.; Grishin, Yuri A.; Vieth, Hans-Martin; Yurkovskaya, Alexandra V.

2016-02-01

A device for performing fast magnetic field-cycling NMR experiments is described. A key feature of this setup is that it combines fast switching of the external magnetic field and high-resolution NMR detection. The field-cycling method is based on precise mechanical positioning of the NMR probe with the mounted sample in the inhomogeneous fringe field of the spectrometer magnet. The device enables field variation over several decades (from 100 μT up to 7 T) within less than 0.3 s; progress in NMR probe design provides NMR linewidths of about 10-3 ppm. The experimental method is very versatile and enables site-specific studies of spin relaxation (NMRD, LLSs) and spin hyperpolarization (DNP, CIDNP, and SABRE) at variable magnetic field and at variable temperature. Experimental examples of such studies are demonstrated; advantages of the experimental method are described and existing challenges in the field are outlined.

Use of NMR and NMR Prediction Software to Identify Components in Red Bull Energy Drinks

ERIC Educational Resources Information Center

Simpson, Andre J.; Shirzadi, Azadeh; Burrow, Timothy E.; Dicks, Andrew P.; Lefebvre, Brent; Corrin, Tricia

2009-01-01

A laboratory experiment designed as part of an upper-level undergraduate analytical chemistry course is described. Students investigate two popular soft drinks (Red Bull Energy Drink and sugar-free Red Bull Energy Drink) by NMR spectroscopy. With assistance of modern NMR prediction software they identify and quantify major components in each…

Acceleration of natural-abundance solid-state MAS NMR measurements on bone by paramagnetic relaxation from gadolinium-DTPA

NASA Astrophysics Data System (ADS)

Mroue, Kamal H.; Zhang, Rongchun; Zhu, Peizhi; McNerny, Erin; Kohn, David H.; Morris, Michael D.; Ramamoorthy, Ayyalusamy

2014-07-01

Reducing the data collection time without affecting the signal intensity and spectral resolution is one of the major challenges for the widespread application of multidimensional nuclear magnetic resonance (NMR) spectroscopy, especially in experiments conducted on complex heterogeneous biological systems such as bone. In most of these experiments, the NMR data collection time is ultimately governed by the proton spin-lattice relaxation times (T1). For over two decades, gadolinium(III)-DTPA (Gd-DTPA, DTPA = Diethylene triamine pentaacetic acid) has been one of the most widely used contrast-enhancement agents in magnetic resonance imaging (MRI). In this study, we demonstrate that Gd-DTPA can also be effectively used to enhance the longitudinal relaxation rates of protons in solid-state NMR experiments conducted on bone without significant line-broadening and chemical-shift-perturbation side effects. Using bovine cortical bone samples incubated in different concentrations of Gd-DTPA complex, the 1H T1 values were calculated from data collected by 1H spin-inversion recovery method detected in natural-abundance 13C cross-polarization magic angle spinning (CPMAS) NMR experiments. Our results reveal that the 1H T1 values can be successfully reduced by a factor of 3.5 using as low as 10 mM Gd-DTPA without reducing the spectral resolution and thus enabling faster data acquisition of the 13C CPMAS spectra. These results obtained from 13C-detected CPMAS experiments were further confirmed using 1H-detected ultrafast MAS experiments on Gd-DTPA doped bone samples. This approach considerably improves the signal-to-noise ratio per unit time of NMR experiments applied to bone samples by reducing the experimental time required to acquire the same number of scans.

Acceleration of natural-abundance solid-state MAS NMR measurements on bone by paramagnetic relaxation from gadolinium-DTPA.

PubMed

Mroue, Kamal H; Zhang, Rongchun; Zhu, Peizhi; McNerny, Erin; Kohn, David H; Morris, Michael D; Ramamoorthy, Ayyalusamy

2014-07-01

Reducing the data collection time without affecting the signal intensity and spectral resolution is one of the major challenges for the widespread application of multidimensional nuclear magnetic resonance (NMR) spectroscopy, especially in experiments conducted on complex heterogeneous biological systems such as bone. In most of these experiments, the NMR data collection time is ultimately governed by the proton spin-lattice relaxation times (T1). For over two decades, gadolinium(III)-DTPA (Gd-DTPA, DTPA=Diethylene triamine pentaacetic acid) has been one of the most widely used contrast-enhancement agents in magnetic resonance imaging (MRI). In this study, we demonstrate that Gd-DTPA can also be effectively used to enhance the longitudinal relaxation rates of protons in solid-state NMR experiments conducted on bone without significant line-broadening and chemical-shift-perturbation side effects. Using bovine cortical bone samples incubated in different concentrations of Gd-DTPA complex, the (1)H T1 values were calculated from data collected by (1)H spin-inversion recovery method detected in natural-abundance (13)C cross-polarization magic angle spinning (CPMAS) NMR experiments. Our results reveal that the (1)H T1 values can be successfully reduced by a factor of 3.5 using as low as 10mM Gd-DTPA without reducing the spectral resolution and thus enabling faster data acquisition of the (13)C CPMAS spectra. These results obtained from (13)C-detected CPMAS experiments were further confirmed using (1)H-detected ultrafast MAS experiments on Gd-DTPA doped bone samples. This approach considerably improves the signal-to-noise ratio per unit time of NMR experiments applied to bone samples by reducing the experimental time required to acquire the same number of scans. Copyright © 2014 Elsevier Inc. All rights reserved.

Selective observation of charge storing ions in supercapacitor electrode materials.

PubMed

Forse, Alexander C; Griffin, John M; Grey, Clare P

2018-02-01

Nuclear magnetic resonance (NMR) spectroscopy has emerged as a useful technique for probing the structure and dynamics of the electrode-electrolyte interface in supercapacitors, as ions inside the pores of the carbon electrodes can be studied separately from bulk electrolyte. However, in some cases spectral resolution can limit the information that can be obtained. In this study we address this issue by showing how cross polarisation (CP) NMR experiments can be used to selectively observe the in-pore ions in supercapacitor electrode materials. We do this by transferring magnetisation from 13 C nuclei in porous carbons to nearby nuclei in the cations ( 1 H) or anions ( 19 F) of an ionic liquid. Two-dimensional NMR experiments and CP kinetics measurements confirm that in-pore ions are located within Ångströms of sp 2 -hybridised carbon surfaces. Multinuclear NMR experiments hold promise for future NMR studies of supercapacitor systems where spectral resolution is limited. Copyright © 2017 University of Cambridge. Published by Elsevier Inc. All rights reserved.

Proteins contribute insignificantly to the intrinsic buffering capacity of yeast cytoplasm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Poznanski, Jaroslaw; Szczesny, Pawel; Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw

Highlights: Black-Right-Pointing-Pointer We predicted buffering capacity of yeast proteome from protein abundance data. Black-Right-Pointing-Pointer We measured total buffering capacity of yeast cytoplasm. Black-Right-Pointing-Pointer We showed that proteins contribute insignificantly to buffering capacity. -- Abstract: Intracellular pH is maintained by a combination of the passive buffering of cytoplasmic dissociable compounds and several active systems. Over the years, a large portion of and possibly most of the cell's intrinsic (i.e., passive non-bicarbonate) buffering effect was attributed to proteins, both in higher organisms and in yeast. This attribution was not surprising, given that the concentration of proteins with multiple protonable/deprotonable groups in themore » cell exceeds the concentration of free protons by a few orders of magnitude. Using data from both high-throughput experiments and in vitro laboratory experiments, we tested this concept. We assessed the buffering capacity of the yeast proteome using protein abundance data and compared it to our own titration of yeast cytoplasm. We showed that the protein contribution is less than 1% of the total intracellular buffering capacity. As confirmed with NMR measurements, inorganic phosphates play a crucial role in the process. These findings also shed a new light on the role of proteomes in maintaining intracellular pH. The contribution of proteins to the intrinsic buffering capacity is negligible, and proteins might act only as a recipient of signals for changes in pH.« less

Functions and ATP-binding responses of the twelve histidine residues in the TF1-ATPase beta subunit.

PubMed

Tozawa, K; Yagi, H; Hisamatsu, K; Ozawa, K; Yoshida, M; Akutsu, H

2001-10-01

The C2 proton signals of all (twelve) histidine residues of the TF1 beta subunit in the 1H-NMR spectrum have been identified and assigned by means of pH change experiments and site-directed substitution of histidines by glutamines. pH and ligand titration experiments were carried out for these signals. Furthermore, the ATPase activity of the reconstituted alpha3beta3gamma complex was examined for the twelve mutant beta subunits. Two of three conserved histidines, namely, His-119 and 324, were found to be important for expression of the ATPase activity. The former fixes the N-terminal domain to the central domain. His-324 is involved in the formation of the interface essential for the alpha3beta3gamma complex assembly. The other conserved residue, His-363, showed a very low pK(a), suggesting that it is involved in the tertiary structure formation. On the binding of a nucleotide, only the signals of His-173, 179, 200, and 324 shifted. These histidines are located in the hinge region, and its proximity, of the beta subunit. This observation provided further support for the conformational change of the beta monomer from the open to the closed form on the binding of a nucleotide proposed by us [Yagi et al. (1999) Biophys. J. 77, 2175-2183]. This conformational change should be one of the essential driving forces in the rotation of the alpha3beta3gamma complex.

Ultrafast-based projection-reconstruction three-dimensional nuclear magnetic resonance spectroscopy.

PubMed

Mishkovsky, Mor; Kupce, Eriks; Frydman, Lucio

2007-07-21

Recent years have witnessed increased efforts toward the accelerated acquisition of multidimensional nuclear magnetic resonance (nD NMR) spectra. Among the methods proposed to speed up these NMR experiments is "projection reconstruction," a scheme based on the acquisition of a reduced number of two-dimensional (2D) NMR data sets constituting cross sections of the nD time domain being sought. Another proposition involves "ultrafast" spectroscopy, capable of completing nD NMR acquisitions within a single scan. Potential limitations of these approaches include the need for a relatively slow 2D-type serial data collection procedure in the former case, and a need for at least n high-performance, linearly independent gradients and a sufficiently high sensitivity in the latter. The present study introduces a new scheme that comes to address these limitations, by combining the basic features of the projection reconstruction and the ultrafast approaches into a single, unified nD NMR experiment. In the resulting method each member within the series of 2D cross sections required by projection reconstruction to deliver the nD NMR spectrum being sought, is acquired within a single scan with the aid of the 2D ultrafast protocol. Full nD NMR spectra can thus become available by backprojecting a small number of 2D sets, collected using a minimum number of scans. Principles, opportunities, and limitations of the resulting approach, together with demonstrations of its practical advantages, are here discussed and illustrated with a series of three-dimensional homo- and heteronuclear NMR correlation experiments.

An advanced NMR protocol for the structural characterization of aluminophosphate glasses.

PubMed

van Wüllen, Leo; Tricot, Grégory; Wegner, Sebastian

2007-10-01

In this work a combination of complementary advanced solid-state nuclear magnetic resonance (NMR) strategies is employed to analyse the network organization in aluminophosphate glasses to an unprecedented level of detailed insight. The combined results from MAS, MQMAS and (31)P-{(27)Al}-CP-heteronuclear correlation spectroscopy (HETCOR) NMR experiments allow for a detailed speciation of the different phosphate and aluminate species present in the glass. The interconnection of these local building units to an extended three-dimensional network is explored employing heteronuclear dipolar and scalar NMR approaches to quantify P-O-Al connectivity by (31)P{(27)Al}-heteronuclear multiple quantum coherence (HMQC), -rotational echo adiabatic passage double resonance (REAPDOR) and -HETCOR NMR as well as (27)Al{(31)P}-rotational echo double resonance (REDOR) NMR experiments, complemented by (31)P-2D-J-RESolved MAS NMR experiments to probe P-O-P connectivity utilizing the through bond scalar J-coupling. The combination of the results from the various NMR approaches enables us to not only quantify the phosphate units present in the glass but also to identify their respective structural environments within the three-dimensional network on a medium length scale employing a modified Q notation, Q(n)(m),(AlO)(x), where n denotes the number of connected tetrahedral phosphate, m gives the number of aluminate species connected to a central phosphate unit and x specifies the nature of the bonded aluminate species (i.e. 4, 5 or 6 coordinate aluminium).

Superstatistics model for T₂ distribution in NMR experiments on porous media.

PubMed

Correia, M D; Souza, A M; Sinnecker, J P; Sarthour, R S; Santos, B C C; Trevizan, W; Oliveira, I S

2014-07-01

We propose analytical functions for T2 distribution to describe transverse relaxation in high- and low-fields NMR experiments on porous media. The method is based on a superstatistics theory, and allows to find the mean and standard deviation of T2, directly from measurements. It is an alternative to multiexponential models for data decay inversion in NMR experiments. We exemplify the method with q-exponential functions and χ(2)-distributions to describe, respectively, data decay and T2 distribution on high-field experiments of fully water saturated glass microspheres bed packs, sedimentary rocks from outcrop and noisy low-field experiment on rocks. The method is general and can also be applied to biological systems. Copyright © 2014 Elsevier Inc. All rights reserved.

Isothermal titration calorimetry for measuring macromolecule-ligand affinity.

PubMed

Duff, Michael R; Grubbs, Jordan; Howell, Elizabeth E

2011-09-07

Isothermal titration calorimetry (ITC) is a useful tool for understanding the complete thermodynamic picture of a binding reaction. In biological sciences, macromolecular interactions are essential in understanding the machinery of the cell. Experimental conditions, such as buffer and temperature, can be tailored to the particular binding system being studied. However, careful planning is needed since certain ligand and macromolecule concentration ranges are necessary to obtain useful data. Concentrations of the macromolecule and ligand need to be accurately determined for reliable results. Care also needs to be taken when preparing the samples as impurities can significantly affect the experiment. When ITC experiments, along with controls, are performed properly, useful binding information, such as the stoichiometry, affinity and enthalpy, are obtained. By running additional experiments under different buffer or temperature conditions, more detailed information can be obtained about the system. A protocol for the basic setup of an ITC experiment is given.

Isothermal Titration Calorimetry for Measuring Macromolecule-Ligand Affinity

PubMed Central

Duff,, Michael R.; Grubbs, Jordan; Howell, Elizabeth E.

2011-01-01

Isothermal titration calorimetry (ITC) is a useful tool for understanding the complete thermodynamic picture of a binding reaction. In biological sciences, macromolecular interactions are essential in understanding the machinery of the cell. Experimental conditions, such as buffer and temperature, can be tailored to the particular binding system being studied. However, careful planning is needed since certain ligand and macromolecule concentration ranges are necessary to obtain useful data. Concentrations of the macromolecule and ligand need to be accurately determined for reliable results. Care also needs to be taken when preparing the samples as impurities can significantly affect the experiment. When ITC experiments, along with controls, are performed properly, useful binding information, such as the stoichiometry, affinity and enthalpy, are obtained. By running additional experiments under different buffer or temperature conditions, more detailed information can be obtained about the system. A protocol for the basic setup of an ITC experiment is given. PMID:21931288

Modified spectrophotometer for multi-dimensional circular dichroism/fluorescence data acquisition in titration experiments: application to the pH and guanidine-HCI induced unfolding of apomyoglobin.

PubMed

Ramsay, G; Ionescu, R; Eftink, M R

1995-08-01

In a previous paper (Ramsay and Eftink, Biophys. J. 66:516-523) we reported the development of a modified spectrophotometer that can make nearly simultaneous circular dichroism (CD) and fluorescence measurements. This arrangement allows multiple data sets to be collected during a single experiment, resulting in a saving of time and material, and improved correlation between the different types of measurements. The usefulness of the instrument was shown by thermal melting experiments on several different protein systems. This CD/fluorometer spectrophotometer has been further modified by interfacing with a syringe pump and a pH meter. This arrangement allows ligand, pH, and chemical denaturation titration experiments to be performed while monitoring changes in the sample's CD, absorbance, fluorescence, and light scattering properties. Our data acquisition program also has an ability to check whether the signals have approached equilibrium before the data is recorded. For performing pH titrations we have developed a procedure which uses the signal from a pH meter in a feedback circuit in order to collect data at evenly spaced pH intervals. We demonstrate the use of this instrument with studies of the unfolding of sperm whale apomyoglobin, as induced by acid pH and by the addition of guanidine-HCI.

Modified spectrophotometer for multi-dimensional circular dichroism/fluorescence data acquisition in titration experiments: application to the pH and guanidine-HCI induced unfolding of apomyoglobin.

PubMed Central

Ramsay, G; Ionescu, R; Eftink, M R

1995-01-01

In a previous paper (Ramsay and Eftink, Biophys. J. 66:516-523) we reported the development of a modified spectrophotometer that can make nearly simultaneous circular dichroism (CD) and fluorescence measurements. This arrangement allows multiple data sets to be collected during a single experiment, resulting in a saving of time and material, and improved correlation between the different types of measurements. The usefulness of the instrument was shown by thermal melting experiments on several different protein systems. This CD/fluorometer spectrophotometer has been further modified by interfacing with a syringe pump and a pH meter. This arrangement allows ligand, pH, and chemical denaturation titration experiments to be performed while monitoring changes in the sample's CD, absorbance, fluorescence, and light scattering properties. Our data acquisition program also has an ability to check whether the signals have approached equilibrium before the data is recorded. For performing pH titrations we have developed a procedure which uses the signal from a pH meter in a feedback circuit in order to collect data at evenly spaced pH intervals. We demonstrate the use of this instrument with studies of the unfolding of sperm whale apomyoglobin, as induced by acid pH and by the addition of guanidine-HCI. Images FIGURE 2 PMID:8527683

Assigning the NMR Spectrum of Glycidol: An Advanced Organic Chemistry Exercise

ERIC Educational Resources Information Center

Helms, Eric; Arpaia, Nicholas; Widener, Melissa

2007-01-01

Various one- and two-dimensional NMR experiments have been found to be extremely useful for assigning the proton and carbon NMR spectra of glycidol. The technique provides extremely valuable information aiding in the complete assignment of the peaks.

Simultaneous acquisition for T2 -T2 Exchange and T1 -T2 correlation NMR experiments

NASA Astrophysics Data System (ADS)

Montrazi, Elton T.; Lucas-Oliveira, Everton; Araujo-Ferreira, Arthur G.; Barsi-Andreeta, Mariane; Bonagamba, Tito J.

2018-04-01

The NMR measurements of longitudinal and transverse relaxation times and its multidimensional correlations provide useful information about molecular dynamics. However, these experiments are very time-consuming, and many researchers proposed faster experiments to reduce this issue. This paper presents a new way to simultaneously perform T2 -T2 Exchange and T1 -T2 correlation experiments by taking the advantage of the storage time and the two steps phase cycling used for running the relaxation exchange experiment. The data corresponding to each step is either summed or subtracted to produce the T2 -T2 and T1 -T2 data, enhancing the information obtained while maintaining the experiment duration. Comparing the results from this technique with traditional NMR experiments it was possible to validate the method.

Quartz Crystal Temperature Sensor for MAS NMR

NASA Astrophysics Data System (ADS)

Simon, Gerald

1997-10-01

Quartz crystal temperature sensors (QCTS) were tested for the first time as wireless thermometers in NMR MAS rotors utilizing the NMR RF technique itself for exiting and receiving electro-mechanical quartz resonances. This new tool in MAS NMR has a high sensitivity, linearity, and precision. When compared to the frequently used calibration of the variable temperature in the NMR system by a solid state NMR chemical shift thermometer (CST), such as lead nitrate, QCTS shows a number of advantages. It is an inert thermometer in close contact with solid samples operating parallel to the NMR experiment. QCTS can be manufactured for any frequency to be near a NMR frequency of interest (typically 1 to 2 MHz below or above). Due to the strong response of the crystal, signal detection is possible without changing the tuning of the MAS probe. The NMR signal is not influenced due to the relative sharp crystal resonance, restricted excitation by finite pulses, high probeQvalues, and commonly used audio filters. The quadratic dependence of the temperature increase on spinning speed is the same for the QCTS and for the CST lead nitrate and is discussed in terms of frictional heat in accordance with the literature about lead nitrate and with the results of a simple rotor speed jump experiment with differently radial located lead nitrate in the rotor.

Screening of biologically important Zn2 + by a chemosensor with fluorescent turn on-off mechanism

NASA Astrophysics Data System (ADS)

Khan, Tanveer A.; Sheoran, Monika; Nikhil Raj M., Venkata; Jain, Surbhi; Gupta, Diksha; Naik, Sunil G.

2018-01-01

Reported herein the synthesis, characterization and biologically important zinc ion binding propensity of a weakly fluorescent chemosensor, 4-methyl-2,6-bis((E)-(2-(4-phenylthiazol-2-yl)hydrazono)methyl)phenol (1). 1H NMR spectroscopic titration experiment reveals the binding knack of 1 to the essential Zn2 +. The photo-physical studies of 1 exhibit an enhancement in the fluorescence by several folds upon binding with the zinc ions attributed to PET-off process, with a binding constant value of 5.22 × 103 M- 1. 1 exhibits an excellent detection range for Zn2 + with lower detection limit value of 2.31 × 10- 8 M. The selectivity of 1 was studied with various mono and divalent metal cations and it was observed that most cations either quenches the fluorescence or remains unchanged except for Cd2 +, which shows a slight enhancement in fluorescence intensity of 1. The ratiometric displacement of Cd2 + ions by Zn2 + ions shows an excellent selectivity towards in-situ detection of Zn2 + ions. Photo-physical studies also support the reversible binding of 1 to Zn2 + ions having on and off mechanism in presence of EDTA. Such recognition of the biologically important zinc ions finds potential application in live cell imaging.

Supramolecular complex of a fused zinc phthalocyanine-zinc porphyrin dyad assembled by two imidazole-C60 units: ultrafast photoevents.

PubMed

Follana-Berná, Jorge; Seetharaman, Sairaman; Martín-Gomis, Luis; Charalambidis, Georgios; Trapali, Adelais; Karr, Paul A; Coutsolelos, Athanassios G; Fernández-Lázaro, Fernando; D'Souza, Francis; Sastre-Santos, Ángela

2018-03-14

A new zinc phthalocyanine-zinc porphyrin dyad (ZnPc-ZnP) fused through a pyrazine ring has been synthesized as a receptor for imidazole-substituted C 60 (C 60 Im) electron acceptor. Self-assembly via metal-ligand axial coordination and the pertinent association constants in solution were determined by 1 H-NMR, UV-Vis and fluorescence titration experiments at room temperature. The designed host was able to bind up to two C 60 Im electron acceptor guest molecules to yield C 60 Im:ZnPc-ZnP:ImC 60 donor-acceptor supramolecular complex. The spectral data showed that the two binding sites behave independently with binding constants similar in magnitude. Steady-state fluorescence studies were indicative of an efficient singlet-singlet energy transfer from zinc porphyrin to zinc phthalocyanine within the fused dyad. Accordingly, the transient absorption studies covering a wide timescale of femto-to-milli seconds revealed ultrafast energy transfer from 1 ZnP* to ZnPc (k EnT ∼ 10 12 s -1 ) in the fused dyad. Further, a photo induced electron transfer was observed in the supramolecularly assembled C 60 Im:ZnPc-ZnP:ImC 60 donor-acceptor complex leading to charge separated states, which persisted for about 200 ns.

Sequence-Selective Formation of Synthetic H-Bonded Duplexes

PubMed Central

2017-01-01

Oligomers equipped with a sequence of phenol and pyridine N-oxide groups form duplexes via H-bonding interactions between these recognition units. Reductive amination chemistry was used to synthesize all possible 3-mer sequences: AAA, AAD, ADA, DAA, ADD, DAD, DDA, and DDD. Pairwise interactions between the oligomers were investigated using NMR titration and dilution experiments in toluene. The measured association constants vary by 3 orders of magnitude (102 to 105 M–1). Antiparallel sequence-complementary oligomers generally form more stable complexes than mismatched duplexes. Mismatched duplexes that have an excess of H-bond donors are stabilized by the interaction of two phenol donors with one pyridine N-oxide acceptor. Oligomers that have a H-bond donor and acceptor on the ends of the chain can fold to form intramolecular H-bonds in the free state. The 1,3-folding equilibrium competes with duplex formation and lowers the stability of duplexes involving these sequences. As a result, some of the mismatch duplexes are more stable than some of the sequence-complementary duplexes. However, the most stable mismatch duplexes contain DDD and compete with the most stable sequence-complementary duplex, AAA·DDD, so in mixtures that contain all eight sequences, sequence-complementary duplexes dominate. Even higher fidelity sequence selectivity can be achieved if alternating donor–acceptor sequences are avoided. PMID:28857551

Quantitative measurement of regional blood flow with gadolinium diethylenetriaminepentaacetate bolus track NMR imaging in cerebral infarcts in rats: validation with the iodo[14C]antipyrine technique.

PubMed Central

Wittlich, F; Kohno, K; Mies, G; Norris, D G; Hoehn-Berlage, M

1995-01-01

NMR bolus track measurements were correlated with autoradiographically determined regional cerebral blood flow (rCBF). The NMR method is based on bolus infusion of the contrast agent gadolinium diethylenetriaminepentaacetate and high-speed T*2-sensitive NMR imaging. The first pass of the contrast agent through the image plane causes a transient decrease of the signal intensity. This time course of the signal intensity is transformed into relative concentrations of the contrast agent in each pixel. The mean transit time and relative blood flow and volume are calculated from such indicator dilution curves. We investigated whether this NMR technique correctly expresses the relative rCBF. The relative blood flow data, calculated from NMR bolus track experiments, and the absolute values of iodo[14C]antipyrine autoradiography were compared. A linear relationship was observed, indicating the proportionality of the transient NMR signal change with CBF. Excellent interindividual reproducibility of calibration constants is observed (r = 0.963). For a given NMR protocol, bolus track measurements calibrated with autoradiography after the experiment allow determination of absolute values for rCBF and regional blood volume. Images Fig. 2 Fig. 3 PMID:7892189

Predicting prolonged dose titration in patients starting warfarin.

PubMed

Finkelman, Brian S; French, Benjamin; Bershaw, Luanne; Brensinger, Colleen M; Streiff, Michael B; Epstein, Andrew E; Kimmel, Stephen E

2016-11-01

Patients initiating warfarin therapy generally experience a dose-titration period of weeks to months, during which time they are at higher risk of both thromboembolic and bleeding events. Accurate prediction of prolonged dose titration could help clinicians determine which patients might be better treated by alternative anticoagulants that, while more costly, do not require dose titration. A prediction model was derived in a prospective cohort of patients starting warfarin (n = 390), using Cox regression, and validated in an external cohort (n = 663) from a later time period. Prolonged dose titration was defined as a dose-titration period >12 weeks. Predictor variables were selected using a modified best subsets algorithm, using leave-one-out cross-validation to reduce overfitting. The final model had five variables: warfarin indication, insurance status, number of doctor's visits in the previous year, smoking status, and heart failure. The area under the ROC curve (AUC) in the derivation cohort was 0.66 (95%CI 0.60, 0.74) using leave-one-out cross-validation, but only 0.59 (95%CI 0.54, 0.64) in the external validation cohort, and varied across clinics. Including genetic factors in the model did not improve the area under the ROC curve (0.59; 95%CI 0.54, 0.65). Relative utility curves indicated that the model was unlikely to provide a clinically meaningful benefit compared with no prediction. Our results suggest that prolonged dose titration cannot be accurately predicted in warfarin patients using traditional clinical, social, and genetic predictors, and that accurate prediction will need to accommodate heterogeneities across clinical sites and over time. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

EASY: a simple tool for simultaneously removing background, deadtime and acoustic ringing in quantitative NMR spectroscopy--part I: basic principle and applications.

PubMed

Jaeger, Christian; Hemmann, Felix

2014-01-01

Elimination of Artifacts in NMR SpectroscopY (EASY) is a simple but very effective tool to remove simultaneously any real NMR probe background signal, any spectral distortions due to deadtime ringdown effects and -specifically- severe acoustic ringing artifacts in NMR spectra of low-gamma nuclei. EASY enables and maintains quantitative NMR (qNMR) as only a single pulse (preferably 90°) is used for data acquisition. After the acquisition of the first scan (it contains the wanted NMR signal and the background/deadtime/ringing artifacts) the same experiment is repeated immediately afterwards before the T1 waiting delay. This second scan contains only the background/deadtime/ringing parts. Hence, the simple difference of both yields clean NMR line shapes free of artefacts. In this Part I various examples for complete (1)H, (11)B, (13)C, (19)F probe background removal due to construction parts of the NMR probes are presented. Furthermore, (25)Mg EASY of Mg(OH)2 is presented and this example shows how extremely strong acoustic ringing can be suppressed (more than a factor of 200) such that phase and baseline correction for spectra acquired with a single pulse is no longer a problem. EASY is also a step towards deadtime-free data acquisition as these effects are also canceled completely. EASY can be combined with any other NMR experiment, including 2D NMR, if baseline distortions are a big problem. © 2013 Published by Elsevier Inc.

"Cooking the sample": radiofrequency induced heating during solid-state NMR experiments.

PubMed

d'Espinose de Lacaillerie, Jean-Baptiste; Jarry, Benjamin; Pascui, Ovidiu; Reichert, Detlef

2005-09-01

Dissipation of radiofrequency (RF) energy as heat during continuous wave decoupling in solid-state NMR experiment was examined outside the conventional realm of such phenomena. A significant temperature increase could occur while performing dynamic NMR measurements provided the sample contains polar molecules and the sequence calls for relatively long applications of RF power. It was shown that the methyl flip motion in dimethylsulfone (DMS) is activated by the decoupling RF energy conversion to heat during a CODEX pulse sequence. This introduced a significant bias in the correlation time-temperature dependency measurement used to obtain the activation energy of the motion. By investigating the dependency of the temperature increase in hydrated lead nitrate on experimental parameters during high-power decoupling one-pulse experiments, the mechanisms for the RF energy deposition was identified. The samples were heated due to dissipation of the energy absorbed by dielectric losses, a phenomenon commonly known as "microwave" heating. It was thus established that during solid-state NMR experiments at moderate B0 fields, RF heating could lead to the heating of samples containing polar molecules such as hydrated polymers and inorganic solids. In particular, this could result in systematic errors for slow dynamics measurements by solid-state NMR.

High-sensitivity NMR beyond 200,000 atmospheres of pressure.

PubMed

Meier, T; Reichardt, S; Haase, J

2015-08-01

Pressure-induced changes in the chemical or electronic structure of solids require pressures well into the Giga-Pascal (GPa) range due to the strong bonding. Anvil cell designs can reach such pressures, but their small and mostly inaccessible sample chamber has severely hampered NMR experiments in the past. With a new cell design that has a radio frequency (RF) micro-coil in the high pressure chamber, NMR experiments beyond 20 Giga-Pascal are reported for the first time. (1)H NMR of water shows sensitivity and resolution obtained with the cells, and (63)Cu NMR on a cuprate superconductor (YBa2Cu3O7-δ) demonstrates that single-crystals can be investigated, as well. (115)In NMR of the ternary chalcogenide AgInTe2 discovers an insulator-metal transition with shift and relaxation measurements. The pressure cells can be mounted easily on standard NMR probes that fit commercial wide-bore magnets with regular cryostats for field- and temperature-dependent measurements ready for many applications in physics and chemistry. Copyright © 2015 Elsevier Inc. All rights reserved.

The role of cysteine 206 in allosteric inhibition of Escherichia coli citrate synthase. Studies by chemical modification, site-directed mutagenesis, and 19F NMR.

PubMed

Donald, L J; Crane, B R; Anderson, D H; Duckworth, H W

1991-11-05

Escherichia coli citrate synthase is strongly and specifically inhibited by NADH, but this inhibition can be prevented by reacting the enzyme with Ellman's reagent. We have now labeled the single reactive cysteine covalently with monobromobimane and isolated and sequenced the bimane-containing cyanogen bromide peptide and identified the cysteine as Cys-206. Modeling studies suggest that this residue is on the subunit surface, 25-30 A from the active site. Mutation of Cys-206 to serine (C206S), or of Gly-207 to alanine (E207A), weakened NADH binding and inhibition; when these mutations were present together, NADH binding was weaker by 18-fold and inhibition by 250-fold. The mutations also had small effects on substrate binding at the active site. Cys-206 of wild type enzyme and of the mutant E207A was alkylated with 1,1,1-trifluorobromoacetone and the environment of the fluorine nuclei studied by 19F NMR. With wild type enzyme, the NMR spectrum consisted of two peaks of about equal intensity but different line widths, at -8.65 ppm (line width 11.2 +/- 0.5 Hz) and -7.6 ppm (line width 57 +/- 4 Hz). As the labeled wild type citrate synthase was titrated with KCl, the narrow peak converted to the broad one. The same range of KCl concentrations was needed for this conversion as for the allosteric activation of E. coli citrate synthase. The E207A mutant gave the broader NMR peak almost exclusively. We propose that the fluorine label in wild type citrate synthase exists in two conformational states with different mobilities, exchanging slowly on the NMR time scale, and that treatment with KCl, or truncation of the Glu-207 side chain by mutagenesis, stabilizes one of these states. Consistent with this explanation is the finding that Cys-206 reacts more quickly with Ellman's reagent in the presence of KCl, and that this rate is faster yet in the E207A mutant.

pytc: Open-Source Python Software for Global Analyses of Isothermal Titration Calorimetry Data.

PubMed

Duvvuri, Hiranmayi; Wheeler, Lucas C; Harms, Michael J

2018-05-08

Here we describe pytc, an open-source Python package for global fits of thermodynamic models to multiple isothermal titration calorimetry experiments. Key features include simplicity, the ability to implement new thermodynamic models, a robust maximum likelihood fitter, a fast Bayesian Markov-Chain Monte Carlo sampler, rigorous implementation, extensive documentation, and full cross-platform compatibility. pytc fitting can be done using an application program interface or via a graphical user interface. It is available for download at https://github.com/harmslab/pytc .

External and internal guest binding of a highly charged supramolecular host in water: deconvoluting the very different thermodynamics.

PubMed

Sgarlata, Carmelo; Mugridge, Jeffrey S; Pluth, Michael D; Tiedemann, Bryan E F; Zito, Valeria; Arena, Giuseppe; Raymond, Kenneth N

2010-01-27

NMR, UV-vis, and isothermal titration calorimetry (ITC) measurements probe different aspects of competing host-guest equilibria as simple alkylammonium guest molecules interact with both the exterior (ion-association) and interior (encapsulation) of the [Ga(4)L(6)](12-) supramolecular assembly in water. Data obtained by each independent technique measure different components of the host-guest equilibria and only when analyzed together does a complete picture of the solution thermodynamics emerge. Striking differences between the internal and external guest binding are found. External binding is enthalpy driven and mainly due to attractive interactions between the guests and the exterior surface of the assembly while encapsulation is entropy driven as a result of desolvation and release of solvent molecules from the host cavity.

EPR Studies of the Binding Properties, Guest Dynamics, and Inner-Space Dimensions of a Water-Soluble Resorcinarene Capsule.

PubMed

Ayhan, Mehmet Menaf; Casano, Gilles; Karoui, Hakim; Rockenbauer, Antal; Monnier, Valérie; Hardy, Micaël; Tordo, Paul; Bardelang, David; Ouari, Olivier

2015-11-09

Nitroxide free radicals have been used to study the inner space of one of Rebek's water-soluble capsules. EPR and (1) H NMR spectroscopy, ESI-MS, and DFT calculations showed a preference for the formation of 1:2 complexes. EPR titrations allowed us to determine binding constants (Ka ) in the order of 10(7)  M(-2) . EPR spectral-shape analysis provided information on the guest rotational dynamics within the capsule. The interplay between optimum hydrogen bonding upon capsule formation and steric strain for guest accommodation highlights some degree of flexibility for guest inclusion, particularly at the center of the capsule where the hydrogen bond seam can be barely distorted or slightly disturbed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A calix[4]arene derivative and its selective interaction with drugs (clofibric acid, diclofenac and aspirin).

PubMed

Danil de Namor, Angela F; Al Nuaim, Maan; Villanueva Salas, Jose A; Bryant, Sophie; Howlin, Brendan

2017-03-30

The synthesis and characterisation of a partially substituted calix[4]arene, namely, 5,11,17,23-tetra-tert-butyl,25,27-bis[aminoethoxy] 26,28-dihydroxycalix[4]arene are reported. Its interaction with commonly used pharmaceuticals (clofibric acid, diclofenac and aspirin) was investigated by spectroscopic ( 1 H NMR and UV), electrochemical (conductance measurements) and thermal (titration calorimetry) techniques. It is concluded on the basis of the experimental work and molecular simulation studies that the receptor interacts selectively with these drugs. Preliminary studies on the selective extraction of these pharmaceuticals from water by the calix receptor are reported and the potential for a carrier mediated sensor based on this ligand for 'on site' monitoring of pharmaceuticals is discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

Highly specific and reversible fluoride sensor based on an organic semiconductor.

PubMed

Aboubakr, Hecham; Brisset, Hugues; Siri, Olivier; Raimundo, Jean-Manuel

2013-10-15

A novel sulfonamide-conjugated benzo-[2,1-b:3,4-b']bithiophene semiconductor has been designed and synthetized in order to develop a probe for specific detection of anions both in the homogeneous (solution) and heterogeneous phase. Its photophysical and electrochemical data were reported in this study. On the basis of the optical and NMR titrations analysis, the chelator was found to be highly selective for fluoride compared to others anions (Ka = 1.6 × 10(4) M(-1) in dimethyl sulfoxide (DMSO)). In addition, from an intricate sample, the novel chelator shows exceptional specificity toward fluoride and reveals a complete reversibility after addition of trifluoroacetic acid (TFA). Sensing films were obtained by electrochemical polymerization of the probe on an electrode surface, which clearly show effective detection of fluoride.

Determination of the Deacetylation Degree of Chitooligosaccharides

PubMed Central

Fu, Chuhan; Wu, Sihui; Liu, Guihua; Guo, Jiao; Su, Zhengquan

2017-01-01

The methods for determination of chitosan content recommended in the Chinese Pharmacopoeia and the European Pharmacopoeia are not applicable for evaluation of the extent of deacetylation (deacetylation degree, DD) in chitooligosaccharides (COS). This study explores two different methods for assessment of DD in COS having relatively high and low molecular weights: an acid-base titration with bromocresol green indicator and a first order derivative UV spectrophotometric method for assessment of DD in COS. The accuracy of both methods as a function of molecular weight was also investigated and compared to results obtained using 1H NMR spectroscopy. Our study demonstrates two simple, fast, widely adaptable, highly precise, accurate, and inexpensive methods for the effective determination of DD in COS, which have the potential for widespread commercial applications in developing country. PMID:29068401

Nano-Saturn: Experimental Evidence of Complex Formation of an Anthracene Cyclic Ring with C60.

PubMed

Yamamoto, Yuta; Tsurumaki, Eiji; Wakamatsu, Kan; Toyota, Shinji

2018-05-30

An anthracene cyclic hexamer was synthesized by the coupling reaction as a macrocyclic hydrocarbon host. This disk-shaped host included a C 60 guest in 1:1 ratio to form a Saturn-type supramolecular complex in solution and in crystals. X-ray analysis unambiguously revealed that the guest molecule was accommodated in the middle of the host cavity with several CH⋅⋅⋅π contacts. The association constant K a determined by NMR titration measurements was 2.3×10 3  L mol -1 at 298 K in toluene. The structural features and the role of CH⋅⋅⋅π interactions are discussed with the aid of DFT calculations. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The influence of water-ethanol mixture on the thermodynamics of complex formation between 18-crown-6 ether and L-phenylalanine

NASA Astrophysics Data System (ADS)

Usacheva, T. R.; Sharnin, V. A.; Chernov, I. V.; Matteoli, E.; Terekhova, I. V.; Kumeev, R. S.

2012-08-01

The influence of water-ethanol mixture composition on the complex formation between 18-crown-6 ether and L-phenylalanine was studied by titration calorimetry at Т = 298.15 K. The standard thermodynamic parameters (ΔrGо, ΔrHо, ТΔrSо) of formation of [Phe18C6] molecular complex were calculated from data obtained by means of the microcalorimetric system TAM III (TA Instruments, USA) at X(EtOH) = 0.0/0.6 mol fraction. The stability of [Phe18C6] and the mechanism of complexation in water were investigated using the 1Н and 13С NMR spectroscopy. The increase of EtOH concentration results in an increase of the complex stability and of the exothermicity of complexation.

Determinations of Carbon Dioxide by Titration: New Experiments for General, Physical, and Quantitative Analysis Courses.

ERIC Educational Resources Information Center

Crossno, S. K.; And Others

1996-01-01

Presents experiments involving the analysis of commercial products such as carbonated beverages and antacids that illustrate the principles of acid-base reactions and present interesting problems in stoichiometry for students. (JRH)

NMR study of the transforming growth factor-alpha (TGF-alpha)-epidermal growth factor receptor complex. Visualization of human TGF-alpha binding determinants through nuclear Overhauser enhancement analysis.

PubMed

McInnes, C; Hoyt, D W; Harkins, R N; Pagila, R N; Debanne, M T; O'Connor-McCourt, M; Sykes, B D

1996-12-13

The study of human transforming growth factor-alpha (TGF-alpha) in complex with the epidermal growth factor (EGF) receptor extracellular domain has been undertaken in order to generate information on the interactions of these molecules. Analysis of 1H NMR transferred nuclear Overhauser enhancement data for titration of the ligand with the receptor has yielded specific data on the residues of the growth factor involved in contact with the larger protein. Significant increases and decreases in nuclear Overhauser enhancement cross-peak intensity occur upon complexation, and interpretation of these changes indicates that residues of the A- and C-loops of TGF-alpha form the major binding interface, while the B-loop provides a structural scaffold for this site. These results corroborate the conclusions from NMR relaxation studies (Hoyt, D. W., Harkins, R. N., Debanne, M. T., O'Connor-McCourt, M., and Sykes, B. D. (1994) Biochemistry 33, 15283-15292), which suggest that the C-terminal residues of the polypeptide are immobilized upon receptor binding, while the N terminus of the molecule retains considerable flexibility, and are consistent with structure-function studies of the TGF-alpha/EGF system indicating a multidomain binding model. These results give a visualization, for the first time, of native TGF-alpha in complex with the EGF receptor and generate a picture of the ligand-binding site based upon the intact molecule. This will undoubtedly be of utility in the structure-based design of TGF-alpha/EGF agonists and/or antagonists.

Measurement of Solution Viscosity via Diffusion-Ordered NMR Spectroscopy (DOSY)

ERIC Educational Resources Information Center

Li, Weibin; Kagan, Gerald; Hopson, Russell; Williard, Paul G.

2011-01-01

Increasingly, the undergraduate chemistry curriculum includes nuclear magnetic resonance (NMR) spectroscopy. Advanced NMR techniques are often taught including two-dimensional gradient-based experiments. An investigation of intermolecular forces including viscosity, by a variety of methods, is often integrated in the undergraduate physical and…

Interaction of phenazinium dyes with double-stranded poly(A): Spectroscopy and isothermal titration calorimetry studies

NASA Astrophysics Data System (ADS)

Khan, Asma Yasmeen; Saha, Baishakhi; Kumar, Gopinatha Suresh

2014-10-01

A comprehensive study on the binding of phenazinium dyes viz. janus green B, indoine blue, safranine O and phenosafranine with double stranded poly(A) using various spectroscopic and calorimetric techniques is presented. A higher binding of janus green B and indoine blue over safranine O and phenosafranine to poly(A) was observed from all experiments. Intercalative mode of binding of the dyes was inferred from fluorescence polarization anisotropy, iodide quenching and viscosity experiments. Circular dichroism study revealed significant perturbation of the secondary structure of poly(A) on binding of these dyes. Results from isothermal titration calorimetry experiments suggested that the binding was predominantly entropy driven with a minor contribution of enthalpy to the standard molar Gibbs energy. The results presented here may open new opportunities in the application of these dyes as RNA targeted therapeutic agents.

Single-Scan Multidimensional NMR Analysis of Mixtures at Sub-Millimolar Concentrations by using SABRE Hyperpolarization.

PubMed

Daniele, Valeria; Legrand, François-Xavier; Berthault, Patrick; Dumez, Jean-Nicolas; Huber, Gaspard

2015-11-16

Signal amplification by reversible exchange (SABRE) is a promising method to increase the sensitivity of nuclear magnetic resonance (NMR) experiments. However, SABRE-enhanced (1)H NMR signals are short lived, and SABRE is often used to record 1D NMR spectra only. When the sample of interest is a complex mixture, this results in severe overlaps for (1)H spectra. In addition, the use of a co-substrate, whose signals may obscure the (1) H spectra, is currently the most efficient way to lower the detection limit of SABRE experiments. Here, we describe an approach to obtain clean, SABRE-hyperpolarized 2D (1)H NMR spectra of mixtures of small molecules at sub-millimolar concentrations in a single scan. The method relies on the use of para-hydrogen together with a deuterated co-substrate for hyperpolarization and ultrafast 2D NMR for acquisition. It is applicable to all substrates that can be polarized with SABRE. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Optimized slice-selective 1H NMR experiments combined with highly accurate quantitative 13C NMR using an internal reference method

NASA Astrophysics Data System (ADS)

Jézéquel, Tangi; Silvestre, Virginie; Dinis, Katy; Giraudeau, Patrick; Akoka, Serge

2018-04-01

Isotope ratio monitoring by 13C NMR spectrometry (irm-13C NMR) provides the complete 13C intramolecular position-specific composition at natural abundance. It represents a powerful tool to track the (bio)chemical pathway which has led to the synthesis of targeted molecules, since it allows Position-specific Isotope Analysis (PSIA). Due to the very small composition range (which represents the range of variation of the isotopic composition of a given nuclei) of 13C natural abundance values (50‰), irm-13C NMR requires a 1‰ accuracy and thus highly quantitative analysis by 13C NMR. Until now, the conventional strategy to determine the position-specific abundance xi relies on the combination of irm-MS (isotopic ratio monitoring Mass Spectrometry) and 13C quantitative NMR. However this approach presents a serious drawback since it relies on two different techniques and requires to measure separately the signal of all the carbons of the analyzed compound, which is not always possible. To circumvent this constraint, we recently proposed a new methodology to perform 13C isotopic analysis using an internal reference method and relying on NMR only. The method combines a highly quantitative 1H NMR pulse sequence (named DWET) with a 13C isotopic NMR measurement. However, the recently published DWET sequence is unsuited for samples with short T1, which forms a serious limitation for irm-13C NMR experiments where a relaxing agent is added. In this context, we suggest two variants of the DWET called Multi-WET and Profiled-WET, developed and optimized to reach the same accuracy of 1‰ with a better immunity towards T1 variations. Their performance is evaluated on the determination of the 13C isotopic profile of vanillin. Both pulse sequences show a 1‰ accuracy with an increased robustness to pulse miscalibrations compared to the initial DWET method. This constitutes a major advance in the context of irm-13C NMR since it is now possible to perform isotopic analysis with high relaxing agent concentrations, leading to a strong reduction of the overall experiment time.

Imidazole as a pH Probe: An NMR Experiment for the General Chemistry Laboratory

ERIC Educational Resources Information Center

Hagan, William J., Jr.; Edie, Dennis L.; Cooley, Linda B.

2007-01-01

The analysis describes an NMR experiment for the general chemistry laboratory, which employs an unknown imidazole solution to measure the pH values. The described mechanism can also be used for measuring the acidity within the isolated cells.

Cation Hydration Constants by Proton NMR: A Physical Chemistry Experiment.

ERIC Educational Resources Information Center

Smith, Robert L.; And Others

1988-01-01

Studies the polarization effect on water by cations and anions. Describes an experiment to illustrate the polarization effect of sodium, lithium, calcium, and strontium ions on the water molecule in the hydration spheres of the ions. Analysis is performed by proton NMR. (MVL)

ODIN-object-oriented development interface for NMR.

PubMed

Jochimsen, Thies H; von Mengershausen, Michael

2004-09-01

A cross-platform development environment for nuclear magnetic resonance (NMR) experiments is presented. It allows rapid prototyping of new pulse sequences and provides a common programming interface for different system types. With this object-oriented interface implemented in C++, the programmer is capable of writing applications to control an experiment that can be executed on different measurement devices, even from different manufacturers, without the need to modify the source code. Due to the clear design of the software, new pulse sequences can be created, tested, and executed within a short time. To post-process the acquired data, an interface to well-known numerical libraries is part of the framework. This allows a transparent integration of the data processing instructions into the measurement module. The software focuses mainly on NMR imaging, but can also be used with limitations for spectroscopic experiments. To demonstrate the capabilities of the framework, results of the same experiment, carried out on two NMR imaging systems from different manufacturers are shown and compared with the results of a simulation.

Surface-Bound Intermediates in Low-Temperature Methanol Synthesis on Copper. Participants and Spectators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Yong; Mei, Donghai; Peden, Charles H.F.

The reactivity of surface adsorbed species present on copper catalysts during methanol synthesis at low temperatures was studied by simultaneous infrared spectroscopy (IR) and mass spectroscopy (MS) measurements during “titration” (transient surface reaction) experiments with isotopic tracing. The results show that adsorbed formate is a major bystander species present on the surface under steady-state methanol synthesis reaction conditions, but it cannot be converted to methanol by reaction with pure H 2, nor with H 2 plus added water. Formate-containing surface adlayers for these experiments were produced during steady state catalysis in (a) H 2:CO 2 (with substantial formate coverage) andmore » (b) moist H 2:CO (with no IR visible formate species). Both these reaction conditions produce methanol at steady state with relatively high rates. Adlayers containing formate were also produced by (c) formic acid adsorption. Various "titration" gases were used to probe these adlayers at modest temperatures (T = 410-450K) and 6 bar total pressure. Methanol gas (up to ~1% monolayer equivalent) was produced in "titration" from the H 2:CO 2 catalytic adlayers by H 2 plus water, but not by dry hydrogen. The decay in the formate IR features accelerated in the presence of added water vapor. The H 2:CO:H 2O catalytic adlayer produced similar methanol titration yields in H 2 plus water but showed no surface formate features in IR (less than 0.2% monolayer coverage). Finally, formate from formic acid chemisorption produced no methanol under any titration conditions. Even under (H 2:CO 2) catalytic reaction conditions, isotope tracing showed that pre-adsorbed formate from formic acid did not contribute to the methanol produced. Although non-formate intermediates exist during low temperature methanol synthesis on copper which can be converted to methanol gas by titration with pure H 2 plus water in sufficient quantities for that intermediate to be observable by IR, formate itself is only a "spectator" in this reaction and gives no observable methanol upon any titration we performed with H 2 or H 2 plus water.« less

Bringing NMR and IR Spectroscopy to High Schools

ERIC Educational Resources Information Center

Bonjour, Jessica L.; Hass, Alisa L.; Pollock, David W.; Huebner, Aaron; Frost, John A.

2017-01-01

Development of benchtop, portable Fourier transform nuclear magnetic resonance (NMR) and infrared (IR) spectrometers has opened up opportunities for creating university-high school partnerships that provide high school students with hands-on experience with NMR and IR instruments. With recent changes to the international baccalaureate chemistry…

Microcalorimetric and potentiometric titration studies on the adsorption of copper by extracellular polymeric substances (EPS), minerals and their composites.

PubMed

Fang, Linchuan; Huang, Qiaoyun; Wei, Xing; Liang, Wei; Rong, Xinming; Chen, Wenli; Cai, Peng

2010-08-01

Equilibrium adsorption experiments, isothermal titration calorimetry and potentiometric titration techniques were employed to investigate the adsorption of Cu(II) by extracellular polymeric substances (EPS) extracted from Pseudomonas putida X4, minerals (montmorillonite and goethite) and their composites. Compared with predicted values of Cu(II) adsorption on composites, the measured values of Cu(II) on EPS-montmorillonite composite increased, however, those on EPS-goethite composite decreased. Potentiometric titration results also showed that more surface sites were observed on EPS-montmorillonite composite and less reactive sites were found on EPS-goethite composite. The adsorption of Cu(II) on EPS molecules and their composites with minerals was an endothermic reaction, while that on minerals was exothermic. The positive values of enthalpy change (Delta H) and entropy change (DeltaS) for Cu(II) adsorption on EPS and mineral-EPS composites indicated that Cu(II) mainly interacts with carboxyl and phosphoryl groups as inner-sphere complexes on EPS molecules and their composites with minerals. (c) 2010 Elsevier Ltd. All rights reserved.

Effects of CO2 injection and Kerogen Maturation on Low-Field Nuclear Magnetic Resonance Response

NASA Astrophysics Data System (ADS)

Prasad, M.; Livo, K.

2017-12-01

Low-field Nuclear Magnetic Resonance (NMR) is commonly used in petrophysical analysis of petroleum reservoir rocks. NMR experiments record the relaxation and polarization of in-situ hydrogen protons present in gaseous phases such as free-gas intervals and solution gas fluids, bulk fluid phases such as oil and aquifer intervals, and immovable fractions of kerogen and bitumen. Analysis of NMR relaxation spectra is performed to record how fluid composition, maturity, and viscosity change NMR experimental results. We present T1-T2 maps as thermal maturity of a water-saturated, sub-mature Woodford shale is increased at temperatures from 125 to 400 degrees Celsius. Experiments with applied fluid pressure in paraffinic mineral oil and DI water with varying fluid pH have been performed to mimic reservoir conditions in analysis of the relaxation of bulk fluid phases. We have recorded NMR spectra, T1-T2 maps, and fluid diffusion coefficients using a low-field (2 MHz) MagritekTM NMR. CO2 was injected at a pressure of 900 psi in an in house developed NMR pressure vessel made of torlon plastic. Observable 2D NMR shifts in immature kerogen formations as thermal maturity is increased show generation of lighter oils with increased maturity. CO2 injection leads to a decrease in bulk fluid relaxation time that is attributed to viscosity modification with gas presence. pH variation with increased CO2 presence were shown to not effect NMR spectra. From this, fluid properties have been shown to greatly affect NMR readings and must be taken into account for more accurate NMR reservoir characterization.

NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment

PubMed Central

Jang, Richard; Wang, Yan

2015-01-01

NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second round of the CASD-NMR experiment. Unlike many molecular dynamics-based methods, NMR-I-TASSER takes a molecular replacement-like approach to the problem by first threading the target through the PDB to identify structural templates which are then used for iterative NOE assignments and fragment structure assembly refinements. The employment of multiple templates allows NMR-I-TASSER to sample different topologies while convergence to a single structure is not required. Retroactive and blind tests of the CASD-NMR targets from Rounds 1 and 2 demonstrate that even without using NOE peak lists I-TASSER can generate correct structure topology with 15 of 20 targets having a TM-score above 0.5. With the addition of NOE-based distance restraints, NMR-I-TASSER significantly improved the I-TASSER models with all models having the TM-score above 0.5. The average RMSD was reduced from 5.29 to 2.14 Å in Round 1 and 3.18 to 1.71 Å in Round 2. There is no obvious difference in the modeling results with using raw and refined peak lists, indicating robustness of the pipeline to the NOE assignment errors. Overall, despite the low-resolution modeling the current NMR-I-TASSER pipeline provides a coarse-grained structure folding approach complementary to traditional molecular dynamics simulations, which can produce fast near-native frameworks for atomic-level structural refinement. PMID:25737244

Effects of radiation damping for biomolecular NMR experiments in solution: a hemisphere concept for water suppression

PubMed Central

Ishima, Rieko

2016-01-01

Abundant solvent nuclear spins, such as water protons in aqueous solution, cause radiation damping in NMR experiments. It is important to know how the effect of radiation damping appears in high-resolution protein NMR because macromolecular studies always require very high magnetic field strengths with a highly sensitive NMR probe that can easily cause radiation damping. Here, we show the behavior of water magnetization after a pulsed-field gradient (PFG) using nutation experiments at 900 MHz with a cryogenic probe: when water magnetization is located in the upper hemisphere (having +Z component, parallel to the external magnetic field), dephasing of the magnetization by a PFG effectively suppresses residual water magnetization in the transverse plane. In contrast, when magnetization is located in the lower hemisphere (having −Z component), the small residual transverse component remaining after a PFG is still sufficient to induce radiation damping. Based on this observation, we designed 1H-15N HSQC experiments in which water magnetization is maintained in the upper hemisphere, but not necessarily along Z, and compared them with the conventional experiments, in which water magnetization is inverted during the t1 period. The result demonstrates moderate gain of signal-to-noise ratio, 0–28%. Designing the experiments such that water magnetization is maintained in the upper hemisphere allows shorter pulses to be used compared to the complete water flip-back and, thereby, is useful as a building block of protein NMR pulse programs in solution. PMID:27524944

A NMR experiment for simultaneous correlations of valine and leucine/isoleucine methyls with carbonyl chemical shifts in proteins.

PubMed

Tugarinov, Vitali; Venditti, Vincenzo; Marius Clore, G

2014-01-01

A methyl-detected 'out-and-back' NMR experiment for obtaining simultaneous correlations of methyl resonances of valine and isoleucine/leucine residues with backbone carbonyl chemical shifts, SIM-HMCM(CGCBCA)CO, is described. The developed pulse-scheme serves the purpose of convenience in recording a single data set for all Ile(δ1), Leu(δ) and Val(γ) (ILV) methyl positions instead of acquiring two separate spectra selective for valine or leucine/isoleucine residues. The SIM-HMCM(CGCBCA)CO experiment can be used for ILV methyl assignments in moderately sized protein systems (up to ~100 kDa) where the backbone chemical shifts of (13)C(α), (13)Cβ and (13)CO are known from prior NMR studies and where some losses in sensitivity can be tolerated for the sake of an overall reduction in NMR acquisition time.

Development of a method for detecting trace metals in aqueous solutions based on the coordination chemistry of hexahydrotriazines.

PubMed

Wojtecki, Rudy J; Yuen, Alexander Y; Zimmerman, Thomas G; Jones, Gavin O; Horn, Hans W; Boday, Dylan J; Hedrick, James L; García, Jeannette M

2015-08-07

The detection of trace amounts (<10 ppb) of heavy metals in aqueous solutions is described using 1,3,5-hexahydro-1,3,5-triazines (HTs) as chemical indicators and a low cost fluorimeter-based detection system. This method takes advantage of the inherent properties of HTs to coordinate strongly with metal ions in solution, a fundamental property that was studied using a combination of analytical tools (UV-Vis titrations, (1)H-NMR titrations and computational modeling). Based on these fundamental studies that show significant changes in the HT UV signature when a metal ion is present, HT compounds were used to prepare indicator strips that resulted in significant fluorescence changes when a metal was present. A portable and economical approach was adopted to test the concept of utilizing HTs to detect heavy metals using a fluorimeter system that consisted of a low-pressure mercury lamp, a photo-detector, a monolithic photodiode and an amplifier, which produces a voltage proportional to the magnitude of the visible fluorescence emission. Readings of the prepared HT test strips were evaluated by exposure to two different heavy metals at the safe threshold concentration described by the U.S. Environmental Protection Agency (EPA) for Cr(3+) and Ag(2+) (100 μg L(-1) and 6.25, respectively). This method of detection could be used to the presence of either metal at these threshold concentrations.

Complexity in Acid–Base Titrations: Multimer Formation Between Phosphoric Acids and Imines

PubMed Central

Malm, Christian; Kim, Heejae; Wagner, Manfred

2017-01-01

Abstract Solutions of Brønsted acids with bases in aprotic solvents are not only common model systems to study the fundamentals of proton transfer pathways but are also highly relevant to Brønsted acid catalysis. Despite their importance the light nature of the proton makes characterization of acid–base aggregates challenging. Here, we track such acid–base interactions over a broad range of relative compositions between diphenyl phosphoric acid and the base quinaldine in dichloromethane, by using a combination of dielectric relaxation and NMR spectroscopy. In contrast to what one would expect for an acid–base titration, we find strong deviations from quantitative proton transfer from the acid to the base. Even for an excess of the base, multimers consisting of one base and at least two acid molecules are formed, in addition to the occurrence of proton transfer from the acid to the base and simultaneous formation of ion pairs. For equimolar mixtures such multimers constitute about one third of all intermolecular aggregates. Quantitative analysis of our results shows that the acid‐base association constant is only around six times larger than that for the acid binding to an acid‐base dimer, that is, to an already protonated base. Our findings have implications for the interpretation of previous studies of reactive intermediates in organocatalysis and provide a rationale for previously observed nonlinear effects in phosphoric acid catalysis. PMID:28597513

Monitoring an Induced Permafrost Warming Experiment Using ERT, Temperature, and NMR in Fairbanks, Alaska

NASA Astrophysics Data System (ADS)

Ulrich, C.; Ajo Franklin, J. B.; Ekblaw, I.; Lindsey, N.; Wagner, A. M.; Saari, S.; Daley, T. M.; Freifeld, B. M.

2016-12-01

As global temperatures continue to rise, permafrost landscapes will experience more rapid changes than other global climate zones. Permafrost thaw is a result of increased temperatures in arctic settings resulting in surface deformation and subsurface hydrology changes. From an engineering perspective, surface deformation poses a threat to the stability of existing infrastructure such as roads, utility piping, and building structures. Preemptively detecting or monitoring subsurface thaw dynamics presents a difficult challenge due to the long time scales as deformation occurs. Increased subsurface moisture content results from permafrost thaw of which electrical resistivity tomography (ERT), soil temperature, and nuclear magnetic resonance (NMR) are directly sensitive. In this experiment we evaluate spatial and temporal changes in subsurface permafrost conditions (moisture content and temperature) at a experimental heating plot in Fairbanks, AK. This study focuses on monitoring thaw signatures using multiple collocated electrical resistivity (ERT), borehole temperature, and borehole nuclear magnetic resonance (NMR) measurements. Timelapse ERT (sensitive to changes in moisture content) was inverted using collocated temperature and NMR to constrain ERT inversions. Subsurface thermal state was monitored with timelapse thermistors, sensitive to soil ice content. NMR was collected in multiple boreholes and is sensitive to changes in moisture content and pore scale distribution. As permafrost thaws more hydrogen, in the form of water, is available resulting in a changing NMR response. NMR requires the availability of liquid water in order to induce spin of the hydrogen molecule, hence, if frozen water molecules will be undetectable. In this study, the permafrost is poised close to 0oC and is mainly silt with small pore dimensions; this combination makes NMR particularly useful due to the possibility of sub-zero thaw conditions within the soil column. Overall this experiment presents a complementary suite of methods that provides feedback on subsurface permafrost state even in cases where soil texture might control unfrozen water content.

Solution state NMR of lignins

Treesearch

John Ralph; Jane M. Marita; Sally A. Ralph; Ronald D. Hatfield; Fachuang Lu; Richard M. Ede; Junpeng Peng; Larry L. Landucci

1999-01-01

Despite the rather random and heterogeneous nature of isolated lignins, many of their intimate structural details are revealed by diagnostic NMR experiments. 13C-NMR was recognized early-on as a high-resolution method for detailed structural characterization, aided by the almost exact agreement between chemical shifts of carbons in good low-molecular...

Heteronuclear Multidimensional Protein NMR in a Teaching Laboratory

ERIC Educational Resources Information Center

Wright, Nathan T.

2016-01-01

Heteronuclear multidimensional NMR techniques are commonly used to study protein structure, function, and dynamics, yet they are rarely taught at the undergraduate level. Here, we describe a senior undergraduate laboratory where students collect, process, and analyze heteronuclear multidimensional NMR experiments using an unstudied Ig domain (Ig2…

Using NMR to Expand Chemistry Research and Educational Experiences at North Carolina Central University, an Historically Black University

DTIC Science & Technology

analytical chemistry . Most students do not get hands-on training with an NMR within their classroom or laboratory courses. The NMR will provide...unique opportunities to our students as they train to become the next generation of scientists, doctors, and engineers .

An Integrated Laboratory Project in NMR Spectroscopy.

ERIC Educational Resources Information Center

Hudson, Reggie L.; Pendley, Bradford D.

1988-01-01

Describes an advanced NMR project that can be done with a 60-MHz continuous-wave proton spectrometer. Points out the main purposes are to give students experience in second-order NMR analysis, the simplification of spectra by raising the frequency, and the effect of non-hydrogen nuclei on proton resonances. (MVL)

On the use of ultracentrifugal devices for routine sample preparation in biomolecular magic-angle-spinning NMR

PubMed Central

Mandal, Abhishek; Boatz, Jennifer C.; Wheeler, Travis; van der Wel, Patrick C. A.

2017-01-01

A number of recent advances in the field of magic-angle-spinning (MAS) solid-state NMR have enabled its application to a range of biological systems of ever increasing complexity. To retain biological relevance, these samples are increasingly studied in a hydrated state. At the same time, experimental feasibility requires the sample preparation process to attain a high sample concentration within the final MAS rotor. We discuss these considerations, and how they have led to a number of different approaches to MAS NMR sample preparation. We describe our experience of how custom-made (or commercially available) ultracentrifugal devices can facilitate a simple, fast and reliable sample preparation process. A number of groups have since adopted such tools, in some cases to prepare samples for sedimentation-style MAS NMR experiments. Here we argue for a more widespread adoption of their use for routine MAS NMR sample preparation. PMID:28229262

Trispyrazolylborate Complexes: An Advanced Synthesis Experiment Using Paramagnetic NMR, Variable-Temperature NMR, and EPR Spectroscopies

ERIC Educational Resources Information Center

Abell, Timothy N.; McCarrick, Robert M.; Bretz, Stacey Lowery; Tierney, David L.

2017-01-01

A structured inquiry experiment for inorganic synthesis has been developed to introduce undergraduate students to advanced spectroscopic techniques including paramagnetic nuclear magnetic resonance and electron paramagnetic resonance. Students synthesize multiple complexes with unknown first row transition metals and identify the unknown metals by…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cho, Ching Chang, E-mail: ccjwo@yahoo.com.tw; Chou, Ruey Hwang, E-mail: rhchou@mail.cmu.edu.tw; Yu, Chin, E-mail: cyu.nthu@gmail.com

The human S100 protein family contains small, dimeric and acidic proteins that contain two EF-hand motifs and bind calcium. When S100A5 binds calcium, its conformation changes and promotes interaction with the target protein. The extracellular domain of RAGE (Receptor of Advanced Glycation End products) contain three domains: C1, C2 and V. The RAGE V domain is the target protein of S100A5 that promotes cell survival, growth and differentiation by activating several signaling pathways. Pentamidine is an apoptotic and antiparasitic drug that is used to treat or prevent pneumonia. Here, we found that pentamidine interacts with S100A5 using HSQC titration. Wemore » elucidated the interactions of S100A5 with RAGE V domain and pentamidine using fluorescence and NMR spectroscopy. We generated two binary models—the S100A5-RAGE V domain and S100A5-Pentamidine complex—and then observed that the pentamidine and RAGE V domain share a similar binding region in mS100A5. We also used the WST-1 assay to investigate the bioactivity of S100A5, RAGE V domain and pentamidine. These results indicated that pentamidine blocks the binding between S100A5 and RAGE V domain. This finding is useful for the development of new anti-proliferation drugs. - Highlights: • The interaction between mS100A5–RAGE V was investigated by fluorescence spectroscopy. • The interfacial residues on mS100A5–RAGE V and mS100A5–pentamidine contact surface were mapped by {sup 1}H-{sup 15}N HSQC experiments. • mS100A5–RAGE V and mS100A5–pentamidine complex models were generated from NMR restraints using HADDOCK program. • The bioactivity of the mS100A5–RAGE V and mS100A5–pentamidine complex was studied using WST-1 assay.« less

Pub1p C-Terminal RRM Domain Interacts with Tif4631p through a Conserved Region Neighbouring the Pab1p Binding Site

PubMed Central

Rico-Lastres, Palma; Pérez-Cañadillas, José Manuel

2011-01-01

Pub1p, a highly abundant poly(A)+ mRNA binding protein in Saccharomyces cerevisiae, influences the stability and translational control of many cellular transcripts, particularly under some types of environmental stresses. We have studied the structure, RNA and protein recognition modes of different Pub1p constructs by NMR spectroscopy. The structure of the C-terminal RRM domain (RRM3) shows a non-canonical N-terminal helix that packs against the canonical RRM fold in an original fashion. This structural trait is conserved in Pub1p metazoan homologues, the TIA-1 family, defining a new class of RRM-type domains that we propose to name TRRM (TIA-1 C-terminal domain-like RRM). Pub1p TRRM and the N-terminal RRM1-RRM2 tandem bind RNA with high selectivity for U-rich sequences, with TRRM showing additional preference for UA-rich ones. RNA-mediated chemical shift changes map to β-sheet and protein loops in the three RRMs. Additionally, NMR titration and biochemical in vitro cross-linking experiments determined that Pub1p TRRM interacts specifically with the N-terminal region (1–402) of yeast eIF4G1 (Tif4631p), very likely through the conserved Box1, a short sequence motif neighbouring the Pab1p binding site in Tif4631p. The interaction involves conserved residues of Pub1p TRRM, which define a protein interface that mirrors the Pab1p-Tif4631p binding mode. Neither protein nor RNA recognition involves the novel N-terminal helix, whose functional role remains unclear. By integrating these new results with the current knowledge about Pub1p, we proposed different mechanisms of Pub1p recruitment to the mRNPs and Pub1p-mediated mRNA stabilization in which the Pub1p/Tif4631p interaction would play an important role. PMID:21931728

Grafting of poly (lactic acid) with maleic anhydride using supercritical carbon dioxide

NASA Astrophysics Data System (ADS)

Khankrua, R.; Pivsa-Art, S.; Hiroyuki, H.; Suttiruengwong, S.

2015-07-01

The aim of this work was to modify poly lactic acid (PLA) via free radical grafting with maleic anhydride (MA) by using supercritical carbon dioxide (SCCO2). Benzoyl peroxide (BPO) was used as an initiator. The solubility of MA in SCCO2 was first determined to estimate the suitable grafting conditions and equilibrium. From the solubility study of MA in SCCO2, it was found that the solubility of MA in SCCO2 increased with the increasing pressure and dissolution time. PLA films were first prepared by compression molding. The ratio of MA to BPO was 2:1. The reaction temperature and pressure were 70°C and 100 bar respectively. The grafting reaction and the degree of grafting were characterized by nuclear magnetic resonance (NMR) spectroscopy and titration, respectively. Scanning electron microscope (SEM) technique and contact angle were used to confirm the changes in physical properties of PLA film grafted MA. NMR spectrum indicated that the grafting of MA onto PLA was successively achieved. Degree of grafting by using SCCO2 was as high as 0.98%. This provided rather high grafting degree compared with other processes. SEM pictures showed the rough surface structure on modified PLA film. In addition, contact angle results showed an improvement of the hydrophilicity by maleic anhydride grafting onto polymers.

Spectroscopic and structural investigation of 2,5-dicarboxy-1-methylpyridinium inner salt

NASA Astrophysics Data System (ADS)

Barczyński, P.; Komasa, A.; Katrusiak, A.; Dega-Szafran, Z.; Nowaczyk, Ł.; Ratajczak-Sitarz, M.; Szafran, M.

2014-03-01

The structure of 2,5-dicarboxy-1-methylpyridinium inner salt (1), has been studied by X-ray diffraction, B3LYP/6-311G(d,p) calculations, FTIR, Raman and NMR spectroscopy. The molecules are linked by short intermolecular and asymmetric Osbnd H⋯O hydrogen bonds of 2.486(2) Å between carboxyl and carboxylate groups of neighboring molecules into infinite chains. The hydrogen bonds in the molecules optimized by the B3LYP/6-311G(d,p) approach in trimer (2) and dimer (3) are slightly longer than in the crystal. The FTIR spectrum of the investigated inner salt is dominated by a broad and intense absorption in the 1500-800 cm-1 region attributed to the νas(OHO) and γ(OHO) vibrations of the strong hydrogen bond. In the Raman spectrum the broad absorption is absent. Linear correlations, δexp = a + b σcalc between the experimental 1H and 13C NMR chemical shifts (δexp) of the investigated inner salt in D2O and the calculated magnetic isotropic shielding constants (σcalc) for the optimized monomer (4a) solvated in water are reported. The pKa value for 1 of 2.31 ± 0.02 was determined by the potentiometric titration.

Methyl group reorientation under ligand binding probed by pseudocontact shifts.

PubMed

Lescanne, Mathilde; Ahuja, Puneet; Blok, Anneloes; Timmer, Monika; Akerud, Tomas; Ubbink, Marcellus

2018-06-02

Liquid-state NMR spectroscopy is a powerful technique to elucidate binding properties of ligands on proteins. Ligands binding in hydrophobic pockets are often in close proximity to methyl groups and binding can lead to subtle displacements of methyl containing side chains to accommodate the ligand. To establish whether pseudocontact shifts can be used to characterize ligand binding and the effects on methyl groups, the N-terminal domain of HSP90 was tagged with caged lanthanoid NMR probe 5 at three positions and titrated with a ligand. Binding was monitored using the resonances of leucine and valine methyl groups. The pseudocontact shifts (PCS) caused by ytterbium result in enhanced dispersion of the methyl spectrum, allowing more resonances to be observed. The effects of tag attachment on the spectrum and ligand binding are small. Significant changes in PCS were observed upon ligand binding, indicating displacements of several methyl groups. By determining the cross-section of PCS iso-surfaces generated by two or three paramagnetic centers, the new position of a methyl group can be estimated, showing displacements in the range of 1-3 Å for methyl groups in the binding site. The information about such subtle but significant changes may be used to improve docking studies and can find application in fragment-based drug discovery.

Spectroscopic characterization of metal bound phytochelatin analogue (Glu-Cys)4-Gly.

PubMed

Cheng, Yongsheng; Yan, Yong-Bin; Liu, Jinyuan

2005-10-01

The metal ion binding properties of a phytochelatin (PC) analogue, (Glu-Cys)4-Gly (named as EC4), have been studied by a divalent metal ion binding assay monitored by UV-visible spectroscopy, circular dichroism and NMR spectroscopy. Spectro- photometric titration with different divalent metal ions have revealed that the stiochoimetry of metal-bound EC4 was 1:1, and its metal binding affinities with different divalent metal ions in the order of Cd(II)>Cu(II)>Zn(II)>Pb(II)>Ni(II)>Co(II). UV-visible spectroscopic analysis of metal complexes indicated that four sulfur atoms in cysteine residues are attributable to ligand-to-metal charge transfer (LMCT) between divalent metal ions and EC4, and further confirmed by 1D H1 NMR study and Circular Dichroism. In addition, Circular Dichroism spectra of both free and metal-bound forms of EC4 revealed that metal coordination drives the nonapeptide chain to fold into a turned conformation. The comprehensive analysis of spectroscopic properties of the nonapeptide complexed with metal ions not only provides a fundamental description of the metal ion binding properties of PC analogue, but also shows a correlation between metal binding affinity of PC analogue and the induction activity of metal ions.

Supramolecular polymeric chemosensor for biomedical applications: design and synthesis of a luminescent zinc metallopolymer as a chemosensor for adenine detection.

PubMed

Chow, Cheuk-Fai

2012-11-01

Adenine is an important bio-molecule that plays many crucial roles in food safety and biomedical diagnostics. Differentiating adenine from a mixture of adenosine and other nucleic bases (guanine, thymine, cytosine, and uracil) is particularly important for both biological and clinical applications. A neutral Zn(II) metallosupramolecular polymer based on acyl hydrazone derived coordination centres (P1) were generated through self-assembly polymerization. It is a linear coordination polymer that behaves like self-standing film. The synthesis, (1)H-NMR characterization, and spectroscopic properties of this supramolecular material are reported. P1 was found to be a chemosensor specific to adenine, with a luminescent enhancement. The binding properties of P1 with common nucleic bases and nucleosides reveal that this supramolecular polymer is very selective to adenine molecules (~20 to 420 times more selectivity than other nucleic bases). The formation constant (K) of P1 to adenine was found to be log K = 4.10 ± 0.02. This polymeric chemosensor produces a specific response to adenine down to 90 ppb. Spectrofluorimetric and (1)H-NMR titration studies showed that the P1 polymer allows each Zn(II) coordination centre to bind to two adenine molecules through hydrogen bonding with their imine and hydrazone protons.

Chemistry Notes

ERIC Educational Resources Information Center

Pinkney, J. N.; And Others

1976-01-01

Describes eleven laboratory experiments, including the catalytic effect of copper in zinc-acid reaction; a study of the rate of polymerization of some aldehydes; and a demonstration automatic potentiometric titrator. (MLH)

Field and In-Lab Determination of Ca[superscript 2+] in Seawater

ERIC Educational Resources Information Center

Stoodley, Robin; Nun~ez, Jose R. Rodriguez; Bartz, Tessa

2014-01-01

Portions of classic undergraduate quantitative analysis experiments in complexiometric titration and potentiometry are combined with a field-sampling experience to create a two period (2 × 3 h) comparison-based experiment for second-year students. A multifunctional chemical analysis device is used with calcium ion-selective electrode for field…

A complete 1H and 13C NMR data assignment for the diterpene methyl (-)-zanzibarate by 2D spectroscopy and NOE experiments.

PubMed

Imamura, P M; Miranda, P C M L; Giacomini, R A

2004-06-01

The 1H and 13C NMR spectra of methyl (-)-zanzibarate (1), an ent-labdanic diterpene isolated from the epicarp of Hymenaea courbaril var. altissima (Leguminosaea, Cesalpinoideae, Detariae), was fully assigned by COSY experiments, 13C/1H shift correlation diagrams and NOE experiments. Copyright 2004 John Wiley & Sons, Ltd.

Diels-Alder Cycloadditions: A MORE Experiment in the Organic Laboratory Including a Diene Identification Exercise Involving NMR Spectroscopy and Molecular Modeling

ERIC Educational Resources Information Center

Shaw, Roosevelt; Severin, Ashika; Balfour, Miguel; Nettles, Columbus

2005-01-01

Two Diels-Alder reactions are described that are suitable for a MORE (microwave-induced organic reaction enhanced) experiment in the organic chemistry laboratory course. A second experiment in which the splitting patterns of the vinyl protons in the nuclear magnetic resonance (NMR) spectra of two MORE adducts are used in conjunction with molecular…

NMR properties of 3He-A in biaxially anisotropic aerogel

NASA Astrophysics Data System (ADS)

Dmitriev, V. V.; Krasnikhin, D. A.; Senin, A. A.; Yudin, A. N.

2012-12-01

Theoretical model of G.E. Volovik for A-like phase of 3He in aerogel suggests formation of Larkin-Imry-Ma state of Anderson-Brinkmann-Morel order parameter. Most of results of NMR studies of A-like phase are in a good agreement with this model in assumption of uniaxial anisotropy, except for some of experiments in weakly anisotropic aerogel samples. We demonstrate that these results can be described in frames of the same model in assumption of biaxial anisotropy. Parameters of anisotropy in these experiments can be determined from the NMR data.

A quasi-optical and corrugated waveguide microwave transmission system for simultaneous dynamic nuclear polarization NMR on two separate 14.1 T spectrometers

PubMed Central

Dubroca, Thierry; Smith, Adam N.; Pike, Kevin J.; Froud, Stuart; Wylde, Richard; Trociewitz, Bianca; McKay, Johannes; Mentink-Vigier, Frederic; van Tol, Johan; Wi, Sungsool; Brey, William; Long, Joanna R.; Frydman, Lucio; Hill, Stephen

2018-01-01

Nuclear magnetic resonance (NMR) is an intrinsically insensitive technique, with Boltzmann distributions of nuclear spin states on the order of parts per million in conventional magnetic fields. To overcome this limitation, dynamic nuclear polarization (DNP) can be used to gain up to three orders of magnitude in signal enhancement, which can decrease experimental time by up to six orders of magnitude. In DNP experiments, nuclear spin polarization is enhanced by transferring the relatively larger electron polarization to NMR active nuclei via microwave irradiation. Here, we describe the design and performance of a quasi-optical system enabling the use of a single 395 GHz gyrotron microwave source to simultaneously perform DNP experiments on two different 14.1 T (1H 600 MHz) NMR spectrometers: one configured for magic angle spinning (MAS) solid state NMR; the other configured for solution state NMR experiments. In particular, we describe how the high power microwave beam is split, transmitted, and manipulated between the two spectrometers. A 13C enhancement of 128 is achieved via the cross effect for alanine, using the nitroxide biradical AMUPol, under MAS-DNP conditions at 110 K, while a 31P enhancement of 160 is achieved via the Overhauser effect for triphenylphosphine using the monoradical BDPA under solution NMR conditions at room temperature. The latter result is the first demonstration of Overhauser DNP in the solution state at a field of 14.1 T (1H 600 MHz). Moreover these results have been produced with large sample volumes (~100 μL, i.e. 3 mm diameter NMR tubes). PMID:29459343

A quasi-optical and corrugated waveguide microwave transmission system for simultaneous dynamic nuclear polarization NMR on two separate 14.1 T spectrometers

NASA Astrophysics Data System (ADS)

Dubroca, Thierry; Smith, Adam N.; Pike, Kevin J.; Froud, Stuart; Wylde, Richard; Trociewitz, Bianca; McKay, Johannes; Mentink-Vigier, Frederic; van Tol, Johan; Wi, Sungsool; Brey, William; Long, Joanna R.; Frydman, Lucio; Hill, Stephen

2018-04-01

Nuclear magnetic resonance (NMR) is an intrinsically insensitive technique, with Boltzmann distributions of nuclear spin states on the order of parts per million in conventional magnetic fields. To overcome this limitation, dynamic nuclear polarization (DNP) can be used to gain up to three orders of magnitude in signal enhancement, which can decrease experimental time by up to six orders of magnitude. In DNP experiments, nuclear spin polarization is enhanced by transferring the relatively larger electron polarization to NMR active nuclei via microwave irradiation. Here, we describe the design and performance of a quasi-optical system enabling the use of a single 395 GHz gyrotron microwave source to simultaneously perform DNP experiments on two different 14.1 T (1H 600 MHz) NMR spectrometers: one configured for magic angle spinning (MAS) solid state NMR; the other configured for solution state NMR experiments. In particular, we describe how the high power microwave beam is split, transmitted, and manipulated between the two spectrometers. A 13C enhancement of 128 is achieved via the cross effect for alanine, using the nitroxide biradical AMUPol, under MAS-DNP conditions at 110 K, while a 31P enhancement of 160 is achieved via the Overhauser effect for triphenylphosphine using the monoradical BDPA under solution NMR conditions at room temperature. The latter result is the first demonstration of Overhauser DNP in the solution state at a field of 14.1 T (1H 600 MHz). Moreover these results have been produced with large sample volumes (∼100 μL, i.e. 3 mm diameter NMR tubes).

A quasi-optical and corrugated waveguide microwave transmission system for simultaneous dynamic nuclear polarization NMR on two separate 14.1 T spectrometers.

PubMed

Dubroca, Thierry; Smith, Adam N; Pike, Kevin J; Froud, Stuart; Wylde, Richard; Trociewitz, Bianca; McKay, Johannes; Mentink-Vigier, Frederic; van Tol, Johan; Wi, Sungsool; Brey, William; Long, Joanna R; Frydman, Lucio; Hill, Stephen

2018-04-01

Nuclear magnetic resonance (NMR) is an intrinsically insensitive technique, with Boltzmann distributions of nuclear spin states on the order of parts per million in conventional magnetic fields. To overcome this limitation, dynamic nuclear polarization (DNP) can be used to gain up to three orders of magnitude in signal enhancement, which can decrease experimental time by up to six orders of magnitude. In DNP experiments, nuclear spin polarization is enhanced by transferring the relatively larger electron polarization to NMR active nuclei via microwave irradiation. Here, we describe the design and performance of a quasi-optical system enabling the use of a single 395 GHz gyrotron microwave source to simultaneously perform DNP experiments on two different 14.1 T ( 1 H 600 MHz) NMR spectrometers: one configured for magic angle spinning (MAS) solid state NMR; the other configured for solution state NMR experiments. In particular, we describe how the high power microwave beam is split, transmitted, and manipulated between the two spectrometers. A 13 C enhancement of 128 is achieved via the cross effect for alanine, using the nitroxide biradical AMUPol, under MAS-DNP conditions at 110 K, while a 31 P enhancement of 160 is achieved via the Overhauser effect for triphenylphosphine using the monoradical BDPA under solution NMR conditions at room temperature. The latter result is the first demonstration of Overhauser DNP in the solution state at a field of 14.1 T ( 1 H 600 MHz). Moreover these results have been produced with large sample volumes (∼100 µL, i.e. 3 mm diameter NMR tubes). Copyright © 2018 Elsevier Inc. All rights reserved.

Sensitivity of the acid-base properties of clays to the methods of preparation and measurement. 2. Evidence from continuous potentiometric titrations.

PubMed

Duc, Myriam; Gaboriaud, Fabien; Thomas, Fabien

2005-09-01

The effects of experimental procedures on the acid-base consumption titration curves of montmorillonite suspension were studied using continuous potentiometric titration. For that purpose, the hysteresis amplitudes between the acid and base branches were found to be useful to systematically evaluate the impacts of storage conditions (wet or dried), the atmosphere in titration reactor, the solid-liquid ratio, the time interval between successive increments, and the ionic strength. In the case of storage conditions, the increase of the hysteresis was significantly higher for longer storage of clay in suspension and drying procedures compared to "fresh" clay suspension. The titration carried out under air demonstrated carbonate contamination that could only be cancelled by performing experiments under inert gas. Interestingly, the increase of the time intervals between successive increments of titrant strongly emphasized the amplitude of hysteresis, which could be correlated with the slow kinetic process specifically observed for acid addition in acid media. Thus, such kinetic behavior is probably associated with dissolution processes of clay particles. However, the resulting curves recorded at different ionic strengths under optimized conditions did not show the common intersection point required to define point of zero charge. Nevertheless, the ionic strength dependence of the point of zero net proton charge suggested that the point of zero charge of sodic montmorillonite could be estimated as lower than 5.

An Oil Spill in a Tube: An Accessible Approach for Teaching Environmental NMR Spectroscopy

ERIC Educational Resources Information Center

Simpson, Andre´ J.; Mitchell, Perry J.; Masoom, Hussain; Mobarhan, Yalda Liaghati; Adamo, Antonio; Dicks, Andrew P.

2015-01-01

NMR spectroscopy has great potential as an instrumental method for environmental chemistry research and monitoring but may be underused in teaching laboratories because of its complexity and the level of expertise required in operating the instrument and interpreting data. This laboratory experiment introduces environmental NMR spectroscopy to…

An NMR Experiment Based on Off-the-Shelf Digital Data-Acquisition Equipment

ERIC Educational Resources Information Center

Hilty, Christian; Bowen, Sean

2010-01-01

Nuclear magnetic resonance (NMR) poses significant challenges for teaching in the context of an undergraduate laboratory, foremost because of high equipment cost. Current off-the-shelf data-acquisition hardware, however, is sufficiently powerful to constitute the core of a fully digital NMR spectrometer operating at the earth's field. We present…

13C cell wall enrichment and ionic liquid NMR analysis: progress towards a high-throughput detailed chemical analysis of the whole plant cell wall.

PubMed

Foston, Marcus; Samuel, Reichel; Ragauskas, Arthur J

2012-09-07

The ability to accurately and rapidly measure plant cell wall composition, relative monolignol content and lignin-hemicellulose inter-unit linkage distributions has become essential to efforts centered on reducing the recalcitrance of biomass by genetic engineering. Growing (13)C enriched transgenic plants is a viable route to achieve the high-throughput, detailed chemical analysis of whole plant cell wall before and after pretreatment and microbial or enzymatic utilization by (13)C nuclear magnetic resonance (NMR) in a perdeuterated ionic liquid solvent system not requiring component isolation. 1D (13)C whole cell wall ionic liquid NMR of natural abundant and (13)C enriched corn stover stem samples suggest that a high level of uniform labeling (>97%) can significantly reduce the total NMR experiment times up to ~220 times. Similarly, significant reduction in total NMR experiment time (~39 times) of the (13)C enriched corn stover stem samples for 2D (13)C-(1)H heteronuclear single quantum coherence NMR was found.

Allosteric Effects of the Anti-Psychotic Drug Trifluoperazine on the Energetics of Calcium Binding by Calmodulin

PubMed Central

Feldkamp, Michael D.; O'Donnell, Susan E.; Yu, Liping; Shea, Madeline A.

2010-01-01

Trifluoperazine (TFP; Stelazine™) is an antagonist of calmodulin (CaM), an essential regulator of calcium-dependent signal transduction. Reports differ regarding whether, or where, TFP binds to apo CaM. Three crystallographic structures (1CTR, 1A29, 1LIN) show TFP bound to (Ca2+)4-CaM in ratios of 1, 2 or 4 TFP per CaM. In all of these, CaM domains adopt the “open” conformation seen in CaM-kinase complexes having increased calcium affinity. Most reports suggest TFP also increases calcium affinity of CaM. To compare TFP binding to apo CaM and (Ca2+)4-CaM, and explore differential effects on the N- and C-domains of CaM, stoichiometric TFP titrations of CaM were monitored by 15N-HSQC NMR. Two TFP bound to apo CaM, while four bound to (Ca2+)4-CaM. In both cases, the preferred site was in the C-domain. During the titrations, biphasic responses for some resonances suggested inter-site interactions. TFP-binding sites in apo CaM appeared distinct from those in (Ca2+)4-CaM. In equilibrium calcium titrations at defined ratios of TFP:CaM, TFP reduced calcium affinity at most levels tested; this is similar to the effect of many IQ-motifs on CaM. However, at the highest level tested, TFP raised the calcium affinity of the N-domain of CaM. A model of conformational switching is proposed to explain how TFP can exert opposing allosteric effects on calcium affinity by binding to different sites in the “closed”, “semi-open” and “open” domains of CaM. In physiological processes, apo CaM, as well as (Ca2+)4-CaM, needs to be considered a potential target of drug action. PMID:20544963

A ferromagnetic shim insert for NMR magnets - Towards an integrated gyrotron for DNP-NMR spectroscopy.

PubMed

Ryan, Herbert; van Bentum, Jan; Maly, Thorsten

2017-04-01

In recent years high-field Dynamic Nuclear Polarization (DNP) enhanced NMR spectroscopy has gained significant interest. In high-field DNP-NMR experiments (⩾400MHz 1 H NMR, ⩾9.4T) often a stand-alone gyrotron is used to generate high microwave/THz power to produce sufficiently high microwave induced B 1e fields at the position of the NMR sample. These devices typically require a second, stand-alone superconducting magnet to operate. Here we present the design and realization of a ferroshim insert, to create two iso-centers inside a commercially available wide-bore NMR magnet. This work is part of a larger project to integrate a gyrotron into NMR magnets, effectively eliminating the need for a second, stand-alone superconducting magnet. Copyright © 2017 Elsevier Inc. All rights reserved.

An NMR Study of Isotope Effect on Keto-Enol Tautomerization: A Physical Organic Chemistry Experiment

ERIC Educational Resources Information Center

Atkinson, D.; Chechik, V.

2004-01-01

Isotope substitution often affects the rate of an organic reaction and can be used to reveal the underlying mechanism. A series of experiments that use (super 1)H NMR to determine primary and secondary isotope effects, activation parameters, and the regioselectivity of butanone enolization are described.

NMR Determination of Hydrogen Bond Thermodynamics in a Simple Diamide: A Physical Chemistry Experiment

ERIC Educational Resources Information Center

Morton, Janine G.; Joe, Candice L.; Stolla, Massiel C.; Koshland, Sophia R.; Londergan, Casey H.; Schofield, Mark H.

2015-01-01

Variable temperature NMR spectroscopy is used to determine the ?H° and ?S° of hydrogen bond formation in a simple diamide. In this two- or three-day experiment, students synthesize N,N'-dimethylmalonamide, dimethylsuccinamide, dimethylglutaramide, or dimethyladipamide from methylamine and the corresponding diester (typically in 50% recrystallized…

The Complexation of the Na(super +) by 18-Crown-6 Studied via Nuclear Magnetic Resonance

ERIC Educational Resources Information Center

Peters, Steven J.; Stevenson, Cheryl D.

2004-01-01

A student friendly experiment that teaches several important concepts of modern nuclear magnetic resonance (NMR), like multinuclear capabilities, the NMR time scale, and time-averaged signals, is described along with some important concepts of thermo chemical equilibria. The mentioned experiment involves safe and inexpensive compounds, such as…

Using Nuclear Magnetic Resonance Spectroscopy for Measuring Ternary Phase Diagrams

ERIC Educational Resources Information Center

Woodworth, Jennifer K.; Terrance, Jacob C.; Hoffmann, Markus M.

2006-01-01

A laboratory experiment is presented for the upper-level undergraduate physical chemistry curriculum in which the ternary phase diagram of water, 1-propanol and n-heptane is measured using proton nuclear magnetic resonance (NMR) spectroscopy. The experiment builds upon basic concepts of NMR spectral analysis, typically taught in the undergraduate…

Recent progress in heteronuclear long-range NMR of complex carbohydrates: 3D H2BC and clean HMBC.

PubMed

Meier, Sebastian; Petersen, Bent O; Duus, Jens Ø; Sørensen, Ole W

2009-11-02

The new NMR experiments 3D H2BC and clean HMBC are explored for challenging applications to a complex carbohydrate at natural abundance of (13)C. The 3D H2BC experiment is crucial for sequential assignment as it yields heteronuclear one- and two-bond together with COSY correlations for the (1)H spins, all in a single spectrum with good resolution and non-informative diagonal-type peaks suppressed. Clean HMBC is a remedy for the ubiquitous problem of strong coupling induced one-bond correlation artifacts in HMBC spectra of carbohydrates. Both experiments work well for one of the largest carbohydrates whose structure has been determined by NMR, not least due to the enhanced resolution offered by the third dimension in 3D H2BC and the improved spectral quality due to artifact suppression in clean HMBC. Hence these new experiments set the scene to take advantage of the sensitivity boost achieved by the latest generation of cold probes for NMR structure determination of even larger and more complex carbohydrates in solution.

Solvent signal suppression for high-resolution MAS-DNP

NASA Astrophysics Data System (ADS)

Lee, Daniel; Chaudhari, Sachin R.; De Paëpe, Gaël

2017-05-01

Dynamic nuclear polarization (DNP) has become a powerful tool to substantially increase the sensitivity of high-field magic angle spinning (MAS) solid-state NMR experiments. The addition of dissolved hyperpolarizing agents usually results in the presence of solvent signals that can overlap and obscure those of interest from the analyte. Here, two methods are proposed to suppress DNP solvent signals: a Forced Echo Dephasing experiment (FEDex) and TRAnsfer of Populations in DOuble Resonance Echo Dephasing (TRAPDORED) NMR. These methods reintroduce a heteronuclear dipolar interaction that is specific to the solvent, thereby forcing a dephasing of recoupled solvent spins and leaving acquired NMR spectra free of associated resonance overlap with the analyte. The potency of these methods is demonstrated on sample types common to MAS-DNP experiments, namely a frozen solution (of L-proline) and a powdered solid (progesterone), both containing deuterated glycerol as a DNP solvent. The proposed methods are efficient, simple to implement, compatible with other NMR experiments, and extendable past spectral editing for just DNP solvents. The sensitivity gains from MAS-DNP in conjunction with FEDex or TRAPDORED then permits rapid and uninterrupted sample analysis.

A study of pH-dependent photodegradation of amiloride by a multivariate curve resolution approach to combined kinetic and acid-base titration UV data.

PubMed

De Luca, Michele; Ioele, Giuseppina; Mas, Sílvia; Tauler, Romà; Ragno, Gaetano

2012-11-21

Amiloride photostability at different pH values was studied in depth by applying Multivariate Curve Resolution Alternating Least Squares (MCR-ALS) to the UV spectrophotometric data from drug solutions exposed to stressing irradiation. Resolution of all degradation photoproducts was possible by simultaneous spectrophotometric analysis of kinetic photodegradation and acid-base titration experiments. Amiloride photodegradation showed to be strongly dependent on pH. Two hard modelling constraints were sequentially used in MCR-ALS for the unambiguous resolution of all the species involved in the photodegradation process. An amiloride acid-base system was defined by using the equilibrium constraint, and the photodegradation pathway was modelled taking into account the kinetic constraint. The simultaneous analysis of photodegradation and titration experiments revealed the presence of eight different species, which were differently distributed according to pH and time. Concentration profiles of all the species as well as their pure spectra were resolved and kinetic rate constants were estimated. The values of rate constants changed with pH and under alkaline conditions the degradation pathway and photoproducts also changed. These results were compared to those obtained by LC-MS analysis from drug photodegradation experiments. MS analysis allowed the identification of up to five species and showed the simultaneous presence of more than one acid-base equilibrium.

Optimized slice-selective 1H NMR experiments combined with highly accurate quantitative 13C NMR using an internal reference method.

PubMed

Jézéquel, Tangi; Silvestre, Virginie; Dinis, Katy; Giraudeau, Patrick; Akoka, Serge

2018-04-01

Isotope ratio monitoring by 13 C NMR spectrometry (irm- 13 C NMR) provides the complete 13 C intramolecular position-specific composition at natural abundance. It represents a powerful tool to track the (bio)chemical pathway which has led to the synthesis of targeted molecules, since it allows Position-specific Isotope Analysis (PSIA). Due to the very small composition range (which represents the range of variation of the isotopic composition of a given nuclei) of 13 C natural abundance values (50‰), irm- 13 C NMR requires a 1‰ accuracy and thus highly quantitative analysis by 13 C NMR. Until now, the conventional strategy to determine the position-specific abundance x i relies on the combination of irm-MS (isotopic ratio monitoring Mass Spectrometry) and 13 C quantitative NMR. However this approach presents a serious drawback since it relies on two different techniques and requires to measure separately the signal of all the carbons of the analyzed compound, which is not always possible. To circumvent this constraint, we recently proposed a new methodology to perform 13 C isotopic analysis using an internal reference method and relying on NMR only. The method combines a highly quantitative 1 H NMR pulse sequence (named DWET) with a 13 C isotopic NMR measurement. However, the recently published DWET sequence is unsuited for samples with short T 1 , which forms a serious limitation for irm- 13 C NMR experiments where a relaxing agent is added. In this context, we suggest two variants of the DWET called Multi-WET and Profiled-WET, developed and optimized to reach the same accuracy of 1‰ with a better immunity towards T 1 variations. Their performance is evaluated on the determination of the 13 C isotopic profile of vanillin. Both pulse sequences show a 1‰ accuracy with an increased robustness to pulse miscalibrations compared to the initial DWET method. This constitutes a major advance in the context of irm- 13 C NMR since it is now possible to perform isotopic analysis with high relaxing agent concentrations, leading to a strong reduction of the overall experiment time. Copyright © 2018 Elsevier Inc. All rights reserved.

Assessment of two theoretical methods to estimate potentiometric titration curves of peptides: comparison with experiment.

PubMed

Makowska, Joanna; Bagiñska, Katarzyna; Makowski, Mariusz; Jagielska, Anna; Liwo, Adam; Kasprzykowski, Franciszek; Chmurzyñski, Lech; Scheraga, Harold A

2006-03-09

We compared the ability of two theoretical methods of pH-dependent conformational calculations to reproduce experimental potentiometric titration curves of two models of peptides: Ac-K5-NHMe in 95% methanol (MeOH)/5% water mixture and Ac-XX(A)7OO-NH2 (XAO) (where X is diaminobutyric acid, A is alanine, and O is ornithine) in water, methanol (MeOH), and dimethyl sulfoxide (DMSO), respectively. The titration curve of the former was taken from the literature, and the curve of the latter was determined in this work. The first theoretical method involves a conformational search using the electrostatically driven Monte Carlo (EDMC) method with a low-cost energy function (ECEPP/3 plus the SRFOPT surface-solvation model, assumming that all titratable groups are uncharged) and subsequent reevaluation of the free energy at a given pH with the Poisson-Boltzmann equation, considering variable protonation states. In the second procedure, molecular dynamics (MD) simulations are run with the AMBER force field and the generalized Born model of electrostatic solvation, and the protonation states are sampled during constant-pH MD runs. In all three solvents, the first pKa of XAO is strongly downshifted compared to the value for the reference compounds (ethylamine and propylamine, respectively); the water and methanol curves have one, and the DMSO curve has two jumps characteristic of remarkable differences in the dissociation constants of acidic groups. The predicted titration curves of Ac-K5-NHMe are in good agreement with the experimental ones; better agreement is achieved with the MD-based method. The titration curves of XAO in methanol and DMSO, calculated using the MD-based approach, trace the shape of the experimental curves, reproducing the pH jump, while those calculated with the EDMC-based approach and the titration curve in water calculated using the MD-based approach have smooth shapes characteristic of the titration of weak multifunctional acids with small differences between the dissociation constants. Nevertheless, quantitative agreement between theoretically predicted and experimental titration curves is not achieved in all three solvents even with the MD-based approach, which is manifested by a smaller pH range of the calculated titration curves with respect to the experimental curves. The poorer agreement obtained for water than for the nonaqueous solvents suggests a significant role of specific solvation in water, which cannot be accounted for by the mean-field solvation models.

The fluorescent property of 3-[(2-hydroxy-1-naphthyl) methylideneamino]benzoic acid and its application as fluorescent chemosensor for Hg2 + and Al3 + ions

NASA Astrophysics Data System (ADS)

Sun, Changyan; Sun, Jiayi; Qiu, Fazheng; Li, Wenjun; Chang, Zhidong; Zhang, Lijun

2018-01-01

This manuscript studies the fluorescent property of 3-[(2-hydroxy-1-naphthyl)methylideneamino]benzoic acid (H2L). Fluorescent spectra show that in different solvents, H2L displays different fluorescent properties, which can be attributed to the interaction between the solvents and H2L. Further study indicates that H2L exhibits a highly selective and sensitive recognition for Hg2 + ions in dimethylsulfoxide (DMSO), Al3 + ions in methanol and N,N‧-dimethylformamide/water (DMF/H2O, 1/1, v/v). The bonding modes and bonding ratio of H2L and metal ions in different solvents are explored by Job's plot, 1H NMR titration, and electrospray ionization mass spectrometry (ESI-MS). The probable mechanisms were discussed.

Interactive Design Strategy for a Multi-Functional PAMAM Dendrimer-Based Nano-Therapeutic Using Computational Models and Experimental Analysis

PubMed Central

Lee, Inhan; Williams, Christopher R.; Athey, Brian D.; Baker, James R.

2010-01-01

Molecular dynamics simulations of nano-therapeutics as a final product and of all intermediates in the process of generating a multi-functional nano-therapeutic based on a poly(amidoamine) (PAMAM) dendrimer were performed along with chemical analyses of each of them. The actual structures of the dendrimers were predicted, based on potentiometric titration, gel permeation chromatography, and NMR. The chemical analyses determined the numbers of functional molecules, based on the actual structure of the dendrimer. Molecular dynamics simulations calculated the configurations of the intermediates and the radial distributions of functional molecules, based on their numbers. This interactive process between the simulation results and the chemical analyses provided a further strategy to design the next reaction steps and to gain insight into the products at each chemical reaction step. PMID:20700476

Tuning Riboswitch Regulation through Conformational Selection

PubMed Central

Wilson, Ross C.; Smith, Angela M.; Fuchs, Ryan T.; Kleckner, Ian R.; Henkin, Tina M.; Foster, Mark P.

2010-01-01

SUMMARY The SMK box riboswitch, which represents one of three known classes of S-adenosylmethionine (SAM)-responsive riboswitches, regulates gene expression in bacteria at the level of translation initiation. In contrast to most riboswitches, which contain separate domains responsible for ligand recognition and gene regulation, the ligand-binding and regulatory domains of the SMK box riboswitch are coincident. This property was exploited to allow the first atomic-level characterization of a functionally intact riboswitch in both the ligand-bound and ligand-free states. NMR spectroscopy revealed distinct mutually exclusive RNA conformations that are differentially populated in the presence or absence of the effector metabolite. Isothermal titration calorimetry and in vivo reporter assay results revealed the thermodynamic and functional consequences of this conformational equilibrium. We present a comprehensive model of the structural, thermodynamic, and functional properties of this compact RNA regulatory element. PMID:21075119

Controlled synthesis and inclusion ability of a hyaluronic acid derivative bearing beta-cyclodextrin molecules.

PubMed

Charlot, Aurélia; Heyraud, Alain; Guenot, Pierre; Rinaudo, Marguerite; Auzély-Velty, Rachel

2006-03-01

A new synthetic route to beta-cyclodextrin-linked hyaluronic acid (HA-CD) was developed. This was based on the preparation of a HA derivative selectively modified with adipic dihydrazide (HA-ADH) and a beta-cyclodextrin derivative possessing an aldehyde function on the primary face, followed by their coupling by a reductive amination-type reaction. The CD-polysaccharide was fully characterized in terms of chemical integrity and purity by high-resolution NMR spectroscopy. The complexation ability of the grafted CD was further demonstrated by isothermal titration calorimetry using sodium adamantane acetate (ADAc) and Ibuprofen as model guest molecules. The thermodynamic parameters for the complexation of these negatively charged guest molecules by the beta-CD grafted on negatively charged HA were shown to be largely influenced by the ionic strength of the aqueous medium.

Preparation and spectroscopic studies on charge-transfer complexes of 2,2'-bipyridine with picric and chloranilic acids

NASA Astrophysics Data System (ADS)

Teleb, Said M.; Gaballa, Akmal S.

2005-11-01

Charge-transfer (CT) complexes formed on the reaction of 2,2'-bipyridine with some acceptors such as picric acid (HPA) and chloranilic acid (H 2CA) have been studied in CHCl 3 and MeOH at room temperature. Based on elemental analysis and IR spectra of the solid CT complexes along with the photometric titration curves for the reactions, the data obtained indicate the formation of 1:1 charge-transfer complexes [(bpyH)(PA)] and [(bpyH 2)(CA)], respectively. The infrared and 1H NMR spectroscopic data indicate a charge-transfer interaction associated with a proton migration from the acceptor to the donor followed by intramolecular hydrogen bonding. The formation constants ( KC) for the complexes were shown to be dependent on the structure of the electron acceptors used.

Preparation and spectroscopic studies on charge-transfer complexes of 2,2'-bipyridine with picric and chloranilic acids.

PubMed

Teleb, Said M; Gaballa, Akmal S

2005-11-01

Charge-transfer (CT) complexes formed on the reaction of 2,2'-bipyridine with some acceptors such as picric acid (HPA) and chloranilic acid (H(2)CA) have been studied in CHCl(3) and MeOH at room temperature. Based on elemental analysis and IR spectra of the solid CT complexes along with the photometric titration curves for the reactions, the data obtained indicate the formation of 1:1 charge-transfer complexes [(bpyH)(PA)] and [(bpyH(2))(CA)], respectively. The infrared and (1)H NMR spectroscopic data indicate a charge-transfer interaction associated with a proton migration from the acceptor to the donor followed by intramolecular hydrogen bonding. The formation constants (K(C)) for the complexes were shown to be dependent on the structure of the electron acceptors used.

Determination of Solvent Effects on Keto-Enol Equilibria of 1,3-Dicarbonyl Compounds Using NMR: Revisiting a Classic Physical Chemistry Experiment

ERIC Educational Resources Information Center

Cook, A. Gilbert; Feltman, Paul M.

2007-01-01

The use of proton NMR to determine the equilibrium position of tautomeric 1,3-dicarbonyl compounds in various solvents has been a classic physical chemistry experiment. We are presenting an expansion of the excellent description of this experiment by Garland, Shoemaker, and Nibler. Often the assumption is made that the keto tautomer is always the…

A novel method for the investigation of liquid/liquid distribution coefficients and interface permeabilities applied to the water-octanol-drug system.

PubMed

Stein, Paul C; di Cagno, Massimiliano; Bauer-Brandl, Annette

2011-09-01

In this work a new, accurate and convenient technique for the measurement of distribution coefficients and membrane permeabilities based on nuclear magnetic resonance (NMR) is described. This method is a novel implementation of localized NMR spectroscopy and enables the simultaneous analysis of the drug content in the octanol and in the water phase without separation. For validation of the method, the distribution coefficients at pH = 7.4 of four active pharmaceutical ingredients (APIs), namely ibuprofen, ketoprofen, nadolol, and paracetamol (acetaminophen), were determined using a classical approach. These results were compared to the NMR experiments which are described in this work. For all substances, the respective distribution coefficients found with the two techniques coincided very well. Furthermore, the NMR experiments make it possible to follow the distribution of the drug between the phases as a function of position and time. Our results show that the technique, which is available on any modern NMR spectrometer, is well suited to the measurement of distribution coefficients. The experiments present also new insight into the dynamics of the water-octanol interface itself and permit measurement of the interface permeability.

Observation of NMR noise from solid samples.

PubMed

Schlagnitweit, Judith; Dumez, Jean-Nicolas; Nausner, Martin; Jerschow, Alexej; Elena-Herrmann, Bénédicte; Müller, Norbert

2010-11-01

We demonstrate that proton NMR noise signals, i.e. NMR spectra without excitation by radio frequency, can be obtained from solid samples. Experimental results are shown for static and magic-angle spinning conditions. In addition, a tuning procedure based on the probes' NMR noise characteristics and similar to the one described previously for liquids probes can also be used to optimize signal-to-noise ratios in ¹H-MAS experiments. Copyright © 2010 Elsevier Inc. All rights reserved.

Thermodynamics of Coupled Folding in the Interaction of Archaeal RNase P Proteins RPP21 and RPP29

PubMed Central

Xu, Yiren; Oruganti, Sri Vidya; Gopalan, Venkat; Foster, Mark P.

2014-01-01

We have used isothermal titration calorimetry (ITC) to identify and describe binding-coupled equilibria in the interaction between two protein subunits of archaeal ribonuclease P (RNase P). In all three domains of life, RNase P is a ribonucleoprotein complex that is primarily responsible for catalyzing the Mg2+-dependent cleavage of the 5′ leader sequence of precursor tRNAs during tRNA maturation. In archaea, RNase P has been shown to be composed of one catalytic RNA and up to five proteins, four of which associate in the absence of RNA as two functional heterodimers, POP5-RPP30 and RPP21-RPP29. NMR studies of the Pyrococcus furiosus RPP21 and RPP29 proteins in their free and complexed states provided evidence for significant protein folding upon binding. ITC experiments were performed over a range of temperatures, ionic strengths, pH values and in buffers with varying ionization potential, and with a folding-deficient RPP21 point mutant. These experiments revealed a negative heat capacity change (ΔCp), nearly twice that predicted from surface accessibility calculations, a strong salt dependence to the interaction and proton release at neutral pH, but a small net contribution from these to the excess ΔCp. We considered potential contributions from protein folding and burial of interfacial water molecules based on structural and spectroscopic data. We conclude that binding-coupled protein folding is likely responsible for a significant portion of the excess ΔCp. These findings provide novel structural-thermodynamic insights into coupled equilibria that enable specificity in macromolecular assemblies. PMID:22243443

Mechanistic insight into formation and changes of nanoparticles in MgF2 sols evidenced by liquid and solid state NMR.

PubMed

Karg, M; Scholz, G; König, R; Kemnitz, E

2012-02-28

The fluorolytic sol-gel reaction of magnesium methoxide with HF in methanol was studied by (19)F, (1)H and (13)C liquid and solid state NMR. In (19)F NMR five different species were identified, three of which belong to magnesium fluoride nanoparticles, i.e. NMR gave access to local structures of solid particles in suspensions. The long-term evolution of (19)F signals was followed and along with (19)F MAS NMR experiments of sols rotating at 13 kHz mechanistic insights into the ageing processes were obtained.

Surface Characteristics and Adhesion Behavior of Escherichia coli O157:H7: Role of Extracellular Macromolecules

USDA-ARS?s Scientific Manuscript database

Surface macromolecule cleavage experiments were conducted on enterohaemorrhagic Escherichia coli O157:H7 cells to investigate the influence of these macromolecules on cell surface properties. Electrophoretic mobility, hydrophobicity, and titration experiments were carried out on proteinase K treate...

Redox Titration of Ferricyanide to Ferrocyanide with Ascorbic Acid: Illustrating the Nernst Equation and Beer-Lambert Law

ERIC Educational Resources Information Center

Huang, Tina H.; Salter, Gail; Kahn, Sarah L.; Gindt, Yvonne M.

2007-01-01

We have developed a simple, resilient experiment that illustrates the Nernst equation and Beer-Lambert law for our second-semester general chemistry students. In the experiment, the students monitor the reduction of ferricyanide ion, [Fe(CN)[subscript 6

Derivatizing weak polyelectrolytes--solution properties, self-aggregation, and association with anionic surfaces of hydrophobically modified poly(ethylene imine).

PubMed

Griffiths, Peter C; Paul, Alison; Fallis, Ian A; Wellappili, Champa; Murphy, Damien M; Jenkins, Robert; Waters, Sarah J; Nilmini, Renuka; Heenan, Richard K; King, Stephen M

2007-10-15

The physical properties of weak polyelectrolytes may be tailored via hydrophobic modification to exhibit useful properties under appropriate pH and ionic strength conditions as a consequence of the often inherently competing effects of electrostatics and hydrophobicity. Pulsed-gradient spin-echo NMR (PGSE-NMR), electron paramagnetic resonance (EPR), small-angle neutron scattering (SANS) surface tension, fluorescence, and pH titration have been used to examine the solution conformation and aggregation behavior of a series of hydrophobically modified hyperbranched poly(ethylene imine) (PEI) polymers in aqueous solution, and their interaction with sodium dodecylsulfate (SDS). PGSE-NMR gave a particularly insightful picture of the apparent molecular weight distribution. The presence of the hydrophobes led to a lower effective charge on the polymer at any given pH, compared to the (parent) nonmodified samples. Analysis of the SANS data showed that the propensity to form highly elliptical or rod-like aggregates at higher pHs, reflecting both the changes in protonation behavior induced by the hydrophobic modification and an hydrophobic interaction, but that these structures were disrupted with decreasing pH (increasing charge). The parent samples were not surface active yet the hydrophobically modified samples show pronounced surface activity and the presence of small hydrophobic domains. The surface activity increased with an increase in the degree of modification. On addition of SDS, the onset of the formation of polymer/surfactant complexes was insensitive to the degree of modification with the resultant PEI/SDS complexes resembling the size and shape of simple SDS micelles. Indeed, the presence of the SDS effectively nullifies the effects of the hydrophobe. Hydrophobic modification is therefore a viable option to tailor pH dependent properties, whose effects may be removed by the presence of surfactant.

Identification and structural mechanism for a novel interaction between a ubiquitin ligase WWP1 and Nogo-A, a key inhibitor for central nervous system regeneration.

PubMed

Qin, Haina; Pu, Helen X; Li, Minfen; Ahmed, Sohail; Song, Jianxing

2008-12-23

Nogo-A has been extensively demonstrated to play key roles in inhibiting central nervous system regeneration, regulating endoplasmic reticulum formation, and maintaining the integrity of the neuromuscular junction. In this study, an E3 ubiquitin ligase WWP1 was first identified to be a novel interacting partner for Nogo-A both in vitro and in vivo. By using CD, ITC, and NMR, we have further conducted extensive studies on all four WWP1 WW domains and their interactions with a Nogo-A peptide carrying the only PPxY motif. The results lead to several striking findings. (1) Despite containing an unstructured region, the 186-residue WWP1 fragment containing all four WW domains is able to interact with the Nogo-A(650-666) peptide with a high affinity, with a dissociation constant (K(d)) of 1.68 microM. (2) Interestingly, four isolated WW domains show differential structural properties in the free states. WW1 and WW2 are only partially folded, while WW4 is well-folded. Nevertheless, they all become well-folded upon binding to Nogo-A(650-666), with K(d) values ranging from 1.03 to 3.85 microM. (3) The solution structure of the best-folded WW4 domain is determined, and the binding-perturbed residues were derived for both WW4 and Nogo-A(650-666) by NMR HSQC titrations. Moreover, on the basis of the NMR data, the complex model is constructed by HADDOCK 2.0. This study provides rationales as well as a template Nogo-A(650-666) for further design of molecules to intervene in the WWP1-Nogo-A interaction which may regulate the Nogo-A protein level by controlling its ubiquitination.

Multivalent binding of formin-binding protein 21 (FBP21)-tandem-WW domains fosters protein recognition in the pre-spliceosome.

PubMed

Klippel, Stefan; Wieczorek, Marek; Schümann, Michael; Krause, Eberhard; Marg, Berenice; Seidel, Thorsten; Meyer, Tim; Knapp, Ernst-Walter; Freund, Christian

2011-11-04

The high abundance of repetitive but nonidentical proline-rich sequences in spliceosomal proteins raises the question of how these known interaction motifs recruit their interacting protein domains. Whereas complex formation of these adaptors with individual motifs has been studied in great detail, little is known about the binding mode of domains arranged in tandem repeats and long proline-rich sequences including multiple motifs. Here we studied the interaction of the two adjacent WW domains of spliceosomal protein FBP21 with several ligands of different lengths and composition to elucidate the hallmarks of multivalent binding for this class of recognition domains. First, we show that many of the proteins that define the cellular proteome interacting with FBP21-WW1-WW2 contain multiple proline-rich motifs. Among these is the newly identified binding partner SF3B4. Fluorescence resonance energy transfer (FRET) analysis reveals the tandem-WW domains of FBP21 to interact with splicing factor 3B4 (SF3B4) in nuclear speckles where splicing takes place. Isothermal titration calorimetry and NMR shows that the tandem arrangement of WW domains and the multivalency of the proline-rich ligands both contribute to affinity enhancement. However, ligand exchange remains fast compared with the NMR time scale. Surprisingly, a N-terminal spin label attached to a bivalent ligand induces NMR line broadening of signals corresponding to both WW domains of the FBP21-WW1-WW2 protein. This suggests that distinct orientations of the ligand contribute to a delocalized and semispecific binding mode that should facilitate search processes within the spliceosome.

Multivalent Binding of Formin-binding Protein 21 (FBP21)-Tandem-WW Domains Fosters Protein Recognition in the Pre-spliceosome*

PubMed Central

Klippel, Stefan; Wieczorek, Marek; Schümann, Michael; Krause, Eberhard; Marg, Berenice; Seidel, Thorsten; Meyer, Tim; Knapp, Ernst-Walter; Freund, Christian

2011-01-01

The high abundance of repetitive but nonidentical proline-rich sequences in spliceosomal proteins raises the question of how these known interaction motifs recruit their interacting protein domains. Whereas complex formation of these adaptors with individual motifs has been studied in great detail, little is known about the binding mode of domains arranged in tandem repeats and long proline-rich sequences including multiple motifs. Here we studied the interaction of the two adjacent WW domains of spliceosomal protein FBP21 with several ligands of different lengths and composition to elucidate the hallmarks of multivalent binding for this class of recognition domains. First, we show that many of the proteins that define the cellular proteome interacting with FBP21-WW1-WW2 contain multiple proline-rich motifs. Among these is the newly identified binding partner SF3B4. Fluorescence resonance energy transfer (FRET) analysis reveals the tandem-WW domains of FBP21 to interact with splicing factor 3B4 (SF3B4) in nuclear speckles where splicing takes place. Isothermal titration calorimetry and NMR shows that the tandem arrangement of WW domains and the multivalency of the proline-rich ligands both contribute to affinity enhancement. However, ligand exchange remains fast compared with the NMR time scale. Surprisingly, a N-terminal spin label attached to a bivalent ligand induces NMR line broadening of signals corresponding to both WW domains of the FBP21-WW1-WW2 protein. This suggests that distinct orientations of the ligand contribute to a delocalized and semispecific binding mode that should facilitate search processes within the spliceosome. PMID:21917930

Synthesis, Physicochemical Properties, and Hydrogen Bonding of 4(5)-Substituted 1-H-Imidazole-2-carboxamide, A Potential Universal Reader for DNA Sequencing by Recognition Tunneling

PubMed Central

Liang, Feng; Li, Shengqing

2012-01-01

We have developed a chemical reagent that recognizes all naturally occurring DNA bases, a so called universal reader, for DNA sequencing by recognition tunnelling in nanopores.[1] The primary requirements for this type of molecules are the ability to form non-covalent complexes with individual DNA bases and to generate recognizable electronic signatures under an electrical bias. 1-H-imidazole-2-carboxamide was designed as such a recognition moiety to interact with the DNA bases through hydrogen bonding. In the present study, we first furnished a synthetic route to 1-H-imidazole-2-carboxamide containing a short ω-functionalized alkyl chain at its 4(5) position for its attachment to metal and carbon electrodes. The acid dissociation constants of the imidazole-2-carboxamide were then determined by UV spectroscopy. The data show that the 1-H-imidazole-2-carboxamide exists in a neutral form between pH 6–10. Density functional theory (DFT) and NMR studies indicate that the imidazole ring exists in prototropic tautomers. We propose an intramolecular mechanism for tautomerization of 1-H-imidazole-2-carboxamide. In addition, the imidazole-2-carboxamide can self-associate to form hydrogen bonded dimers. NMR titration found that naturally occurring nucleosides interacted with 1-H-imidazole-2-carboxamide through hydrogen bonding in a tendency of dG>dC≫dT> dA. These studies are indispensable to assisting us in understanding the molecular recognition that takes place in the nanopore where routinely used analytical tools such as NMR and FTIR cannot be conveniently applied. PMID:22461259

Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein–DNA Complex

PubMed Central

2016-01-01

Metal ion cofactors can alter the energetics and specificity of sequence specific protein–DNA interactions, but it is unknown if the underlying effects on structure and dynamics are local or dispersed throughout the protein–DNA complex. This work uses EcoRV endonuclease as a model, and catalytically inactive lanthanide ions, which replace the Mg2+ cofactor. Nuclear magnetic resonance (NMR) titrations indicate that four Lu3+ or two La3+ cations bind, and two new crystal structures confirm that Lu3+ binding is confined to the active sites. NMR spectra show that the metal-free EcoRV complex with cognate (GATATC) DNA is structurally distinct from the nonspecific complex, and that metal ion binding sites are not assembled in the nonspecific complex. NMR chemical shift perturbations were determined for 1H–15N amide resonances, for 1H–13C Ile-δ-CH3 resonances, and for stereospecifically assigned Leu-δ-CH3 and Val-γ-CH3 resonances. Many chemical shifts throughout the cognate complex are unperturbed, so metal binding does not induce major conformational changes. However, some large perturbations of amide and side chain methyl resonances occur as far as 34 Å from the metal ions. Concerted changes in specific residues imply that local effects of metal binding are propagated via a β-sheet and an α-helix. Both amide and methyl resonance perturbations indicate changes in the interface between subunits of the EcoRV homodimer. Bound metal ions also affect amide hydrogen exchange rates for distant residues, including a distant subdomain that contacts DNA phosphates and promotes DNA bending, showing that metal ions in the active sites, which relieve electrostatic repulsion between protein and DNA, cause changes in slow dynamics throughout the complex. PMID:27786446

Identification and MS-assisted interpretation of genetically influenced NMR signals in human plasma

PubMed Central

2013-01-01

Nuclear magnetic resonance spectroscopy (NMR) provides robust readouts of many metabolic parameters in one experiment. However, identification of clinically relevant markers in 1H NMR spectra is a major challenge. Association of NMR-derived quantities with genetic variants can uncover biologically relevant metabolic traits. Using NMR data of plasma samples from 1,757 individuals from the KORA study together with 655,658 genetic variants, we show that ratios between NMR intensities at two chemical shift positions can provide informative and robust biomarkers. We report seven loci of genetic association with NMR-derived traits (APOA1, CETP, CPS1, GCKR, FADS1, LIPC, PYROXD2) and characterize these traits biochemically using mass spectrometry. These ratios may now be used in clinical studies. PMID:23414815

Characterizing slow chemical exchange in nucleic acids by carbon CEST and low spin-lock field R(1ρ) NMR spectroscopy.

PubMed

Zhao, Bo; Hansen, Alexandar L; Zhang, Qi

2014-01-08

Quantitative characterization of dynamic exchange between various conformational states provides essential insights into the molecular basis of many regulatory RNA functions. Here, we present an application of nucleic-acid-optimized carbon chemical exchange saturation transfer (CEST) and low spin-lock field R(1ρ) relaxation dispersion (RD) NMR experiments in characterizing slow chemical exchange in nucleic acids that is otherwise difficult if not impossible to be quantified by the ZZ-exchange NMR experiment. We demonstrated the application on a 47-nucleotide fluoride riboswitch in the ligand-free state, for which CEST and R(1ρ) RD profiles of base and sugar carbons revealed slow exchange dynamics involving a sparsely populated (p ~ 10%) and shortly lived (τ ~ 10 ms) NMR "invisible" state. The utility of CEST and low spin-lock field R(1ρ) RD experiments in studying slow exchange was further validated in characterizing an exchange as slow as ~60 s(-1).

Characterizing Slow Chemical Exchange in Nucleic Acids by Carbon CEST and Low Spin-Lock Field R1ρ NMR Spectroscopy

PubMed Central

Zhao, Bo; Hansen, Alexandar L.; Zhang, Qi

2016-01-01

Quantitative characterization of dynamic exchange between various conformational states provides essential insights into the molecular basis of many regulatory RNA functions. Here, we present an application of nucleic-acid-optimized carbon chemical exchange saturation transfer (CEST) and low spin-lock field R1ρ relaxation dispersion (RD) NMR experiments in characterizing slow chemical exchange in nucleic acids that is otherwise difficult if not impossible to be quantified by the ZZ-exchange NMR experiment. We demonstrated the application on a 47-nucleotide fluoride riboswitch in the ligand-free state, for which CEST and R1ρ RD profiles of base and sugar carbons revealed slow exchange dynamics involving a sparsely populated (p ~ 10%) and shortly lived (τ ~ 10 ms) NMR “invisible” state. The utility of CEST and low spin-lock field R1ρ RD experiments in studying slow exchange was further validated in characterizing an exchange as slow as ~60 s−1. PMID:24299272

Orphan spin operators enable the acquisition of multiple 2D and 3D magic angle spinning solid-state NMR spectra

NASA Astrophysics Data System (ADS)

Gopinath, T.; Veglia, Gianluigi

2013-05-01

We propose a general method that enables the acquisition of multiple 2D and 3D solid-state NMR spectra for U-13C, 15N-labeled proteins. This method, called MEIOSIS (Multiple ExperIments via Orphan SpIn operatorS), makes it possible to detect four coherence transfer pathways simultaneously, utilizing orphan (i.e., neglected) spin operators of nuclear spin polarization generated during 15N-13C cross polarization (CP). In the MEIOSIS experiments, two phase-encoded free-induction decays are decoded into independent nuclear polarization pathways using Hadamard transformations. As a proof of principle, we show the acquisition of multiple 2D and 3D spectra of U-13C, 15N-labeled microcrystalline ubiquitin. Hadamard decoding of CP coherences into multiple independent spin operators is a new concept in solid-state NMR and is extendable to many other multidimensional experiments. The MEIOSIS method will increase the throughput of solid-state NMR techniques for microcrystalline proteins, membrane proteins, and protein fibrils.

Changes in NMR relaxation times of adjacent muscle after implantation of malignant and normal tissue.

PubMed Central

Ling, C. R.; Foster, M. A.; Mallard, J. R.

1979-01-01

In separate experiments, normal foreign tissue and malignant tumour were implanted s.c. into the rat thigh. NMR T1 values of the adjacent normal muscle, resulting from local inflammatory reactions or from malignant invasion, were measured. Elevations in T1 of the underlying muscle occurred within 24 h in both experiments, and it is believed these were caused by rapid inflammatory and immunological reactions to the implants. However the T1 values of muscle samples adjacent to the non-malignant implants decreased during the 11 days after implantation, dropping to values within the normal range. In the second experiment there was progressive malignant invasion into the normal adjacent tissue and the elevated T1 values were maintained throughout the 12-day period. The effects of the implantation on tissue water content are discussed in relation to NMR T1 relaxation times, and the relevance to whole-body NMR imaging of elevated T1 values due to nonmalignant pathological states is considered. PMID:526431

Dynamic Nuclear Polarization-Enhanced Biomolecular NMR Spectroscopy at High Magnetic Field with Fast Magic-Angle Spinning.

PubMed

Jaudzems, Kristaps; Bertarello, Andrea; Chaudhari, Sachin R; Pica, Andrea; Cala-De Paepe, Diane; Barbet-Massin, Emeline; Pell, Andrew J; Akopjana, Inara; Kotelovica, Svetlana; Gajan, David; Ouari, Olivier; Tars, Kaspars; Pintacuda, Guido; Lesage, Anne

2018-06-18

Dynamic nuclear polarization (DNP) is a powerful way to overcome the sensitivity limitation of magic-angle-spinning (MAS) NMR experiments. However, the resolution of the DNP NMR spectra of proteins is compromised by severe line broadening associated with the necessity to perform experiments at cryogenic temperatures and in the presence of paramagnetic radicals. High-quality DNP-enhanced NMR spectra of the Acinetobacter phage 205 (AP205) nucleocapsid can be obtained by combining high magnetic field (800 MHz) and fast MAS (40 kHz). These conditions yield enhanced resolution and long coherence lifetimes allowing the acquisition of resolved 2D correlation spectra and of previously unfeasible scalar-based experiments. This enables the assignment of aromatic resonances of the AP205 coat protein and its packaged RNA, as well as the detection of long-range contacts, which are not observed at room temperature, opening new possibilities for structure determination. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

qHNMR Analysis of Purity of Common Organic Solvents--An Undergraduate Quantitative Analysis Laboratory Experiment

ERIC Educational Resources Information Center

Bell, Peter T.; Whaley, W. Lance; Tochterman, Alyssa D.; Mueller, Karl S.; Schultz, Linda D.

2017-01-01

NMR spectroscopy is currently a premier technique for structural elucidation of organic molecules. Quantitative NMR (qNMR) methodology has developed more slowly but is now widely accepted, especially in the areas of natural product and medicinal chemistry. However, many undergraduate students are not routinely exposed to this important concept.…

Consensus on Insulin Dose and Titration Algorithms in Ambulatory Care of Type 2 Diabetes in India.

PubMed

Kovil, Rajiv; Chawla, Manoj; Rajput, Rajesh; Singh, A K; Sinha, Binayak; Ghosal, Samit; Ballani, Piya; Gupta, Sunil; Tanna, Snehal; Bandukwala, S M; Shah, Tejas; Negalur, Vijay; Bhoraskar, Anil; Aravind, S R; Zargar, Abdul H; Kesavadev, Jothydev; Das, Ashok Kumar

2017-02-01

Insulin is the oldest of the currently available treatment options in Type 2 diabetes mellitus (T2DM) and is considered as the most effective glucose lowering agent. Despite this, decision on starting insulin therapy is often delayed in India as well as worldwide due to various barriers at both patient and physician levels. Appropriate insulin dosing and titration is also critical to the successful achievement of tight glycaemic control. To provide simple and easily implementable guidelines to primary care physicians on appropriate insulin dosing and titration of various insulin regimens for both initiation and intensification. Each insulin regimen (once daily [OD] basal, OD, twice daily and thrice daily premixed, basal-plus and basal-bolus) was presented and evaluated for dosing and titration based on established guidelines, data from approved pack inserts, and published scientific literature. These evaluations were then factored into the national context based on the expert committee representatives patient-physician experience in their clinical practice and common therapeutic practices followed in India. Recommendations for dosing and titration of basal, basal-plus, premixed and basal-bolus insulins were developed. The key recommendations are that insulin doses can be adjusted once or twice weekly; adjustment can be based on lowest/mean of three recent self-monitoring of plasma glucose pre-meal/fasting plasma glucose (FPG) values. The titration should be based on FPG or pre-meal value of 80-130 mg/dL and the dose should be reduced by 10-20% for patients reporting hypoglycaemia(<70mg/dL). The consensus based recommendations mentioned in this paper will be a useful reference tool for health care practitioners, to initiate, optimise and intensify insulin therapy and to successfully achieve optimal glucose control.

Surfactant titration of nanoparticle-protein corona.

PubMed

Maiolo, Daniele; Bergese, Paolo; Mahon, Eugene; Dawson, Kenneth A; Monopoli, Marco P

2014-12-16

Nanoparticles (NP), when exposed to biological fluids, are coated by specific proteins that form the so-called protein corona. While some adsorbing proteins exchange with the surroundings on a short time scale, described as a "dynamic" corona, others with higher affinity and long-lived interaction with the NP surface form a "hard" corona (HC), which is believed to mediate NP interaction with cellular machineries. In-depth NP protein corona characterization is therefore a necessary step in understanding the relationship between surface layer structure and biological outcomes. In the present work, we evaluate the protein composition and stability over time and we systematically challenge the formed complexes with surfactants. Each challenge is characterized through different physicochemical measurements (dynamic light scattering, ζ-potential, and differential centrifugal sedimentation) alongside proteomic evaluation in titration type experiments (surfactant titration). 100 nm silicon oxide (Si) and 100 nm carboxylated polystyrene (PS-COOH) NPs cloaked by human plasma HC were titrated with 3-[(3-Cholamidopropyl) dimethylammonio]-1-propanesulfonate (CHAPS, zwitterionic), Triton X-100 (nonionic), sodium dodecyl sulfate (SDS, anionic), and dodecyltrimethylammonium bromide (DTAB, cationic) surfactants. Composition and density of HC together with size and ζ-potential of NP-HC complexes were tracked at each step after surfactant titration. Results on Si NP-HC complexes showed that SDS removes most of the HC, while DTAB induces NP agglomeration. Analogous results were obtained for PS NP-HC complexes. Interestingly, CHAPS and Triton X-100, thanks to similar surface binding preferences, enable selective extraction of apolipoprotein AI (ApoAI) from Si NP hard coronas, leaving unaltered the dispersion physicochemical properties. These findings indicate that surfactant titration can enable the study of NP-HC stability through surfactant variation and also selective separation of certain proteins from the HC. This approach thus has an immediate analytical value as well as potential applications in HC engineering.

Titrating Oxygen Requirements During Exercise: Evaluation of a Standardized Single Walk Test Protocol.

PubMed

Giovacchini, Coral X; Mathews, Anne M; Lawlor, Brian R; MacIntyre, Neil R

2018-04-01

Oxygen supplementation for exercise-induced hypoxemia is a common clinical practice that improves exercise tolerance. However, we know of no standardized exercise oxygen titration protocol using a single walk test. We report our experience with a protocol developed in our laboratory. Our protocol is based on the 6-min walk test (6MWT). Pulse oximetry readings (oxygen saturation [Spo 2 ]) are monitored, and supplemental oxygen is added in 2 L/min increments to keep Spo 2 > 88%. This continues for at least 6 min of walking with the Spo 2 remaining > 88% for at least 3 min. The records of consecutive patients over 4 months undergoing this procedure were reviewed for test performance, oxygen titration results, and adverse events. Two hundred twenty-two patients were tested; only two prematurely terminated the protocol because of intractable dyspnea. One hundred fifty-six patients (38%) required oxygen supplementation, with the first titration most commonly occurring between 1 and 2 min of walking. Nine of the patients had the first titration after 5 min of walking. The average test duration was 7 min (maximum, 15 min). The average number of titrations was 2.2 (maximum six). Sixteen patients could not maintain Spo 2 > 88% for 3 min despite administration of 15 L/min of supplemental oxygen (maximal dose). Our protocol was easily performed as a modification of a standard 6MWT with no serious adverse events. Because it is based on a widely accepted measurement of functional capabilities, and because it determined a stable final oxygen dose for ≥ 3 min of walking in most patients, we believe this protocol can be easily adapted for clinical use. Copyright © 2017 American College of Chest Physicians. Published by Elsevier Inc. All rights reserved.

Titration of biologically active amyloid–β seeds in a transgenic mouse model of Alzheimer's disease

PubMed Central

Morales, Rodrigo; Bravo-Alegria, Javiera; Duran-Aniotz, Claudia; Soto, Claudio

2015-01-01

Experimental evidence in animal models suggests that misfolded Amyloid-β (Aβ) spreads in disease following a prion-like mechanism. Several properties characteristics of infectious prions have been shown for the induction of Aβ aggregates. However, a detailed titration of Aβ misfolding transmissibility and estimation of the minimum concentration of biologically active Aβ seeds able to accelerate pathological changes has not yet been performed. In this study, brain extracts from old tg2576 animals were serially diluted and intra-cerebrally injected into young subjects from the same transgenic line. Animals were sacrificed several months after treatment and brain slices were analyzed for amyloid pathology. We observed that administration of misfolded Aβ was able to significantly accelerate amyloid deposition in young mice, even when the original sample was diluted a million times. The titration curve obtained in this experiment was compared to the natural Aβ load spontaneously accumulated by these mice overtime. Our findings suggest that administration of the largest dose of Aβ seeds led to an acceleration of pathology equivalent to over a year. These results show that active Aβ seeds present in the brain can seed amyloidosis in a titratable manner, similarly as observed for infectious prions. PMID:25879692

Charge-Neutral Constant pH Molecular Dynamics Simulations Using a Parsimonious Proton Buffer.

PubMed

Donnini, Serena; Ullmann, R Thomas; Groenhof, Gerrit; Grubmüller, Helmut

2016-03-08

In constant pH molecular dynamics simulations, the protonation states of titratable sites can respond to changes of the pH and of their electrostatic environment. Consequently, the number of protons bound to the biomolecule, and therefore the overall charge of the system, fluctuates during the simulation. To avoid artifacts associated with a non-neutral simulation system, we introduce an approach to maintain neutrality of the simulation box in constant pH molecular dynamics simulations, while maintaining an accurate description of all protonation fluctuations. Specifically, we introduce a proton buffer that, like a buffer in experiment, can exchange protons with the biomolecule enabling its charge to fluctuate. To keep the total charge of the system constant, the uptake and release of protons by the buffer are coupled to the titration of the biomolecule with a constraint. We find that, because the fluctuation of the total charge (number of protons) of a typical biomolecule is much smaller than the number of titratable sites of the biomolecule, the number of buffer sites required to maintain overall charge neutrality without compromising the charge fluctuations of the biomolecule, is typically much smaller than the number of titratable sites, implying markedly enhanced simulation and sampling efficiency.

Analysis of Bromination of Ethylbenzene Using a 45 MHz NMR Spectrometer: An Undergraduate Organic Chemistry Laboratory Experiment

ERIC Educational Resources Information Center

Isaac-Lam, Meden F.

2014-01-01

A 45 MHz benchtop NMR spectrometer is used to identify the structures and determine the amount of 1-bromoethylbenzene and 1,1-dibromoethylbenzene produced from free-radical bromination of ethylbenzene. The experiment is designed for nonchemistry majors, specifically B.S. Biology students, in a predominantly undergraduate institution with…

Double cross-polarization MAS NMR in the assignment of abundant-spin resonances: ¹⁹F-{²⁹Si}-¹⁹F FBCP/MAS NMR of fluoride ions incorporated in calcium silicate hydrate (C-S-H) phases.

PubMed

Tran, Thuan T; Bildsøe, Henrik; Jakobsen, Hans J; Skibsted, Jørgen

2012-08-01

A new version of the double cross-polarization MAS NMR experiment, which transfers polarization Forth and Back (FBCP) between high- and low-γ spin nuclei, is presented. The pulse sequence is demonstrated by ¹⁹F-{²⁹Si}-¹⁹F and ¹⁹F-{¹³C}-¹⁹F FBCP NMR spectra of a mixture of cuspidine (Ca₄Si₂O₇F₂) and Teflon (-CF₂-)(n). The experiment is useful for assignment of the high-γ spin resonances, as demonstrated by ¹⁹F-{²⁹Si}-¹⁹F FBCP NMR of a fluoride-containing calcium-silicate-hydrate (C-S-H) phase, where the ¹⁹F resonance from fluoride ions incorporated in the interlayer structure of the C-S-H phase is identified. Copyright © 2012 Elsevier Inc. All rights reserved.

A general algorithm for peak-tracking in multi-dimensional NMR experiments.

PubMed

Ravel, P; Kister, G; Malliavin, T E; Delsuc, M A

2007-04-01

We present an algorithmic method allowing automatic tracking of NMR peaks in a series of spectra. It consists in a two phase analysis. The first phase is a local modeling of the peak displacement between two consecutive experiments using distance matrices. Then, from the coefficients of these matrices, a value graph containing the a priori set of possible paths used by these peaks is generated. On this set, the minimization under constraint of the target function by a heuristic approach provides a solution to the peak-tracking problem. This approach has been named GAPT, standing for General Algorithm for NMR Peak Tracking. It has been validated in numerous simulations resembling those encountered in NMR spectroscopy. We show the robustness and limits of the method for situations with many peak-picking errors, and presenting a high local density of peaks. It is then applied to the case of a temperature study of the NMR spectrum of the Lipid Transfer Protein (LTP).

NMR reaction monitoring in flow synthesis

PubMed Central

Gomez, M Victoria

2017-01-01

Recent advances in the use of flow chemistry with in-line and on-line analysis by NMR are presented. The use of macro- and microreactors, coupled with standard and custom made NMR probes involving microcoils, incorporated into high resolution and benchtop NMR instruments is reviewed. Some recent selected applications have been collected, including synthetic applications, the determination of the kinetic and thermodynamic parameters and reaction optimization, even in single experiments and on the μL scale. Finally, software that allows automatic reaction monitoring and optimization is discussed. PMID:28326137

NMR reaction monitoring in flow synthesis.

PubMed

Gomez, M Victoria; de la Hoz, Antonio

2017-01-01

Recent advances in the use of flow chemistry with in-line and on-line analysis by NMR are presented. The use of macro- and microreactors, coupled with standard and custom made NMR probes involving microcoils, incorporated into high resolution and benchtop NMR instruments is reviewed. Some recent selected applications have been collected, including synthetic applications, the determination of the kinetic and thermodynamic parameters and reaction optimization, even in single experiments and on the μL scale. Finally, software that allows automatic reaction monitoring and optimization is discussed.

Sampling Error in a Particulate Mixture: An Analytical Chemistry Experiment.

ERIC Educational Resources Information Center

Kratochvil, Byron

1980-01-01

Presents an undergraduate experiment demonstrating sampling error. Selected as the sampling system is a mixture of potassium hydrogen phthalate and sucrose; using a self-zeroing, automatically refillable buret to minimize titration time of multiple samples and employing a dilute back-titrant to obtain high end-point precision. (CS)

Oxygen from Hydrogen Peroxide. A Safe Molar Volume-Molar Mass Experiment.

ERIC Educational Resources Information Center

Bedenbaugh, John H.; And Others

1988-01-01

Describes a molar volume-molar mass experiment for use in general chemistry laboratories. Gives background technical information, procedures for the titration of aqueous hydrogen peroxide with standard potassium permanganate and catalytic decomposition of hydrogen peroxide to produce oxygen, and a discussion of the results obtained in three…

Dose titration of sericea lespedeza leaf meal on Haemonchus contortus infection in lambs and kids

USDA-ARS?s Scientific Manuscript database

The objective of three experiments was to determine the impact of supplementing sericea lespedeza (Lespedeza cuneata; SL) in three concentrations in a loose or pelleted diet on gastrointestinal nematodes (GIN) in small ruminants. Experiments on lambs were conducted at the USDA, Agricultural Research...

[Synthesis and Spectroscopic Study of a Chemosensor for Naked Eye Recognition of Cu2+ and Hg2+].

PubMed

Cao, Li; Qian, Ya-ao; Huang, Yan; Cao, Juan; Jia, Chun-man; Liu, Chun-ling; Zhang, Qi; Lu, Zheng-rong

2015-07-01

Compound L, as the procedural sensor for the detection of Cu2+ and Hg2+, was designed and synthesized based on the coumarin-modified rhodamine derivative. The structure of compound L was characterized by NMR, high resolution mass spectrometry and infrared method. Its sensing behavior toward various metal ions was investigated with absorbance methods. The study found that L had good selectivity and sensitivity for Cu2+. When addition of various metal ions (Zn2+, Hg2+, Cu2+, Fe3+, Cd2+, CO2+, Ni2+, Mg2+, Ca2+, Al3+, La3+, K+, Na+, Mn2+, Pb2+ and Ag+), only Cu2+ could induce a visible change of solution from colourless to pink and a new absorption band centered at 534 nm appear, which indicated that compound L could be used for the naked eye detection of Cu2+. From UV titration, the detection limit was about 1.9 X 10(-8) mol x L(-1). Test strips based on L were fabricated, and this test strips could act as a convenient and efficient Cu2+ test kit. The binding ratio of the complex of L-Cu2+ was 1:1 according to the Job's plot and high resolution mass spectrometer (HRMS) experiments. Moreover, Upon addition of 1 equiv. EDTA to the mixture of L and Cu2+ in DMSO solution, colour changed from pink to almost colourless, indicating that the EDTA replaced the receptor L to coordinate with Cu2+. Therefore, L could be classified as a reversible sensor for Cu2+. In addition, when adding Hg2+ to L-Cu2+ complexes, a visible change of solution from pink to colourless was observed, while other metal ions didn't cause this change. Thus, L-Cu2+ complex also could be used for the naked eye recognition of Hg2+, and the detection limit was calculated about 2.9 x 10(-1) mol x L(-1) according to the UV titration. Consequently, this procedural sensor L could be use for the orderly naked eye recognition of Cu2+ and Hg2+.

Characterization of Pharmaceutical Cocrystals and Salts by Dynamic Nuclear Polarization-Enhanced Solid-State NMR Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Li; Hanrahan, Michael P.; Chakravarty, Paroma

Multicomponent solids such as cocrystals have emerged as a way to control and engineer the stability, solubility and manufacturability of solid active pharmaceutical ingredients (APIs). Cocrystals are typically formed by solution- or solid-phase reactions of APIs with suitable cocrystal coformers, which are often weak acids. One key structural question about a given multicomponent solid is whether it should be classified as a salt, where the basic API is protonated by the acid, or as a cocrystal, where the API and coformer remain neutral and engage in hydrogen bonding interactions. It has previously been demonstrated that solid-state NMR spectroscopy is amore » powerful probe of structure in cocrystals and salts of APIs, however, the poor sensitivity of solid-state NMR spectroscopy usually restricts the types of experiments that can be performed. Here relayed dynamic nuclear polarization (DNP) was applied to reduce solid-state NMR experiments by one to two orders of magnitude for salts and cocrystals of a complex API. The large sensitivity gains from DNP facilitates rapid acquisition of natural isotopic abundance 13C and 15N solid-state NMR spectra. Critically, DNP enables double resonance 1H-15N solid-state NMR experiments such as 2D 1H-15N HETCOR, 1H-15N CP-build up, 15N{1H} J-resolved/attached proton tests, 1H-15N DIPSHIFT and 1H-15N PRESTO. The latter two experiments allow 1H-15N dipolar coupling constants and H-N bond lengths to be accurately measured, providing an unambiguous assignment of nitrogen protonation state and definitive classification of the multi-component solids as cocrystals or salts. In conclusion, these types of measurements should also be extremely useful in the context of polymorph discrimination, NMR crystallography structure determination and for probing hydrogen bonding in a variety of organic materials.« less

Characterization of Pharmaceutical Cocrystals and Salts by Dynamic Nuclear Polarization-Enhanced Solid-State NMR Spectroscopy

DOE PAGES

Zhao, Li; Hanrahan, Michael P.; Chakravarty, Paroma; ...

2018-02-15

Multicomponent solids such as cocrystals have emerged as a way to control and engineer the stability, solubility and manufacturability of solid active pharmaceutical ingredients (APIs). Cocrystals are typically formed by solution- or solid-phase reactions of APIs with suitable cocrystal coformers, which are often weak acids. One key structural question about a given multicomponent solid is whether it should be classified as a salt, where the basic API is protonated by the acid, or as a cocrystal, where the API and coformer remain neutral and engage in hydrogen bonding interactions. It has previously been demonstrated that solid-state NMR spectroscopy is amore » powerful probe of structure in cocrystals and salts of APIs, however, the poor sensitivity of solid-state NMR spectroscopy usually restricts the types of experiments that can be performed. Here relayed dynamic nuclear polarization (DNP) was applied to reduce solid-state NMR experiments by one to two orders of magnitude for salts and cocrystals of a complex API. The large sensitivity gains from DNP facilitates rapid acquisition of natural isotopic abundance 13C and 15N solid-state NMR spectra. Critically, DNP enables double resonance 1H-15N solid-state NMR experiments such as 2D 1H-15N HETCOR, 1H-15N CP-build up, 15N{1H} J-resolved/attached proton tests, 1H-15N DIPSHIFT and 1H-15N PRESTO. The latter two experiments allow 1H-15N dipolar coupling constants and H-N bond lengths to be accurately measured, providing an unambiguous assignment of nitrogen protonation state and definitive classification of the multi-component solids as cocrystals or salts. In conclusion, these types of measurements should also be extremely useful in the context of polymorph discrimination, NMR crystallography structure determination and for probing hydrogen bonding in a variety of organic materials.« less

Motions and entropies in proteins as seen in NMR relaxation experiments and molecular dynamics simulations.

PubMed

Allnér, Olof; Foloppe, Nicolas; Nilsson, Lennart

2015-01-22

Molecular dynamics simulations of E. coli glutaredoxin1 in water have been performed to relate the dynamical parameters and entropy obtained in NMR relaxation experiments, with results extracted from simulated trajectory data. NMR relaxation is the most widely used experimental method to obtain data on dynamics of proteins, but it is limited to relatively short timescales and to motions of backbone amides or in some cases (13)C-H vectors. By relating the experimental data to the all-atom picture obtained in molecular dynamics simulations, valuable insights on the interpretation of the experiment can be gained. We have estimated the internal dynamics and their timescales by calculating the generalized order parameters (O) for different time windows. We then calculate the quasiharmonic entropy (S) and compare it to the entropy calculated from the NMR-derived generalized order parameter of the amide vectors. Special emphasis is put on characterizing dynamics that are not expressed through the motions of the amide group. The NMR and MD methods suffer from complementary limitations, with NMR being restricted to local vectors and dynamics on a timescale determined by the rotational diffusion of the solute, while in simulations, it may be difficult to obtain sufficient sampling to ensure convergence of the results. We also evaluate the amount of sampling obtained with molecular dynamics simulations and how it is affected by the length of individual simulations, by clustering of the sampled conformations. We find that two structural turns act as hinges, allowing the α helix between them to undergo large, long timescale motions that cannot be detected in the time window of the NMR dipolar relaxation experiments. We also show that the entropy obtained from the amide vector does not account for correlated motions of adjacent residues. Finally, we show that the sampling in a total of 100 ns molecular dynamics simulation can be increased by around 50%, by dividing the trajectory into 10 replicas with different starting velocities.

Characterization of active phosphorus surface sites at synthetic carbonate-free fluorapatite using single-pulse 1H, 31P, and 31P CP MAS NMR.

PubMed

Jarlbring, Mathias; Sandström, Dan E; Antzutkin, Oleg N; Forsling, Willis

2006-05-09

The chemically active phosphorus surface sites defined as PO(x), PO(x)H, and PO(x)H2, where x = 1, 2, or 3, and the bulk phosphorus groups of PO4(3-) at synthetic carbonate-free fluorapatite (Ca5(PO4)3F) have been studied by means of single-pulse 1H,31P, and 31P CP MAS NMR. The changes in composition and relative amounts of each surface species are evaluated as a function of pH. By combining spectra from single-pulse 1H and 31P MAS NMR and data from 31P CP MAS NMR experiments at varying contact times in the range 0.2-3.0 ms, it has been possible to distinguish between resonance lines in the NMR spectra originating from active surface sites and bulk phosphorus groups and also to assign the peaks in the NMR spectra to the specific phosphorus species. In the 31P CP MAS NMR experiments, the spinning frequency was set to 4.2 kHz; in the single-pulse 1H MAS NMR experiments, the spinning frequency was 10 kHz. The 31P CP MAS NMR spectrum of fluorapatite at pH 5.9 showed one dominating resonance line at 2.9 ppm assigned to originate from PO4(3-) groups and two weaker shoulder peaks at 5.4 and 0.8 ppm which were assigned to the unprotonated PO(x) (PO, PO2-, and PO3(2-)) and protonated PO(x)H (PO2H and PO3H-) surface sites. At pH 12.7, the intensity of the peak representing unprotonated PO(x) surface sites has increased 1.7% relative to the bulk peak, while the intensity of the peaks of the protonated species PO(x)H have decreased 1.4% relative to the bulk peak. At pH 3.5, a resonance peak at -4.5 ppm has appeared in the 31P CP MAS NMR spectrum assigned to the surface species PO(x)H2 (PO3H2). The results from the 1H MAS and 31P CP MAS NMR measurements indicated that H+, OH-, and physisorbed H2O at the surface were released during the drying process at 200 degrees C.

Wet Labs, Computers, and Spreadsheets.

ERIC Educational Resources Information Center

Durham, Bill

1990-01-01

Described are some commonly encountered chemistry experiments that have been modified for computerized data acquisition. Included are exercises in radioactivity, titration, calorimetry, kinetics, and electrochemistry. Software considerations and laboratory procedures are discussed. (CW)

The dominant role of side chains in supramolecular double helical organisation in synthetic tripeptides

NASA Astrophysics Data System (ADS)

Sharma, Ankita; Tiwari, Priyanka; Dutt Konar, Anita

2018-06-01

Peptide self-assembled nanostructures have attracted attention recently owing to their promising applications in diversified avenues. To validate the importance of sidechains in supramolecular architectural stabilization, herein this report describes the self-assembly propensities involving weak interactions in a series of model tripeptides Boc-Xaa-Aib-Yaa-OMe I-IV, (where Xaa = 4-F-Phe/NMeSer/Ile & Yaa = Tyr in peptide I-III respectively and Xaa = 4-F-Phe & Yaa = Ile in peptide IV) differing in terminal side chains. The solid state structural analysis reveals that tripeptide (I) displays supramolecular preference for double helical architecture. However, when slight modification has been introduced in the N-terminal side chains disfavour the double helical organisation (Peptide II and III). Indeed the peptides display sheet like ensemble within the framework. Besides replacement of C-terminal Tyr by Ile in peptide I even do not promote the architecture, emphasizing the dominant role of balance of side chains in stabilizing double helical organisation. The CD measurements, concentration dependant studies, NMR titrations and ROESY spectra are well in agreement with the solid state conformational investigation. Moreover the morphological experiments utilizing FE-SEM, support the heterogeneity present in the peptides. Thus this work may not only hold future promise in understanding the structure and function of neurodegenerative diseases but also assist in rational design of protein modification in biologically active peptides.

Highly sensitive oligothiophene-phenylamine-based dual-functional fluorescence "turn-on" sensor for rapid and simultaneous detection of Al3+ and Fe3+ in environment and food samples.

PubMed

Guo, Zongrang; Niu, Qingfen; Li, Tianduo

2018-07-05

Developing low-cost and efficient sensors for rapid, selective and sensitive detection of the transition metal ions in environmental and food science is very important. In this study, a novel dual-functional fluorescent "turn-on" sensor 3TP based on oligothiophene-phenylamine Schiff base has been synthesized for discrimination and simultaneous detection of both Al 3+ and Fe 3+ ions with high selectivity and anti-interference over other metal ions. Sensor 3TP displayed a very fast fluorescence-enhanced response towards Al 3+ and Fe 3+ ions with low detection limits (0.177μM for Al 3+ and 0.172μM for Fe 3+ ) and wide pH response range (4.0-12.0). The Al 3+ /Fe 3+ sensing mechanisms were investigated by fluorescence experiments, 1 H NMR titrations, FT-IR and ESI-MS spectra. Importantly, sensor 3TP was served as an efficient solid material for the highly sensitive and selective detection of Fe 3+ on TLC plates. Moreover, the sensor 3TP has been successfully used to detect trace Al 3+ and Fe 3+ in environment and food samples with satisfactory results and good recoveries, revealing a convenient, reliable and accurate method for Al 3+ and Fe 3+ analysis in real samples. Copyright © 2018 Elsevier B.V. All rights reserved.

Interactions of Enolizable Barbiturate Dyes.

PubMed

Schade, Alexander; Schreiter, Katja; Rüffer, Tobias; Lang, Heinrich; Spange, Stefan

2016-04-11

The specific barbituric acid dyes 1-n-butyl-5-(2,4-dinitro-phenyl) barbituric acid and 1-n-butyl-5-{4-[(1,3-dioxo-1H-inden-(3 H)-ylidene)methyl]phenyl}barbituric acid were used to study complex formation with nucleobase derivatives and related model compounds. The enol form of both compounds shows a strong bathochromic shift of the UV/Vis absorption band compared to the rarely coloured keto form. The keto-enol equilibria of the five studied dyes are strongly dependent on the properties of the environment as shown by solvatochromic studies in ionic liquids and a set of organic solvents. Enol form development of the barbituric acid dyes is also associated with alteration of the hydrogen bonding pattern from the ADA to the DDA type (A=hydrogen bond acceptor site, D=donor site). Receptor-induced altering of ADA towards DDA hydrogen bonding patterns of the chromophores are utilised to study supramolecular complex formation. As complementary receptors 9-ethyladenine, 1-n-butylcytosine, 1-n-butylthymine, 9-ethylguanidine and 2,6-diacetamidopiridine were used. The UV/Vis spectroscopic response of acid-base reaction compared to supramolecular complex formation is evaluated by (1)H NMR titration experiments and X-ray crystal structure analyses. An increased acidity of the barbituric acid derivative promotes genuine salt formation. In contrast, supramolecular complex formation is preferred for the weaker acidic barbituric acid. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Highly sensitive oligothiophene-phenylamine-based dual-functional fluorescence "turn-on" sensor for rapid and simultaneous detection of Al3+ and Fe3+ in environment and food samples

NASA Astrophysics Data System (ADS)

Guo, Zongrang; Niu, Qingfen; Li, Tianduo

2018-07-01

Developing low-cost and efficient sensors for rapid, selective and sensitive detection of the transition metal ions in environmental and food science is very important. In this study, a novel dual-functional fluorescent "turn-on" sensor 3TP based on oligothiophene-phenylamine Schiff base has been synthesized for discrimination and simultaneous detection of both Al3+ and Fe3+ ions with high selectivity and anti-interference over other metal ions. Sensor 3TP displayed a very fast fluorescence-enhanced response towards Al3+ and Fe3+ ions with low detection limits (0.177 μM for Al3+ and 0.172 μM for Fe3+) and wide pH response range (4.0-12.0). The Al3+/Fe3+ sensing mechanisms were investigated by fluorescence experiments, 1H NMR titrations, FT-IR and ESI-MS spectra. Importantly, sensor 3TP was served as an efficient solid material for the highly sensitive and selective detection of Fe3+ on TLC plates. Moreover, the sensor 3TP has been successfully used to detect trace Al3+ and Fe3+ in environment and food samples with satisfactory results and good recoveries, revealing a convenient, reliable and accurate method for Al3+ and Fe3+ analysis in real samples.

[superscript 31]P NMR of the Pyruvate Kinase Reaction: An Undergraduate Experiment in Enzyme Kinetics

ERIC Educational Resources Information Center

Werner, R. Marshall; Johnson, Austin

2017-01-01

Understanding how to perform an enzyme assay is a critical learning skill in the undergraduate biochemistry curriculum. Students in biochemistry typically have been exposed to the use of NMR spectroscopy as a tool to determine chemical structure, but rarely are they exposed to the utility of NMR to evaluate enzyme kinetics. Furthermore, coverage…

Determination of Molecular Self-Diffusion Coefficients Using Pulsed-Field-Gradient NMR: An Experiment for Undergraduate Physical Chemistry Laboratory

ERIC Educational Resources Information Center

Harmon, Jennifer; Coffman, Cierra; Villarrial, Spring; Chabolla, Steven; Heisel, Kurt A.; Krishnan, Viswanathan V.

2012-01-01

NMR spectroscopy has become one of the primary tools that chemists utilize to characterize a range of chemical species in the solution phase, from small organic molecules to medium-sized proteins. A discussion of NMR spectroscopy is an essential component of physical and biophysical chemistry lecture courses, and a number of instructional…

Organic Spectroscopy Laboratory: Utilizing IR and NMR in the Identification of an Unknown Substance

ERIC Educational Resources Information Center

Glagovich, Neil M.; Shine, Timothy D.

2005-01-01

A laboratory experiment that emphasizes the interpretation of both infrared (IR) and nuclear magnetic resonance (NMR) spectra in the elucidation of the structure of an unknown compound was developed. The method helps students determine [to the first power]H- and [to the thirteenth power]C-NMR spectra from the structures of compounds and to…

Dynamic NMR of Intramolecular Exchange Processes in EDTA Complexes of Sc[superscript 3+], Y[superscript 3+], and La[superscript 3+

ERIC Educational Resources Information Center

Ba, Yong; Han, Steven; Ni, Lily; Su, Tony; Garcia, Andres

2006-01-01

Dynamic NMR makes use of the effect of chemical exchanges on NMR spectra to study kinetics and thermodynamics. An advanced physical chemistry lab experiment was developed to study the intramolecular exchange processes of EDTA (the disodium salt of ethylenediaminetetraacetic acid) metal complexes. EDTA is an important chelating agent, used in…

A Robust Magnetic Resonance Imager For Ground and Flight Based Measurements of Fluid Physics Phenomena

NASA Technical Reports Server (NTRS)

2002-01-01

Nuclear magnetic resonance (NMR) is a powerful and versatile, noninvasive method for studying fluid transport problems, However, its applications to these types of investigations have been limited. A primary factor that limits the application of NMR has been the lack of a user-friendly, versatile, and inexpensive NMR imaging apparatus that can be used by scientists who are not familiar with sophisticated NMR. To rectify this situation, we developed a user-friendly, NMR imager for projects of relevance to the MRD science community. To that end, we performed preliminary collaborative experiments between NASA, NCMR, and New Mexico Resonance in the high field NMR set up at New Mexico Resonance to track wetting front dynamics in foams under gravity. The experiments were done in a 30 cm, 1.9T Oxford magnet with a TECMAG Libra spectrometer (Tecmag, Inc., Houston, TX). We used two different imaging strategies depending on whether the water in the foam sample was static or moving. Stationary water distributions were imaged with the standard Fourier imaging method, as used in medical MRI, in which data are acquired from all parts of the region of interest at all times and Fourier transformed into a static spatial image.

Behavior of atypical amphiphilic molecules

NASA Astrophysics Data System (ADS)

Ko, John

1997-08-01

The physical behavior of several atypical amphiphilic molecules was studied in various environments including micelles, model bilayer membranes, and emulsions. The molecules under investigation were nor-chenodeoxycholic acid (nor-CDCA), ursodeoxycholic acid (UDCA), sphingosine (Sp), sphingosine hydrochloride (SpċHCl), and tetrahydrolipstatin (THL). The bile acids, nor-CDCA and UDCA, were studied using 13C-Nuclear Magnetic Resonance ([13C) -NMR) in micelles of taurocholate and in bilayers of phosphatidylcholine. The pK a values of the bile acids in each environment were determined by [13C) -NMR and are as follows: 6.08 ±.03 for nor-CDCA and 6.27 ±.01 for UDCA in micelles, and 7.04 ± 12 for nor-CDCA and 6.89 ±.05 for UDCA in vesicles. Using line shape analysis, the transbilayer movement rate at 36oC for nor-CDCA and UDCA was calculated to be 580 sec--1 and 409 sec-1, respectively. [13C) -NMR titration of Sp gave pK a values of 9.09 ±.02 in micelles and 9.69 ±.21 in bilayers. Differential scanning calorimetry (DSC) and X-ray diffraction were used to establish the Spċwater and SpċHClċwater phase diagrams. Anhydrous and hydrated samples ranging from 5- 90% water were analyzed. The DSC thermograms traced out the transition temperatures of each molecule while the X- ray diffraction patterns revealed their chain and crystalline lattice packing structures. In general, sphingosine exists as a hydrated crystal with β packing phase below 43oC and melts into an Lα phase. Sphingosine hydrochloride, however, exists as a gel phase (L_beta or /beta/sp') below 42oC that swells to 61% hydration. At low water concentrations (0-64%), a lamellar liquid crystal phase (L_alpha) is formed above the chain melting transition of 42oC. At medium concentration (65%), a Hexagonal I phase is present, and at high water concentrations (66-90%), a micellar phase is present. THL, a specific inhibitor of lipases, was analyzed with [ 13C) -NMR to study its behavior in various environments, ranging from carbon tetrachloride to water to pure triolein. THL was also incorporated into phosphatidylcholine bilayers and into microemulsions of triolein and phosphatidylcholine. [ 13C) -NMR analysis revealed that THL gets incorporated into the surface of vesicles, and into both the surface and core of microemulsion particles.

1H-detected MAS solid-state NMR experiments enable the simultaneous mapping of rigid and dynamic domains of membrane proteins

NASA Astrophysics Data System (ADS)

Gopinath, T.; Nelson, Sarah E. D.; Veglia, Gianluigi

2017-12-01

Magic angle spinning (MAS) solid-state NMR (ssNMR) spectroscopy is emerging as a unique method for the atomic resolution structure determination of native membrane proteins in lipid bilayers. Although 13C-detected ssNMR experiments continue to play a major role, recent technological developments have made it possible to carry out 1H-detected experiments, boosting both sensitivity and resolution. Here, we describe a new set of 1H-detected hybrid pulse sequences that combine through-bond and through-space correlation elements into single experiments, enabling the simultaneous detection of rigid and dynamic domains of membrane proteins. As proof-of-principle, we applied these new pulse sequences to the membrane protein phospholamban (PLN) reconstituted in lipid bilayers under moderate MAS conditions. The cross-polarization (CP) based elements enabled the detection of the relatively immobile residues of PLN in the transmembrane domain using through-space correlations; whereas the most dynamic region, which is in equilibrium between folded and unfolded states, was mapped by through-bond INEPT-based elements. These new 1H-detected experiments will enable one to detect not only the most populated (ground) states of biomacromolecules, but also sparsely populated high-energy (excited) states for a complete characterization of protein free energy landscapes.

Moissanite anvil cell design for Giga-Pascal nuclear magnetic resonance.

PubMed

Meier, Thomas; Herzig, Tobias; Haase, Jürgen

2014-04-01

A new design of a non-magnetic high-pressure anvil cell for nuclear magnetic resonance (NMR) experiments at Giga-Pascal pressures is presented, which uses a micro-coil inside the pressurized region for high-sensitivity NMR. The comparably small cell has a length of 22 mm and a diameter of 18 mm, so it can be used with most NMR magnets. The performance of the cell is demonstrated with external-force vs. internal-pressure experiments, and the cell is shown to perform well at pressures up to 23.5 GPa using 800 μm 6H-SiC large cone Boehler-type anvils. (1)H, (23)Na, (27)Al, (69)Ga, and (71)Ga NMR test measurements are presented, which show a resolution of better than 4.5 ppm, and an almost maximum possible signal-to-noise ratio.

Protein-nucleotide contacts in motor proteins detected by DNP-enhanced solid-state NMR.

PubMed

Wiegand, Thomas; Liao, Wei-Chih; Ong, Ta Chung; Däpp, Alexander; Cadalbert, Riccardo; Copéret, Christophe; Böckmann, Anja; Meier, Beat H

2017-11-01

DNP (dynamic nuclear polarization)-enhanced solid-state NMR is employed to directly detect protein-DNA and protein-ATP interactions and identify the residue type establishing the intermolecular contacts. While conventional solid-state NMR can detect protein-DNA interactions in large oligomeric protein assemblies in favorable cases, it typically suffers from low signal-to-noise ratios. We show here, for the oligomeric DnaB helicase from Helicobacter pylori complexed with ADP and single-stranded DNA, that this limitation can be overcome by using DNP-enhanced spectroscopy. Interactions are established by DNP-enhanced 31 P- 13 C polarization-transfer experiments followed by the recording of a 2D 13 C- 13 C correlation experiment. The NMR spectra were obtained in less than 2 days and allowed the identification of residues of the motor protein involved in nucleotide binding.

The structure of poly(carbonsuboxide) on the atomic scale: a solid-state NMR study.

PubMed

Schmedt auf der Günne, Jörn; Beck, Johannes; Hoffbauer, Wilfried; Krieger-Beck, Petra

2005-07-18

In this contribution we present a study of the structure of amorphous poly(carbonsuboxide) (C3O2)x by 13C solid-state NMR spectroscopy supported by infrared spectroscopy and chemical analysis. Poly(carbonsuboxide) was obtained by polymerization of carbonsuboxide C3O2, which in turn was synthesized from malonic acid bis(trimethylsilylester). Two different 13C labeling schemes were applied to probe inter- and intramonomeric bonds in the polymer by dipolar solid-state NMR methods and also to allow quantitative 13C MAS NMR spectra. Four types of carbon environments can be distinguished in the NMR spectra. Double-quantum and triple-quantum 2D correlation experiments were used to assign the observed peaks using the through-space and through-bond dipolar coupling. In order to obtain distance constraints for the intermonomeric bonds, double-quantum constant-time experiments were performed. In these experiments an additional filter step was applied to suppress contributions from not directly bonded 13C,13C spin pairs. The 13C NMR intensities, chemical shifts, connectivities and distances gave constraints for both the polymerization mechanism and the short-range order of the polymer. The experimental results were complemented by bond lengths predicted by density functional theory methods for several previously suggested models. Based on the presented evidence we can unambiguously exclude models based on gamma-pyronic units and support models based on alpha-pyronic units. The possibility of planar ladder- and bracelet-like alpha-pyronic structures is discussed.

Improving reliability of chemometric models for authentication of species origin of heparin by switching from 1D to 2D NMR experiments.

PubMed

Monakhova, Yulia B; Fareed, Jawed; Yao, Yiming; Diehl, Bernd W K

2018-05-10

Nuclear magnetic resonance (NMR) spectroscopy is regarded as one of the most powerful and versatile analytical approaches to assure the quality of heparin preparations. In particular, it was recently demonstrated that by using 1 H NMR coupled with chemometrics heparin and low molecular weight heparin (LMWH) samples derived from three major animal species (porcine, ovine and bovine) can be differentiated [Y.B. Monakhova et al. J. Pharm. Anal. 149 (2018) 114-119]. In this study, significant improvement of existing chemometric models was achieved by switching to 2D NMR experiments (heteronuclear multiple-quantum correlation (HMQC) and diffusion-ordered spectroscopy (DOSY)). Two representative data sets (sixty-nine heparin and twenty-two LMWH) belonged to different batches and distributed by different commercial companies were investigated. A trend for animal species differentiation was observed in the principal component analysis (PCA) score plot built based on the DOSY data. A superior model was constructed using HMQC experiments, where individual heparin (LMWH) clusters as well as their blends were clearly differentiated. The predictive power of different classification methods as well as unsupervised techniques (independent components analysis, ICA) clearly proved applicability of the model for routine heparin and LMWH analysis. The switch from 1D to 2D NMR techniques provides a wealth of additional information, which is beneficial for multivariate modeling of NMR spectroscopic data for heparin preparations. Copyright © 2018 Elsevier B.V. All rights reserved.

Iron Analysis by Redox Titration. A General Chemistry Experiment.

ERIC Educational Resources Information Center

Kaufman, Samuel; DeVoe, Howard

1988-01-01

Describes a simplified redox method for total iron analysis suitable for execution in a three-hour laboratory period by general chemistry students. Discusses materials, procedures, analyses, and student performance. (CW)

Edible Acid-Base Indicators.

ERIC Educational Resources Information Center

Mebane, Robert C.; Rybolt, Thomas R.

1985-01-01

Reports on the colors observed during titrations of 15 natural indicators obtained from common fruits and vegetables. These edible indicators can be used for a variety of teacher demonstrations or for simple student experiments. (JN)