Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Precise measurement of long-range heteronuclear coupling constants by a novel broadband proton-proton-decoupled CPMG-HSQMBC method.

ABSTRACT: A broadband proton-proton-decoupled CPMG-HSQMBC method for the precise and direct measurement of long-range heteronuclear coupling constants is presented. The Zangger-Sterk-based homodecoupling scheme reported herein efficiently removes unwanted proton-proton splittings from the heteronuclear multiplets, so that the desired heteronuclear couplings can be determined simply by measuring frequency differences between singlet maxima in the resulting spectra. The proposed pseudo-1D/2D pulse sequences were tested on nucleotides, a metal complex incorporating P heterocycles, and diglycosyl (di)selenides, as well as on other carbohydrate derivatives, for the extraction of (n) J((1) H,(31) P), (n) J((1) H,(77) Se), and (n) J((1) H,(13) C) values, respectively.

SUBMITTER: Timari I

PROVIDER: S-EPMC4338765 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Precise measurement of long-range heteronuclear coupling constants by a novel broadband proton-proton-decoupled CPMG-HSQMBC method.

Timári István I Illyés Tünde Z TZ Adams Ralph W RW Nilsson Mathias M Szilágyi László L Morris Gareth A GA Kövér Katalin E KE

Chemistry (Weinheim an der Bergstrasse, Germany) 20150108 8

A broadband proton-proton-decoupled CPMG-HSQMBC method for the precise and direct measurement of long-range heteronuclear coupling constants is presented. The Zangger-Sterk-based homodecoupling scheme reported herein efficiently removes unwanted proton-proton splittings from the heteronuclear multiplets, so that the desired heteronuclear couplings can be determined simply by measuring frequency differences between singlet maxima in the resulting spectra. The proposed pseudo-1D/2D pulse sequences ...[more]

PMID: 25573660

Similar Datasets

CSSF-CLIP-HSQMBC: measurement of heteronuclear coupling constants in severely crowded spectral regions.

Project description:A new pulse program development, a chemical shift selective filtration clean in-phase HSQMBC (CSSF-CLIP-HSQMBC), is presented for the user-friendly measurement of long-range heteronuclear coupling constants in severely crowded spectral regions. The introduction of the chemical shift selective filter makes the experiment extremely efficient at resolving overlapped multiplets and produces a clean selective CLIP-HSQMBC spectrum, in which the desired coupling constants can easily be measured as an extra proton-carbon splitting in f2. The pulse sequence is also provided as a real-time homonuclear decoupled version in which the heteronuclear coupling constant can be directly measured as the peak splitting in f2. The same principle is readily applicable to IPAP and AP versions of the same sequence as well as the optional TOCSY transfer, or in principle to any other selective heteronuclear experiment that relies on a clean 1H multiplet.

| S-EPMC9074913 | biostudies-literature

Rapid Measurement of Heteronuclear Coupling Constants in Complex NMR Spectra.

Project description:The NMR analysis of fluorine-containing molecules, increasingly widespread due to their importance in pharmaceuticals and biochemistry, poses significant challenges. Severe peak overlap in the proton spectrum often hinders the extraction of critical structural information in the form of heteronuclear scalar coupling constants, which are crucial for determining pharmaceutical properties and biological activity. Here, a new method, IPAP-FESTA, is reported that drastically simplifies measurements of the signs and magnitudes of proton-fluorine couplings. Its usefulness is demonstrated for the structural study of the steroidal drug fluticasone propionate extracted from a commercial formulation and for assessing solvent effects on the conformational equilibrium in a physically inseparable fluorohydrin mixture.

| S-EPMC10510310 | biostudies-literature

Heteronuclear proton assisted recoupling.

Project description:We describe a theoretical framework for understanding the heteronuclear version of the third spin assisted recoupling polarization transfer mechanism and demonstrate its potential for detecting long-distance intramolecular and intermolecular (15)N-(13)C contacts in biomolecular systems. The pulse sequence, proton assisted insensitive nuclei cross polarization (PAIN-CP) relies on a cross term between (1)H-(15)N and (1)H-(13)C dipolar couplings to mediate zero- and∕or double-quantum (15)N-(13)C recoupling. In particular, using average Hamiltonian theory we derive effective Hamiltonians for PAIN-CP and show that the transfer is mediated by trilinear terms of the form N(±)C(∓)H(z) (ZQ) or N(±)C(±)H(z) (DQ) depending on the rf field strengths employed. We use analytical and numerical simulations to explain the structure of the PAIN-CP optimization maps and to delineate the appropriate matching conditions. We also detail the dependence of the PAIN-CP polarization transfer with respect to local molecular geometry and explain the observed reduction in dipolar truncation. In addition, we demonstrate the utility of PAIN-CP in structural studies with (15)N-(13)C spectra of two uniformly (13)C,(15)N labeled model microcrystalline proteins-GB1, a 56 amino acid peptide, and Crh, a 85 amino acid domain swapped dimer (MW=2×10.4 kDa). The spectra acquired at high magic angle spinning frequencies (ω(r)∕2π>20 kHz) and magnetic fields (ω(0H)∕2π=700-900 MHz) using moderate rf fields, yield multiple long-distance intramonomer and intermonomer (15)N-(13)C contacts. We use these distance restraints, in combination with the available x-ray structure as a homology model, to perform a calculation of the monomer subunit of the Crh protein.

| S-EPMC3064688 | biostudies-literature

Selenoglycosides as Lectin Ligands: <sup>77</sup> Se-Edited CPMG-HSQMBC NMR Spectroscopy To Monitor Biomedically Relevant Interactions.

Project description:The fundamental importance of protein-glycan recognition calls for specific and sensitive high-resolution techniques for their detailed analysis. After the introduction of 19 F NMR spectroscopy to study the recognition of fluorinated glycans, a new 77 Se NMR spectroscopy method is presented for complementary studies of selenoglycans with optimised resolution and sensitivity, in which direct NMR spectroscopy detection on 77 Se is replaced by its indirect observation in a 2D 1 H,77 Se HSQMBC spectrum. In contrast to OH/F substitution, O/Se exchange allows the glycosidic bond to be targeted. As an example, selenodigalactoside recognition by three human galectins and a plant toxin is readily indicated by signal attenuation and line broadening in the 2D 1 H,77 Se HSQMBC spectrum, in which CPMG-INEPT long-range transfer ensures maximal detection sensitivity, clean signal phases, and reliable ligand ranking. By monitoring competitive displacement of a selenated spy ligand, the selective 77 Se NMR spectroscopy approach may also be used to screen non-selenated compounds. Finally, 1 H,77 Se CPMG-INEPT transfer allows further NMR sensors of molecular interaction to be combined with the specificity and resolution of 77 Se NMR spectroscopy.

| S-EPMC6618100 | biostudies-literature

Fast proton exchange in histidine: measurement of rate constants through indirect detection by NMR spectroscopy.

Project description:Owing to its imidazole side chain, histidine participates in various processes such as enzyme catalysis, pH regulation, metal binding, and phosphorylation. The determination of exchange rates of labile protons for such a system is important for understanding its functions. However, these rates are too fast to be measured directly in an aqueous solution by using NMR spectroscopy. We have obtained the exchange rates of the NH3(+) amino protons and the labile NH(?2) and NH(?1) protons of the imidazole ring by indirect detection through nitrogen-15 as a function of temperature (272?K<T<293?K) and pH (1.3<pH<4.9) of uniformly nitrogen-15- and carbon-13-labeled L-histidine?HCl?H2O. Exchange rates up to 8.5×10(4)?s(-1) could be determined (i.e., lifetimes as short as 12??s). The three chemical shifts ?H(i) of the invisible exchanging protons H(i) and the three one-bond scalar coupling constants (1)J(N,H(i)) could also be determined accurately.

| S-EPMC4497323 | biostudies-literature

Measurement of long-range 1H-19F scalar coupling constants and their glycosidic torsion dependence in 5-fluoropyrimidine-substituted RNA.

Project description:Long-range scalar 5J(H1',F) couplings were observed in 5-fluoropyrimidine-substituted RNA. We developed a novel S3E-19F-alpha,beta-edited NOESY experiment for quantitation of these long-range scalar 5J(H1',F) couplings, where the J-couplings can be extracted from inspection of intraresidual (H1',H6) NOE cross-peaks. Quantum chemical calculations were exploited to investigate the relation between scalar couplings and conformations around the glycosidic bond in oligonucleotides. The theoretical dependence of the observed 5J(H1',F) couplings on the torsion angle chi can be described by a generalized Karplus relationship. The corresponding density functional theory (DFT) analysis is outlined. Additional NMR experiments facilitating the resonance assignments of 5-fluoropyrimidine-substituted RNAs are described, and chemical shift changes due to altered shielding in the presence of fluorine-19 (19F) are presented.

| S-EPMC2556634 | biostudies-literature

Simultaneous Broadband Suppression of Homonuclear and Heteronuclear Couplings in <sup>1</sup> H NMR Spectroscopy.

Project description:The 1 H NMR analysis of species containing NMR-active heteronuclei can be difficult due to signal overlap caused by the combined effects of homonuclear and heteronuclear scalar (J) couplings. Here, a general pure shift method is presented for obtaining ultra-high resolution 1 H NMR spectra where spectral overlap is drastically reduced by suppressing both homonuclear and heteronuclear J-couplings, giving one single signal per 1 H chemical environment. Its usefulness is demonstrated in the analysis of fluorine- and phosphorus-containing compounds of pharmaceutical and biochemical interest.

| S-EPMC10099583 | biostudies-literature

Proton range verification in inhomogeneous tissue: Treatment planning system vs. measurement vs. Monte Carlo simulation.

Project description:In particle radiotherapy, range uncertainty is an important issue that needs to be overcome. Because high-dose conformality can be achieved using a particle beam, a small uncertainty can affect tumor control or cause normal-tissue complications. From this perspective, the treatment planning system (TPS) must be accurate. However, there is a well-known inaccuracy regarding dose computation in heterogeneous media. This means that verifying the uncertainty level is one of the prerequisites for TPS commissioning. We evaluated the range accuracy of the dose computation algorithm implemented in a commercial TPS, and Monte Carlo (MC) simulation against measurement using a CT calibration phantom. A treatment plan was produced for eight different materials plugged into a phantom, and two-dimensional doses were measured using a chamber array. The measurement setup and beam delivery were simulated by MC code. For an infinite solid water phantom, the gamma passing rate between the measurement and TPS was 97.7%, and that between the measurement and MC was 96.5%. However, gamma passing rates between the measurement and TPS were 49.4% for the lung and 67.8% for bone, and between the measurement and MC were 85.6% for the lung and 100.0% for bone tissue. For adipose, breast, brain, liver, and bone mineral, the gamma passing rates computed by TPS were 91.7%, 90.6%, 81.7%, 85.6%, and 85.6%, respectively. The gamma passing rates for MC for adipose, breast, brain, liver, and bone mineral were 100.0%, 97.2%, 95.0%, 98.9%, and 97.8%, respectively. In conclusion, the described procedure successfully evaluated the allowable range uncertainty for TPS commissioning. The TPS dose calculation is inefficient in heterogeneous media with large differences in density, such as lung or bone tissue. Therefore, the limitations of TPS in heterogeneous media should be understood and applied in clinical practice.

| S-EPMC5837130 | biostudies-literature

Resolution Enhancement in SEA XLOC for Heteronuclear NMR Long-Range Correlation.

Project description:It is shown how the resolution in SEA XLOC NMR spectra for distinguishing between heteronuclear two- and three-bond correlations for all 13C multiplicities can be improved by a modified experiment delivering absorptive profiles in the indirect dimension. The method is demonstrated with applications to ibuprofen and strychnine.

| S-EPMC6709521 | biostudies-literature

Resolution and measurement of heteronuclear dipolar couplings of a noncrystalline protein immobilized in a biological supramolecular assembly by proton-detected MAS solid-state NMR spectroscopy.

Project description:Two-dimensional (15)N chemical shift/(1)H chemical shift and three-dimensional (1)H-(15)N dipolar coupling/(15)N chemical shift/(1)H chemical shift MAS solid-state NMR correlation spectra of the filamentous bacteriophage Pf1 major coat protein show single-site resolution in noncrystalline, intact-phage preparations. The high sensitivity and resolution result from (1)H detection at 600MHz under 50kHz magic angle spinning using ∼0.5mg of perdeuterated and uniformly (15)N-labeled protein in which the exchangeable amide sites are partially or completely back-exchanged (reprotonated). Notably, the heteronuclear (1)H-(15)N dipolar coupling frequency dimension is shown to select among (15)N resonances, which will be useful in structural studies of larger proteins where the resonances exhibit a high degree of overlap in multidimensional chemical shift correlation spectra.

| S-EPMC3915937 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data