Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Staphylococcus aureus peptidoglycan stem packing by rotational-echo double resonance NMR spectroscopy.

ABSTRACT: Staphylococcus aureus grown in the presence of an alanine-racemase inhibitor was labeled with d-[1-(13)C]alanine and l-[(15)N]alanine to characterize some details of the peptidoglycan tertiary structure. Rotational-echo double-resonance NMR of intact whole cells was used to measure internuclear distances between (13)C and (15)N of labeled amino acids incorporated in the peptidoglycan, and from those labels to (19)F of a glycopeptide drug specifically bound to the peptidoglycan. The observed (13)C-(15)N average distance of 4.1-4.4 Å between d- and l-alanines in nearest-neighbor peptide stems is consistent with a local, tightly packed, parallel-stem architecture for a repeating structural motif within the peptidoglycan of S. aureus.

SUBMITTER: Kim SJ

PROVIDER: S-EPMC3796188 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Staphylococcus aureus peptidoglycan stem packing by rotational-echo double resonance NMR spectroscopy.

Kim Sung Joon SJ Singh Manmilan M Preobrazhenskaya Maria M Schaefer Jacob J

Biochemistry 20130514 21

Staphylococcus aureus grown in the presence of an alanine-racemase inhibitor was labeled with d-[1-(13)C]alanine and l-[(15)N]alanine to characterize some details of the peptidoglycan tertiary structure. Rotational-echo double-resonance NMR of intact whole cells was used to measure internuclear distances between (13)C and (15)N of labeled amino acids incorporated in the peptidoglycan, and from those labels to (19)F of a glycopeptide drug specifically bound to the peptidoglycan. The observed (13) ...[more]

PMID: 23617832

Similar Datasets

Transferred-Rotational-Echo Double Resonance.

Project description:Internuclear distance determination is the foundation for NMR-based structure calculation. However, high-precision distance measurement is a laborious process requiring lengthy data acquisitions due to the large set of multidimensional spectra needed at different mixing times. This prevents application to large or challenging molecular systems. Here, we present a new approach, transferred-rotational-echo double resonance (TREDOR), a heteronuclear transfer method in which we simultaneously detect both starting and transferred signals in a single spectrum. This co-acquisition is used to compensate for coherence decay, resulting in accurate and precise distance determination by a single parameter fit using a single spectrum recorded at an ideal mixing time. We showcase TREDOR with the microcrystalline SH3 protein using 3D spectra to resolve resonances. By combining the measured N-C and H-C distances, we calculate the structure of SH3, which converges to the correct fold, with a root-mean-square deviation of 2.1 Å compared to a reference X-ray structure. The TREDOR data used in the structure calculation were acquired in only 4 days on a 600 MHz instrument. This is achieved due to the more than 2-fold time saving afforded by co-acquisition of additional information and demonstrates TREDOR as a fast and straightforward method for determining structures via magic-angle spinning NMR.

| S-EPMC7884007 | biostudies-literature

Internuclear (31)P-(51)V distance measurements in polyoxoanionic solids using rotational echo adiabatic passage double resonance NMR spectroscopy.

Project description:We report the first results establishing rotational echo adiabatic passage double resonance (REAPDOR) experiments for distance measurements between a spin-1/2 (31P) and spin-7/2 (51V) pair in a series of vanadium-substituted polyoxoanionic solids from the Keggin and Wells-Dawson families. We have quantitatively measured 31P-51V distances in monovanadium substituted K4PVW11O40, 1-K7P2VW17O62, and 4-K7P2VW17O62. Numerical simulations of the experimental data yield very good agreement with the averaged P-W/P-V distances determined from the X-ray diffraction measurements in the same or related compounds. REAPDOR is therefore a very sensitive P-V distance probe anticipated to be especially useful in the absence of long-range order. Our results suggest that REAPDOR spectroscopy could be broadly applicable for interatomic distance measurements in other spin-7/2-spin-1/2 nuclear pairs.

| S-EPMC3985602 | biostudies-literature

Rotational-echo double-resonance NMR distance measurements for the tubulin-bound Paclitaxel conformation.

Project description:The important anticancer drug Taxol (paclitaxel, PTX) owes its unique activity to its ability to bind to tubulin in a stoichiometric ratio and promote its assembly into microtubules. The conformation of the microtubule-bound drug has been the focus of numerous research efforts, since the inability of polymerized tubulin to form crystals precludes structure proof by X-ray crystallography. Likewise, although the alpha,beta-tubulin dimer structure has been solved by electron crystallography, the 3.7 A resolution is too low to permit direct determination of either ligand conformation or binding pose. In this article, we present experimental results from 2H{19F} REDOR NMR that provide direct confirmation that paclitaxel adopts a T-shaped conformation when it is bound to tubulin.

| S-EPMC2432525 | biostudies-literature

Toward a biorelevant structure of protein kinase C bound modulators: design, synthesis, and evaluation of labeled bryostatin analogues for analysis with rotational echo double resonance NMR spectroscopy.

Project description:Protein kinase C (PKC) modulators are currently of great importance in preclinical and clinical studies directed at cancer, immunotherapy, HIV eradication, and Alzheimer's disease. However, the bound conformation of PKC modulators in a membrane environment is not known. Rotational echo double resonance (REDOR) NMR spectroscopy could uniquely address this challenge. However, REDOR NMR requires strategically labeled, high affinity ligands to determine interlabel distances from which the conformation of the bound ligand in the PKC-ligand complex could be identified. Here we report the first computer-guided design and syntheses of three bryostatin analogues strategically labeled for REDOR NMR analysis. Extensive computer analyses of energetically accessible analogue conformations suggested preferred labeling sites for the identification of the PKC-bound conformers. Significantly, three labeled analogues were synthesized, and, as required for REDOR analysis, all proved highly potent with PKC affinities (?1 nM) on par with bryostatin. These potent and strategically labeled bryostatin analogues are new structural leads and provide the necessary starting point for projected efforts to determine the PKC-bound conformation of such analogues in a membrane environment, as needed to design new PKC modulators and understand PKC-ligand-membrane structure and dynamics.

| S-EPMC4405261 | biostudies-literature

Localization of Cl-35 nuclei in biological solids using rotational-echo double-resonance experiments.

Project description:Chloride ions play important roles in many chemical and biological processes. This paper investigates the possibility of localizing 35Cl nuclei using solid-state NMR. It demonstrates that distances shorter than 3.8Å, between 13C atoms and 35Cl atoms in 10% uniformly labeled 13C L-tyrosine·HCl and natural abundance Glycine·HCl can be measured using rotational-echo (adiabatic passage) double-resonance (RE(AP)DOR). Furthermore the effect of quadrupolar interaction on the REDOR/REAPDOR experiment is quantified. The dephasing curve is plotted in a three dimensional chart as a function of the dephasing time and of the strength of quadrupolar interaction felt by each orientation. During spinning each orientation feels a quadrupolar interaction that varies in time, and therefore at each moment in time we reorder the crystallite orientations as a function of their contribution to the dephasing curve. In this way the effect of quadrupolar interaction on the dipolar dephasing curve can be fitted with a polynomial function. The numerical investigation performed allows us to generate REDOR/REAPDOR curves which are then used to simulate the experimental data.

| S-EPMC5378917 | biostudies-literature

Nutrient-dependent structural changes in S. aureus peptidoglycan revealed by solid-state NMR spectroscopy.

Project description:The bacterial cell wall is essential to cell survival and is a major target of antibiotics. The main component of the bacterial cell wall is peptidoglycan, a cage-like macromolecule that preserves cellular integrity and maintains cell shape. The insolubility and heterogeneity of peptidoglycan pose a challenge to conventional structural analyses. Here we use solid-state NMR combined with specific isotopic labeling to probe a key structural feature of the Staphylococcus aureus peptidoglycan quantitatively and nondestructively. We observed that both the cell-wall morphology and the peptidoglycan structure are functions of growth stage in S. aureus synthetic medium (SASM). Specifically, S. aureus cells at stationary phase have thicker cell walls with nonuniformly thickened septa compared to cells in exponential phase, and remarkably, 12% (±2%) of the stems in their peptidoglycan do not have pentaglycine bridges attached. Mechanistically, we determined that these observations are triggered by the depletion of glycine in the nutrient medium, which is coincident with the start of the stationary phase, and that the production of the structurally altered peptidoglycan can be prevented by the addition of excess glycine. We also demonstrated that the structural changes primarily arise within newly synthesized peptidoglycan rather than through the modification of previously synthesized peptidoglycan. Collectively, our observations emphasize the plasticity in bacterial cell-wall assembly and the possibility to manipulate peptidoglycan structure with external stimuli.

| S-EPMC3554850 | biostudies-literature

Electron-nuclear double resonance spectroscopy (and electron spin-echo envelope modulation spectroscopy) in bioinorganic chemistry.

Project description:This perspective discusses the ways that advanced paramagnetic resonance techniques, namely electron-nuclear double resonance (ENDOR) and electron spin-echo envelope modulation (ESEEM) spectroscopies, can help us understand how metal ions function in biological systems.

| S-EPMC152963 | biostudies-other

Atomic resolution protein structure determination by three-dimensional transferred echo double resonance solid-state nuclear magnetic resonance spectroscopy.

Project description:We show that quantitative internuclear (15)N-(13)C distances can be obtained in sufficient quantity to determine a complete, high-resolution structure of a moderately sized protein by magic-angle spinning solid-state NMR spectroscopy. The three-dimensional ZF-TEDOR pulse sequence is employed in combination with sparse labeling of (13)C sites in the beta1 domain of the immunoglobulin binding protein G (GB1), as obtained by bacterial expression with 1,3-(13)C or 2-(13)C-glycerol as the (13)C source. Quantitative dipolar trajectories are extracted from two-dimensional (15)N-(13)C planes, in which approximately 750 cross peaks are resolved. The experimental data are fit to exact theoretical trajectories for spin clusters (consisting of one (13)C and several (15)N each), yielding quantitative precision as good as 0.1 A for approximately 350 sites, better than 0.3 A for another 150, and approximately 1.0 A for 150 distances in the range of 5-8 A. Along with isotropic chemical shift-based (TALOS) dihedral angle restraints, the distance restraints are incorporated into simulated annealing calculations to yield a highly precise structure (backbone RMSD of 0.25+/-0.09 A), which also demonstrates excellent agreement with the most closely related crystal structure of GB1 (2QMT, bbRMSD 0.79+/-0.03 A). Moreover, side chain heavy atoms are well restrained (0.76+/-0.06 A total heavy atom RMSD). These results demonstrate for the first time that quantitative internuclear distances can be measured throughout an entire solid protein to yield an atomic-resolution structure.

| S-EPMC2832044 | biostudies-literature

Characterization of peptidoglycan in fem-deletion mutants of methicillin-resistant Staphylococcus aureus by solid-state NMR.

Project description:Compositional analysis of the peptidoglycan (PG) of a wild-type methicillin-resistant Staphylococcus aureus and its fem-deletion mutants has been performed on whole cells and cell walls using stable-isotope labeling and rotational-echo double-resonance NMR. The labels included [1-(13)C,(15)N]glycine and l-[epsilon-(15)N]lysine (for a direct measure of the number of glycyl residues in the bridging segment), [1-(13)C]glycine and l-[epsilon-(15)N]lysine (concentration of bridge links), and d-[1-(13)C]alanine and [(15)N]glycine (concentrations of cross-links and wall teichoic acids). The bridging segment length changed from 5.0 glycyl residues (wild-type strain) to 2.5 +/- 0.1 (FemB) with modest changes in cross-link and bridge-link concentrations. This accurate in situ measurement for the FemB mutant indicates a heterogeneous PG structure with 25% monoglycyl and 75% triglycyl bridges. When the bridging segment was reduced to a single glycyl residue 1.0 +/- 0.1 (FemA), the level of cross-linking decreased by more than 20%, resulting in a high concentration of open N-terminal glycyl segments.

| S-EPMC2785074 | biostudies-literature

Nonlinear two-dimensional terahertz photon echo and rotational spectroscopy in the gas phase.

Project description:Ultrafast 2D spectroscopy uses correlated multiple light-matter interactions for retrieving dynamic features that may otherwise be hidden under the linear spectrum; its extension to the terahertz regime of the electromagnetic spectrum, where a rich variety of material degrees of freedom reside, remains an experimental challenge. We report a demonstration of ultrafast 2D terahertz spectroscopy of gas-phase molecular rotors at room temperature. Using time-delayed terahertz pulse pairs, we observe photon echoes and other nonlinear signals resulting from molecular dipole orientation induced by multiple terahertz field-dipole interactions. The nonlinear time domain orientation signals are mapped into the frequency domain in 2D rotational spectra that reveal J-state-resolved nonlinear rotational dynamics. The approach enables direct observation of correlated rotational transitions and may reveal rotational coupling and relaxation pathways in the ground electronic and vibrational state.

| S-EPMC5081644 | 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