Relative CSA–Dipolar Orientation from REDOR Sidebands

O’Connor, Robert; Schaefer, Jacob

doi:10.1006/jmre.2001.2461

Cited by 36 publications

(37 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Expanded frequency scale plots of the carbonyl carbon regions of the REDOR spectra after eight rotor cycles of dipolar evolution (only the signal of the labeled carbonyl carbon nearest to 19 F is dephased) are shown to the right of the figure. The dissimilarity of the REDOR difference and full-echo spectra (dotted lines) indicates an orientational preference for the 13 C-19 F internuclear vector relative to the [ 13 C]carbonyl carbon chemical shift tensor(51).…”

mentioning

confidence: 99%

Rotational-Echo Double Resonance Characterization of Vancomycin Binding Sites in Staphylococcus aureus

et al. 2002

Self Cite

View full text Add to dashboard Cite

Solid-state NMR experiments with stable isotope-labeled Staphylococcus aureus have provided insight into the structure of the peptidoglycan binding site of a potent fluorobiphenyl derivative of chloroeremomycin (Eli Lilly LY329332). Rotational-echo double resonance (REDOR) NMR provided internuclear distances from the 19F of this glycopeptide antibiotic to natural-abundance 31P and to specific 13C and 15N labels biosynthetically incorporated into the bacteria from labeled alanine, glycine, or lysine in the growth medium. Results from experiments with intact late log phase bacteria and cell walls indicated homogeneous drug-peptidoglycan binding. Drug dimers were not detected in situ, and the hydrophobic fluorobiphenyl group of LY329332 did not insert into the bilayer membrane. A model of the binding site consistent with the REDOR results positions the vancomycin cleft around an un-cross-linked D-Ala-D-Ala peptide stem with the fluorobiphenyl moiety of the antibiotic near the base of a second, proximate stem in a locally ordered peptidoglycan matrix.

show abstract

mentioning

confidence: 99%

Rotational-Echo Double Resonance Characterization of Vancomycin Binding Sites in Staphylococcus aureus

et al. 2002

Self Cite

View full text Add to dashboard Cite

show abstract

“…A plot of Δ S/S 0 with respect to time ( t=NT r ), yields the dipolar coupling constant and hence the internuclear distance ( r IS ). The distance and spin-pair concentration (asymptotic dephasing maximum) were allowed to vary to minimize the root-mean-square deviation between the experimental and calculated dephasing (12). …”

Section: Methodsmentioning

confidence: 99%

REDOR constraints on the peptidoglycan lattice architecture of Staphylococcus aureus and its FemA mutant

Singh¹,

Kim²,

Sharif³

et al. 2015

Biochimica et Biophysica Acta (BBA) - Biomembranes

Self Cite

View full text Add to dashboard Cite

The peptidoglycan of Gram-positive bacteria consists of glycan chains with attached short peptide stems cross-linked to one another by glycyl bridges. The bridge of Staphylococcus aureus has five glycyl units and that of its FemA mutant has one. These long- and short-bridge cross-links create totally different cell-wall architectures. S. aureus and its FemA mutant grown in the presence of an alanine-racemase inhibitor were labeled with D-[1-13C]alanine, L-[3-13C]alanine, [2-13C]glycine, and L-[5-19F]lysine to characterize some details of the peptidoglycan tertiary structure. Rotational-echo double-resonance (REDOR) NMR of isolated cell walls was used to measure internuclear distances between 13C-labeled alanines and 19F-labeled lysine incorporated in the peptidoglycan. The alanyl 13C labels in the parent strain were preselected for C{F} and C{P} REDOR measurement by their proximity to the glycine label using 13C-13C spin diffusion. The observed 13C-13C and 13C-31P distances are consistent with a tightly packed architecture containing only parallel stems in a repeating structural motif within the peptidoglycan. Dante selection of D-alanine and L-alanine frequencies followed by 13C-13C spin diffusion rules out scrambling of carbon labels. Cell walls of FemA were also labeled by a combination of D-[1-13C]alanine and L-[15N]alanine. Proximity of chains was measured by C{N} and N{C} REDOR distances and asymptotic plateaus, and both were consistent with a mixed-geometry model. Binding of an 19F-labeled eremomycin analogue in the FemA cell wall matches that of binding to the parent-strain cell wall and reveals the proximity of parallel stems in the alternating parallel-perpendicular mixed-geometry model for the FemA peptidoglycan lattice.

show abstract

“…6) of each sideband to numerical simulations explained previously [32]. The weighted χ 2 ,

χ_{ν}^{2}

, was minimized to fit the data.…”

Section: Experimental Methodsmentioning

confidence: 99%

High-resolution solid-state NMR structure of Alanyl-Prolyl-Glycine

Barnes¹,

Andreas²,

Huber³

et al. 2009

Journal of Magnetic Resonance

View full text Add to dashboard Cite

We present a de novo high-resolution structure of the peptide Alanyl-Prolyl-Glycine using a combination of sensitive solid-state NMR techniques that each yield precise structural constraints. High-quality 13C–13C distance constraints are extracted by fitting rotational resonance width (R2W) experiments using Multimode Multipole Floquet Theory and experimental chemical shift anisotropy (CSA) orientations. In this strategy, a structure is first calculated using DANTE-REDOR and torsion angle measurements and the resulting relative CSA orientations are used as an input parameter in the 13C–13C distance calculations. Finally, a refined structure is calculated using all the constraints. We investigate the effect of different structural constraints on structure quality, as determined by comparison to the crystal structure and also self-consistency of the calculated structures. Inclusion of all or subsets of these constraints into CNS calculations resulted in high-quality structures (0.02 Å backbone RMSD using all 11 constraints).

show abstract

Relative CSA–Dipolar Orientation from REDOR Sidebands

Cited by 36 publications

References 32 publications

Rotational-Echo Double Resonance Characterization of Vancomycin Binding Sites in Staphylococcus aureus

Rotational-Echo Double Resonance Characterization of Vancomycin Binding Sites in Staphylococcus aureus

REDOR constraints on the peptidoglycan lattice architecture of Staphylococcus aureus and its FemA mutant

High-resolution solid-state NMR structure of Alanyl-Prolyl-Glycine

Contact Info

Product

Resources

About