Rotational-echo Double-resonance Nuclear Magnetic Resonance Research Articles

The Carboxyl Terminus of Eremomycin Facilitates Binding to the Non-d-Ala-d-Ala Segment of the Peptidoglycan Pentapeptide Stem.

Glycopeptide antibiotics inhibit cell wall biosynthesis in Gram-positive bacteria by targeting the peptidoglycan (PG) pentapeptide stem structure (l-Ala-d-iso-Gln-l-Lys-d-Ala-d-Ala). Structures of the glycopeptide complexed with a PG stem mimic have shown that the d-Ala-d-Ala segment is the primary drug binding site; however, biochemical evidence suggests that the glycopeptide-PG interaction involves more than d-Ala-d-Ala binding. Interactions of the glycopeptide with the non-d-Ala-d-Ala segment of the PG stem were investigated using solid-state nuclear magnetic resonance (NMR). LCTA-1421, a double (15)N-enriched eremomycin derivative with a C-terminal [(15)N]amide and [(15)N]Asn amide, was complexed with whole cells of Staphylococcus aureus grown in a defined medium containing l-[3-(13)C]Ala and d-[1-(13)C]Ala in the presence of alanine racemase inhibitor alaphosphin. (13)C{(15)N} and (15)N{(13)C} rotational-echo double-resonance (REDOR) NMR measurements determined the (13)C-(15)N internuclear distances between the [(15)N]Asn amide of LCTA-1421 and the (13)C atoms of the bound d-[1-(13)C]Ala-d-[1-(13)C]Ala to be 5.1 and 4.8 Å, respectively. These measurements also determined the distance from the C-terminal [(15)N]amide of LCTA-1421 to the l-[3-(13)C]Ala of PG to be 3.5 Å. The measured REDOR distance constraints position the C-terminus of the glycopeptide in the proximity of the l-Ala of the PG, suggesting that the C-terminus of the glycopeptide interacts near the l-Ala segment of the PG stem. In vivo REDOR measurements provided structural insight into how C-terminally modified glycopeptide antibiotics operate.

The isotridecanyl side chain of plusbacin-A3 is essential for the transglycosylase inhibition of peptidoglycan biosynthesis.

Plusbacin-A3 (pb-A3) is a cyclic lipodepsipeptide that exhibits antibacterial activity against multidrug-resistant Gram-positive pathogens. Plusbacin-A3 is thought not to enter the cell cytoplasm, and its lipophilic isotridecanyl side chain is presumed to insert into the membrane bilayer, thereby facilitating either lipid II binding or some form of membrane disruption. Analogues of pb-A3, [(2)H]pb-A3 and deslipo-pb-A3, were synthesized to test membrane insertion as a key to the mode of action. [(2)H]pb-A3 has an isotopically (2)H-labeled isopropyl subunit of the lipid side chain, and deslipo-pb-A3 is missing the isotridecanyl side chain. Both analogues have the pb-A3 core structure. The loss of antimicrobial activity in deslipo-pb-A3 showed that the isotridecanyl side chain is crucial for the mode of action of the drug. However, rotational-echo double-resonance nuclear magnetic resonance characterization of [(2)H]pb-A3 bound to [1-(13)C]glycine-labeled whole cells of Staphylococcus aureus showed that the isotridecanyl side chain does not insert into the lipid membrane but instead is found in the staphylococcal cell wall, positioned near the pentaglycyl cross-bridge of the cell-wall peptidoglycan. Addition of [(2)H]pb-A3 during the growth of S. aureus resulted in the accumulation of Park's nucleotide, consistent with the inhibition of the transglycosylation step of peptidoglycan biosynthesis.

Structural Study on Small Molecules in Biological Solid Samples by Using Solid State NMR

Many small molecule drugs have molecular targets that are non-crystalline and insoluble biological matrices, such as proteins embedded in lipid membrane, cell membranes, and cell walls. To understand the action mechanisms, it is essential to determine the binding structure with atomic-level resolution. Although solution nuclear magnetic resonance (NMR) and X-ray crystallography have been used to determine molecular structures of cell membrane and membrane proteins, these methods are unable to reproduce the complexity of biological systems because either solubilization or crystallization of target molecules is requisite. For structural studies of insoluble non-crystalline biological samples, so-called "biological solids", high resolution distance measurements using solid-state NMR are indispensable techniques, of which rotational-echo double-resonance (REDOR) is one of the most widely used methods. In this paper, a brief introduction to REDOR NMR and its applications to structural studies on the antifungal amphotericin B-membrane phospholipid complex and a structural elucidation of photorespiration metabolites in plant cells without extraction or isolation is provided.

Application of REDOR NMR in natural product chemistry

Many natural products have molecular targets that are non-crystalline and insoluble biological matrices, such as proteins embedded in lipid membrane, cell membranes, and cell walls. To understand the action mechanisms, it is essential to determine the binding structure with atomic-level resolution. For structural studies of biological solids, high resolution distance measurements using solid-state nuclear magnetic resonance (NMR) are indispensable techniques, of which rotational-echo double-resonance (REDOR) is one of the most widely used methods. This feature article introduces the basic concepts of REDOR NMR and its application to the structural study of natural products in biological matrices.

Vancomycin derivative with damaged D-Ala-D-Ala binding cleft binds to cross-linked peptidoglycan in the cell wall of Staphylococcus aureus.

Des-N-methylleucyl-4-(4-fluorophenyl)benzyl-vancomycin (DFPBV) retains activity against vancomycin-resistant pathogens despite its damaged d-Ala-d-Ala binding cleft. Using solid-state nuclear magnetic resonance (NMR), a DFPBV binding site in the cell walls of whole cells of Staphylococcus aureus has been identified. The cell walls were labeled with d-[1-(13)C]alanine, [1-(13)C]glycine, and l-[epsilon-(15)N]lysine. Internuclear distances from (19)F of the DFPBV to the (13)C and (15)N labels of the cell-wall peptidoglycan were determined by rotational-echo double-resonance (REDOR) NMR. The (13)C{(19)F} and (15)N{(19)F} REDOR spectra show that, in situ, DFPBV binds to the peptidoglycan as a monomer with its vancosamine hydrophobic side chain positioned near a pentaglycyl bridge. This result suggests that the antimicrobial activity of other vancosamine-modified glycopeptides depends upon both d-Ala-d-Ala stem-terminus recognition (primary binding site) and stem-bridge recognition (secondary binding site).

Site connectivities in silver borophosphate glasses: new results from 11B{ 31P} and 31P{ 11B} rotational echo double resonance NMR spectroscopy

Local and medium range order in the glass system 50Ag 2O–50[(B 2O 3) x –(P 2O 5) 1− x ] ( x=0, 0.1, 0.2, 0.3, 0.4, 0.5, and 0.6) have been investigated by high-resolution solid state nuclear magnetic resonance (NMR) techniques. The detailed local site distribution has been derived from deconvolution analysis of the 11B and 31P magic-angle spinning (MAS) NMR signals. Quantitative information regarding the extent of boron–oxygen–phosphorus connectivity has been obtained on the basis of 11B[ 31P} and 31P{ 11B} rotational echo double resonance experiments. Incorporation of borate into silver metaphosphate glasses produces four-coordinate BO 4/2 − sites, which crosslink the metaphosphate chains, resulting in a significant increase in the glass transition temperature. Furthermore, the presence of borate favors the disproportionation of P (2) chain-like units into P (1) and P (3) sites, an effect not observed in binary alkali phosphate glasses. Finally, borate incorporation beyond x=0.3 results in the formation of neutral BO 3/2 units, indicating some net charge transfer from the borate to the phosphate network former species. This latter result corresponds to the general metal ion scavenging effect observed for phosphate species in other mixed network former glass systems. In the present system, the effect is relatively moderate, however, suggesting that anionic BO 4/2 − groups are stabilized by the interaction with the phosphate groups.

Dephasing of spin echoes by multiple heteronuclear dipolar interactions in rotational echo double resonance NMR experiments

The application of rotational echo double resonance (REDOR) nuclear magnetic resonance (NMR) for accurate distance measurements has thus far been largely restricted to isolated heteronuclear two-spin systems. In the present paper, the informational content of REDOR curves is explored for systems characterized by multi-spin interactions. To this end, numerical REDOR simulations are presented for cases in which single observe spins S are dipolarly coupled to groups of spins I in distinct geometries. To develop the utility of REDOR for characterizing dipolar couplings in unknown and/or ill-defined geometries, the validity ranges and systematic errors of certain analytical approximations are studied. In the limit of short dipolar evolution times where 0≤ ΔS S 0 ≤0.2 to 0.3 , the REDOR difference signal intensity increases approximately proportional to the square of the dipolar evolution time. Here, the curvature depends simply on the second moment M 2 characterizing the overall strength of the heterodipolar coupling, irrespective of specific molecular geometries. Fitting experimental REDOR data in this manner produces slight systematic underestimates of M 2. However, these errors tend to be counterbalanced by additional systematic errors made by neglecting weak couplings to more remote spins and distribution effects caused by disorder. Based on these findings, the results suggest a convenient method of obtaining site-resolved second moment information in disordered materials.

Introduction to rotational‐echo, double‐resonance NMR

Rotational-echo, double-resonance nuclear magnetic resonance (REDOR) is a magic-angle spinning experiment for measuring internuclear distances between heteronuclear spin pairs. The basic principles of the REDOR technique are presented. The experimental requirements necessary for quantitative REDOR measurements are also provided. ©1998 John Wiley & Sons, Inc. Concepts Magn Reson 10: 277–289, 1998

Introduction to rotational-echo, double-resonance NMR

Rotational-echo, double-resonance nuclear magnetic resonance (REDOR) is a magic-angle spinning experiment for measuring internuclear distances between heteronuclear spin pairs. The basic principles of the REDOR technique are presented. The experimental requirements necessary for quantitative REDOR measurements are also provided. ©1998 John Wiley & Sons, Inc. Concepts Magn Reson 10: 277–289, 1998

Solid-state REDOR NMR distance measurements at the ligand site of a bacterial chemotaxis membrane receptor.

The Escherichia coli serine receptor senses serine levels in the environment and transmits this information across the bacterial inner membrane to modulate a protein phosphorylation cascade which controls swimming behavior. Solid-state nuclear magnetic resonance (NMR) has been used to characterize specific structural features of the ligand binding site interactions in the intact, membrane-bound Ser receptor. Rotational-echo double-resonance (REDOR) experiments on [15N]Ser bound to a [1-13C]Phe-receptor preparation are used to measure distances between the ligand amino group and the carbonyls of two phenylalanine residues in the ligand binding pocket. The results indicate two 4.0 +/- 0.2 A distances, in excellent agreement with the X-ray crystal structure of a soluble fragment of the homologous aspartate receptor [Milburn et al. (1991) Science 254, 1342-1347]. These results confirm the similarity of the binding sites of the Asp and Ser receptors, and demonstrate the feasibility of using solid-state NMR measurements to obtain specific structural information on the 120 kDa intact receptor for probing transmembrane signaling mechanisms.

Local Packing in Glassy Polycarbonate by Carbon-Deuterium Rotational-Echo Double-Resonance Nuclear Magnetic Resonance. 2

Continuing our work of measuring intermolecular distances in 13 C, 2 H-labeled polycarbonate using rotational-echo double-resonance 13 C NMR with 1 H dephasing, we report average nearest-neighbor interchain ring-carbon to ring-deuterium and ring-carbon to methyl-deuterium distances of 2.6 and 3.2 A, respectively. The short ring-ring distance indicates that the phenyl groups are tightly packed, consistent with the observation that cooperative intermolecular motion is required for ring flips

An investigation of the ligand-binding site of the glutamine-binding protein of Escherichia coli using rotational-echo double-resonance NMR.

Glutamine-binding protein (GlnBP) is an essential component of the glutamine transport system in Escherichia coli. Rotational-echo double-resonance (REDOR) solid-state nuclear magnetic resonance (NMR) has been used to determine internuclear distances in the complex of GlnBP and its ligand, L-glutamine. REDOR, combined with strategically placed isotopic labels, is effective in obtaining model-independent internuclear distances and thus detailed structural information on the ligand-binding site of GlnBP. The existence of a single histidine residue (His156) in the binding site has provided an excellent probe for distance measurements between protein and ligand. REDOR distances up to 6.3 A have been observed between 13C labels in L-glutamine and 15N labels in His156. These results have unambiguously determined the ligand orientation with respect to the imidazole ring of His156, which is an important first step in refining the ligand-binding-site model of GlnBP in general. The measured distances were also used as constraints in restrained molecular dynamics calculations of the complex using the unliganded crystal structure of GlnBP as the starting point. The simulations clearly show consistency between calculated distances and those measured by REDOR.