1
|
Toke O. Three Decades of REDOR in Protein Science: A Solid-State NMR Technique for Distance Measurement and Spectral Editing. Int J Mol Sci 2023; 24:13637. [PMID: 37686450 PMCID: PMC10487747 DOI: 10.3390/ijms241713637] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
Solid-state NMR (ss-NMR) is a powerful tool to investigate noncrystallizable, poorly soluble molecular systems, such as membrane proteins, amyloids, and cell walls, in environments that closely resemble their physical sites of action. Rotational-echo double resonance (REDOR) is an ss-NMR methodology, which by reintroducing heteronuclear dipolar coupling under magic angle spinning conditions provides intramolecular and intermolecular distance restraints at the atomic level. In addition, REDOR can be exploited as a selection tool to filter spectra based on dipolar couplings. Used extensively as a spectroscopic ruler between isolated spins in site-specifically labeled systems and more recently as a building block in multidimensional ss-NMR pulse sequences allowing the simultaneous measurement of multiple distances, REDOR yields atomic-scale information on the structure and interaction of proteins. By extending REDOR to the determination of 1H-X dipolar couplings in recent years, the limit of measurable distances has reached ~15-20 Å, making it an attractive method of choice for the study of complex biomolecular assemblies. Following a methodological introduction including the most recent implementations, examples are discussed to illustrate the versatility of REDOR in the study of biological systems.
Collapse
Affiliation(s)
- Orsolya Toke
- Laboratory for NMR Spectroscopy, Structural Research Centre, Research Centre for Natural Sciences, 2 Magyar tudósok körútja, H-1117 Budapest, Hungary
| |
Collapse
|
2
|
Sehrawat N, Nehra E, Kumar Rohilla K, Kobayashi T, Nishiyama Y, Kumar Pandey M. Determination of the relative orientation between 15N- 1H dipolar coupling and 1H chemical shift anisotropy tensors under fast MAS solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 350:107428. [PMID: 37018911 DOI: 10.1016/j.jmr.2023.107428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 05/10/2023]
Abstract
In this work, we have proposed a proton-detected three-dimensional (3D) 15N-1H dipolar coupling (DIP)/1H chemical shift anisotropy (CSA)/1H chemical shift (CS) correlation experiment to measure the relative orientation between the 15N-1H dipolar coupling and the 1H CSA tensors under fast magic angle spinning (MAS) solid-state NMR. In the 3D correlation experiment, the 15N-1H dipolar coupling and 1H CSA tensors are recoupled using our recently developed windowless C-symmetry-based C331-ROCSA (recoupling of chemical shift anisotropy) DIPSHIFT and C331-ROCSA pulse-based methods, respectively. The 2D 15N-1H DIP/1H CSA powder lineshapes extracted using the proposed 3D correlation method are shown to be sensitive to the sign and asymmetry of the 1H CSA tensor, a feature that allows the determination of the relative orientation between the two correlating tensors with improved accuracy. The experimental method developed in this study is demonstrated on a powdered U-15N L-Histidine.HCl·H2O sample.
Collapse
Affiliation(s)
- Neelam Sehrawat
- Indian Institute of Technology (IIT) Ropar, Rupnagar, Punjab 140001, India
| | - Ekta Nehra
- Indian Institute of Technology (IIT) Ropar, Rupnagar, Punjab 140001, India
| | | | - Takeshi Kobayashi
- U.S. DOE, Ames Laboratory, Iowa State University, Ames, IA 50011-3020, United States
| | - Yusuke Nishiyama
- RIKEN-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan; JEOL Ltd., Musashino, Akishima, Tokyo 196-8558, Japan.
| | - Manoj Kumar Pandey
- Indian Institute of Technology (IIT) Ropar, Rupnagar, Punjab 140001, India.
| |
Collapse
|
3
|
Ruhland K, Frenzel R, Horny R, Nizamutdinova A, van Wüllen L, Moosburger-Will J, Horn S. Investigation of the chemical changes during thermal treatment of polyacrylonitrile and 15N-labelled polyacrylonitrile by means of in-situ FTIR and 15N NMR spectroscopy. Polym Degrad Stab 2017. [DOI: 10.1016/j.polymdegradstab.2017.10.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
4
|
Wilson BW, Parker AA, Gullion T. Determining the relative orientation between the chemical shift anisotropy and heteronuclear dipolar tensors in static solids by SEDOR NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2016; 79:1-5. [PMID: 27690305 DOI: 10.1016/j.ssnmr.2016.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/07/2016] [Accepted: 09/18/2016] [Indexed: 06/06/2023]
Abstract
The measurement of the dipolar interaction between two spins provides the distance between nuclei. A better structural picture emerges when the distance is combined with the orientation of the internuclear vector in the principal axis system of the chemical shift anisotropy tensor. The SEDOR experiment is used on a static sample of alanine to show that the orientation of the vector connecting the nitrogen and carboxylate carbon nuclei can be accurately determined in the CSA PAS of the 13C carboxylate spin.
Collapse
Affiliation(s)
- Brendan W Wilson
- Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States
| | - Arlo A Parker
- Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States
| | - Terry Gullion
- Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States.
| |
Collapse
|
5
|
Pandey MK, Nishiyama Y. Determination of relative orientation between (1)H CSA tensors from a 3D solid-state NMR experiment mediated through (1)H/(1)H RFDR mixing under ultrafast MAS. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2015; 70:15-20. [PMID: 26065628 DOI: 10.1016/j.ssnmr.2015.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/14/2015] [Accepted: 05/07/2015] [Indexed: 06/04/2023]
Abstract
To obtain piercing insights into inter and intramolecular H-bonding, and π-electron interactions measurement of (1)H chemical shift anisotropy (CSA) tensors is gradually becoming an obvious choice. While the magnitude of CSA tensors provides unique information about the local electronic environment surrounding the nucleus, the relative orientation between these tensors can offer further insights into the spatial arrangement of interacting nuclei in their respective three-dimensional (3D) space. In this regard, we present a 3D anisotropic/anisotropic/isotropic proton chemical shift (CSA/CSA/CS) correlation experiment mediated through (1)H/(1)H radio frequency-driven recoupling (RFDR) which enhances spin diffusion through recoupled (1)H-(1)H dipolar couplings under ultrafast magic angle spinning (MAS) frequency (70kHz). Relative orientation between two interacting 1H CSA tensors is obtained by fitting two-interacting (1)H CSA tensors by fitting two-dimensional (2D) (1)H/(1)H CSA/CSA spectral slices through extensive numerical simulations. To recouple (1)H CSAs in the indirect frequency dimensions of a 3D experiment we have employed γ-encoded radio frequency (RF) pulse sequence based on R-symmetry (R188(7)) with a series of phase-alternated 2700(°)-90180(°) composite-180° pulses on citric acid sample. Due to robustness of applied (1)H CSA recoupling sequence towards the presence of RF field inhomogeneity, we have successfully achieved an excellent (1)H/(1)H CSA/CSA cross-correlation efficiency between H-bonded sites of citric acid.
Collapse
Affiliation(s)
- Manoj Kumar Pandey
- RIKEN CLST-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Yusuke Nishiyama
- RIKEN CLST-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan; JEOL RESONANCE Inc., Musashino, Akishima, Tokyo 196-8558, Japan.
| |
Collapse
|
6
|
Singh M, Kim SJ, Sharif S, Preobrazhenskaya M, Schaefer J. REDOR constraints on the peptidoglycan lattice architecture of Staphylococcus aureus and its FemA mutant. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1848:363-8. [PMID: 24990251 PMCID: PMC4254387 DOI: 10.1016/j.bbamem.2014.05.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 05/22/2014] [Indexed: 11/23/2022]
Abstract
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 ¹³C¹³C spin diffusion. The observed ¹³C¹³C and ¹³C³¹P 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 ¹³C¹³C 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 analog 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.
Collapse
Affiliation(s)
- Manmilan Singh
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Sung Joon Kim
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76706, USA
| | - Shasad Sharif
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Maria Preobrazhenskaya
- Gause Institute of New Antibiotics, Russian Academy of Medical Sciences, Moscow 119021, Russia
| | - Jacob Schaefer
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA.
| |
Collapse
|
7
|
Kim SJ, Singh M, Sharif S, Schaefer J. Cross-link formation and peptidoglycan lattice assembly in the FemA mutant of Staphylococcus aureus. Biochemistry 2014; 53:1420-7. [PMID: 24517508 PMCID: PMC3985804 DOI: 10.1021/bi4016742] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/09/2014] [Indexed: 11/29/2022]
Abstract
Staphylococcus aureus FemA mutant grown in the presence of an alanine-racemase inhibitor was labeled with d-[1-(13)C]alanine, l-[3-(13)C]alanine, [2-(13)C]glycine, and l-[5-(19)F]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 (13)C-labeled alanines and (19)F-labeled lysine incorporated in the peptidoglycan. The alanyl (13)C labels were preselected for REDOR measurement by their proximity to the glycine label using (13)C-(13)C spin diffusion. The observed (13)C-(13)C and (13)C-(19)F distances are consistent with a tightly packed, hybrid architecture containing both parallel and perpendicular stems in a repeating structural motif within the peptidoglycan.
Collapse
Affiliation(s)
- Sung Joon Kim
- Department
of Chemistry and Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Manmilan Singh
- Department
of Chemistry, Washington University, St. Louis, Missouri 63130, United
States
| | - Shasad Sharif
- Department
of Chemistry, Washington University, St. Louis, Missouri 63130, United
States
| | - Jacob Schaefer
- Department
of Chemistry, Washington University, St. Louis, Missouri 63130, United
States
| |
Collapse
|
8
|
Cegelski L. REDOR NMR for drug discovery. Bioorg Med Chem Lett 2013; 23:5767-75. [PMID: 24035486 PMCID: PMC4038398 DOI: 10.1016/j.bmcl.2013.08.064] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 08/12/2013] [Accepted: 08/14/2013] [Indexed: 11/19/2022]
Abstract
Rotational-echo double-resonance (REDOR) NMR is a powerful and versatile solid-state NMR measurement that has been recruited to elucidate drug modes of action and to drive the design of new therapeutics. REDOR has been implemented to examine composition, structure, and dynamics in diverse macromolecular and whole-cell systems, including taxol-bound microtubules, enzyme-cofactor-inhibitor ternary complexes, and antibiotic-whole-cell complexes. The REDOR approach involves the integrated design of specific isotopic labeling strategies and the selection of appropriate REDOR experiments. By way of example, this digest illustrates the versatility of the REDOR approach, with an emphasis on the practical considerations of experimental design and data interpretation.
Collapse
Affiliation(s)
- Lynette Cegelski
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
9
|
Kim SJ, Singh M, Preobrazhenskaya M, Schaefer J. Staphylococcus aureus peptidoglycan stem packing by rotational-echo double resonance NMR spectroscopy. Biochemistry 2013; 52:3651-9. [PMID: 23617832 PMCID: PMC3796188 DOI: 10.1021/bi4005039] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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.
Collapse
Affiliation(s)
- Sung Joon Kim
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76706
| | - Manmilan Singh
- Department of Chemistry, Washington University, St. Louis, MO 63130
| | - Maria Preobrazhenskaya
- Gause Institute of New Antibiotics, Russian Academy of Medical Sciences, Moscow 119021, Russia
| | - Jacob Schaefer
- Department of Chemistry, Washington University, St. Louis, MO 63130
| |
Collapse
|
10
|
Kim SJ, Tanaka KSE, Dietrich E, Rafai Far A, Schaefer J. Locations of the hydrophobic side chains of lipoglycopeptides bound to the peptidoglycan of Staphylococcus aureus. Biochemistry 2013; 52:3405-14. [PMID: 23607653 DOI: 10.1021/bi400054p] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glycopeptides whose aminosugars have been modified by attachment of hydrophobic side chains are frequently active against vancomycin-resistant microorganisms. We have compared the conformations of six such fluorinated glycopeptides (with side chains of varying length) complexed to cell walls labeled with d-[1-(13)C]alanine, [1-(13)C]glycine, and l-[ε-(15)N]lysine in whole cells of Staphylococcus aureus. The internuclear distances from (19)F of the bound drug to the (13)C and (15)N labels of the peptidoglycan, and to the natural abundance (31)P of lipid membranes and teichoic acids, were determined by rotational-echo double resonance NMR. The drugs did not dimerize, and their side chains did not form membrane anchors but instead became essential parts of secondary binding to pentaglycyl bridge segments of the cell-wall peptidoglycan.
Collapse
Affiliation(s)
- Sung Joon Kim
- Department of Chemistry and Biochemistry, Baylor University , Waco, Texas 76798, United States
| | | | | | | | | |
Collapse
|
11
|
Barnes AB, Andreas LB, Huber M, Ramachandran R, van der Wel PC, Veshtort M, Griffin RG, Mehta MA. High-resolution solid-state NMR structure of alanyl-prolyl-glycine. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 200:95-100. [PMID: 19596601 PMCID: PMC4133121 DOI: 10.1016/j.jmr.2009.06.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2009] [Revised: 06/05/2009] [Accepted: 06/10/2009] [Indexed: 05/21/2023]
Abstract
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 (13)C-(13)C distance constraints are extracted by fitting rotational resonance width (R(2)W) 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 (13)C-(13)C 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 (0.02A backbone RMSD using all 11 constraints).
Collapse
Affiliation(s)
- Alexander B. Barnes
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts, Institute of Technology, Cambridge, MA 02139, USA
| | - Loren B. Andreas
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts, Institute of Technology, Cambridge, MA 02139, USA
- Department of Chemistry, Oberlin College, 119 Woodland Street, Oberlin, OH 44074, USA
| | - Matthias Huber
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts, Institute of Technology, Cambridge, MA 02139, USA
- ETH Zurich, Physical Chemistry, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Ramesh Ramachandran
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts, Institute of Technology, Cambridge, MA 02139, USA
- Indian Institute of Science Education Research (IISER), Mohali, Chandigarh, India
| | - Patrick C.A. van der Wel
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts, Institute of Technology, Cambridge, MA 02139, USA
- University of Pittsburgh, Department of Structural Biology, Pittsburgh, PA 15260, USA
| | - Mikhail Veshtort
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts, Institute of Technology, Cambridge, MA 02139, USA
| | - Robert G. Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts, Institute of Technology, Cambridge, MA 02139, USA
| | - Manish A. Mehta
- Department of Chemistry, Oberlin College, 119 Woodland Street, Oberlin, OH 44074, USA
| |
Collapse
|
12
|
Matsuoka S, Inoue M. Application of REDOR NMR in natural product chemistry. Chem Commun (Camb) 2009:5664-75. [DOI: 10.1039/b910230b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
13
|
Yu TY, Schaefer J. REDOR NMR characterization of DNA packaging in bacteriophage T4. J Mol Biol 2008; 382:1031-42. [PMID: 18703073 PMCID: PMC2633174 DOI: 10.1016/j.jmb.2008.07.077] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 07/20/2008] [Accepted: 07/26/2008] [Indexed: 11/25/2022]
Abstract
Bacteriophage T4 is a large-tailed Escherichia coli virus whose capsid is 120x86 nm. ATP-driven DNA packaging of the T4 capsid results in the loading of a 171-kb genome in less than 5 min during viral infection. We have isolated 50-mg quantities of uniform (15)N- and [epsilon-(15)N]lysine-labeled bacteriophage T4. We have also introduced (15)NH(4)(+) into filled, unlabeled capsids from synthetic medium by exchange. We have examined lyo- and cryoprotected lyophilized T4 using (15)N{(31)P} and (31)P{(15)N} rotational-echo double resonance. The results of these experiments have shown that (i) packaged DNA is in an unperturbed duplex B-form conformation; (ii) the DNA phosphate negative charge is balanced by lysyl amines (3.2%), polyamines (5.8%), and monovalent cations (40%); and (iii) 11% of lysyl amines, 40% of -NH(2) groups of polyamines, and 80% of monovalent cations within the lyophilized T4 capsid are involved in the DNA charge balance. The NMR evidence suggests that DNA enters the T4 capsid in a charge-unbalanced state. We propose that electrostatic interactions may provide free energy to supplement the nanomotor-driven T4 DNA packaging.
Collapse
Affiliation(s)
- Tsyr-Yan Yu
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | | |
Collapse
|
14
|
Kim SJ, Schaefer J. Hydrophobic side-chain length determines activity and conformational heterogeneity of a vancomycin derivative bound to the cell wall of Staphylococcus aureus. Biochemistry 2008; 47:10155-61. [PMID: 18759499 DOI: 10.1021/bi800838c] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Disaccharide-modified glycopeptides with hydrophobic side chains are active against vancomycin-resistant enterococci and vancomycin-resistant Staphylococcus aureus. The activity depends on the length of the side chain. The benzyl side chain of N-(4-fluorobenzyl)vancomycin (FBV) has the minimal length sufficient for enhancement in activity against vancomycin-resistant pathogens. The conformation of FBV bound to the peptidoglycan in whole cells of S. aureus has been determined using rotational-echo double resonance NMR by measuring internuclear distances from the (19)F of FBV to (13)C and (15)N labels incorporated into the cell-wall peptidoglycan. The hydrophobic side chain and aglycon of FBV form a cleft around the pentaglycyl bridge. FBV binds heterogeneously to the peptidoglycan as a monomer with the (19)F positioned near the middle of the pentaglycyl bridge, approximately 7 A from the bridge link. This differs from the situation for N-(4-(4-fluorophenyl)benzyl)vancomycin complexed to the peptidoglycan where the (19)F is located at the end of pentaglycyl bridge, 7 A from the cross-link.
Collapse
Affiliation(s)
- Sung Joon Kim
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA
| | | |
Collapse
|
15
|
Kim SJ, Matsuoka S, Patti GJ, Schaefer J. Vancomycin derivative with damaged D-Ala-D-Ala binding cleft binds to cross-linked peptidoglycan in the cell wall of Staphylococcus aureus. Biochemistry 2008; 47:3822-31. [PMID: 18302341 PMCID: PMC2778263 DOI: 10.1021/bi702232a] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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).
Collapse
Affiliation(s)
- Sung Joon Kim
- Department of Chemistry, Washington University, St. Louis, MO 63130
| | | | - Gary J. Patti
- Department of Chemistry, Washington University, St. Louis, MO 63130
| | - Jacob Schaefer
- Department of Chemistry, Washington University, St. Louis, MO 63130
| |
Collapse
|
16
|
Andreas LB, Mehta AK, Mehta MA. Determination of Global Structure from Distance and Orientation Constraints in Biological Solids Using Solid-State NMR Spectroscopy. J Am Chem Soc 2007; 129:15233-9. [DOI: 10.1021/ja074789q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Loren B. Andreas
- Contribution from the Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, and Department of Chemistry, Emory University, Atlanta, Georgia 30322
| | - Anil K. Mehta
- Contribution from the Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, and Department of Chemistry, Emory University, Atlanta, Georgia 30322
| | - Manish A. Mehta
- Contribution from the Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, and Department of Chemistry, Emory University, Atlanta, Georgia 30322
| |
Collapse
|
17
|
Toke O, Cegelski L, Schaefer J. Peptide antibiotics in action: Investigation of polypeptide chains in insoluble environments by rotational-echo double resonance. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2006; 1758:1314-29. [PMID: 16616889 DOI: 10.1016/j.bbamem.2006.02.031] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Revised: 02/16/2006] [Accepted: 02/28/2006] [Indexed: 11/22/2022]
Abstract
Rotational-echo double resonance (REDOR) is a solid-state NMR technique that has the capability of providing intra- and intermolecular distance and orientational restraints in non-crystallizable, poorly soluble heterogeneous molecular systems such as cell membranes and cell walls. In this review, we will present two applications of REDOR: the investigation of a magainin-related antimicrobial peptide in lipid bilayers and the study of a vancomycin-like glycopeptide in the cell walls of Staphylococcus aureus.
Collapse
Affiliation(s)
- Orsolya Toke
- Institute for Structural Chemistry, Chemical Research Center of the Hungarian Academy of Sciences, Pusztaszeri út 59-67, H-1025 Budapest, Hungary
| | | | | |
Collapse
|
18
|
Stueber D, Mehta AK, Chen Z, Wooley KL, Schaefer J. Local order in polycarbonate glasses by 13
C{19
F} rotational-echo double-resonance NMR. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/polb.20931] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
19
|
Kim SJ, Cegelski L, Preobrazhenskaya M, Schaefer J. Structures of Staphylococcus aureus cell-wall complexes with vancomycin, eremomycin, and chloroeremomycin derivatives by 13C{19F} and 15N{19F} rotational-echo double resonance. Biochemistry 2006; 45:5235-50. [PMID: 16618112 PMCID: PMC2504515 DOI: 10.1021/bi052660s] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solid-state NMR has been used to examine isolated cell walls and intact whole cells of Staphylococcus aureus complexed to five different vancomycin, eremomycin, and chloroeremomycin derivatives. The cell walls and whole cells were specifically labeled with d-[1-(13)C]alanine, or a combination of [1-(13)C]glycine and [epsilon-(15)N]lysine. Each of the bound glycopeptides had a (19)F-labeled substituent at either its C-terminus or its disaccharide position. The (13)C{(19)F} rotational-echo double-resonance (REDOR) dephasing for the cell-wall (13)C-labeled bridging pentaglycyl segment connecting a glycopeptide-complexed peptidoglycan stem with its neighboring stem indicates that the fluorine labels for all bound glycopeptides are positioned at one or the other end of the bridge. An exception is N'-(p-trifluoromethoxybenzyl)chloroeremomycin, whose hydrophobic substituent differs in length by one phenyl group compared to that of oritavancin, N'-4-[(4-chlorophenyl)benzyl)]chloroeremomycin. For this drug, the fluorine label is near the middle of the pentaglycyl segment. (15)N{(19)F} REDOR dephasing shows the proximity of the fluorine to the bridge-link site of the pentaglycyl bridge for C-terminus-substituted moieties and the cross-link site for disaccharide-substituted moieties. Full-echo REDOR spectra of cell-wall complexes from cells labeled by d-[1-(13)C]alanine (in the presence of an alanine racemase inhibitor) reveal three different carbonyl carbon chemical-shift environments, arising from the d-Ala-d-Ala binding site and the d-Ala-Gly-1 cross-link site. The REDOR results indicate a single fluorine dephasing center in each peptidoglycan complex. Molecular models of the mature cell-wall complexes that are consistent with internuclear distances obtained from (13)C{(19)F} and (15)N{(19)F} REDOR dephasing allow a correlation of structure and antimicrobial activity of the glycopeptides.
Collapse
Affiliation(s)
- Sung Joon Kim
- Department of Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | | | | | | |
Collapse
|
20
|
Cegelski L, Rice CV, O'Connor RD, Caruano AL, Tochtrop GP, Cai ZY, Covey DF, Schaefer J. Mapping the locations of estradiol and potent neuroprotective analogues in phospholipid bilayers by REDOR. Drug Dev Res 2006. [DOI: 10.1002/ddr.20048] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
21
|
Riedel K, Leppert J, Ohlenschläger O, Görlach M, Ramachandran R. Heteronuclear decoupling in rotating solids via symmetry-based adiabatic RF pulse schemes. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.07.106] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
22
|
Mehta AK, Shayo Y, Vankayalapati H, Hurley LH, Schaefer J. Structure of a Quinobenzoxazine−G-Quadruplex Complex by REDOR NMR. Biochemistry 2004; 43:11953-8. [PMID: 15379535 DOI: 10.1021/bi049697h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rotational-echo double resonance solid-state (31)P[(19)F] and (13)C[(19)F] NMR spectra have been used to locate the binding of a fluoroquinobenzoxazine to a DNA G-quadruplex labeled by phosphorothioation and [methyl-(13)C]thymidine.
Collapse
Affiliation(s)
- Anil K Mehta
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA
| | | | | | | | | |
Collapse
|
23
|
Toke O, O'Connor RD, Weldeghiorghis TK, Maloy WL, Glaser RW, Ulrich AS, Schaefer J. Structure of (KIAGKIA)3 aggregates in phospholipid bilayers by solid-state NMR. Biophys J 2004; 87:675-87. [PMID: 15240501 PMCID: PMC1304391 DOI: 10.1529/biophysj.103.032714] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2003] [Accepted: 03/04/2004] [Indexed: 11/18/2022] Open
Abstract
The interchain (13)C-(19)F dipolar coupling measured in a rotational-echo double-resonance (REDOR) experiment performed on mixtures of differently labeled KIAGKIA-KIAGKIA-KIAGKIA (K3) peptides (one specifically (13)C labeled, and the other specifically (19)F labeled) in multilamellar vesicles of dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylglycerol (1:1) shows that K3 forms close-packed clusters, primarily dimers, in bilayers at a lipid/peptide molar ratio (L/P) of 20. Dipolar coupling to additional peptides is weaker than that within the dimers, consistent with aggregates of monomers and dimers. Analysis of the sideband dephasing rates indicates a preferred orientation between the peptide chains of the dimers. The combination of the distance and orientation information from REDOR is consistent with a parallel (N-N) dimer structure in which two K3 helices intersect at a cross-angle of approximately 20 degrees. Static (19)F NMR experiments performed on K3 in oriented lipid bilayers show that between L/P = 200 and L/P = 20, K3 chains change their absolute orientation with respect to the membrane normal. This result suggests that the K3 dimers detected by REDOR at L/P = 20 are not on the surface of the bilayer but are in a membrane pore.
Collapse
Affiliation(s)
- Orsolya Toke
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA
| | | | | | | | | | | | | |
Collapse
|
24
|
Toke O, Maloy WL, Kim SJ, Blazyk J, Schaefer J. Secondary structure and lipid contact of a peptide antibiotic in phospholipid bilayers by REDOR. Biophys J 2004; 87:662-74. [PMID: 15240500 PMCID: PMC1304390 DOI: 10.1529/biophysj.103.032706] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2003] [Accepted: 03/04/2004] [Indexed: 11/18/2022] Open
Abstract
The chemical shifts of specific (13)C and (15)N labels distributed throughout KIAGKIA-KIAGKIA-KIAGKIA (K3), an amphiphilic 21-residue antimicrobial peptide, prove that the peptide is in an all alpha-helical conformation in the bilayers of multilamellar vesicles (MLVs) containing dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylglycerol (1:1). Rotational-echo double-resonance (REDOR) (13)C[(31)P] and (15)N[(31)P] experiments on the same labeled MLVs show that on partitioning into the bilayer, the peptide chains remain in contact with lipid headgroups. The amphipathic lysine side chains of K3 in particular appear to play a key role in the electrostatic interactions with the acidic lipid headgroups. In addition to the extensive peptide-headgroup contact, (13)C[(19)F] REDOR experiments on MLVs containing specifically (19)F-labeled lipid tails suggest that a portion of the peptide is surrounded by a large number of lipid acyl chains. Complementary (31)P[(19)F] REDOR experiments on these MLVs show an enhanced headgroup-lipid tail contact resulting from the presence of K3. Despite these distortions, static (31)P NMR lineshapes indicate that the lamellar structure of the membrane is preserved.
Collapse
Affiliation(s)
- Orsolya Toke
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA
| | | | | | | | | |
Collapse
|
25
|
Grage SL, Watts JA, Watts A. 2H[19F] REDOR for distance measurements in biological solids using a double resonance spectrometer. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2004; 166:1-10. [PMID: 14675813 DOI: 10.1016/j.jmr.2003.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A new approach for distance measurements in biological solids employing 2H[19F] rotational echo double resonance was developed and validated on 2H,19F-D-alanine and an imidazopyridine based inhibitor of the gastric H+/K+-ATPase. The 2H-19F double resonance experiments presented here were performed without 1H decoupling using a double resonance NMR spectrometer. In this way, it was possible to benefit from the relatively longer distance range of fluorine without the need of specialized fluorine equipment. A distance of 2.5 +/- 0.3 A was measured in the alanine derivative, indicating a gauche conformation of the two labels. In the case of the imidazopyridine compound a lower distance limit of 5.2 A was determined and is in agreement with an extended conformation of the inhibitor. Several REDOR variants were compared, and their advantages and limitations discussed. Composite fluorine dephasing pulses were found to enhance the frequency bandwidth significantly, and to reduce the dependence of the performance of the experiment on the exact choice of the transmitter frequency.
Collapse
Affiliation(s)
- Stephan L Grage
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK
| | | | | |
Collapse
|
26
|
Mehta AK, Cegelski L, O'Connor RD, Schaefer J. REDOR with a relative full-echo reference. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2003; 163:182-187. [PMID: 12852922 DOI: 10.1016/s1090-7807(03)00078-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
REDOR and REDOR-like 13C[19F] and 2H[19F] NMR experiments have been performed on lyophilized whole cells of Staphylococcus aureus. The bacteria were grown to maturity on media containing L-[13C(3)]alanine or L-[methyl-d(3)]alanine, and then complexed with the 4-fluorobiphenyl derivative of chloroeremomycin, an analogue of the widely used antibiotic, vancomycin. The position of the 19F of the drug bound in the bacterial cell wall was determined relative to L-alanine 13C and 2H labels in the peptidoglycan peptide stem that was closest to the fluorinated biphenyl moiety of the drug. These determinations were made by dipolar recoupling methods that do not require an absolute measurement of the REDOR full echo (the signal observed without rotor-synchronized dephasing pulses) of the labels in the peptide stem.
Collapse
Affiliation(s)
- Anil K Mehta
- Department of Chemistry, Washington University, One Brookings Dr., Campus Box 1134, St. Louis, MO 63130, USA
| | | | | | | |
Collapse
|
27
|
Kim SJ, Cegelski L, Studelska DR, O'Connor RD, Mehta AK, Schaefer J. Rotational-echo double resonance characterization of vancomycin binding sites in Staphylococcus aureus. Biochemistry 2002; 41:6967-77. [PMID: 12033929 DOI: 10.1021/bi0121407] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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.
Collapse
Affiliation(s)
- Sung Joon Kim
- Department of Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63130, USA
| | | | | | | | | | | |
Collapse
|
28
|
O'Connor RD, Byers JA, Arnold WD, Oldfield E, Wooley KL, Schaefer J. Chain Packing in Ethoxyphenyl−Polycarbonate by 13C{2H} REDOR. Macromolecules 2002. [DOI: 10.1021/ma010918q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Robert D. O'Connor
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, and Department of Chemistry, University of Illinois, Urbana, Illinois 61801
| | - Jeffery A. Byers
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, and Department of Chemistry, University of Illinois, Urbana, Illinois 61801
| | - William D. Arnold
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, and Department of Chemistry, University of Illinois, Urbana, Illinois 61801
| | - Eric Oldfield
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, and Department of Chemistry, University of Illinois, Urbana, Illinois 61801
| | - Karen L. Wooley
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, and Department of Chemistry, University of Illinois, Urbana, Illinois 61801
| | - Jacob Schaefer
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, and Department of Chemistry, University of Illinois, Urbana, Illinois 61801
| |
Collapse
|
29
|
O'Connor RD, Poliks B, Bolton DH, Goetz JM, Byers JA, Wooley KL, Schaefer J. Chain Packing in Linear Phenol−Polycarbonate by 13C{2H} REDOR. Macromolecules 2002. [DOI: 10.1021/ma010919i] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert D. O'Connor
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, and Department of Physics, Binghamton University, Binghamton, New York 13902
| | - Barbara Poliks
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, and Department of Physics, Binghamton University, Binghamton, New York 13902
| | - Daniel H. Bolton
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, and Department of Physics, Binghamton University, Binghamton, New York 13902
| | - Jon M. Goetz
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, and Department of Physics, Binghamton University, Binghamton, New York 13902
| | - Jeffery A. Byers
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, and Department of Physics, Binghamton University, Binghamton, New York 13902
| | - Karen L. Wooley
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, and Department of Physics, Binghamton University, Binghamton, New York 13902
| | - Jacob Schaefer
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, and Department of Physics, Binghamton University, Binghamton, New York 13902
| |
Collapse
|