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Vugmeyster L, Ostrovsky D, Fu R. Carbon-detected deuterium solid-state NMR rotating frame relaxation measurements for protein methyl groups under magic angle spinning. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2024; 130:101922. [PMID: 38417233 PMCID: PMC11015826 DOI: 10.1016/j.ssnmr.2024.101922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024]
Abstract
Deuterium rotating frame solid-state NMR relaxation measurements (2H R1ρ) are important tools in quantitative studies of molecular dynamics. We demonstrate how 2H to 13C cross-polarization (CP) approaches under 10-40 kHz magic angle spinning rates can be combined with the 2H R1ρ blocks to allow for extension of deuterium rotating frame relaxation studies to methyl groups in biomolecules. This extension permits detection on the 13C nuclei and, hence, for the achievement of site-specific resolution. The measurements are demonstrated using a nine-residue low complexity peptide with the sequence GGKGMGFGL, in which a single selective -13CD3 label is placed at the methionine residue. Carbon-detected measurements are compared with the deuterium direct-detection results, which allows for fine-tuning of experimental approaches. In particular, we show how the adiabatic respiration CP scheme and the double adiabatic sweep on the 2H and 13C channels can be combined with the 2H R1ρ relaxation rates measurement. Off-resonance 2H R1ρ measurements are investigated in addition to the on-resonance condition, as they extent the range of effective spin-locking field.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, CO, 80204, USA.
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver, CO, 80204, USA
| | - Riqiang Fu
- National High Field Magnetic Laboratory, Tallahassee, FL, 32310, USA
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2
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Akbey Ü. Site-specific protein backbone deuterium 2H α quadrupolar patterns by proton-detected quadruple-resonance 3D 2H αc αNH MAS NMR spectroscopy. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2023; 125:101861. [PMID: 36989552 DOI: 10.1016/j.ssnmr.2023.101861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/23/2023] [Accepted: 03/06/2023] [Indexed: 06/11/2023]
Abstract
A novel deuterium-excited and proton-detected quadruple-resonance three-dimensional (3D) 2HαcαNH MAS nuclear magnetic resonance (NMR) method is presented to obtain site-specific 2Hα deuterium quadrupolar couplings from protein backbone, as an extension to the 2D version of the experiment reported earlier. Proton-detection results in high sensitivity compared to the heteronuclei detection methods. Utilizing four independent radiofrequency (RF) channels (quadruple-resonance), we managed to excite the 2Hα, then transfer deuterium polarization to its attached Cα, followed by polarization transfers to the neighboring backbone nitrogen and then to the amide proton for detection. This experiment results in an easy to interpret HSQC-like 2D 1H-15N fingerprint NMR spectrum, which contains site-specific deuterium quadrupolar patterns in the indirect third dimension. Provided that four-channel NMR probe technology is available, the setup of the 2HαcαNH experiment is relatively straightforward, by using low power deuterium excitation and polarization transfer schemes we have been developing. To our knowledge, this is the first demonstration of a quadruple-resonance MAS NMR experiment to link 2Hα quadrupolar couplings to proton-detection, extending our previous triple-resonance demonstrations. Distortion-free excitation and polarization transfer of ∼160-170 kHz 2Hα quadrupolar coupling were presented by using a deuterium RF strength of ∼20 kHz. From these 2Hα patterns, an average backbone order parameter of S = 0.92 was determined on a deuterated SH3 sample, with an average η = 0.22. These indicate that SH3 backbone represents sizable dynamics in the microsecond timescale where the 2Hα lineshape is sensitive. Moreover, site-specific 2Hα T1 relaxation times were obtained for a proof of concept. This 3D 2HαcαNH NMR experiment has the potential to determine structure and dynamics of perdeuterated proteins by utilizing deuterium as a novel reporter.
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Affiliation(s)
- Ümit Akbey
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, 15261, United States.
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3
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Welton C, Raval P, Trébosc J, Reddy GNM. Chemical exchange of labile protons by deuterium enables selective detection of pharmaceuticals in solid formulations. Chem Commun (Camb) 2022; 58:11551-11554. [PMID: 36165029 DOI: 10.1039/d2cc04585k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemically assisted swapping of labile protons by deuterons is presented for amino acids, polysaccharides, pharmaceutical compounds, and their solid formulations. Solid-state packing interactions in these compounds are elucidated by 1H-2H isotope correlation NMR spectroscopy (iCOSY). A minuscule concentration of dopamine, 5 wt% or ∼100 μg, in a solid formulation can be detected by 2H NMR at 28.2 T (1H, 1200 MHz) in under a minute.
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Affiliation(s)
- Claire Welton
- University of Lille, CNRS, Centrale Lille Institut, Univ. Artois, UMR 8181 - UCCS - Unité de Catalyse et Chimie du Solide, F-59000, Lille, France.
| | - Parth Raval
- University of Lille, CNRS, Centrale Lille Institut, Univ. Artois, UMR 8181 - UCCS - Unité de Catalyse et Chimie du Solide, F-59000, Lille, France.
| | - Julien Trébosc
- University of Lille, CNRS, INRAE, Centrale Lille, Univ. Artois, FR 2638 - IMEC - Institut Michel-Eugène Chevreul, F-59000, Lille, France
| | - G N Manjunatha Reddy
- University of Lille, CNRS, Centrale Lille Institut, Univ. Artois, UMR 8181 - UCCS - Unité de Catalyse et Chimie du Solide, F-59000, Lille, France.
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Borcik C, Eason IR, Vanderloop B, Wylie BJ. 2H, 13C-Cholesterol for Dynamics and Structural Studies of Biological Membranes. ACS OMEGA 2022; 7:17151-17160. [PMID: 35647452 PMCID: PMC9134247 DOI: 10.1021/acsomega.2c00796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/08/2022] [Indexed: 05/19/2023]
Abstract
We present a cost-effective means of 2H and 13C enrichment of cholesterol. This method exploits the metabolism of 2H,13C-acetate into acetyl-CoA, the first substrate in the mevalonate pathway. We show that growing the cholesterol producing strain RH6827 of Saccharomyces cerevisiae in 2H,13C-acetate-enriched minimal media produces a skip-labeled pattern of deuteration. We characterize this cholesterol labeling pattern by mass spectrometry and solid-state nuclear magnetic resonance spectroscopy. It is confirmed that most 2H nuclei retain their original 2H-13C bonds from acetate throughout the biosynthetic pathway. We then quantify the changes in 13C chemical shifts brought by deuteration and the impact upon 13C-13C spin diffusion. Finally, using adiabatic rotor echo short pulse irradiation cross-polarization (RESPIRATIONCP), we acquire the 2H-13C correlation spectra to site specifically quantify cholesterol dynamics in two model membranes as a function of temperature. These measurements show that cholesterol acyl chains at physiological temperatures in mixtures of 1-palmitoyl-2-oleoylphosphatidylcholine (POPC), sphingomyelin, and cholesterol are more dynamic than cholesterol in POPC. However, this overall change in motion is not uniform across the cholesterol molecule. This result establishes that this cholesterol labeling pattern will have great utility in reporting on cholesterol dynamics and orientation in a variety of environments and with different membrane bilayer components, as well as monitoring the mevalonate pathway product interactions within the bilayer. Finally, the flexibility and universality of acetate labeling will allow this technique to be widely applied to a large range of lipids and other natural products.
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Vugmeyster L, Ostrovsky D, Greenwood A, Fu R. Deuteron rotating frame relaxation for the detection of slow motions in rotating solids. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 337:107171. [PMID: 35219160 PMCID: PMC8994516 DOI: 10.1016/j.jmr.2022.107171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 06/06/2023]
Abstract
We demonstrate experimental and computational approaches for measuring 2H rotating frame NMR relaxation for solid samples under magic angle spinning (MAS) conditions. The relaxation properties of the deuterium spin-1 system are dominated by the reorientation of the anisotropic quadrupolar tensors, with the effective quadrupolar coupling constant around 55 kHz for methyl groups. The technique is demonstrated using the model compound dimethyl-sulfone at MAS rates of 10 and 60 kHz as well as for an amyloid fibril sample comprising an amyloid-β (1-40) protein with a selective methyl group labeled in the disordered domain of the fibrils, at an MAS rate of 8 kHz. For both systems, the motional parameters fall well within the ranges determined by other techniques, thus validating its feasibility. Experimental and computational factors such as i) the probe's radio frequency inhomogeneity profiles, ii) rotary resonances at conditions for which the spin-lock field strength matches the half- or full-integer of the MAS rate, iii) the choice of MAS rates and spin-lock field strengths, and iv) simulations that account for the interconversion of multiple coherences for the spin-1 system under MAS and deviations from the analytical Redfield treatment are thoroughly considered.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, CO 80204, USA.
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver, CO 80204, USA
| | - Alexander Greenwood
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221-0172, USA
| | - Riqiang Fu
- National High Field Magnetic Laboratory, Tallahassee, FL 32310, USA
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Akbey Ü. Site-specific protein methyl deuterium quadrupolar patterns by proton-detected 3D 2H- 13C- 1H MAS NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2022; 76:23-28. [PMID: 34997409 DOI: 10.1007/s10858-021-00388-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Determination of protein structure and dynamics is key to understand the mechanism of protein action. Perdeuterated proteins have been used to obtain high resolution/sensitivty NMR experiments via proton-detection. These methods utilizes 1H, 13C and 15N nuclei for chemical shift dispersion or relaxation probes, despite the existing abundant deuterons. However, a high-sensitivity NMR method to utilize deuterons and e.g. determine site-specific deuterium quadrupolar pattern information has been lacking due to technical difficulties associated with deuterium's large quadrupolar couplings. Here, we present a novel deuterium-excited and proton-detected three-dimensional 2H-13C-1H MAS NMR experiment to utilize deuterons and to obtain site-specific methyl 2H quadrupolar patterns on detuterated proteins for the first time. A high-resolution fingerprint 1H-15N HSQC-spectrum is correlated with the anisotropic deuterium quadrupolar tensor in the third dimension. Results from a model perdeuterated protein has been shown.
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Affiliation(s)
- Ümit Akbey
- Radboud University, Magnetic Resonance Research Center, Institute for Molecules and Materials, Nijmegen, The Netherlands.
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, USA.
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Gelenter MD, Chen KJ, Hong M. Off-resonance 13C- 2H REDOR NMR for site-resolved studies of molecular motion. JOURNAL OF BIOMOLECULAR NMR 2021; 75:335-345. [PMID: 34342847 PMCID: PMC8830769 DOI: 10.1007/s10858-021-00377-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/19/2021] [Indexed: 06/06/2023]
Abstract
We introduce a 13C-2H Rotational Echo DOuble Resonance (REDOR) technique that uses the difference between on-resonance and off-resonance 2H irradiation to detect dynamic segments in deuterated molecules. By selectively inverting specific regions of the 2H magic-angle spinning (MAS) sideband manifold to recouple some of the deuterons to nearby carbons, we distinguish dynamic and rigid residues in 1D and 2D 13C spectra. We demonstrate this approach on deuterated GB1, H/D exchanged GB1, and perdeuterated bacterial cellulose. Numerical simulations reproduce the measured mixing-time and 2H carrier-frequency dependence of the REDOR dephasing of bacterial cellulose. Combining numerical simulations with experiments thus allow the extraction of motionally averaged quadrupolar couplings from REDOR dephasing values.
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Affiliation(s)
- Martin D Gelenter
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, MA, 02139, Cambridge, USA
| | - Kelly J Chen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, MA, 02139, Cambridge, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, MA, 02139, Cambridge, USA.
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Vugmeyster L, Ostrovsky D, Greenwood A, Fu R. Deuteron Chemical Exchange Saturation Transfer for the Detection of Slow Motions in Rotating Solids. Front Mol Biosci 2021; 8:705572. [PMID: 34386521 PMCID: PMC8353179 DOI: 10.3389/fmolb.2021.705572] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/12/2021] [Indexed: 01/10/2023] Open
Abstract
We utilized the 2H Chemical Exchange Saturation Transfer (CEST) technique under magic angle spinning (MAS) conditions to demonstrate the feasibility of the method for studies of slow motions in the solid state. For the quadrupolar anisotropic interaction, the essence of CEST is to scan the saturation pattern over a range of offsets corresponding to the entire spectral region(s) for all conformational states involved, which translates into a range of −60–+ 60 kHz for methyl groups. Rotary resonances occur when the offsets are at half-and full-integer of the MAS rates. The choice of the optimal MAS rate is governed by the condition to reduce the number of rotary resonances in the CEST profile patterns and retain a sufficiently large quadrupolar interaction active under MAS to maintain sensitivity to motions. As examples, we applied this technique to a well-known model compound dimethyl-sulfone (DMS) as well as amyloid-β fibrils selectively deuterated at a single methyl group of A2 belonging to the disordered domain. It is demonstrated that the obtained exchange rate between the two rotameric states of DMS at elevated temperatures fell within known ranges and the fitted model parameters for the fibrils agree well with the previously obtained value using static 2H NMR techniques. Additionally, for the fibrils we have observed characteristic broadening of rotary resonances in the presence of conformational exchange, which provides implications for model selection and refinement. This work sets the stage for future potential extensions of the 2H CEST under MAS technique to multiple-labeled samples in small molecules and proteins.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver, CO, United States
| | - Alexander Greenwood
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, United States
| | - Riqiang Fu
- National High Field Magnetic Laboratory, Tallahassee, FL, United States
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9
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Akbey Ü. Dynamics of uniformly labelled solid proteins between 100 and 300 K: A 2D 2H- 13C MAS NMR approach. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 327:106974. [PMID: 33823335 DOI: 10.1016/j.jmr.2021.106974] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/20/2021] [Accepted: 03/20/2021] [Indexed: 06/12/2023]
Abstract
We describe a 2H based MAS nuclear magnetic resonance (NMR) method to obtain site-specific molecular dynamics of biomolecules. The method utilizes the use of deuterium nucleus as a spin label that is proven to be very useful in dynamics studies of solid biological and functional materials. The aim is to understand overall characteristics of protein backbone and side-chain motions for CD3, CD2 and CD groups, in terms of timescale, type and activation energy of the underlying processes. Variable temperature two-dimensional (2D) 2H-13C correlation MAS NMR spectra were recorded for the uniformly 2H,13C,15N labelled Alanine and microcrystalline SH3 at a broad temperature range, from 320 K down to 100 K. First, the deuterium quadrupolar-coupling constant from specific D-C sites is obtained with the 2D experiment by utilizing carbon chemical shifts. Second, the static quadrupolar patterns are obtained at 100 K. Third, variable temperature approach enabled the observation of quadrupolar pattern over different motional regimes; slow, intermediate and fast. And finally, the apparent activation energies for C-D sites are determined and compared, by evaluating the temperature induced signal intensities. This information led to the determination of the dynamic processes for different D-C sites at a broad range of temperature and motional timescales. This is a first representation of 2D 2H-13C MAS NMR approach applied to fully isotope labelled deuterated protein covering 220 K temperature range.
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Affiliation(s)
- Ümit Akbey
- Weizmann Institute of Science, Department of Chemical and Biological Physics, Perlman Chemical Sciences Building, P.O. Box 26, Rehovot 76100, Israel.
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10
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Vugmeyster L. Recent developments in deuterium solid-state NMR for the detection of slow motions in proteins. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2021; 111:101710. [PMID: 33450712 PMCID: PMC7903970 DOI: 10.1016/j.ssnmr.2020.101710] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/19/2020] [Accepted: 12/05/2020] [Indexed: 05/14/2023]
Abstract
Slow timescale dynamics in proteins are essential for a variety of biological functions spanning ligand binding, enzymatic catalysis, protein folding and misfolding regulations, as well as protein-protein and protein-nucleic acid interactions. In this review, we focus on the experimental and theoretical developments of 2H static NMR methods applicable for studies of microsecond to millisecond motional modes in proteins, particularly rotating frame relaxation dispersion (R1ρ), quadrupolar Carr-Purcell-Meiboom-Gill (QCPMG) relaxation dispersion, and quadrupolar chemical exchange saturation transfer NMR experiments (Q-CEST). With applications chosen from amyloid-β fibrils, we show the complementarity of these approaches for elucidating the complexities of conformational ensembles in disordered domains in the non-crystalline solid state, with the employment of selective deuterium labels. Combined with recent advances in relaxation dispersion backbone measurements for 15N/13C/1H nuclei, these techniques provide powerful tools for studies of biologically relevant timescale dynamics in disordered domains in the solid state.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, CO, 80204, USA.
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11
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Makrinich M, Goldbourt A. 1H-Detected quadrupolar spin-lattice relaxation measurements under magic-angle spinning solid-state NMR. Chem Commun (Camb) 2019; 55:5643-5646. [PMID: 31026003 DOI: 10.1039/c9cc01176e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Proton detection and phase-modulated pulse saturation enable the measurement of spin-lattice relaxation times of "invisible" quadrupolar nuclei with extensively large quadrupolar couplings. For nitrogen-14, efficient cross-polarization is obtained with a long-duration preparation pulse. The experiment paves the way to the characterization of a large variety of materials containing halogens, metals and more.
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Affiliation(s)
- Maria Makrinich
- School of Chemistry, Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Tel Aviv, Israel.
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12
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Gelenter MD, Hong M. Efficient 15N- 13C Polarization Transfer by Third-Spin-Assisted Pulsed Cross-Polarization Magic-Angle-Spinning NMR for Protein Structure Determination. J Phys Chem B 2018; 122:8367-8379. [PMID: 30106585 DOI: 10.1021/acs.jpcb.8b06400] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We introduce a pulsed third-spin-assisted recoupling experiment that produces high-intensity long-range 15N-13C cross peaks using low radiofrequency (rf) energy. This Proton-Enhanced Rotor-echo Short-Pulse IRradiATION Cross-Polarization (PERSPIRATIONCP) pulse sequence operates with the same principle as the Proton-Assisted Insensitive-Nuclei Cross-Polarization (PAINCP) experiment but uses only a fraction of the rf energy by replacing continuous-wave 13C and 15N irradiation with rotor-echo 90° pulses. Using formyl-Met-Leu-Phe (f-MLF) and β1 immunoglobulin binding domain of protein G (GB1) as model proteins, we demonstrate experimentally how PERSPIRATIONCP polarization transfer depends on the CP contact time, rf power, pulse flip angle, and 13C carrier frequency and compare the PERSPIRATIONCP performance with the performances of PAINCP, RESPIRATIONCP, and SPECIFICCP for measuring 15N-13C cross peaks. PERSPIRATIONCP achieves long-range 15N-13C transfer and yields higher cross peak-intensities than that of the other techniques. Numerical simulations reproduce the experimental trends and moreover indicate that PERSPIRATIONCP relies on 15N-1H and 13C-1H dipolar couplings rather than 15N-13C dipolar coupling for polarization transfer. Therefore, PERSPIRATIONCP is an rf-efficient and higher-sensitivity alternative to PAINCP for measuring long-range 15N-13C correlations, which are essential for protein resonance assignment and structure determination. Using cross peaks from two PERSPIRATIONCP 15N-13C correlation spectra as the sole distance restraints, supplemented with (φ, ψ) torsion angles obtained from chemical shifts, we calculated the GB1 structure and obtained a backbone root-mean-square deviation of 2.0 Å from the high-resolution structure of the protein. Therefore, this rf-efficient PERSPIRATIONCP method is useful for obtaining many long-range distance restraints for protein structure determination.
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Affiliation(s)
- Martin D Gelenter
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Mei Hong
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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13
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Collier KA, Sengupta S, Espinosa CA, Kelly JE, Kelz JI, Martin RW. Design and construction of a quadruple-resonance MAS NMR probe for investigation of extensively deuterated biomolecules. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 285:8-17. [PMID: 29059553 PMCID: PMC6317732 DOI: 10.1016/j.jmr.2017.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 10/03/2017] [Accepted: 10/06/2017] [Indexed: 05/22/2023]
Abstract
Extensive deuteration is frequently used in solid-state NMR studies of biomolecules because it dramatically reduces both homonuclear (1H-1H) and heteronuclear (1H-13C and 1H-15N) dipolar interactions. This approach greatly improves resolution, enables low-power rf decoupling, and facilitates 1H-detected experiments even in rigid solids at moderate MAS rates. However, the resolution enhancement is obtained at some cost due the reduced abundance of protons available for polarization transfer. Although deuterium is a useful spin-1 NMR nucleus, in typical experiments the deuterons are not directly utilized because the available probes are usually triple-tuned to 1H,13C and 15N. Here we describe a 1H/13C/2H/15N MAS ssNMR probe designed for solid-state NMR of extensively deuterated biomolecules. The probe utilizes coaxial coils, with a modified Alderman-Grant resonator for the 1H channel, and a multiply resonant solenoid for 13C/2H/15N. A coaxial tuning-tube design is used for all four channels in order to efficiently utilize the constrained physical space available inside the magnet bore. Isolation among the channels is likewise achieved using short, adjustable transmission line elements. We present benchmarks illustrating the tuning of each channel and isolation among them and the magnetic field profiles at each frequency of interest. Finally, representative NMR data are shown demonstrating the performance of both the detection and decoupling circuits.
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Affiliation(s)
- Kelsey A Collier
- Department of Physics & Astronomy, UC Irvine, Irvine, CA 92697-4575, United States
| | - Suvrajit Sengupta
- Department of Chemistry, UC Irvine, Irvine, CA 92697-2025, United States
| | | | - John E Kelly
- Department of Chemistry, UC Irvine, Irvine, CA 92697-2025, United States
| | - Jessica I Kelz
- Department of Chemistry, UC Irvine, Irvine, CA 92697-2025, United States
| | - Rachel W Martin
- Department of Chemistry, UC Irvine, Irvine, CA 92697-2025, United States; Department of Molecular Biology & Biochemistry, UC Irvine, Irvine, CA 92697-3900, United States.
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14
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Gelenter MD, Wang T, Liao SY, O'Neill H, Hong M. 2H- 13C correlation solid-state NMR for investigating dynamics and water accessibilities of proteins and carbohydrates. JOURNAL OF BIOMOLECULAR NMR 2017; 68:257-270. [PMID: 28674916 PMCID: PMC6908442 DOI: 10.1007/s10858-017-0124-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 06/29/2017] [Indexed: 05/29/2023]
Abstract
Site-specific determination of molecular motion and water accessibility by indirect detection of 2H NMR spectra has advantages over dipolar-coupling based techniques due to the large quadrupolar couplings and the ensuing high angular resolution. Recently, a Rotor Echo Short Pulse IRrAdiaTION mediated cross polarization (RESPIRATIONCP) technique was developed, which allowed efficient transfer of 2H magnetization to 13C at moderate 2H radiofrequency field strengths available on most commercial MAS probes. In this work, we investigate the 2H-13C magnetization transfer characteristics of one-bond perdeuterated CD n spin systems and two-bond H/D exchanged C-(O)-D and C-(N)-D spin systems in carbohydrates and proteins. Our results show that multi-bond, broadband 2H-13C polarization transfer can be achieved using 2H radiofrequency fields of ~50 kHz, relatively short contact times of 1.3-1.7 ms, and with sufficiently high sensitivity to enable 2D 2H-13C correlation experiments with undistorted 2H spectra in the indirect dimension. To demonstrate the utility of this 2H-13C technique for studying molecular motion, we show 2H-13C correlation spectra of perdeuterated bacterial cellulose, whose surface glucan chains exhibit a motionally averaged C6 2H quadrupolar coupling that indicates fast trans-gauche isomerization about the C5-C6 bond. In comparison, the interior chains in the microfibril core are fully immobilized. Application of the 2H-13C correlation experiment to H/D exchanged Arabidopsis primary cell walls show that the O-D quadrupolar spectra of the highest polysaccharide peaks can be fit to a two-component model, in which 74% of the spectral intensity, assigned to cellulose, has a near-rigid-limit coupling, while 26% of the intensity, assigned to matrix polysaccharides, has a weakened coupling of 50 kHz. The latter O-D quadrupolar order parameter of 0.22 is significantly smaller than previously reported C-D dipolar order parameters of 0.46-0.55 for pectins, suggesting that additional motions exist at the C-O bonds in the wall polysaccharides. 2H-13C polarization transfer profiles are also compared between statistically deuterated and H/D exchanged GB1.
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Affiliation(s)
- Martin D Gelenter
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tuo Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Shu-Yu Liao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Hugh O'Neill
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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Shi X, Rienstra CM. Site-Specific Internal Motions in GB1 Protein Microcrystals Revealed by 3D ²H-¹³C-¹³C Solid-State NMR Spectroscopy. J Am Chem Soc 2016; 138:4105-19. [PMID: 26849428 PMCID: PMC4819898 DOI: 10.1021/jacs.5b12974] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Indexed: 02/04/2023]
Abstract
(2)H quadrupolar line shapes deliver rich information about protein dynamics. A newly designed 3D (2)H-(13)C-(13)C solid-state NMR magic angle spinning (MAS) experiment is presented and demonstrated on the microcrystalline β1 immunoglobulin binding domain of protein G (GB1). The implementation of (2)H-(13)C adiabatic rotor-echo-short-pulse-irradiation cross-polarization (RESPIRATION CP) ensures the accuracy of the extracted line shapes and provides enhanced sensitivity relative to conventional CP methods. The 3D (2)H-(13)C-(13)C spectrum reveals (2)H line shapes for 140 resolved aliphatic deuterium sites. Motional-averaged (2)H quadrupolar parameters obtained from the line-shape fitting identify side-chain motions. Restricted side-chain dynamics are observed for a number of polar residues including K13, D22, E27, K31, D36, N37, D46, D47, K50, and E56, which we attribute to the effects of salt bridges and hydrogen bonds. In contrast, we observe significantly enhanced side-chain flexibility for Q2, K4, K10, E15, E19, N35, N40, and E42, due to solvent exposure and low packing density. T11, T16, and T17 side chains exhibit motions with larger amplitudes than other Thr residues due to solvent interactions. The side chains of L5, V54, and V29 are highly rigid because they are packed in the core of the protein. High correlations were demonstrated between GB1 side-chain dynamics and its biological function. Large-amplitude side-chain motions are observed for regions contacting and interacting with immunoglobulin G (IgG). In contrast, rigid side chains are primarily found for residues in the structural core of the protein that are absent from protein binding and interactions.
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Affiliation(s)
- Xiangyan Shi
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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17
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Rossini AJ, Hanrahan MP, Thuo M. Rapid acquisition of wideline MAS solid-state NMR spectra with fast MAS, proton detection, and dipolar HMQC pulse sequences. Phys Chem Chem Phys 2016; 18:25284-25295. [DOI: 10.1039/c6cp04279a] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fast MAS and proton detection are applied to rapidly acquire wideline solid-state NMR spectra of spin-1/2 and half-integer quadrupolar nuclei.
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Affiliation(s)
- Aaron J. Rossini
- Iowa State University
- Department of Chemistry
- Ames
- USA
- US DOE Ames Laboratory
| | | | - Martin Thuo
- US DOE Ames Laboratory
- Ames
- USA
- Iowa State University
- Materials Science and Engineering Department
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18
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Shen M, Trébosc J, Lafon O, Gan Z, Pourpoint F, Hu B, Chen Q, Amoureux JP. Solid-state NMR indirect detection of nuclei experiencing large anisotropic interactions using spinning sideband-selective pulses. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2015; 72:104-117. [PMID: 26411981 DOI: 10.1016/j.ssnmr.2015.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/04/2015] [Accepted: 09/04/2015] [Indexed: 06/05/2023]
Abstract
Under Magic-Angle Spinning (MAS), a long radio-frequency (rf) pulse applied on resonance achieves the selective excitation of the center-band of a wide NMR spectrum. We show herein that these rf pulses can be applied on the indirect channel of Hetero-nuclear Multiple-Quantum Correlation (HMQC) sequences, which facilitate the indirect detection via spin-1/2 isotopes of nuclei exhibiting wide spectra. Numerical simulations show that this indirect excitation method is applicable to spin-1/2 nuclei experiencing a large chemical shift anisotropy, as well as to spin-1 isotopes subject to a large quadrupole interaction, such as (14)N. The performances of the long pulses are analyzed by the numerical simulations of scalar-mediated HMQC (J-HMQC) experiments indirectly detecting spin-1/2 or spin-1 nuclei, as well as by dipolar-mediated HMQC (D-HMQC) experiments achieving indirect detection of (14)N nuclei via (1)H in crystalline γ-glycine and N-acetyl-valine samples at a MAS frequency of 60kHz. We show on these solids that for the acquisition of D-HMQC spectra between (1)H and (14)N nuclei, the efficiency of selective moderate excitation with long-pulses at the (14)N Larmor frequency, ν0((14)N), is comparable to those with strong excitation pulses at ν0((14)N) or 2ν0((14)N) frequencies, given the rf field delivered by common solid-state NMR probes. Furthermore, the D-HMQC experiments also demonstrate that the use of long pulses does not produce significant spectral distortions along the (14)N dimension. In summary, the use of center-band selective weak pulses is advantageous for HMQC experiments achieving the indirect detection of wide spectra since it (i) requires a moderate rf field, (ii) can be easily optimized, (iii) displays a high robustness to CSAs, offsets, rf-field inhomogeneities, and fluctuations in MAS frequency, and (iv) is little dependent on the quadrupolar coupling constant.
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Affiliation(s)
- Ming Shen
- UCCS, CNRS, UMR 8181, University of Lille, Villeneuve d'Ascq 59652, France; Physics Department & Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062, China
| | - Julien Trébosc
- UCCS, CNRS, UMR 8181, University of Lille, Villeneuve d'Ascq 59652, France
| | - Olivier Lafon
- UCCS, CNRS, UMR 8181, University of Lille, Villeneuve d'Ascq 59652, France.
| | - Zhehong Gan
- Center of Interdisciplinary Magnetic Resonance, NHMFL, Tallahassee, FL 32310, USA
| | | | - Bingwen Hu
- Physics Department & Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062, China
| | - Qun Chen
- Physics Department & Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062, China
| | - Jean-Paul Amoureux
- UCCS, CNRS, UMR 8181, University of Lille, Villeneuve d'Ascq 59652, France; Physics Department & Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062, China.
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Lesot P, Lafon O, Berdagué P. Correlation 2D-NMR experiments involving both 13C and 2H isotopes in oriented media: methodological developments and analytical applications. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2014; 52:595-613. [PMID: 25209071 DOI: 10.1002/mrc.4118] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/06/2014] [Accepted: 07/07/2014] [Indexed: 06/03/2023]
Abstract
Correlation 2D-NMR experiments for (13)C and (2)H isotopes turn out to be powerful methods for the assignment of the quadrupolar doublets in the (2)H NMR spectra of isotopically modified (polydeuterated or perdeuterated) or unmodified solutes in homogeneously oriented solvents, such as thermotropic systems or lyotropic liquid crystals. We review here the different pulse sequences, which have been employed, their properties, and their most salient applications. These 2D-NMR sequences have been used for (i) (13)C-(2)H correlation with and without (1)H relay and (ii) (2)H-(2)H correlation with (13)C relay. The (13)C-(2) H correlation experiments without (1)H relay have been achieved for specifically deuterated or non-selectively deuterated analytes, but also more recently for isotopically unmodified ones thanks to the high sensitivity of very high-field NMR spectrometers (21.1 T) equipped with cryogenic probes. The (13)C-(2)H correlation 2D-NMR experiments are especially useful for the assignment of overcrowded deuterium spectra because the (2)H signals are correlated to (13)C signals, which benefit from a much larger dispersion of chemical shifts. In this contribution, particular attention will be paid to the use of correlation 2D-NMR experiments for (2)H and (13)C nuclei in weakly aligning, polypeptide oriented chiral solvents, because these methods are useful and original tools for enantiomeric and enantiotopic analyses.
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Affiliation(s)
- Philippe Lesot
- RMN en Milieu Orienté, ICMMO, UMR-CNRS 8182, Université de Paris-Sud, Orsay, F-91405, Orsay CEDEX, France
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Basse K, Jain SK, Bakharev O, Nielsen NC. Efficient polarization transfer between spin-1/2 and ¹⁴N nuclei in solid-state MAS NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 244:85-89. [PMID: 24880881 DOI: 10.1016/j.jmr.2014.04.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 04/15/2014] [Accepted: 04/21/2014] [Indexed: 06/03/2023]
Abstract
Polarization transfer between spin-1/2 nuclei and quadrupolar spin-1 nuclei such as (14)N in solid-state NMR is severely challenged by the typical presence of large quadrupole coupling interactions. This has effectively prevented the use of the abundant (14)N spin as a probe to structural information and its use as an element in multi-dimensional solid-state NMR correlation experiments for assignment and structural characterization. In turn, this has been a contributing factor to the extensive use of isotope labeling in biological solid-state NMR, where (14)N is replaced with (15)N. The alternative strategy of using the abundant (14)N spins calls for methods enabling efficient polarization transfer between (14)N and its binding partners. This work demonstrates that the recently introduced (RESPIRATION)CP transfer method can be optimized to achieve efficient (1)H ↔(14)N polarization transfer under magic angle spinning conditions. The method is demonstrated numerically and experimentally on powder samples of NH4NO3 and L-alanine.
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Affiliation(s)
- Kristoffer Basse
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Sheetal Kumar Jain
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Oleg Bakharev
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Niels Chr Nielsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
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