1
|
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: 3] [Impact Index Per Article: 3.0] [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.
Collapse
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.
| |
Collapse
|
2
|
Nishiyama Y, Hou G, Agarwal V, Su Y, Ramamoorthy A. Ultrafast Magic Angle Spinning Solid-State NMR Spectroscopy: Advances in Methodology and Applications. Chem Rev 2023; 123:918-988. [PMID: 36542732 PMCID: PMC10319395 DOI: 10.1021/acs.chemrev.2c00197] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Solid-state NMR spectroscopy is one of the most commonly used techniques to study the atomic-resolution structure and dynamics of various chemical, biological, material, and pharmaceutical systems spanning multiple forms, including crystalline, liquid crystalline, fibrous, and amorphous states. Despite the unique advantages of solid-state NMR spectroscopy, its poor spectral resolution and sensitivity have severely limited the scope of this technique. Fortunately, the recent developments in probe technology that mechanically rotate the sample fast (100 kHz and above) to obtain "solution-like" NMR spectra of solids with higher resolution and sensitivity have opened numerous avenues for the development of novel NMR techniques and their applications to study a plethora of solids including globular and membrane-associated proteins, self-assembled protein aggregates such as amyloid fibers, RNA, viral assemblies, polymorphic pharmaceuticals, metal-organic framework, bone materials, and inorganic materials. While the ultrafast-MAS continues to be developed, the minute sample quantity and radio frequency requirements, shorter recycle delays enabling fast data acquisition, the feasibility of employing proton detection, enhancement in proton spectral resolution and polarization transfer efficiency, and high sensitivity per unit sample are some of the remarkable benefits of the ultrafast-MAS technology as demonstrated by the reported studies in the literature. Although the very low sample volume and very high RF power could be limitations for some of the systems, the advantages have spurred solid-state NMR investigation into increasingly complex biological and material systems. As ultrafast-MAS NMR techniques are increasingly used in multidisciplinary research areas, further development of instrumentation, probes, and advanced methods are pursued in parallel to overcome the limitations and challenges for widespread applications. This review article is focused on providing timely comprehensive coverage of the major developments on instrumentation, theory, techniques, applications, limitations, and future scope of ultrafast-MAS technology.
Collapse
Affiliation(s)
- Yusuke Nishiyama
- JEOL Ltd., Akishima, Tokyo196-8558, Japan
- RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa230-0045, Japan
| | - Guangjin Hou
- State Key Laboratory of Catalysis, Dalian National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian116023, China
| | - Vipin Agarwal
- Tata Institute of Fundamental Research, Sy. No. 36/P, Gopanpally, Hyderabad500 046, India
| | - Yongchao Su
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey07065, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, Michigan41809-1055, United States
| |
Collapse
|
3
|
Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
Collapse
Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| |
Collapse
|
4
|
Reif B. Deuteration for High-Resolution Detection of Protons in Protein Magic Angle Spinning (MAS) Solid-State NMR. Chem Rev 2021; 122:10019-10035. [PMID: 34870415 DOI: 10.1021/acs.chemrev.1c00681] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proton detection developed in the last 20 years as the method of choice to study biomolecules in the solid state. In perdeuterated proteins, proton dipolar interactions are strongly attenuated, which allows yielding of high-resolution proton spectra. Perdeuteration and backsubstitution of exchangeable protons is essential if samples are rotated with MAS rotation frequencies below 60 kHz. Protonated samples can be investigated directly without spin dilution using proton detection methods in case the MAS frequency exceeds 110 kHz. This review summarizes labeling strategies and the spectroscopic methods to perform experiments that yield assignments, quantitative information on structure, and dynamics using perdeuterated samples. Techniques for solvent suppression, H/D exchange, and deuterium spectroscopy are discussed. Finally, experimental and theoretical results that allow estimation of the sensitivity of proton detected experiments as a function of the MAS frequency and the external B0 field in a perdeuterated environment are compiled.
Collapse
Affiliation(s)
- Bernd Reif
- Bayerisches NMR Zentrum (BNMRZ) at the Department of Chemistry, Technische Universität München (TUM), Lichtenbergstr. 4, 85747 Garching, Germany.,Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Institute of Structural Biology (STB), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| |
Collapse
|
5
|
Duong NT, Kuprov I, Nishiyama Y. Indirect detection of 10B (I = 3) overtone NMR at very fast magic angle spinning. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 291:27-31. [PMID: 29677601 DOI: 10.1016/j.jmr.2018.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/05/2018] [Accepted: 04/09/2018] [Indexed: 06/08/2023]
Abstract
The application of overtone nuclear magnetic resonance (OT NMR) to symmetric spin transitions of integer quadrupolar nuclei is of considerable interest since this transition is immune to the first-order quadrupolar interaction, thus resulting in narrow NMR lines. Owing to its roles in nature and its high natural abundance, 14N (I = 1) OT NMR has been explored, in which the indirect and/or direct acquisitions of 14N OT were experimentally demonstrated. However, other than 14N nucleus, no OT NMR observation of other integer quadrupolar nuclei has been reported in the literature. In this work, we extend the application of OT NMR to another integer quadrupolar nucleus, namely 10B (I = 3). However, this is not straightforward owing to the unfavorable characteristics of 10B isotope. Here, for the first time, we present the selective acquisition of 10B central (-1 ↔ +1) OT NMR via detection of 1H nuclei on perborate monohydrate sample. Numerical calculations are in a good agreement with the experimental results. Both show that the optimal sensitivity is achieved when the carrier frequency is applied at the second OT spinning sideband, i.e. an offset of twice of the spinning frequency from the center band.
Collapse
Affiliation(s)
- Nghia Tuan Duong
- RIKEN CLST-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Ilya Kuprov
- School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Yusuke Nishiyama
- RIKEN CLST-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan; JEOL RESONANCE Inc., Musashino, Akishima, Tokyo 196-8558, Japan.
| |
Collapse
|
6
|
Asakura T, Nishimura A, Kametani S, Kawanishi S, Aoki A, Suzuki F, Kaji H, Naito A. Refined Crystal Structure of Samia cynthia ricini Silk Fibroin Revealed by Solid-State NMR Investigations. Biomacromolecules 2017; 18:1965-1974. [DOI: 10.1021/acs.biomac.7b00441] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Tetsuo Asakura
- Department
of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Akio Nishimura
- Department
of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Shunsuke Kametani
- Department
of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Shuto Kawanishi
- Department
of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Akihiro Aoki
- Department
of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Furitsu Suzuki
- Institute
for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hironori Kaji
- Institute
for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Akira Naito
- Department
of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| |
Collapse
|
7
|
Agarwal RA, Mukherjee S. One dimensional coordination polymers of Cd(II) and Zn(II): Synthesis, structure, polar packing through strong inter-chain hydrogen bonding and gas adsorption studies. Polyhedron 2016. [DOI: 10.1016/j.poly.2015.12.061] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
8
|
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.
Collapse
Affiliation(s)
- Philippe Lesot
- RMN en Milieu Orienté, ICMMO, UMR-CNRS 8182, Université de Paris-Sud, Orsay, F-91405, Orsay CEDEX, France
| | | | | |
Collapse
|
9
|
Linser R, Sarkar R, Krushelnitzky A, Mainz A, Reif B. Dynamics in the solid-state: perspectives for the investigation of amyloid aggregates, membrane proteins and soluble protein complexes. JOURNAL OF BIOMOLECULAR NMR 2014; 59:1-14. [PMID: 24595988 DOI: 10.1007/s10858-014-9822-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/26/2014] [Indexed: 06/03/2023]
Abstract
Aggregates formed by amyloidogenic peptides and proteins and reconstituted membrane protein preparations differ significantly in terms of the spectral quality that they display in solid-state NMR experiments. Structural heterogeneity and dynamics can both in principle account for that observation. This perspectives article aims to point out challenges and limitations, but also potential opportunities in the investigation of these systems.
Collapse
Affiliation(s)
- Rasmus Linser
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA, 02115, USA
| | | | | | | | | |
Collapse
|
10
|
Akbey Ü, Nieuwkoop AJ, Wegner S, Voreck A, Kunert B, Bandara P, Engelke F, Nielsen NC, Oschkinat H. Quadruple-Resonance Magic-Angle Spinning NMR Spectroscopy of Deuterated Solid Proteins. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201308927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
11
|
Akbey Ü, Nieuwkoop AJ, Wegner S, Voreck A, Kunert B, Bandara P, Engelke F, Nielsen NC, Oschkinat H. Quadruple-resonance magic-angle spinning NMR spectroscopy of deuterated solid proteins. Angew Chem Int Ed Engl 2014; 53:2438-42. [PMID: 24474388 DOI: 10.1002/anie.201308927] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 12/03/2013] [Indexed: 11/12/2022]
Abstract
(1)H-detected magic-angle spinning NMR experiments facilitate structural biology of solid proteins, which requires using deuterated proteins. However, often amide protons cannot be back-exchanged sufficiently, because of a possible lack of solvent exposure. For such systems, using (2)H excitation instead of (1)H excitation can be beneficial because of the larger abundance and shorter longitudinal relaxation time, T1, of deuterium. A new structure determination approach, "quadruple-resonance NMR spectroscopy", is presented which relies on an efficient (2)H-excitation and (2)H-(13)C cross-polarization (CP) step, combined with (1)H detection. We show that by using (2)H-excited experiments better sensitivity is possible on an SH3 sample recrystallized from 30 % H2O. For a membrane protein, the ABC transporter ArtMP in native lipid bilayers, different sets of signals can be observed from different initial polarization pathways, which can be evaluated further to extract structural properties.
Collapse
Affiliation(s)
- Ümit Akbey
- Leibniz Institute for Molecular Pharmacology, Robert Roessle Str. 10, 13125 Berlin (Germany).
| | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Jain SK, Nielsen AB, Hiller M, Handel L, Ernst M, Oschkinat H, Akbey Ü, Nielsen NC. Low-power polarization transfer between deuterons and spin-1/2 nuclei using adiabatic RESPIRATIONCP in solid-state NMR. Phys Chem Chem Phys 2014; 16:2827-30. [DOI: 10.1039/c3cp54419b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
13
|
Shi X, Yarger JL, Holland GP. 2H-13C HETCOR MAS NMR for indirect detection of 2H quadrupole patterns and spin-lattice relaxation rates. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 226:1-12. [PMID: 23174312 DOI: 10.1016/j.jmr.2012.10.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/17/2012] [Accepted: 10/22/2012] [Indexed: 06/01/2023]
Abstract
Two-dimensional (2D) cross-polarization magic angle spinning (CP-MAS) (2)H-(13)C heteronuclear correlation (HETCOR) experiments were utilized to indirectly detect site-specific deuterium MAS powder patterns. The (2)H-(13)C cross-polarization efficiency is orientation-dependent and non-uniform for all crystallites. This leads to difficulty in extracting the correct (2)H MAS quadrupole powder patterns. In order to obtain accurate deuterium line shapes, (13)C spin lock rf field, spin lock rf ramp and CP contact time were carefully calibrated with the assistance of theoretical simulations. The extracted quadrupole patterns for U-[(2)H/(13)C/(15)N]-alanine indicate that the methyl deuterium undergoes classic, three-site jumping in the fast motion regime (10(-8)-10(-12)s) and the methine deuterium has a rigid deuterium powder pattern. For U-[(2)H/(13)C/(15)N]-phenylalanine, indirectly detected deuterium line shapes illustrate that the aromatic ring undergoes 180° flips in the fast motion regime while (2)Hβ and (2)Hα are completely rigid. The experimental deuterium line shapes for U-[(2)H/(13)C/(15)N]-proline reflect that (2)Hβ, (2)Hγ and (2)Hδ are subjected to fast, two-site reorientations at an angle of (15±5)°, (30±5)° and (25±10)° respectively. In addition, an approach that combines a composite inversion pulse with (2)H-(13)C CP-MAS is applied to measure (2)H spin-lattice relaxation times in a site-specific, (13)C-detected fashion.
Collapse
Affiliation(s)
- Xiangyan Shi
- Department of Chemistry and Biochemistry, Magnetic Resonance Research Center, Arizona State University, Tempe, AZ 85287-1604, United States
| | | | | |
Collapse
|
14
|
Akbey U, Rossum BJV, Oschkinat H. Practical aspects of high-sensitivity multidimensional ¹³C MAS NMR spectroscopy of perdeuterated proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 217:77-85. [PMID: 22440428 DOI: 10.1016/j.jmr.2012.02.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 02/13/2012] [Accepted: 02/18/2012] [Indexed: 05/31/2023]
Abstract
The double nucleus enhanced recoupling (DONER) experiment employs simultaneous irradiation of protons and deuterons to promote spin diffusion processes in a perdeuterated protein. This results in 4-5 times higher sensitivity in 2D (13)C-(13)C correlation experiments as compared to PDSD [1]. Here, a quantitative comparison of PDSD, (1)H-DARR, (2)H-DARR, and (1)H+(2)H DONER has been performed to analyze the influence of spin diffusion on polarization transfer processes. Cross peak buildup curves were analyzed to obtain guidelines for choosing the best experimental parameters. The largest cross peak intensities were observed for the DONER experiments. The fastest build-up rate was observed in the (2)H-DARR experiment within a buildup range of ∼18-45 ms, whereas values between 24 and 69 ms are observed for the DONER experiment. Furthermore, the effects of direct excitation and cross polarization (CP) are compared. A comparison between DONER and RFDR experiments reveal ∼50% more intense cross peaks in the C(α)-CO and C(α)-C(alip) regions of the 2D (13)C-(13)C DONER spectrum applying proton CP ((1)H-(13)C). As a parameter determining the S/N in (13)C-(13)C correlation experiments, proton CP efficiency is investigated using deuterated samples with proton/deuterium ratios at 20%, 40%, and 100% H(2)O. Sufficiently strong (13)C CPMAS signal intensity is observed for such proteins even with very low proton concentration. The effect of proton and/or deuterium decoupling is analyzed at various MAS spinning frequencies. Deuterium decoupling was found most crucial for obtaining high resolution. Long range correlations are readily observed representing distances up to ∼6 Å by using DONER approach.
Collapse
Affiliation(s)
- Umit Akbey
- NMR Supported Structural Biology, Leibniz-Institut für Molekulare Pharmakologie, Robert-Roessle Str. 10, 13125 Berlin, Germany.
| | | | | |
Collapse
|
15
|
Reif B. Ultra-high resolution in MAS solid-state NMR of perdeuterated proteins: implications for structure and dynamics. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 216:1-12. [PMID: 22280934 DOI: 10.1016/j.jmr.2011.12.017] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 12/20/2011] [Accepted: 12/22/2011] [Indexed: 05/14/2023]
Abstract
High resolution proton spectra are obtained in MAS solid-state NMR in case samples are prepared using perdeuterated protein and D(2)O in the recrystallization buffer. Deuteration reduces drastically (1)H, (1)H dipolar interactions and allows to obtain amide proton line widths on the order of 20 Hz. Similarly, high-resolution proton spectra of aliphatic groups can be obtained if specifically labeled precursors for biosynthesis of methyl containing side chains are used, or if limited amounts of H(2)O in the bacterial growth medium is employed. This review summarizes recent spectroscopic developments to access structure and dynamics of biomacromolecules in the solid-state, and shows a number of applications to amyloid fibrils and membrane proteins.
Collapse
Affiliation(s)
- Bernd Reif
- Munich Center for Integrated Protein Science (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany.
| |
Collapse
|
16
|
Reif B. Deuterated peptides and proteins: structure and dynamics studies by MAS solid-state NMR. Methods Mol Biol 2012; 831:279-301. [PMID: 22167680 DOI: 10.1007/978-1-61779-480-3_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Perdeuteration and back substitution of exchangeable protons in microcrystalline proteins, in combination with recrystallization from D(2)O-containing buffers, significantly reduce (1)H, (1)H dipolar interactions. This way, amide proton line widths on the order of 20 Hz are obtained. Aliphatic protons are accessible either via specifically protonated precursors or by using low amounts of H(2)O in the bacterial growth medium. The labeling scheme enables characterization of structure and dynamics in the solid-state without dipolar truncation artifacts.
Collapse
Affiliation(s)
- Bernd Reif
- Munich Center for Integrated Protein Science (CIPSM) at Department Chemie, Technische Universität München, Garching, Germany.
| |
Collapse
|
17
|
Asami S, Reif B. Assignment strategies for aliphatic protons in the solid-state in randomly protonated proteins. JOURNAL OF BIOMOLECULAR NMR 2012; 52:31-9. [PMID: 22138787 DOI: 10.1007/s10858-011-9591-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2011] [Accepted: 09/25/2011] [Indexed: 05/26/2023]
Abstract
Biological solid-state nuclear magnetic resonance spectroscopy developed rapidly in the past two decades and emerged as an important tool for structural biology. Resonance assignment is an essential prerequisite for structure determination and the characterization of motional properties of a molecule. Experiments, which rely on carbon or nitrogen detection, suffer, however, from low sensitivity. Recently, we introduced the RAP (Reduced Adjoining Protonation) labeling scheme, which allows to detect backbone and sidechain protons with high sensitivity and resolution. We present here a (1)H-detected 3D (H)CCH experiment for assignment of backbone and sidechain proton resonances. Resolution is significantly improved by employing simultaneous (13)CO and (13)Cβ J-decoupling during evolution of the (13)Cα chemical shift. In total, ~90% of the (1)Hα-(13)Cα backbone resonances of chicken α-spectrin SH3 could be assigned.
Collapse
Affiliation(s)
- Sam Asami
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | | |
Collapse
|
18
|
Bjerring M, Paaske B, Oschkinat H, Akbey U, Nielsen NC. Rapid solid-state NMR of deuterated proteins by interleaved cross-polarization from ¹H and ²H nuclei. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 214:324-328. [PMID: 22130517 DOI: 10.1016/j.jmr.2011.10.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 10/27/2011] [Accepted: 10/29/2011] [Indexed: 05/31/2023]
Abstract
We present a novel sampling strategy, interleaving acquisition of multiple NMR spectra by exploiting initial polarization subsequently from (1)H and (2)H spins, taking advantage of their different T(1) relaxation times. Different (1)H- and (2)H-polarization based spectra are in this way simultaneously recorded improving either information content or sensitivity by adding spectra. The so-called Relaxation-optimized Acquisition of Proton Interleaved with Deuterium (RAPID) (1)H→(13)C/(2)H→(13)C CP/MAS multiple-acquisition method is demonstrated by 1D and 2D experiments using a uniformly (2)H, (15)N,(13)C-labeled α-spectrin SH3 domain sample with all or 30% back-exchanged labile (2)H to (1)H. It is demonstrated how 1D (13)C CP/MAS or 2D (13)C-(13)C correlation spectra initialized with polarization from either (1)H or (2)H may be recorded simultaneously with flexibility to be added or used individually for spectral editing. It is also shown how 2D (13)C-(13)C correlation spectra may be recorded interleaved with (2)H-(13)C correlation spectra to obtain (13)C-(13)C correlations along with information about dynamics from (2)H sideband patterns.
Collapse
Affiliation(s)
- Morten Bjerring
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | | | | | | | | |
Collapse
|
19
|
Lalli D, Schanda P, Chowdhury A, Retel J, Hiller M, Higman VA, Handel L, Agarwal V, Reif B, van Rossum B, Akbey U, Oschkinat H. Three-dimensional deuterium-carbon correlation experiments for high-resolution solid-state MAS NMR spectroscopy of large proteins. JOURNAL OF BIOMOLECULAR NMR 2011; 51:477-485. [PMID: 22038621 DOI: 10.1007/s10858-011-9578-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 09/23/2011] [Indexed: 05/31/2023]
Abstract
Well-resolved (2)H-(13)C correlation spectra, reminiscent of (1)H-(13)C correlations, are obtained for perdeuterated ubiquitin and for perdeuterated outer-membrane protein G (OmpG) from E. coli by exploiting the favorable lifetime of (2)H double-quantum (DQ) states. Sufficient signal-to-noise was achieved due to the short deuterium T (1), allowing for high repetition rates and enabling 3D experiments with a (2)H-(13)C transfer step in a reasonable time. Well-resolved 3D (2)H(DQ)-(13)C-(13)C correlations of ubiquitin and OmpG were recorded within 3.5 days each. An essentially complete assignment of (2)H(DQα) shifts and of a substantial fraction of (2)H(DQβ) shifts were obtained for ubiquitin. In the case of OmpG, (2)H(DQα) and (2)H(DQβ) chemical shifts of a considerable number of threonine, serine and leucine residues were assigned. This approach provides the basis for a general heteronuclear 3D MAS NMR assignment concept utilizing pulse sequences with (2)H(DQ)-(13)C transfer steps and evolution of deuterium double-quantum chemical shifts.
Collapse
Affiliation(s)
- Daniela Lalli
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Breen NF, Li K, Olsen GL, Drobny GP. Deuterium magic angle spinning NMR used to study the dynamics of peptides adsorbed onto polystyrene and functionalized polystyrene surfaces. J Phys Chem B 2011; 115:9452-60. [PMID: 21650191 DOI: 10.1021/jp1101829] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
LKα14 is a 14 amino acid peptide with a periodic sequence of leucine and lysine residues consistent with an amphipathic α-helix. This "hydrophobic periodicity" has been found to result in an α-helical secondary structure at air-water interfaces and on both polar and nonpolar solid polymer surfaces. In this paper, the dynamics of LKα14 peptides, selectively deuterated at a single leucine and adsorbed onto polystyrene and carboxylated polystyrene beads, are studied using (2)H magic angle spinning (MAS) solid state NMR over a 100 °C temperature range. We first demonstrate the sensitivity enhancement possible with (2)H MAS techniques, which in turn enables us to obtain high-quality (2)H NMR spectra for selectively deuterated peptides adsorbed onto solid polymer surfaces. The extensive literature shows that the dynamics of leucine side chains are sensitive to the local structural environment of the protein. Therefore, the degree to which the dynamics of leucine side chains and the backbone of the peptide LKα14 are influenced by surface proximity and surface chemistry is studied as a function of temperature with (2)H MAS NMR. It is found that the dynamics of the leucine side chains in LKα14 depend strongly upon the orientation of the polymer on the surface, which in turn depends on whether the LKα14 peptide adsorbs onto a polar or nonpolar surface. (2)H MAS line shapes therefore permit probes of surface orientation over a wide temperature range.
Collapse
Affiliation(s)
- Nicholas F Breen
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | | | | | | |
Collapse
|
21
|
Akbey Ü, Camponeschi F, van Rossum BJ, Oschkinat H. Triple Resonance Cross-Polarization for More Sensitive 13C MAS NMR Spectroscopy of Deuterated Proteins. Chemphyschem 2011; 12:2092-6. [DOI: 10.1002/cphc.201100084] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 05/12/2011] [Indexed: 11/05/2022]
|
22
|
Wei D, Akbey Ü, Paaske B, Oschkinat H, Reif B, Bjerring M, Nielsen NC. Optimal (2)H rf Pulses and (2)H-(13)C Cross-Polarization Methods for Solid-State (2)H MAS NMR of Perdeuterated Proteins. J Phys Chem Lett 2011; 2:1289-94. [PMID: 26295423 DOI: 10.1021/jz200511b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We present a novel concept for rf pulses and optimal control designed cross-polarization experiments for quadrupolar nuclei. The methods are demonstrated for (2)H CP-MAS and (2)H multiple-pulse NMR of perdeuterated proteins, for which sensitivity enhancements up to an order of magnitude are presented relative to commonly used approaches. The so-called RESPIRATION rf pulses combines the concept of short broad-band pulses with generation of pulses with large flip angles through distribution of the rf pulse over several rotor echoes. This lead to close-to-ideal rf pulses, facilitating implementation of experiments relying on the ability to realize high-performance 90 and 180° pulses, as, for example, in refocused INEPT and double-to-single quantum coherence experiments, or just pulses that provide a true representation of the quadrupolar powder pattern to extract information about the structure or dynamics. The optimal control (2)H → (13)C CP-MAS method demonstrates transfer efficiencies up to around 85% while being extremely robust toward rf inhomogeneity and resonance offsets.
Collapse
Affiliation(s)
- Daxiu Wei
- †Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
- ‡Shanghai Key Lab Magnetic Resonance, East China Normal University, Shanghai 200062, Peoples Republic China
| | - Ümit Akbey
- §NMR Supported Structural Biology, Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert Roessle Strasse 10, D-13125 Berlin, Germany
| | - Berit Paaske
- †Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Hartmut Oschkinat
- §NMR Supported Structural Biology, Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert Roessle Strasse 10, D-13125 Berlin, Germany
| | - Bernd Reif
- §NMR Supported Structural Biology, Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert Roessle Strasse 10, D-13125 Berlin, Germany
- ⊥Center for Integrated Protein Science Munich (CIPS-M) at Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany, and Helmholtz-Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Morten Bjerring
- †Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Niels Chr Nielsen
- †Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| |
Collapse
|
23
|
Asami S, Schmieder P, Reif B. High resolution 1H-detected solid-state NMR spectroscopy of protein aliphatic resonances: access to tertiary structure information. J Am Chem Soc 2011; 132:15133-5. [PMID: 20939587 DOI: 10.1021/ja106170h] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biological magic angle spinning (MAS) solid-state nuclear magnetic resonance spectroscopy has developed rapidly over the past two decades. For the structure determination of a protein by solid-state NMR, routinely (13)C,(13)C distance restraints as well as dihedral restraints are employed. In protonated samples, this is achieved by growing the bacterium on a medium which contains [1,3]-(13)C glycerol or [2]-(13)C glycerol to dilute the (13)C spin system. Labeling schemes, which rely on heteronuclei, are insensitive both for detection and in terms of quantification of distances, since they are relying on low-γ nuclei. Proton detection can in principle provide a gain in sensitivity by a factor of 8 and 31, compared to the (13)C or (15)N detected version of the experiment. We report here a new labeling scheme, which enables (1)H-detection of aliphatic resonances with high resolution in MAS solid-state NMR spectroscopy. We prepared microcrystals of the SH3 domain of chicken α-spectrin with 5% protonation at nonexchangeable sites and obtained line widths on the order of 25 Hz for aliphatic (1)H resonances. We show further that (13)C resolved 3D-(1)H,(1)H correlation experiments yield access to long-range proton-proton distances in the protein.
Collapse
Affiliation(s)
- Sam Asami
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Roessle-Str. 10, 13125 Berlin, Germany
| | | | | |
Collapse
|
24
|
Maly T, Andreas LB, Smith AA, Griffin RG. 2H-DNP-enhanced 2H-13C solid-state NMR correlation spectroscopy. Phys Chem Chem Phys 2010; 12:5872-8. [PMID: 20458422 DOI: 10.1039/c003705b] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Perdeuteration of biological macromolecules for magic angle spinning solid-state NMR spectroscopy can yield high-resolution (2)H-(13)C correlation spectra and the method is therefore of great interest for the structural biology community. Here we demonstrate that the combination of sample deuteration and dynamic nuclear polarization yields resolved (2)H-(13)C correlation spectra with a signal enhancement of epsilon > or = 700 compared to a spectrum recorded with microwaves off and otherwise identical conditions. To our knowledge, this is the first time that (2)H-DNP has been employed to enhance MAS-NMR spectra of a biologically relevant system. The DNP process is studied using several polarizing agents and the technique is applied to obtain (2)H-(13)C correlation spectra of U-[(2)H, (13)C] proline.
Collapse
Affiliation(s)
- Thorsten Maly
- Francis Bitter Magnet Laboratory and Department of Chemistry, Cambridge, MA 02139, USA
| | | | | | | |
Collapse
|
25
|
Linser R, Fink U, Reif B. Narrow carbonyl resonances in proton-diluted proteins facilitate NMR assignments in the solid-state. JOURNAL OF BIOMOLECULAR NMR 2010; 47:1-6. [PMID: 20232230 DOI: 10.1007/s10858-010-9404-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 03/01/2010] [Indexed: 05/28/2023]
Abstract
HNCO/HNCACO type correlation experiments are an alternative for assignment of backbone resonances in extensively deuterated proteins in the solid-state, given the fact that line widths on the order of 14-17 Hz are achieved in the carbonyl dimension without the need of high power decoupling. The achieved resolution demonstrates that MAS solid-state NMR on extensively deuterated proteins is able to compete with solution-state NMR spectroscopy if proteins are investigated with correlation times tau(c) that exceed 25 ns.
Collapse
Affiliation(s)
- Rasmus Linser
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle Str. 10, 13125, Berlin, Germany
| | | | | |
Collapse
|
26
|
Murakami M, Shimizu T, Tansho M, Takegoshi K. Improvement of 1H-2H cross polarization under magic-angle spinning by using amplitude/frequency modulation. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2009; 36:172-176. [PMID: 19954932 DOI: 10.1016/j.ssnmr.2009.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Revised: 10/14/2009] [Accepted: 10/29/2009] [Indexed: 05/28/2023]
Abstract
In 1H-2H cross polarization (CP) under magic-angle spinning (MAS), it has been pointed out that modulation of a H2 resonance frequency caused by MAS acts as adiabatic frequency sweep and efficient CP over the broad H2 powder pattern can be achieved. The adiabaticity, however, does not hold when the MAS frequency becomes faster, leading to insufficient CP enhancement. In this work, it is demonstrated that by applying amplitude/frequency modulation for H2 irradiation during CP, CP efficiency at faster MAS can be improved appreciably. By examining 1H-2H CP spectra taken at off-amplitude or off-resonance conditions, it is suggested that the improvement is ascribed to accumulation of CP signals from various parts of the broad H2 resonance, whose orientational dependence is time-dependent and is partially averaged under MAS.
Collapse
Affiliation(s)
- Miwa Murakami
- National Institute for Materials Science, 3-13 Sakura, Tsukuba, Ibaraki 305-0003, Japan.
| | | | | | | |
Collapse
|
27
|
Brown SP. Recent Advances in Solid-State MAS NMR Methodology for Probing Structure and Dynamics in Polymeric and Supramolecular Systems. Macromol Rapid Commun 2009; 30:688-716. [DOI: 10.1002/marc.200800816] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Accepted: 02/06/2009] [Indexed: 01/12/2023]
|