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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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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: 22] [Impact Index Per Article: 22.0] [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.
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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
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3
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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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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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5
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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: 4] [Impact Index Per Article: 1.3] [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.
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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
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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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7
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Reif B, Ashbrook SE, Emsley L, Hong M. Solid-state NMR spectroscopy. NATURE REVIEWS. METHODS PRIMERS 2021; 1:2. [PMID: 34368784 PMCID: PMC8341432 DOI: 10.1038/s43586-020-00002-1] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/29/2020] [Indexed: 12/18/2022]
Abstract
Solid-state nuclear magnetic resonance (NMR) spectroscopy is an atomic-level method used to determine the chemical structure, three-dimensional structure, and dynamics of solids and semi-solids. This Primer summarizes the basic principles of NMR as applied to the wide range of solid systems. The fundamental nuclear spin interactions and the effects of magnetic fields and radiofrequency pulses on nuclear spins are the same as in liquid-state NMR. However, because of the anisotropy of the interactions in the solid state, the majority of high-resolution solid-state NMR spectra is measured under magic-angle spinning (MAS), which has profound effects on the types of radiofrequency pulse sequences required to extract structural and dynamical information. We describe the most common MAS NMR experiments and data analysis approaches for investigating biological macromolecules, organic materials, and inorganic solids. Continuing development of sensitivity-enhancement approaches, including 1H-detected fast MAS experiments, dynamic nuclear polarization, and experiments tailored to ultrahigh magnetic fields, is described. We highlight recent applications of solid-state NMR to biological and materials chemistry. The Primer ends with a discussion of current limitations of NMR to study solids, and points to future avenues of development to further enhance the capabilities of this sophisticated spectroscopy for new applications.
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Affiliation(s)
- Bernd Reif
- Technische Universität München, Department Chemie, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Sharon E. Ashbrook
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Lyndon Emsley
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des sciences et ingénierie chimiques, CH-1015 Lausanne, Switzerland
| | - Mei Hong
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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8
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Asami S, Reif B. Accessing Methyl Groups in Proteins via 1H-detected MAS Solid-state NMR Spectroscopy Employing Random Protonation. Sci Rep 2019; 9:15903. [PMID: 31685894 PMCID: PMC6828780 DOI: 10.1038/s41598-019-52383-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/16/2019] [Indexed: 11/09/2022] Open
Abstract
We recently introduced RAP (reduced adjoining protonation) labelling as an easy to implement and cost-effective strategy to yield selectively methyl protonated protein samples. We show here that even though the amount of H2O employed in the bacterial growth medium is rather low, the intensities obtained in MAS solid-state NMR 1H,13C correlation spectra are comparable to spectra obtained for samples in which α-ketoisovalerate was employed as precursor. In addition to correlations for Leu and Val residues, RAP labelled samples yield also resonances for all methyl containing side chains. The labelling scheme has been employed to quantify order parameters, together with the respective asymmetry parameters. We obtain a very good correlation between the order parameters measured using a GlcRAP (glucose carbon source) and a α-ketoisovalerate labelled sample. The labelling scheme holds the potential to be very useful for the collection of long-range distance restraints among side chain atoms. Experiments are demonstrated using RAP and α-ketoisovalerate labelled samples of the α-spectrin SH3 domain, and are applied to fibrils formed from the Alzheimer's disease Aβ1-40 peptide.
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Affiliation(s)
- Sam Asami
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany.
| | - Bernd Reif
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, 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
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9
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Martin RW, Kelly JE, Kelz JI. Advances in instrumentation and methodology for solid-state NMR of biological assemblies. J Struct Biol 2018; 206:73-89. [PMID: 30205196 DOI: 10.1016/j.jsb.2018.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 07/08/2018] [Accepted: 09/06/2018] [Indexed: 01/11/2023]
Abstract
Many advances in instrumentation and methodology have furthered the use of solid-state NMR as a technique for determining the structures and studying the dynamics of molecules involved in complex biological assemblies. Solid-state NMR does not require large crystals, has no inherent size limit, and with appropriate isotopic labeling schemes, supports solving one component of a complex assembly at a time. It is complementary to cryo-EM, in that it provides local, atomic-level detail that can be modeled into larger-scale structures. This review focuses on the development of high-field MAS instrumentation and methodology; including probe design, benchmarking strategies, labeling schemes, and experiments that enable the use of quadrupolar nuclei in biomolecular NMR. Current challenges facing solid-state NMR of biological assemblies and new directions in this dynamic research area are also discussed.
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Affiliation(s)
- Rachel W Martin
- Department of Chemistry, University of California, Irvine 92697-2025, United States; Department of Molecular Biology and Biochemistry, University of California, Irvine 92697-3900, United States.
| | - John E Kelly
- Department of Chemistry, University of California, Irvine 92697-2025, United States
| | - Jessica I Kelz
- Department of Chemistry, University of California, Irvine 92697-2025, United States
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10
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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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11
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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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12
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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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13
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Shi X, Holland GP, Yarger JL. Molecular Dynamics of Spider Dragline Silk Fiber Investigated by 2H MAS NMR. Biomacromolecules 2015; 16:852-9. [DOI: 10.1021/bm5017578] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Xiangyan Shi
- Department
of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Gregory P. Holland
- Department
of Chemistry and Biochemistry, San Diego State University, 5500
Campanile Drive, San Diego, California 92182-1030, United States
| | - Jeffery L. Yarger
- Department
of Chemistry and Biochemistry, Magnetic Resonance Research Center, Arizona State University, Tempe, Arizona 85287-1604, United States
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14
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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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15
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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.
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Affiliation(s)
- Rasmus Linser
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA, 02115, USA
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16
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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]
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17
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Bjerring M, Jain S, Paaske B, Vinther JM, Nielsen NC. Designing dipolar recoupling and decoupling experiments for biological solid-state NMR using interleaved continuous wave and RF pulse irradiation. Acc Chem Res 2013; 46:2098-107. [PMID: 23557787 DOI: 10.1021/ar300329g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Rapid developments in solid-state NMR methodology have boosted this technique into a highly versatile tool for structural biology. The invention of increasingly advanced rf pulse sequences that take advantage of better hardware and sample preparation have played an important part in these advances. In the development of these new pulse sequences, researchers have taken advantage of analytical tools, such as average Hamiltonian theory or lately numerical methods based on optimal control theory. In this Account, we focus on the interplay between these strategies in the systematic development of simple pulse sequences that combines continuous wave (CW) irradiation with short pulses to obtain improved rf pulse, recoupling, sampling, and decoupling performance. Our initial work on this problem focused on the challenges associated with the increasing use of fully or partly deuterated proteins to obtain high-resolution, liquid-state-like solid-state NMR spectra. Here we exploit the overwhelming presence of (2)H in such samples as a source of polarization and to gain structural information. The (2)H nuclei possess dominant quadrupolar couplings which complicate even the simplest operations, such as rf pulses and polarization transfer to surrounding nuclei. Using optimal control and easy analytical adaptations, we demonstrate that a series of rotor synchronized short pulses may form the basis for essentially ideal rf pulse performance. Using similar approaches, we design (2)H to (13)C polarization transfer experiments that increase the efficiency by one order of magnitude over standard cross polarization experiments. We demonstrate how we can translate advanced optimal control waveforms into simple interleaved CW and rf pulse methods that form a new cross polarization experiment. This experiment significantly improves (1)H-(15)N and (15)N-(13)C transfers, which are key elements in the vast majority of biological solid-state NMR experiments. In addition, we demonstrate how interleaved sampling of spectra exploiting polarization from (1)H and (2)H nuclei can substantially enhance the sensitivity of such experiments. Finally, we present systematic development of (1)H decoupling methods where CW irradiation of moderate amplitude is interleaved with strong rotor-synchronized refocusing pulses. We show that these sequences remove residual cross terms between dipolar coupling and chemical shielding anisotropy more effectively and improve the spectral resolution over that observed in current state-of-the-art methods.
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Affiliation(s)
- Morten Bjerring
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Denmark
| | - Sheetal Jain
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Denmark
| | - Berit Paaske
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Denmark
| | - Joachim M. Vinther
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Denmark
| | - Niels Chr. Nielsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Denmark
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18
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Krushelnitsky A, Reichert D, Saalwächter K. Solid-state NMR approaches to internal dynamics of proteins: from picoseconds to microseconds and seconds. Acc Chem Res 2013; 46:2028-36. [PMID: 23875699 DOI: 10.1021/ar300292p] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Solid-state nuclear magnetic resonance (NMR) spectroscopy has matured to the point that it is possible to determine the structure of proteins in immobilized states, such as within microcrystals or embedded in membranes. Currently, researchers continue to develop and apply NMR techniques that can deliver site-resolved dynamic information toward the goal of understanding protein function at the atomic scale. As a widely-used, natural approach, researchers have mostly measured longitudinal (T1) relaxation times, which, like in solution-state NMR, are sensitive to picosecond and nanosecond motions, and motionally averaged dipolar couplings, which provide an integral amplitude of all motions with a correlation time of up to a few microseconds. While overall Brownian tumbling in solution mostly precludes access to slower internal dynamics, dedicated solid-state NMR approaches are now emerging as powerful new options. In this Account, we give an overview of the classes of solid-state NMR experiments that have expanded the accessible range correlation times from microseconds to many milliseconds. The measurement of relaxation times in the rotating frame, T1ρ, now allows researchers to access the microsecond range. Using our recent theoretical work, researchers can now quantitatively analyze this data to distinguish relaxation due to chemical-shift anisotropy (CSA) from that due to dipole-dipole couplings. Off-resonance irradiation allows researchers to extend the frequency range of such experiments. We have built multidimensional analogues of T2-type or line shape experiments using variants of the dipolar-chemical shift correlation (DIPSHIFT) experiment that are particularly suited to extract intermediate time scale motions in the millisecond range. In addition, we have continuously improved variants of exchange experiments, mostly relying on the recoupling of anisotropic interactions to address ultraslow motions in the ms to s ranges. The NH dipolar coupling offers a useful probe of local dynamics, especially with proton-depleted samples that suppress the adverse effect of strong proton dipolar couplings. We demonstrate how these techniques have provided a concise picture of the internal dynamics in a popular model system, the SH3 domain of α-spectrin. T1-based methods have shown that large-amplitude bond orientation fluctuations in the picosecond range and slower 10 ns low-amplitude motions coexist in these structures. When we include T1ρ data, we observe that many residues undergo low amplitude motions slower than 100 ns. On the millisecond to second scale, mostly localized but potentially cooperative motions occur. Comparing different exchange experiments, we found that terminal NH2 groups in side chains can even undergo a combination of ultraslow large-angle two-site jumps accompanied by small-angle fluctuations that occur 10 times more quickly.
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Affiliation(s)
- Alexey Krushelnitsky
- Institut für Physik − NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 7, D-06120 Halle (Saale), Germany
| | - Detlef Reichert
- Institut für Physik − NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 7, D-06120 Halle (Saale), Germany
| | - Kay Saalwächter
- Institut für Physik − NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 7, D-06120 Halle (Saale), Germany
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19
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Asami S, Reif B. Proton-detected solid-state NMR spectroscopy at aliphatic sites: application to crystalline systems. Acc Chem Res 2013; 46:2089-97. [PMID: 23745638 DOI: 10.1021/ar400063y] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
When applied to biomolecules, solid-state NMR suffers from low sensitivity and resolution. The major obstacle to applying proton detection in the solid state is the proton dipolar network, and deuteration can help avoid this problem. In the past, researchers had primarily focused on the investigation of exchangeable protons in these systems. In this Account, we review NMR spectroscopic strategies that allow researchers to observe aliphatic non-exchangeable proton resonances in proteins with high sensitivity and resolution. Our labeling scheme is based on u-[(2)H,(13)C]-glucose and 5-25% H2O (95-75% D2O) in the M9 bacterial growth medium, known as RAP (reduced adjoining protonation). We highlight spectroscopic approaches for obtaining resonance assignments, a prerequisite for any study of structure and dynamics of a protein by NMR spectroscopy. Because of the dilution of the proton spin system in the solid state, solution-state NMR (1)HCC(1)H type strategies cannot easily be transferred to these experiments. Instead, we needed to pursue ((1)H)CC(1)H, CC(1)H, (1)HCC or ((2)H)CC(1)H type experiments. In protonated samples, we obtained distance restraints for structure calculations from samples grown in bacteria in media containing [1,3]-(13)C-glycerol, [2]-(13)C-glycerol, or selectively enriched glucose to dilute the (13)C spin system. In RAP-labeled samples, we obtained a similar dilution effect by randomly introducing protons into an otherwise deuterated matrix. This isotopic labeling scheme allows us to measure the long-range contacts among aliphatic protons, which can then serve as restraints for the three-dimensional structure calculation of a protein. Due to the high gyromagnetic ratio of protons, longer range contacts are more easily accessible for these nuclei than for carbon nuclei in homologous experiments. Finally, the RAP labeling scheme allows access to dynamic parameters, such as longitudinal relaxation times T1, and order parameters S(2) for backbone and side chain carbon resonances. We expect that these measurements will open up new opportunities to obtain a more detailed description of protein backbone and side chain dynamics.
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Affiliation(s)
- Sam Asami
- Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU), Helmholtz-Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Bernd Reif
- Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU), Helmholtz-Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
- Munich Center for Integrated Protein Science (CIPSM) at Department of Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, D-85747 Garching, Germany
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20
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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: 9] [Impact Index Per Article: 0.8] [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.
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Affiliation(s)
- Xiangyan Shi
- Department of Chemistry and Biochemistry, Magnetic Resonance Research Center, Arizona State University, Tempe, AZ 85287-1604, United States
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21
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Huang W, Bardaro MF, Varani G, Drobny GP. Preparation of RNA samples with narrow line widths for solid state NMR investigations. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 223:51-54. [PMID: 22967888 DOI: 10.1016/j.jmr.2012.07.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Revised: 07/19/2012] [Accepted: 07/22/2012] [Indexed: 06/01/2023]
Abstract
Solid state NMR can provide detailed structural and dynamic information on biological systems that cannot be studied under solution conditions, and can investigate motions which occur with rates that cannot be fully studied by solution NMR. This approach has successfully been used to study proteins, but the application of multidimensional solid state NMR to RNA has been limited because reported line widths have been too broad to execute most multidimensional experiments successfully. A reliable method to generate spectra with narrow line widths is necessary to apply the full range of solid state NMR spectroscopic approaches to RNA. Using the HIV-1 transactivation response (TAR) RNA as a model, we present an approach based on precipitation with polyethylene glycol that improves the line width of (13)C signals in TAR from >6 ppm to about 1 ppm, making solid state 2D NMR studies of selectively enriched RNAs feasible at ambient temperature.
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Affiliation(s)
- Wei Huang
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195, USA
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22
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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: 63] [Impact Index Per Article: 5.3] [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.
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Affiliation(s)
- Bernd Reif
- Munich Center for Integrated Protein Science (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany.
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23
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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.
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Affiliation(s)
- Bernd Reif
- Munich Center for Integrated Protein Science (CIPSM) at Department Chemie, Technische Universität München, Garching, Germany.
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24
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Verardi R, Traaseth NJ, Masterson LR, Vostrikov VV, Veglia G. Isotope labeling for solution and solid-state NMR spectroscopy of membrane proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 992:35-62. [PMID: 23076578 PMCID: PMC3555569 DOI: 10.1007/978-94-007-4954-2_3] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this chapter, we summarize the isotopic labeling strategies used to obtain high-quality solution and solid-state NMR spectra of biological samples, with emphasis on integral membrane proteins (IMPs). While solution NMR is used to study IMPs under fast tumbling conditions, such as in the presence of detergent micelles or isotropic bicelles, solid-state NMR is used to study the structure and orientation of IMPs in lipid vesicles and bilayers. In spite of the tremendous progress in biomolecular NMR spectroscopy, the homogeneity and overall quality of the sample is still a substantial obstacle to overcome. Isotopic labeling is a major avenue to simplify overlapped spectra by either diluting the NMR active nuclei or allowing the resonances to be separated in multiple dimensions. In the following we will discuss isotopic labeling approaches that have been successfully used in the study of IMPs by solution and solid-state NMR spectroscopy.
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Affiliation(s)
- Raffaello Verardi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
| | | | | | | | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455
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25
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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.
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Affiliation(s)
- Nicholas F Breen
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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26
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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: 15] [Impact Index Per Article: 1.2] [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.
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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
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27
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Krushelnitsky A, Zinkevich T, Reichert D, Chevelkov V, Reif B. Microsecond Time Scale Mobility in a Solid Protein As Studied by the 15N R1ρ Site-Specific NMR Relaxation Rates. J Am Chem Soc 2010; 132:11850-3. [DOI: 10.1021/ja103582n] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexey Krushelnitsky
- Kazan Institute of Biochemistry and Biophysics, Kazan, Russia, Kazan Physical Technical Institute, Kazan, Russia, Institut für Physik - NMR, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, and Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - Tatiana Zinkevich
- Kazan Institute of Biochemistry and Biophysics, Kazan, Russia, Kazan Physical Technical Institute, Kazan, Russia, Institut für Physik - NMR, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, and Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - Detlef Reichert
- Kazan Institute of Biochemistry and Biophysics, Kazan, Russia, Kazan Physical Technical Institute, Kazan, Russia, Institut für Physik - NMR, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, and Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - Veniamin Chevelkov
- Kazan Institute of Biochemistry and Biophysics, Kazan, Russia, Kazan Physical Technical Institute, Kazan, Russia, Institut für Physik - NMR, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, and Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - Bernd Reif
- Kazan Institute of Biochemistry and Biophysics, Kazan, Russia, Kazan Physical Technical Institute, Kazan, Russia, Institut für Physik - NMR, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany, and Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
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28
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Chevelkov V, Fink U, Reif B. Accurate determination of order parameters from 1H,15N dipolar couplings in MAS solid-state NMR experiments. J Am Chem Soc 2009; 131:14018-22. [PMID: 19743845 DOI: 10.1021/ja902649u] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A reliable site-specific estimate of the individual N-H bond lengths in the protein backbone is the fundamental basis of any relaxation experiment in solution and in the solid-state NMR. The N-H bond length can in principle be influenced by hydrogen bonding, which would result in an increased N-H distance. At the same time, dynamics in the backbone induces a reduction of the experimental dipolar coupling due to motional averaging. We present a 3D dipolar recoupling experiment in which the (1)H,(15)N dipolar coupling is reintroduced in the indirect dimension using phase-inverted CP to eliminate effects from rf inhomogeneity. We find no variation of the N-H dipolar coupling as a function of hydrogen bonding. Instead, variations in the (1)H,(15)N dipolar coupling seem to be due to dynamics of the protein backbone. This is supported by the observed correlation between the H(N)-N dipolar coupling and the amide proton chemical shift. The experiment is demonstrated for a perdeuterated sample of the alpha-spectrin SH3 domain. Perdeuteration is a prerequisite to achieve high accuracy. The average error in the analysis of the H-N dipolar couplings is on the order of +/-370 Hz (+/-0.012 A) and can be as small as 150 Hz, corresponding to a variation of the bond length of +/-0.005 A.
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Affiliation(s)
- Veniamin Chevelkov
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, D-13125 Berlin, Germany
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29
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Krushelnitsky A, deAzevedo E, Linser R, Reif B, Saalwächter K, Reichert D. Direct observation of millisecond to second motions in proteins by dipolar CODEX NMR spectroscopy. J Am Chem Soc 2009; 131:12097-9. [PMID: 19673476 DOI: 10.1021/ja9038888] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a site-resolved study of slow (ms to s) motions in a protein in the solid (microcrystalline) state performed with the use of a modified version of the centerband-only detection of exchange (CODEX) NMR experiment. CODEX was originally based on measuring changes in molecular orientation by means of the chemical shift anisotropy (CSA) tensor, and in our modification, angular reorientations of internuclear vectors are observed. The experiment was applied to the study of slow (15)N-(1)H motions of the SH3 domain of chicken alpha-spectrin. The protein was perdeuterated with partial back-exchange of protons at labile sites. This allowed indirect (proton) detection of (15)N nuclei and thus a significant enhancement of sensitivity. The diluted proton system also made negligible proton-driven spin diffusion between (15)N nuclei, which interferes with the molecular exchange (motion) and hampers the acquisition of dynamic parameters. The experiment has shown that approximately half of the peaks in the 2D (15)N-(1)H correlation spectrum exhibit exchange in a different extent. The correlation time of the slow motion for most peaks is 1 to 3 s. This is the first NMR study of the internal dynamics of proteins in the solid state on the millisecond to second time scale with site-specific spectral resolution that provides both time-scale and geometry information about molecular motions.
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Böckmann A, Gardiennet C, Verel R, Hunkeler A, Loquet A, Pintacuda G, Emsley L, Meier BH, Lesage A. Characterization of different water pools in solid-state NMR protein samples. JOURNAL OF BIOMOLECULAR NMR 2009; 45:319-27. [PMID: 19779834 DOI: 10.1007/s10858-009-9374-3] [Citation(s) in RCA: 199] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Accepted: 09/04/2009] [Indexed: 05/09/2023]
Abstract
We observed and characterized two distinct signals originating from different pools of water protons in solid-state NMR protein samples, namely from crystal water which exchanges polarization with the protein (on the NMR timescale) and is located in the protein-rich fraction at the periphery of the magic-angle spinning (MAS) sample container, and supernatant water located close to the axis of the sample container. The polarization transfer between the water and the protein can be probed by two-dimensional exchange spectroscopy, and we show that the supernatant water does not interact with protein on the timescale of the experiments. The two water pools have different spectroscopic properties, including resonance frequency, longitudinal, transverse and rotating frame relaxation times. The supernatant water can be removed almost completely physically or can be frozen selectively. Both measures lead to an enhancement of the quality factor of the probe circuit, accompanied by an improvement of the experimental signal/noise, and greatly simplify solvent-suppression by substantially reducing the water signal. We also present a tool, which allows filling solid-state NMR sample containers in a more efficient manner, greatly reducing the amount of supernatant water and maximizing signal/noise.
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Affiliation(s)
- Anja Böckmann
- Institut de Biologie et Chimie des Protéines, Université de Lyon, UMR 5086 CNRS/UCB-Lyon 1, 7 passage du Vercors, 69367 Lyon, France.
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Chevelkov V, Fink U, Reif B. Quantitative analysis of backbone motion in proteins using MAS solid-state NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2009; 45:197-206. [PMID: 19629713 DOI: 10.1007/s10858-009-9348-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2009] [Accepted: 06/26/2009] [Indexed: 05/13/2023]
Abstract
We present a comprehensive analysis of protein dynamics for a micro-crystallin protein in the solid-state. Experimental data include (15)N T (1) relaxation times measured at two different magnetic fields as well as (1)H-(15)N dipole, (15)N CSA cross correlated relaxation rates which are sensitive to the spectral density function J(0) and are thus a measure of T (2) in the solid-state. In addition, global order parameters are included from a (1)H,(15)N dipolar recoupling experiment. The data are analyzed within the framework of the extended model-free Clore-Lipari-Szabo theory. We find slow motional correlation times in the range of 5 and 150 ns. Assuming a wobbling in a cone motion, the amplitude of motion of the respective amide moiety is on the order of 10 degrees for the half-opening angle of the cone in most of the cases. The experiments are demonstrated using a perdeuterated sample of the chicken alpha-spectrin SH3 domain.
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Affiliation(s)
- Veniamin Chevelkov
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, Berlin, Germany
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Xu J, Xue Y, Skrynnikov NR. Detection of nanosecond time scale side-chain jumps in a protein dissolved in water/glycerol solvent. JOURNAL OF BIOMOLECULAR NMR 2009; 45:57-72. [PMID: 19582374 DOI: 10.1007/s10858-009-9336-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Accepted: 06/06/2009] [Indexed: 05/28/2023]
Abstract
In solution, the correlation time of the overall protein tumbling, tau(R), plays a role of a natural dynamics cutoff-internal motions with correlation times on the order of tau ( R ) or longer cannot be reliably identified on the basis of spin relaxation data. It has been proposed some time ago that the 'observation window' of solution experiments can be expanded by changing the viscosity of solvent to raise the value of tau(R). To further explore this concept, we prepared a series of samples of alpha-spectrin SH3 domain in solvent with increasing concentration of glycerol. In addition to the conventional (15)N labeling, the protein was labeled in the Val, Leu methyl positions ((13)CHD(2) on a deuterated background). The collected relaxation data were used in asymmetric fashion: backbone (15)N relaxation rates were used to determine tau(R) across the series of samples, while methyl (13)C data were used to probe local dynamics (side-chain motions). In interpreting the results, it has been initially suggested that addition of glycerol leads only to increases in tau(R), whereas local motional parameters remain unchanged. Thus the data from multiple samples can be analyzed jointly, with tau(R) playing the role of experimentally controlled variable. Based on this concept, the extended model-free model was constructed with the intent to capture the effect of ns time-scale rotameric jumps in valine and leucine side chains. Using this model, we made a positive identification of nanosecond dynamics in Val-23 where ns motions were already observed earlier. In several other cases, however, only tentative identification was possible. The lack of definitive results was due to the approximate character of the model-contrary to what has been assumed, addition of glycerol led to a gradual 'stiffening' of the protein. This and other observations also shed light on the interaction of the protein with glycerol, which is one of the naturally occurring osmoprotectants. In particular, it has been found that the overall protein tumbling is controlled by the bulk solvent, and not by a thin solvation layer which contains a higher proportion of water.
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Affiliation(s)
- Jun Xu
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA
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Agarwal V, Faelber K, Schmieder P, Reif B. High-Resolution Double-Quantum Deuterium Magic Angle Spinning Solid-State NMR Spectroscopy of Perdeuterated Proteins. J Am Chem Soc 2008; 131:2-3. [DOI: 10.1021/ja803620r] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vipin Agarwal
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany, and Charité Universitätsmedizin, 10115 Berlin, Germany
| | - Katja Faelber
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany, and Charité Universitätsmedizin, 10115 Berlin, Germany
| | - Peter Schmieder
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany, and Charité Universitätsmedizin, 10115 Berlin, Germany
| | - Bernd Reif
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany, and Charité Universitätsmedizin, 10115 Berlin, Germany
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Agarwal V, Xue Y, Reif B, Skrynnikov NR. Protein Side-Chain Dynamics As Observed by Solution- and Solid-State NMR Spectroscopy: A Similarity Revealed. J Am Chem Soc 2008; 130:16611-21. [PMID: 19049457 DOI: 10.1021/ja804275p] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vipin Agarwal
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany, and Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084
| | - Yi Xue
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany, and Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084
| | - Bernd Reif
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany, and Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084
| | - Nikolai R. Skrynnikov
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany, and Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084
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Biocatalyst activity in nonaqueous environments correlates with centisecond-range protein motions. Proc Natl Acad Sci U S A 2008; 105:15672-7. [PMID: 18840689 DOI: 10.1073/pnas.0804566105] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent studies exploring the relationship between enzymatic catalysis and protein dynamics in the aqueous phase have yielded evidence that dynamics and enzyme activity are strongly correlated. Given that protein dynamics are significantly attenuated in organic solvents and that proteins exhibit a wide range of motions depending on the specific solvent environment, the nonaqueous milieu provides a unique opportunity to examine the role of protein dynamics in enzyme activity. Variable-temperature kinetic measurements, X-band electron spin resonance spectroscopy, (1)H NMR relaxation, and (19)F NMR spectroscopy experiments were performed on subtilisin Carlsberg colyophilized with several inorganic salts and suspended in organic solvents. The results indicate that salt activation induces a greater degree of transition-state flexibility, reflected by a more positive DeltaDeltaS(dagger), for the more active biocatalyst preparations in organic solvents. In contrast, DeltaDeltaH(dagger) was negligible regardless of salt type or salt content. Electron spin resonance spectroscopy and (1)H NMR relaxation measurements, including spin-lattice relaxation, spin-lattice relaxation in the rotating frame, and longitudinal magnetization exchange, revealed that the enzyme's turnover number (k(cat)) was strongly correlated with protein motions in the centisecond time regime, weakly correlated with protein motions in the millisecond regime, and uncorrelated with protein motions on the piconanosecond timescale. In addition, (19)F chemical shift measurements and hyperfine tensor measurements of biocatalyst formulations inhibited with 4-fluorobenzenesulfonyl fluoride and 4-ethoxyfluorophosphinyl-oxy-TEMPO, respectively, suggest that enzyme activation was only weakly affected by changes in active-site polarity.
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Agarwal V, Reif B. Residual methyl protonation in perdeuterated proteins for multi-dimensional correlation experiments in MAS solid-state NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 194:16-24. [PMID: 18571955 DOI: 10.1016/j.jmr.2008.05.021] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Accepted: 05/19/2008] [Indexed: 05/26/2023]
Abstract
NMR studies involving perdeuterated proteins focus in general on exchangeable amide protons. However, non-exchangeable sites contain as well a small amount of protons as the employed precursors for protein biosynthesis are not completely proton depleted. The degree of methyl group protonation is in the order of 9% for CD2H using >97% deuterium enriched glucose. We show in this manuscript that this small amount of residual protonation is sufficient to perform 2D and 3D MAS solid-state NMR experiments. In particular, we suggest a HCCH-TOBSY type experiment which we successfully employ to assign the methyl resonances in aliphatic side chains in a perdeuterated sample of the SH3 domain of chicken alpha-spectrin.
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Affiliation(s)
- Vipin Agarwal
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Strase 10, D-13125 Berlin, Germany
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Linser R, Fink U, Reif B. Proton-detected scalar coupling based assignment strategies in MAS solid-state NMR spectroscopy applied to perdeuterated proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 193:89-93. [PMID: 18462963 DOI: 10.1016/j.jmr.2008.04.021] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Revised: 04/04/2008] [Accepted: 04/14/2008] [Indexed: 05/10/2023]
Abstract
Assignment of proteins in MAS (magic angle spinning) solid-state NMR relies so far on correlations among heteronuclei. This strategy is based on well dispersed resonances in the (15)N dimension. In many complex cases like membrane proteins or amyloid fibrils, an additional frequency dimension is desirable in order to spread the amide resonances. We show here that proton detected HNCO, HNCA, and HNCACB type experiments can successfully be implemented in the solid-state. Coherences are sufficiently long lived to allow pulse schemes of a duration greater than 70 ms before incrementation of the first indirect dimension. The achieved resolution is comparable to the resolution obtained in solution-state NMR experiments. We demonstrate the experiments using a triply labeled sample of the SH3 domain of chicken alpha-spectrin, which was re-crystallized in H(2)O/D(2)O using a ratio of 1/9. We employ paramagnetic relaxation enhancement (PRE) using EDTA chelated Cu(II) to enable rapid data acquisition.
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Affiliation(s)
- Rasmus Linser
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle Strasse 10, 13125 Berlin, Germany
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Sackewitz M, Scheidt HA, Lodderstedt G, Schierhorn A, Schwarz E, Huster D. Structural and Dynamical Characterization of Fibrils from a Disease-Associated Alanine Expansion Domain Using Proteolysis and Solid-State NMR Spectroscopy. J Am Chem Soc 2008; 130:7172-3. [DOI: 10.1021/ja800120s] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mirko Sackewitz
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle, Germany, Max Planck Research Unit for Enzymology of Protein Folding, D-06120 Halle, Germany, and Institute of Medical Physics and Biophysics, D-04107 Leipzig, Germany
| | - Holger A. Scheidt
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle, Germany, Max Planck Research Unit for Enzymology of Protein Folding, D-06120 Halle, Germany, and Institute of Medical Physics and Biophysics, D-04107 Leipzig, Germany
| | - Grit Lodderstedt
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle, Germany, Max Planck Research Unit for Enzymology of Protein Folding, D-06120 Halle, Germany, and Institute of Medical Physics and Biophysics, D-04107 Leipzig, Germany
| | - Angelika Schierhorn
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle, Germany, Max Planck Research Unit for Enzymology of Protein Folding, D-06120 Halle, Germany, and Institute of Medical Physics and Biophysics, D-04107 Leipzig, Germany
| | - Elisabeth Schwarz
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle, Germany, Max Planck Research Unit for Enzymology of Protein Folding, D-06120 Halle, Germany, and Institute of Medical Physics and Biophysics, D-04107 Leipzig, Germany
| | - Daniel Huster
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle, Germany, Max Planck Research Unit for Enzymology of Protein Folding, D-06120 Halle, Germany, and Institute of Medical Physics and Biophysics, D-04107 Leipzig, Germany
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Helmus JJ, Nadaud PS, Höfer N, Jaroniec CP. Determination of methyl 13C-15N dipolar couplings in peptides and proteins by three-dimensional and four-dimensional magic-angle spinning solid-state NMR spectroscopy. J Chem Phys 2008; 128:052314. [PMID: 18266431 DOI: 10.1063/1.2817638] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We describe three- and four-dimensional semiconstant-time transferred echo double resonance (SCT-TEDOR) magic-angle spinning solid-state nuclear magnetic resonance (NMR) experiments for the simultaneous measurement of multiple long-range (15)N-(13)C(methyl) dipolar couplings in uniformly (13)C, (15)N-enriched peptides and proteins with high resolution and sensitivity. The methods take advantage of (13)C spin topologies characteristic of the side-chain methyl groups in amino acids alanine, isoleucine, leucine, methionine, threonine, and valine to encode up to three distinct frequencies ((15)N-(13)C(methyl) dipolar coupling, (15)N chemical shift, and (13)C(methyl) chemical shift) within a single SCT evolution period of initial duration approximately 1(1)J(CC) (where (1)J(CC) approximately 35 Hz, is the one-bond (13)C(methyl)-(13)C J-coupling) while concurrently suppressing the modulation of NMR coherences due to (13)C-(13)C and (15)N-(13)C J-couplings and transverse relaxation. The SCT-TEDOR schemes offer several important advantages over previous methods of this type. First, significant (approximately twofold to threefold) gains in experimental sensitivity can be realized for weak (15)N-(13)C(methyl) dipolar couplings (corresponding to structurally interesting, approximately 3.5 A or longer, distances) and typical (13)C(methyl) transverse relaxation rates. Second, the entire SCT evolution period can be used for (13)C(methyl) and/or (15)N frequency encoding, leading to increased spectral resolution with minimal additional coherence decay. Third, the experiments are inherently "methyl selective," which results in simplified NMR spectra and obviates the use of frequency-selective pulses or other spectral filtering techniques. Finally, the (15)N-(13)C cross-peak buildup trajectories are purely dipolar in nature (i.e., not influenced by J-couplings or relaxation), which enables the straightforward extraction of (15)N-(13)C(methyl) distances using an analytical model. The SCT-TEDOR experiments are demonstrated on a uniformly (13)C, (15)N-labeled peptide, N-acetyl-valine, and a 56 amino acid protein, B1 immunoglobulin-binding domain of protein G (GB1), where the measured (15)N-(13)C(methyl) dipolar couplings provide site-specific information about side-chain dihedral angles and the packing of protein molecules in the crystal lattice.
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Affiliation(s)
- Jonathan J Helmus
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
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Gardiennet C, Loquet A, Etzkorn M, Heise H, Baldus M, Böckmann A. Structural constraints for the Crh protein from solid-state NMR experiments. JOURNAL OF BIOMOLECULAR NMR 2008; 40:239-50. [PMID: 18320329 PMCID: PMC2579321 DOI: 10.1007/s10858-008-9229-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Accepted: 02/06/2008] [Indexed: 05/11/2023]
Abstract
We demonstrate that short, medium and long-range constraints can be extracted from proton mediated, rare-spin detected correlation solid-state NMR experiments for the microcrystalline 10.4 x 2 kDa dimeric model protein Crh. Magnetization build-up curves from cross signals in NHHC and CHHC spectra deliver detailed information on side chain conformers and secondary structure for interactions between spin pairs. A large number of medium and long-range correlations can be observed in the spectra, and an analysis of the resolved signals reveals that the constraints cover the entire sequence, also including inter-monomer contacts between the two molecules forming the domain-swapped Crh dimer. Dynamic behavior is shown to have an impact on cross signals intensities, as indicated for mobile residues or regions by contacts predicted from the crystal structure, but absent in the spectra. Our work validates strategies involving proton distance measurements for large and complex proteins as the Crh dimer, and confirms the magnetization transfer properties previously described for small molecules in solid protein samples.
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Affiliation(s)
- Carole Gardiennet
- Institut de Biologie et Chimie des Protéines, UMR 5086 C.N.R.S./Université de Lyon, 7, passage du Vercors, 69367 Lyon Cedex 07, France
| | - Antoine Loquet
- Institut de Biologie et Chimie des Protéines, UMR 5086 C.N.R.S./Université de Lyon, 7, passage du Vercors, 69367 Lyon Cedex 07, France
| | - Manuel Etzkorn
- Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR, Am Fassberg 11, 37077 Gottingen, Germany
| | - Henrike Heise
- Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR, Am Fassberg 11, 37077 Gottingen, Germany
| | - Marc Baldus
- Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR, Am Fassberg 11, 37077 Gottingen, Germany
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, UMR 5086 C.N.R.S./Université de Lyon, 7, passage du Vercors, 69367 Lyon Cedex 07, France
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Linser R, Chevelkov V, Diehl A, Reif B. Sensitivity enhancement using paramagnetic relaxation in MAS solid-state NMR of perdeuterated proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 189:209-16. [PMID: 17923428 DOI: 10.1016/j.jmr.2007.09.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2007] [Revised: 09/06/2007] [Accepted: 09/13/2007] [Indexed: 05/15/2023]
Abstract
Previously, Ishii et al., could show that chelated paramagnetic ions can be employed to significantly decrease the recycle delay of a MAS solid-state NMR experiment [N.P. Wickramasinghe, M. Kotecha, A. Samoson, J. Past, Y. Ishii, Sensitivity enhancement in C-13 solid-state NMR of protein microcrystals by use of paramagnetic metal ions for optimizing H-1 T-1 relaxation, J. Magn. Reson. 184 (2007) 350-356]. Application of the method is limited to very robust samples, for which sample stability is not compromised by RF induced heating. In addition, probe integrity might be perturbed in standard MAS PRE experiments due to the use of very short duty cycles. We show that these deleterious effects can be avoided if perdeuterated proteins are employed that have been re-crystallized from D(2)O:H(2)O=9:1 containing buffer solutions. The experiments are demonstrated using the SH3 domain of chicken alpha-spectrin as a model system. The labeling scheme allows to record proton detected (1)H, (15)N correlation spectra with very high resolution in the absence of heteronuclear dipolar decoupling. Cu-edta as a doping reagent yields a reduction of the recycle delay by up to a factor of 15. In particular, we find that the (1)H T(1) for the bulk H(N) magnetization is reduced from 4.4s to 0.3s if the Cu-edta concentration is increased from 0mM to 250 mM. Possible perturbations like chemical shift changes or line broadening due to the paramagnetic chelate complex are minimal. No degradation of our samples was observed in the course of the experiments.
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Affiliation(s)
- Rasmus Linser
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle Str. 10, 13125, Berlin, Germany
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42
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Chevelkov V, Diehl A, Reif B. Quantitative measurement of differential 15N-H(alpha/beta)T2 relaxation rates in a perdeuterated protein by MAS solid-state NMR spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S156-60. [PMID: 18157805 DOI: 10.1002/mrc.2129] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Dynamic parameters become more and more accessible in the study of uniformly isotopically enriched proteins by MAS solid-state NMR. We demonstrate that T(2)-related relaxation properties can quantitatively be determined in a sample of a perdeuterated microcrystalline protein by the measurement of (15)N,(1)H dipole, (15)N CSA cross-correlated relaxation rates. We find that the measured cross-correlated relaxation rates are independent of the MAS rotation frequency, and therefore reflect local dynamic fluctuations of the protein structure.
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Böckmann A. High-resolution solid-state MAS NMR of proteins-Crh as an example. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S24-S31. [PMID: 18081212 DOI: 10.1002/mrc.2106] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Revised: 09/04/2007] [Accepted: 09/12/2007] [Indexed: 05/25/2023]
Abstract
Solid-state NMR spectroscopy provides unique possibilities for the structural investigation of insoluble molecules at the atomic level. Recent efforts aim at solving the complete structures of biological macromolecules using high-resolution magic angle spinning NMR. Structurally homogenous samples of [(13)C,(15)N]-labeled proteins have to be used in this type of studies. Microcrystalline model proteins present valuable tools for the developments of methods towards this goal. This review discusses recent progress in the field, using the Crh protein as an illustrative example. We discuss strategies for resonance assignments and for the determination of structure and dynamics, as well as techniques for the detection of protein interaction partners and folding mechanisms by solid-state NMR methods.
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Affiliation(s)
- Anja Böckmann
- IFR 128 BioSciences Lyon-Gerland, IBCP UMR 5086 CNRS/Université de Lyon Claude Bernard, 7 passage du Vercors, 69367 Lyon, France.
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Agarwal V, Diehl A, Skrynnikov N, Reif B. High resolution 1H detected 1H,13C correlation spectra in MAS solid-state NMR using deuterated proteins with selective 1H,2H isotopic labeling of methyl groups. J Am Chem Soc 2007; 128:12620-1. [PMID: 17002335 DOI: 10.1021/ja064379m] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
MAS solid-state NMR experiments applied to biological solids are still hampered by low sensitivity and resolution. In this work, we employ a deuteration scheme in which individual methyl groups are selectively protonated. This labeling scheme allows the acquisition of proton carbon correlation spectra with a resolution comparable to that in solution-state NMR experiments. We observe an increase in resolution by a factor of 10-15 compared to standard heteronuclear correlation experiments using PMLG for 1H,1H dipolar decoupling in the indirect dimension. At the same time, the full sensitivity of the proton-based experiment is retained. In comparison to the heteronuclear detected version of the experiment, a gain in sensitivity of a factor of approximately 4.7 is achieved.
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Affiliation(s)
- Vipin Agarwal
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
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Xue Y, Pavlova MS, Ryabov YE, Reif B, Skrynnikov NR. Methyl rotation barriers in proteins from 2H relaxation data. Implications for protein structure. J Am Chem Soc 2007; 129:6827-38. [PMID: 17488010 DOI: 10.1021/ja0702061] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Side-chain 2H and backbone 15N relaxation data have been collected at multiple temperatures in the samples of the SH3 domain from alpha-spectrin. Combined analyses of the data allowed for determination of the temperature-dependent correlation times tauf characterizing fast methyl motion. Molecular dynamics simulations confirmed that tauf are dominated by methyl rotation; the corresponding activation energies approximate methyl rotation barriers. For 33 methyl groups in the alpha-spectrin SH3 domain the average barrier height was thus determined to be 2.8 +/- 0.9 kcal/mol. This value is deemed representative of the "fluid" hydrophobic protein core where some barriers are increased and others are lowered because of the contacts with surrounding atoms, but there is no local order that could produce systematically higher (lower) barriers. For comparison, the MD simulation predicts the average barrier of 3.1 kcal/mol (calculated via the potential of mean force) or 3.4-3.5 kcal/mol (rigid barriers after appropriate averaging over multiple MD snapshots). The latter result prompted us to investigate rigid methyl rotation barriers in a series of NMR structures from the Protein Databank. In most cases the barriers proved to be higher than expected, 4-6 kcal/mol. To a certain degree, this is caused by tight packing of the side chains in the NMR structures and stems from the structure calculation procedure where the coordinates are first annealed toward the temperature of 0 K and then subjected to energy minimization. In several cases the barriers >10 kcal/mol are indicative of van der Waals violations. The notable exceptions are (i) the structures solved using the GROMOS force field where tight methyl packing is avoided (3.0-3.6 kcal/mol) and (ii) the structure solved by means of the dynamic ensemble refinement method (Lindorff-Larsen, K.; Best, R. B.; DePristo, M. A.; Dobson, C. M.; Vendruscolo, M. Nature 2005, 433, 128) (3.5 kcal/mol). These results demonstrate that methyl rotation barriers, derived from the experiments that are traditionally associated with studies of protein dynamics, can be also used in the context of structural work. This is particularly interesting in view of the recent efforts to incorporate dynamics data in the process of protein structure elucidation.
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Affiliation(s)
- Yi Xue
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette Indiana 47907-2084, USA
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Sein J, Giraud N, Blackledge M, Emsley L. The role of (15)N CSA and CSA/dipole cross-correlation in (15)N relaxation in solid proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 186:26-33. [PMID: 17280844 DOI: 10.1016/j.jmr.2007.01.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Revised: 01/15/2007] [Accepted: 01/16/2007] [Indexed: 05/13/2023]
Abstract
The influence of the (15)N CSA on (15)N longitudinal relaxation is investigated for an amide group in solid proteins in powder form under MAS. This contribution is determined to be typically 20-33% of the overall longitudinal relaxation rate, at 11.74 and 16.45 T, respectively. The improved treatment is used to analyze the internal dynamics in the protein Crh, in the frame of a motional model of diffusion in a cone, using the explicit average sum approach. Significant variations with respect to the determined dynamics parameters are observed when properly accounting for the contribution of (15)N CSA fluctuations. In general, the fit of experimental data including CSA led to the determination of diffusion times (tau(w)) which are longer than when considering only an (15)N-(1)H dipolar relaxation mechanism. CSA-Dipole cross-correlation is shown to play little or no role in protonated solids, in direct contrast to the liquid state case.
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Affiliation(s)
- Julien Sein
- Laboratoire de Chimie (UMR 5182 CNRS/ENS Lyon), Ecole Normale Supérieure de Lyon, 69364 Lyon, France
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Heller M, Sukopp M, Tsomaia N, John M, Mierke DF, Reif B, Kessler H. The Conformation of cyclo(−d-Pro−Ala4−) as a Model for Cyclic Pentapeptides of the dL4 Type. J Am Chem Soc 2006; 128:13806-14. [PMID: 17044709 DOI: 10.1021/ja063174a] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conformation of the cyclic pentapeptide cyclo(-D-Pro-Ala(4)-) in solution and in the solid state was reinvestigated using modern NMR techniques. To allow unequivocal characterization of hydrogen bonds, relaxation behavior, and intramolecular distances, differently labeled isotopomers were synthesized. The NMR results, supported by extensive MD simulations, demonstrate unambiguously that the preferred conformation previously described by us, but recently questioned, is indeed correct. The validation of the conformational preferences of this cyclic peptide is important given that this system is a template for several bioactive compounds and for controlled "spatial screening" for the search of bioactive conformations.
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Affiliation(s)
- Markus Heller
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
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Reif B, Xue Y, Agarwal V, Pavlova MS, Hologne M, Diehl A, Ryabov YE, Skrynnikov NR. Protein Side-Chain Dynamics Observed by Solution- and Solid-State NMR: Comparative Analysis of Methyl 2H Relaxation Data. J Am Chem Soc 2006; 128:12354-5. [PMID: 16984151 DOI: 10.1021/ja062808a] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rapid advances in solid-state MAS NMR made it possible to probe protein dynamics on a per-residue basis, similar to solution experiments. In this work we compare methyl 2H relaxation rates measured in the solid and liquid samples of alpha-spectrin SH3 domain. The solution data are treated using a model-free approach to separate the contributions from the overall molecular tumbling and fast internal motion. The latter part forms the basis for comparison with the solid-state data. Although the accuracy of solid-state measurements is limited by deuterium spin diffusion, the results suggest a significant similarity between methyl dynamics in the two samples. This is a potentially important observation, preparing the ground for combined analysis of the dynamics data by solid- and solution-state NMR.
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Affiliation(s)
- Bernd Reif
- Forschunginstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
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Chevelkov V, Rehbein K, Diehl A, Reif B. Ultrahigh Resolution in Proton Solid-State NMR Spectroscopy at High Levels of Deuteration. Angew Chem Int Ed Engl 2006; 45:3878-81. [PMID: 16646097 DOI: 10.1002/anie.200600328] [Citation(s) in RCA: 281] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Veniamin Chevelkov
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany.
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Chevelkov V, Rehbein K, Diehl A, Reif B. Ultrahochaufgelöste1H-MAS-Festkörper-NMR-Spektren unter Verwendung von hohen Deuterierungsgraden. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600328] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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