1
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Southern SA, Perras FA. Comparison of methods for the NMR measurement of motionally averaged dipolar couplings. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 364:107710. [PMID: 38901172 DOI: 10.1016/j.jmr.2024.107710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/31/2024] [Accepted: 06/07/2024] [Indexed: 06/22/2024]
Abstract
Motionally averaged dipolar couplings are an important tool for understanding the complex dynamics of catalysts, polymers, and biomolecules. While there is a plethora of solid-state NMR pulse sequences available for their measurement, in can be difficult to gauge the methods' strengths and weaknesses. In particular, there has not been a comprehensive comparison of their performance in natural abundance samples, where 1H homonuclear dipolar couplings are important and the use of large MAS rotors may be required for sensitivity reasons. In this work, we directly compared some of the more common methods for measuring C-H dipolar couplings in natural abundance samples using L-alanine (L-Ala) and the N-formyl-L-methionyl-L-leucyl-L-phenylalanine (fMLF) tripeptide as model systems. We evaluated their performance in terms of accuracy, resolution, sensitivity, and ease of implementation. We found that, despite the presence of 1H homonuclear dipolar interactions, all methods, with the exception of REDOR, were able to yield the reasonable dipolar coupling strengths for both mobile and static moieties. Of these methods, PDLF provides the most convenient workflow and precision at the expense of low sensitivity. In low-sensitivity cases, MAS-PISEMA and DIPSHIFT appear to be the better options.
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Affiliation(s)
- Scott A Southern
- Chemical and Biological Sciences Division, Ames National Laboratory, Ames, IA 50011, USA
| | - Frédéric A Perras
- Chemical and Biological Sciences Division, Ames National Laboratory, Ames, IA 50011, USA; Department of Chemistry, Iowa State University, Ames, IA 50011, USA.
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2
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Toke O. Three Decades of REDOR in Protein Science: A Solid-State NMR Technique for Distance Measurement and Spectral Editing. Int J Mol Sci 2023; 24:13637. [PMID: 37686450 PMCID: PMC10487747 DOI: 10.3390/ijms241713637] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
Solid-state NMR (ss-NMR) is a powerful tool to investigate noncrystallizable, poorly soluble molecular systems, such as membrane proteins, amyloids, and cell walls, in environments that closely resemble their physical sites of action. Rotational-echo double resonance (REDOR) is an ss-NMR methodology, which by reintroducing heteronuclear dipolar coupling under magic angle spinning conditions provides intramolecular and intermolecular distance restraints at the atomic level. In addition, REDOR can be exploited as a selection tool to filter spectra based on dipolar couplings. Used extensively as a spectroscopic ruler between isolated spins in site-specifically labeled systems and more recently as a building block in multidimensional ss-NMR pulse sequences allowing the simultaneous measurement of multiple distances, REDOR yields atomic-scale information on the structure and interaction of proteins. By extending REDOR to the determination of 1H-X dipolar couplings in recent years, the limit of measurable distances has reached ~15-20 Å, making it an attractive method of choice for the study of complex biomolecular assemblies. Following a methodological introduction including the most recent implementations, examples are discussed to illustrate the versatility of REDOR in the study of biological systems.
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Affiliation(s)
- Orsolya Toke
- Laboratory for NMR Spectroscopy, Structural Research Centre, Research Centre for Natural Sciences, 2 Magyar tudósok körútja, H-1117 Budapest, Hungary
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3
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Wurl A, Saalwächter K, Mendes Ferreira T. Time-domain proton-detected local-field NMR for molecular structure determination in complex lipid membranes. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2023; 4:115-127. [PMID: 37904803 PMCID: PMC10583295 DOI: 10.5194/mr-4-115-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 04/03/2023] [Indexed: 11/01/2023]
Abstract
Proton-detected local-field (PDLF) NMR spectroscopy, using magic-angle spinning and dipolar recoupling, is presently the most powerful experimental technique for obtaining atomistic structural information from small molecules undergoing anisotropic motion. Common examples include peptides, drugs, or lipids in model membranes and molecules that form liquid crystals. The measurements on complex systems are however compromised by the larger number of transients required. Retaining sufficient spectral quality in the direct dimension requires that the indirect time-domain modulation becomes too short for yielding dipolar splittings in the frequency domain. In such cases, the dipolar couplings can be obtained by fitting the experimental data; however ideal models often fail to fit PDLF data properly due to effects of radiofrequency field (RF) spatial inhomogeneity. Here, we demonstrate that by accounting for RF spatial inhomogeneity in the modeling of R-symmetry-based PDLF NMR experiments, the fitting accuracy is improved, facilitating the analysis of the experimental data. In comparison to the analysis of dipolar splittings without any fitting procedure, the accurate modeling of PDLF measurements makes possible three important improvements: the use of shorter experiments that enable the investigation of samples with a higher level of complexity, the measurement of C-H bond order parameters with smaller magnitudes | S CH | and of smaller variations of | S CH | caused by perturbations of the system, and the determination of | S CH | values with small differences from distinct sites having the same chemical shift. The increase in fitting accuracy is demonstrated by comparison with 2 H NMR quadrupolar echo experiments on mixtures of deuterated and non-deuterated dimyristoylphosphatidylcholine (DMPC) and with 1-palmitoyl-2-oleoyl-s n -glycero-3-phosphoethanolamine (POPE) membranes. Accurate modeling of PDLF NMR experiments is highly useful for investigating complex membrane systems. This is exemplified by application of the proposed fitting procedure for the characterization of membranes composed of a brain lipid extract with many distinct lipid types.
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Affiliation(s)
- Anika Wurl
- NMR group, Institute for Physics, Martin Luther University Halle–Wittenberg, Halle (Saale), Germany
| | - Kay Saalwächter
- NMR group, Institute for Physics, Martin Luther University Halle–Wittenberg, Halle (Saale), Germany
| | - Tiago Mendes Ferreira
- NMR group, Institute for Physics, Martin Luther University Halle–Wittenberg, Halle (Saale), Germany
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4
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Taware PP, Jain MG, Raran-Kurussi S, Agarwal V, Madhu PK, Mote KR. Measuring Dipolar Order Parameters in Nondeuterated Proteins Using Solid-State NMR at the Magic-Angle-Spinning Frequency of 100 kHz. J Phys Chem Lett 2023; 14:3627-3635. [PMID: 37026698 DOI: 10.1021/acs.jpclett.3c00492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Proteins are dynamic molecules, relying on conformational changes to carry out function. Measurement of these conformational changes can provide insight into how function is achieved. For proteins in the solid state, this can be done by measuring the decrease in the strength of anisotropic interactions due to motion-induced fluctuations. The measurement of one-bond heteronuclear dipole-dipole coupling at magic-angle-spinning (MAS) frequencies >60 kHz is ideal for this purpose. However, rotational-echo double resonance (REDOR), an otherwise gold-standard technique for the quantitative measurement of these couplings, is difficult to implement under these conditions, especially in nondeuterated samples. We present here a combination of strategies based on REDOR variants ϵ-REDOR and DEDOR (deferred REDOR) and simultaneously measure residue-specific 15N-1H and 13Cα-1Hα dipole-dipole couplings in nondeuterated systems at the MAS frequency of 100 kHz. These strategies open up avenues to access dipolar order parameters in a variety of systems at the increasingly fast MAS frequencies that are now available.
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Affiliation(s)
- Pravin P Taware
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - Mukul G Jain
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - Sreejith Raran-Kurussi
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - P K Madhu
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, Telangana, India
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5
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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: 36] [Impact Index Per Article: 36.0] [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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6
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Chevelkov V, Lange S, Sawczyc H, Lange A. Accurate Determination of Motional Amplitudes in Biomolecules by Solid-State NMR. ACS PHYSICAL CHEMISTRY AU 2023; 3:199-206. [PMID: 36968444 PMCID: PMC10037497 DOI: 10.1021/acsphyschemau.2c00053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023]
Abstract
Protein dynamics are an intrinsically important factor when considering a protein's biological function. Understanding these motions is often limited through the use of static structure determination methods, namely, X-ray crystallography and cryo-EM. Molecular simulations have allowed for the prediction of global and local motions of proteins from these static structures. Nevertheless, determining local dynamics at residue-specific resolution through direct measurement remains crucial. Solid-state nuclear magnetic resonance (NMR) is a powerful tool for studying dynamics in rigid or membrane-bound biomolecules without prior structural knowledge with the help of relaxation parameters such as T 1 and T 1ρ. However, these provide only a combined result of amplitude and correlation times in the nanosecond-millisecond frequency range. Thus, direct and independent determination of the amplitude of motions might considerably improve the accuracy of dynamics studies. In an ideal situation, the use of cross-polarization would be the optimal method for measuring the dipolar couplings between chemically bound heterologous nuclei. This would unambiguously provide the amplitude of motion per residue. In practice, however, the inhomogeneity of the applied radio-frequency fields across the sample leads to significant errors. Here, we present a novel method to eliminate this issue through including the radio-frequency distribution map in the analysis. This allows for direct and accurate measurement of residue-specific amplitudes of motion. Our approach has been applied to the cytoskeletal protein BacA in filamentous form, as well as to the intramembrane protease GlpG in lipid bilayers.
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Affiliation(s)
- Veniamin Chevelkov
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125Berlin, Germany
| | - Sascha Lange
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125Berlin, Germany
| | - Henry Sawczyc
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125Berlin, Germany
| | - Adam Lange
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125Berlin, Germany
- Institut für Biologie, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115Berlin, Germany
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7
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Le Marchand T, Schubeis T, Bonaccorsi M, Paluch P, Lalli D, Pell AJ, Andreas LB, Jaudzems K, Stanek J, Pintacuda G. 1H-Detected Biomolecular NMR under Fast Magic-Angle Spinning. Chem Rev 2022; 122:9943-10018. [PMID: 35536915 PMCID: PMC9136936 DOI: 10.1021/acs.chemrev.1c00918] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Indexed: 02/08/2023]
Abstract
Since the first pioneering studies on small deuterated peptides dating more than 20 years ago, 1H detection has evolved into the most efficient approach for investigation of biomolecular structure, dynamics, and interactions by solid-state NMR. The development of faster and faster magic-angle spinning (MAS) rates (up to 150 kHz today) at ultrahigh magnetic fields has triggered a real revolution in the field. This new spinning regime reduces the 1H-1H dipolar couplings, so that a direct detection of 1H signals, for long impossible without proton dilution, has become possible at high resolution. The switch from the traditional MAS NMR approaches with 13C and 15N detection to 1H boosts the signal by more than an order of magnitude, accelerating the site-specific analysis and opening the way to more complex immobilized biological systems of higher molecular weight and available in limited amounts. This paper reviews the concepts underlying this recent leap forward in sensitivity and resolution, presents a detailed description of the experimental aspects of acquisition of multidimensional correlation spectra with fast MAS, and summarizes the most successful strategies for the assignment of the resonances and for the elucidation of protein structure and conformational dynamics. It finally outlines the many examples where 1H-detected MAS NMR has contributed to the detailed characterization of a variety of crystalline and noncrystalline biomolecular targets involved in biological processes ranging from catalysis through drug binding, viral infectivity, amyloid fibril formation, to transport across lipid membranes.
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Affiliation(s)
- Tanguy Le Marchand
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Tobias Schubeis
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Marta Bonaccorsi
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Biochemistry and Biophysics, Stockholm
University, Svante Arrhenius
väg 16C SE-106 91, Stockholm, Sweden
| | - Piotr Paluch
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Daniela Lalli
- Dipartimento
di Scienze e Innovazione Tecnologica, Università
del Piemonte Orientale “A. Avogadro”, Viale Teresa Michel 11, 15121 Alessandria, Italy
| | - Andrew J. Pell
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16 C, SE-106
91 Stockholm, Sweden
| | - Loren B. Andreas
- Department
for NMR-Based Structural Biology, Max-Planck-Institute
for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Kristaps Jaudzems
- Latvian
Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006 Latvia
- Faculty
of Chemistry, University of Latvia, Jelgavas 1, Riga LV-1004, Latvia
| | - Jan Stanek
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Guido Pintacuda
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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8
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Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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9
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Liang L, Ji Y, Chen K, Gao P, Zhao Z, Hou G. Solid-State NMR Dipolar and Chemical Shift Anisotropy Recoupling Techniques for Structural and Dynamical Studies in Biological Systems. Chem Rev 2022; 122:9880-9942. [PMID: 35006680 DOI: 10.1021/acs.chemrev.1c00779] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With the development of NMR methodology and technology during the past decades, solid-state NMR (ssNMR) has become a particularly important tool for investigating structure and dynamics at atomic scale in biological systems, where the recoupling techniques play pivotal roles in modern high-resolution MAS NMR. In this review, following a brief introduction on the basic theory of recoupling in ssNMR, we highlight the recent advances in dipolar and chemical shift anisotropy recoupling methods, as well as their applications in structural determination and dynamical characterization at multiple time scales (i.e., fast-, intermediate-, and slow-motion). The performances of these prevalent recoupling techniques are compared and discussed in multiple aspects, together with the representative applications in biomolecules. Given the recent emerging advances in NMR technology, new challenges for recoupling methodology development and potential opportunities for biological systems are also discussed.
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Affiliation(s)
- Lixin Liang
- State Key Laboratory of Catalysis, 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, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Ji
- State Key Laboratory of Catalysis, 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, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuizhi Chen
- State Key Laboratory of Catalysis, 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, Dalian 116023, China
| | - Pan Gao
- State Key Laboratory of Catalysis, 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, Dalian 116023, China
| | - Zhenchao Zhao
- State Key Laboratory of Catalysis, 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, Dalian 116023, China
| | - Guangjin Hou
- State Key Laboratory of Catalysis, 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, Dalian 116023, China
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10
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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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11
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Abstract
Relaxation in nuclear magnetic resonance is a powerful method for obtaining spatially resolved, timescale-specific dynamics information about molecular systems. However, dynamics in biomolecular systems are generally too complex to be fully characterized based on NMR data alone. This is a familiar problem, addressed by the Lipari-Szabo model-free analysis, a method that captures the full information content of NMR relaxation data in case all internal motion of a molecule in solution is sufficiently fast. We investigate model-free analysis, as well as several other approaches, and find that model-free, spectral density mapping, LeMaster's approach, and our detector analysis form a class of analysis methods, for which behavior of the fitted parameters has a well-defined relationship to the distribution of correlation times of motion, independent of the specific form of that distribution. In a sense, they are all "model-free." Of these methods, only detectors are generally applicable to solid-state NMR relaxation data. We further discuss how detectors may be used for comparison of experimental data to data extracted from molecular dynamics simulation, and how simulation may be used to extract details of the dynamics that are not accessible via NMR, where detector analysis can be used to connect those details to experiments. We expect that combined methodology can eventually provide enough insight into complex dynamics to provide highly accurate models of motion, thus lending deeper insight into the nature of biomolecular dynamics.
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Affiliation(s)
- Kai Zumpfe
- Institute for Medical Physics and Biophysics, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Albert A Smith
- Institute for Medical Physics and Biophysics, Medical Faculty, Leipzig University, Leipzig, Germany
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12
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Goldbourt A. Distance measurements to quadrupolar nuclei: Evolution of the rotational echo double resonance technique. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:908-919. [PMID: 33729630 DOI: 10.1002/mrc.5150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
Molecular structure determination is the basis for understanding chemical processes and the property of materials. The direct dependence of the magnetic dipolar interaction on the distance makes solid-state nuclear magnetic resonance (NMR) an excellent tool to study molecular structure when X-ray crystallography fails to provide atomic-resolution data. Although techniques to measure distances between pairs of isolated nuclear spin-1/2 pairs are routine and easy to implement using the rotational echo double resonance (REDOR) experiment (Gullion & Schaefer, 1989), the existence of a nucleus with a spin > 1/2, appearing in approximately 75% of the elements in the periodic table, poses a challenge due to difficulties stemming from the large nuclear quadrupolar coupling constant (QCC). This mini-review presents the existing solid-state magic-angle spinning NMR techniques aimed toward the efficient and accurate determination of internuclear distances between a spin-1/2 and a "quadrupolar" nucleus having a spin larger than one half. Analytical expressions are provided for the various recoupling curves stemming from different techniques, and a coherent nomenclature for these various techniques is suggested. Treatment of some special cases such as multiple spin effects and spins with close Larmor frequencies is also discussed. The most advanced methods can recouple spins with quadrupolar frequencies up to tens of megahertz and beyond, expanding the distance measurement capabilities of solid-state NMR to an increasingly growing number of applications and nuclear spin systems.
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Affiliation(s)
- Amir Goldbourt
- School of Chemistry, Tel Aviv University, Tel Aviv, Israel
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13
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Aebischer K, Tošner Z, Ernst M. Effects of radial radio-frequency field inhomogeneity on MAS solid-state NMR experiments. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:523-543. [PMID: 37904774 PMCID: PMC10539735 DOI: 10.5194/mr-2-523-2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/14/2021] [Indexed: 11/01/2023]
Abstract
Radio-frequency field inhomogeneity is one of the most common imperfections in NMR experiments. They can lead to imperfect flip angles of applied radio-frequency (rf) pulses or to a mismatch of resonance conditions, resulting in artefacts or degraded performance of experiments. In solid-state NMR under magic angle spinning (MAS), the radial component becomes time-dependent because the rf irradiation amplitude and phase is modulated with integer multiples of the spinning frequency. We analyse the influence of such time-dependent MAS-modulated rf fields on the performance of some commonly used building blocks of solid-state NMR experiments. This analysis is based on analytical Floquet calculations and numerical simulations, taking into account the time dependence of the rf field. We find that, compared to the static part of the rf field inhomogeneity, such time-dependent modulations play a very minor role in the performance degradation of the investigated typical solid-state NMR experiments.
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Affiliation(s)
- Kathrin Aebischer
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Zdeněk Tošner
- Department of Chemistry, Faculty of Science, Charles University, Hlavova 8, 12842 Prague 2, Czech Republic
| | - Matthias Ernst
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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14
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Dasgupta R, Gupta KBSS, Elam D, Ubbink M, de Groot HJM. Dipolar dephasing for structure determination in a paramagnetic environment. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2021; 113:101728. [PMID: 33744671 DOI: 10.1016/j.ssnmr.2021.101728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/26/2021] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
We demonstrate the efficacy of the REDOR-type sequences in determining dipolar coupling strength in a paramagnetic environment. Utilizing paramagnetic effects of enhanced relaxation rates and rapid electronic fluctuations in Cu(II)-(DL-Ala)2.H2O, the dipolar coupling for the methyl C-H that is 4.20 Å (methyl carbon) away from the Cu2+ ion, was estimated to be 8.8 ± 0.6 kHz. This coupling is scaled by a factor of ~0.3 in comparison to the rigid limit value of ~32 kHz, in line with partial averaging of the dipolar interaction by rotational motion of the methyl group. Limited variation in the scaling factor of the dipolar coupling strength at different temperatures is observed. The C-H internuclear distance derived from the size of the dipolar coupling is similar to that observed in the crystal structure. The errors in the dipolar coupling strength observed in the REDOR-type experiments are similar to those reported for diamagnetic systems. Increase in resolution due to the Fermi contact shifts, coupled with MAS frequencies of 30-35 kHz allowed to estimate the hyperfine coupling strengths for protons and carbons from the temperature dependence of the chemical shift and obtain a high resolution 1H-1H spin diffusion spectrum. This study shows the utility of REDOR-type sequences in obtaining reliable structural and dynamical information from a paramagnetic complex. We believe that this can help in studying the active site of paramagnetic metalloproteins at high resolution.
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Affiliation(s)
- Rubin Dasgupta
- Leiden University, Leiden Institute of Chemistry, Gorlaeus Laboratories, Einsteinweg, 55 2333 CC, Leiden, the Netherlands
| | - Karthick B S S Gupta
- Leiden University, Leiden Institute of Chemistry, Gorlaeus Laboratories, Einsteinweg, 55 2333 CC, Leiden, the Netherlands
| | - Derek Elam
- Leiden University, Leiden Institute of Chemistry, Gorlaeus Laboratories, Einsteinweg, 55 2333 CC, Leiden, the Netherlands
| | - Marcellus Ubbink
- Leiden University, Leiden Institute of Chemistry, Gorlaeus Laboratories, Einsteinweg, 55 2333 CC, Leiden, the Netherlands
| | - Huub J M de Groot
- Leiden University, Leiden Institute of Chemistry, Gorlaeus Laboratories, Einsteinweg, 55 2333 CC, Leiden, the Netherlands.
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15
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Duong NT, Gan Z, Nishiyama Y. Selective 1H- 14N Distance Measurements by 14N Overtone Solid-State NMR Spectroscopy at Fast MAS. Front Mol Biosci 2021; 8:645347. [PMID: 33898521 PMCID: PMC8061749 DOI: 10.3389/fmolb.2021.645347] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 01/28/2021] [Indexed: 01/25/2023] Open
Abstract
Accurate distance measurements between proton and nitrogen can provide detailed information on the structures and dynamics of various molecules. The combination of broadband phase-modulated (PM) pulse and rotational-echo saturation-pulse double-resonance (RESPDOR) sequence at fast magic-angle spinning (MAS) has enabled the measurement of multiple 1H-14N distances with high accuracy. However, complications may arise when applying this sequence to systems with multiple inequivalent 14N nuclei, especially a single 1H sitting close to multiple 14N atoms. Due to its broadband characteristics, the PM pulse saturates all 14N atoms; hence, the single 1H simultaneously experiences the RESPDOR effect from multiple 1H-14N couplings. Consequently, no reliable H-N distances are obtained. To overcome the problem, selective 14N saturation is desired, but it is difficult because 14N is an integer quadrupolar nucleus. Alternatively, 14N overtone (OT) NMR spectroscopy can be employed owing to its narrow bandwidth for selectivity. Moreover, owing to the sole presence of two energy levels (m = ± 1), the 14N OT spin dynamics behaves similarly to that of spin-1/2. This allows the interchangeability between RESPDOR and rotational-echo double-resonance (REDOR) since their principles are the same except the degree of 14N OT population transfer; saturation for the former whereas inversion for the latter. As the ideal saturation/inversion is impractical due to the slow and orientation-dependent effective nutation of 14N OT, the working condition is usually an intermediate between REDOR and RESPDOR. The degree of 14N OT population transfer can be determined from the results of protons with short distances to 14N and then can be used to obtain long-distance determination of other protons to the same 14N site. Herein, we combine the 14N OT and REDOR/RESPDOR to explore the feasibility of selective 1H-14N distance measurements. Experimental demonstrations on simple biological compounds of L-tyrosine.HCl, N-acetyl-L-alanine, and L-alanyl-L-alanine were performed at 14.1 T and MAS frequency of 62.5 kHz. The former two consist of a single 14N site, whereas the latter consists of two 14N sites. The experimental optimizations and reliable fittings by the universal curves are described. The extracted 1H-14N distances by OT-REDOR are in good agreement with those determined by PM-RESPDOR and diffraction techniques.
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Affiliation(s)
- Nghia Tuan Duong
- NMR Science and Development Division, RIKEN SPring-8 Center, Nano-Crystallography Unit, RIKEN-JEOL Collaboration Center, Yokohama, Japan
| | - Zhehong Gan
- Centre of Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Tallahassee, FL, United States
| | - Yusuke Nishiyama
- NMR Science and Development Division, RIKEN SPring-8 Center, Nano-Crystallography Unit, RIKEN-JEOL Collaboration Center, Yokohama, Japan
- JEOL RESONANCE Inc., Tokyo, Japan
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16
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Ji Y, Liang L, Bao X, Hou G. Recent progress in dipolar recoupling techniques under fast MAS in solid-state NMR spectroscopy. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2021; 112:101711. [PMID: 33508579 DOI: 10.1016/j.ssnmr.2020.101711] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 12/04/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
With the recent advances in NMR hardware and probe design technology, magic-angle spinning (MAS) rates over 100 kHz are accessible now, even on commercial solid NMR probes. Under such fast MAS conditions, excellent spectral resolution has been achieved by efficient suppression of anisotropic interactions, which also opens an avenue to the proton-detected NMR experiments in solids. Numerous methods have been developed to take full advantage of fast MAS during the last decades. Among them, dipolar recoupling techniques under fast MAS play vital roles in the determination of the molecular structure and dynamics, and are also key elements in multi-dimensional correlation NMR experiments. Herein, we review the dipolar recoupling techniques, especially those developed in the past two decades for fast-to-ultrafast MAS conditions. A major focus for our discussion is the ratio of RF field strength (in frequency) to MAS frequency, ν1/νr, in different pulse sequences, which determines whether these dipolar recoupling techniques are suitable for NMR experiments under fast MAS conditions. Systematic comparisons are made among both heteronuclear and homonuclear dipolar recoupling schemes. In addition, the schemes developed specially for proton-detection NMR experiments under ultrafast MAS conditions are highlighted as well.
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Affiliation(s)
- Yi Ji
- State Key Laboratory of Catalysis, 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, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lixin Liang
- State Key Laboratory of Catalysis, 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, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinhe Bao
- State Key Laboratory of Catalysis, 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, Dalian, 116023, China
| | - Guangjin Hou
- State Key Laboratory of Catalysis, 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, Dalian, 116023, China.
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17
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Zhang X, Forster MC, Nimerovsky E, Movellan KT, Andreas LB. Transferred-Rotational-Echo Double Resonance. J Phys Chem A 2021; 125:754-769. [PMID: 33464081 PMCID: PMC7884007 DOI: 10.1021/acs.jpca.0c09033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/11/2020] [Indexed: 12/21/2022]
Abstract
Internuclear distance determination is the foundation for NMR-based structure calculation. However, high-precision distance measurement is a laborious process requiring lengthy data acquisitions due to the large set of multidimensional spectra needed at different mixing times. This prevents application to large or challenging molecular systems. Here, we present a new approach, transferred-rotational-echo double resonance (TREDOR), a heteronuclear transfer method in which we simultaneously detect both starting and transferred signals in a single spectrum. This co-acquisition is used to compensate for coherence decay, resulting in accurate and precise distance determination by a single parameter fit using a single spectrum recorded at an ideal mixing time. We showcase TREDOR with the microcrystalline SH3 protein using 3D spectra to resolve resonances. By combining the measured N-C and H-C distances, we calculate the structure of SH3, which converges to the correct fold, with a root-mean-square deviation of 2.1 Å compared to a reference X-ray structure. The TREDOR data used in the structure calculation were acquired in only 4 days on a 600 MHz instrument. This is achieved due to the more than 2-fold time saving afforded by co-acquisition of additional information and demonstrates TREDOR as a fast and straightforward method for determining structures via magic-angle spinning NMR.
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Affiliation(s)
| | | | - Evgeny Nimerovsky
- NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Kumar Tekwani Movellan
- NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Loren B. Andreas
- NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
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18
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Jain MG, Rajalakshmi G, Madhu PK, Agarwal V, Mote KR. Overcoming Prohibitively Large Radiofrequency Demands for the Measurement of Internuclear Distances with Solid-State NMR under Fast Magic-Angle Spinning. J Phys Chem B 2020; 124:1444-1451. [DOI: 10.1021/acs.jpcb.9b11849] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Mukul G. Jain
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad, Telangana 500107, India
| | - G. Rajalakshmi
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad, Telangana 500107, India
| | - P. K. Madhu
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad, Telangana 500107, India
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad, Telangana 500107, India
| | - Kaustubh R. Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad, Telangana 500107, India
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19
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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: 11] [Impact Index Per Article: 2.2] [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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20
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Duong NT, Rossi F, Makrinich M, Goldbourt A, Chierotti MR, Gobetto R, Nishiyama Y. Accurate 1H- 14N distance measurements by phase-modulated RESPDOR at ultra-fast MAS. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 308:106559. [PMID: 31345769 DOI: 10.1016/j.jmr.2019.07.046] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/12/2019] [Accepted: 07/12/2019] [Indexed: 06/10/2023]
Abstract
The combination of a phase-modulated (PM) saturation pulse and symmetry-based dipolar recoupling into a rotational-echo saturation-pulse double-resonance (RESPDOR) sequence has been employed to measure 1H-14N distances. Such a measurement is challenging owing to the quadrupolar interaction of 14N nucleus and the intense 1H-1H homonuclear dipolar interactions. Thanks to the recent advances in probe technology, the homonuclear dipolar interaction can be sufficiently suppressed at a fast MAS frequency (νR ≥ 60 kHz). PM pulse is robust to large variations of parameters on quadrupolar spins, but it has not been demonstrated under very fast MAS conditions. On the other hand, the RESPDOR sequence is applicable to such condition when it employs symmetry-based pulses during the recoupling period, but a prior knowledge on the system is required. In this article, we demonstrated the PM-RESPDOR combination for providing accurate 1H-14N distances at a very fast MAS frequency of 70 kHz on two samples, namely L-tyrosine⋅HCl and N-acetyl-L-alanine. This sequence, supported by simulations and experiments, has shown its feasibility at νR = 70 kHz as well as the robustness to the 14N quadrupolar interaction. It is applicable to a wide range of 1H-14N dipolar coupling constants when a radio frequency field on the 14N channel is approximately 80 kHz or more, while the PM pulse length lasts 10 rotor periods. For the first time, multiple 1H-14N heteronuclear dipolar couplings, thus multiple quantitative distances, are simultaneously and reliably extracted by fitting the experimental fraction curves with the analytical expression. The size of the 1H-14N dipolar interaction is solely used as a fitting parameter. These determined distances are in excellent agreement with those derived from diffraction techniques.
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Affiliation(s)
- Nghia Tuan Duong
- NMR Science and Development Division, RIKEN SPring-8 Center, and Nano-Crystallography Unit, RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan
| | - Federica Rossi
- Department of Chemistry and NIS Centre, University of Torino, V.P. Giuria 7, 10125, Italy
| | - Maria Makrinich
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 6997801, Israel
| | - Amir Goldbourt
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 6997801, Israel
| | - Michele R Chierotti
- Department of Chemistry and NIS Centre, University of Torino, V.P. Giuria 7, 10125, Italy
| | - Roberto Gobetto
- Department of Chemistry and NIS Centre, University of Torino, V.P. Giuria 7, 10125, Italy
| | - Yusuke Nishiyama
- NMR Science and Development Division, RIKEN SPring-8 Center, and Nano-Crystallography Unit, RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan; JEOL RESONANCE Inc., Musashino, Akishima, Tokyo 196-8558, Japan.
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21
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Xue K, Mamone S, Koch B, Sarkar R, Reif B. Determination of methyl order parameters using solid state NMR under off magic angle spinning. JOURNAL OF BIOMOLECULAR NMR 2019; 73:471-475. [PMID: 31407204 DOI: 10.1007/s10858-019-00253-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/07/2019] [Indexed: 06/10/2023]
Abstract
Quantification of dipolar couplings in biological solids is important for the understanding of dynamic processes. Under Magic Angle Spinning (MAS), order parameters are normally obtained by recoupling of anisotropic interactions involving the application of radio frequency pulses. We have recently shown that amide backbone order parameters can be estimated accurately in a spin-echo experiment in case the rotor spinning angle is slightly mis-calibrated. In this work, we apply this method to determine methyl order parameters in a deuterated sample of the SH3 domain of chicken α-spectrin in which the methyl containing side chains valine and leucine are selectively protonated.
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Affiliation(s)
- Kai Xue
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Salvatore Mamone
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Benita Koch
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Riddhiman Sarkar
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany.
| | - Bernd Reif
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany.
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22
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Gauto DF, Macek P, Barducci A, Fraga H, Hessel A, Terauchi T, Gajan D, Miyanoiri Y, Boisbouvier J, Lichtenecker R, Kainosho M, Schanda P. Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 kDa Enzyme by Specific 1H- 13C Labeling and Fast Magic-Angle Spinning NMR. J Am Chem Soc 2019; 141:11183-11195. [PMID: 31199882 DOI: 10.1021/jacs.9b04219] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Aromatic residues are located at structurally important sites of many proteins. Probing their interactions and dynamics can provide important functional insight but is challenging in large proteins. Here, we introduce approaches to characterize the dynamics of phenylalanine residues using 1H-detected fast magic-angle spinning (MAS) NMR combined with a tailored isotope-labeling scheme. Our approach yields isolated two-spin systems that are ideally suited for artifact-free dynamics measurements, and allows probing motions effectively without molecular weight limitations. The application to the TET2 enzyme assembly of ∼0.5 MDa size, the currently largest protein assigned by MAS NMR, provides insights into motions occurring on a wide range of time scales (picoseconds to milliseconds). We quantitatively probe ring-flip motions and show the temperature dependence by MAS NMR measurements down to 100 K. Interestingly, favorable line widths are observed down to 100 K, with potential implications for DNP NMR. Furthermore, we report the first 13C R1ρ MAS NMR relaxation-dispersion measurements and detect structural excursions occurring on a microsecond time scale in the entry pore to the catalytic chamber and at a trimer interface that was proposed as the exit pore. We show that the labeling scheme with deuteration at ca. 50 kHz MAS provides superior resolution compared to 100 kHz MAS experiments with protonated, uniformly 13C-labeled samples.
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Affiliation(s)
- Diego F Gauto
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
| | - Pavel Macek
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
| | - Alessandro Barducci
- Centre de Biochimie Structurale (CBS) , INSERM, CNRS, Université de Montpellier , Montpellier , France
| | - Hugo Fraga
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France.,Departamento de Biomedicina , Faculdade de Medicina da Universidade do Porto , Porto , Portugal.,i3S, Instituto de Investigação e Inovação em Saúde , Universidade do Porto , Porto , Portugal
| | - Audrey Hessel
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
| | - Tsutomu Terauchi
- Graduate School of Science , Tokyo Metropolitan University , 1-1 Minami-ohsawa , Hachioji , Tokyo 192-0397 , Japan.,SI Innovation Center , Taiyo Nippon Sanso Corp. , 2008-2 Wada , Tama-city , Tokyo 206-0001 , Japan
| | - David Gajan
- Université de Lyon , Centre de RMN à Hauts Champs de Lyon CRMN, FRE 2034, Université de Lyon, CNRS, ENS Lyon, UCB Lyon 1 , 69100 Villeurbanne , France
| | - Yohei Miyanoiri
- Institute of Protein Research , Osaka University , 3-2 Yamadaoka , Suita , Osaka 565-0871 , Japan.,Structural Biology Research Center, Graduate School of Sciences , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602 , Japan
| | - Jerome Boisbouvier
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
| | - Roman Lichtenecker
- Institute of Organic Chemistry , University of Vienna , Währinger Str. 38 , 1090 Vienna , Austria
| | - Masatsune Kainosho
- Graduate School of Science , Tokyo Metropolitan University , 1-1 Minami-ohsawa , Hachioji , Tokyo 192-0397 , Japan.,Structural Biology Research Center, Graduate School of Sciences , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602 , Japan
| | - Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
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23
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Jain MG, Mote KR, Hellwagner J, Rajalakshmi G, Ernst M, Madhu PK, Agarwal V. Measuring strong one-bond dipolar couplings using REDOR in magic-angle spinning solid-state NMR. J Chem Phys 2019; 150:134201. [DOI: 10.1063/1.5088100] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mukul G. Jain
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Sy. No. 36/P, Gopanpally, Hyderabad 500 107, India
| | - Kaustubh R. Mote
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Sy. No. 36/P, Gopanpally, Hyderabad 500 107, India
| | - Johannes Hellwagner
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - G. Rajalakshmi
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Sy. No. 36/P, Gopanpally, Hyderabad 500 107, India
| | - Matthias Ernst
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - P. K. Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Sy. No. 36/P, Gopanpally, Hyderabad 500 107, India
| | - Vipin Agarwal
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Sy. No. 36/P, Gopanpally, Hyderabad 500 107, India
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24
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Xue K, Mühlbauer M, Mamone S, Sarkar R, Reif B. Accurate Determination of
1
H‐
15
N Dipolar Couplings Using Inaccurate Settings of the Magic Angle in Solid‐State NMR Spectroscopy. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kai Xue
- Helmholtz-Zentrum München (HMGU)Deutsches Forschungszentrum für Gesundheit und Umwelt Ingolstädter Landstr. 1 85764 Neuherberg Germany
| | - Max Mühlbauer
- Helmholtz-Zentrum München (HMGU)Deutsches Forschungszentrum für Gesundheit und Umwelt Ingolstädter Landstr. 1 85764 Neuherberg Germany
| | - Salvatore Mamone
- Max Planck Institute for Biophysical Chemistry Göttingen Germany
| | - Riddhiman Sarkar
- Helmholtz-Zentrum München (HMGU)Deutsches Forschungszentrum für Gesundheit und Umwelt Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Munich Center for Integrated Protein Science (CIPS-M), Department ChemieTechnische Universität München (TUM) Lichtenbergstr. 4 85747 Garching Germany
| | - Bernd Reif
- Helmholtz-Zentrum München (HMGU)Deutsches Forschungszentrum für Gesundheit und Umwelt Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Munich Center for Integrated Protein Science (CIPS-M), Department ChemieTechnische Universität München (TUM) Lichtenbergstr. 4 85747 Garching Germany
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25
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Xue K, Mühlbauer M, Mamone S, Sarkar R, Reif B. Accurate Determination of 1 H- 15 N Dipolar Couplings Using Inaccurate Settings of the Magic Angle in Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2019; 58:4286-4290. [PMID: 30694593 DOI: 10.1002/anie.201814314] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Indexed: 11/10/2022]
Abstract
Magic-angle spinning (MAS) is an essential ingredient in a wide variety of solid-state NMR experiments. The standard procedures to adjust the rotor angle are not highly accurate, resulting in a slight misadjustment of the rotor from the magic angle ( θ R L = tan - 1 2 ) on the order of a few millidegrees. This small missetting has no significant impact on the overall spectral resolution, but is sufficient to reintroduce anisotropic interactions. Shown here is that site-specific 1 H-15 N dipolar couplings can be accurately measured in a heavily deuterated protein. This method can be applied at arbitrarily high MAS frequencies, since neither rotor synchronization nor particularly high radiofrequency field strengths are required. The off-MAS method allows the quantification of order parameters for very dynamic residues, which often escape an analysis using existing methods.
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Affiliation(s)
- Kai Xue
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Max Mühlbauer
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Salvatore Mamone
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Riddhiman Sarkar
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Munich Center for Integrated Protein Science (CIPS-M), Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Bernd Reif
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Munich Center for Integrated Protein Science (CIPS-M), Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
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26
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Smith AA, Ernst M, Meier BH. Optimized "detectors" for dynamics analysis in solid-state NMR. J Chem Phys 2018; 148:045104. [PMID: 29390848 DOI: 10.1063/1.5013316] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Relaxation in nuclear magnetic resonance (NMR) results from stochastic motions that modulate anisotropic NMR interactions. Therefore, measurement of relaxation-rate constants can be used to characterize molecular-dynamic processes. The motion is often characterized by Markov processes using an auto-correlation function, which is assumed to be a sum of multiple decaying exponentials. We have recently shown that such a model can lead to severe misrepresentation of the real motion, when the real correlation function is more complex than the model. Furthermore, multiple distributions of motion may yield the same set of dynamics data. Therefore, we introduce optimized dynamics "detectors" to characterize motions which are linear combinations of relaxation-rate constants. A detector estimates the average or total amplitude of motion for a range of motional correlation times. The information obtained through the detectors is less specific than information obtained using an explicit model, but this is necessary because the information contained in the relaxation data is ambiguous, if one does not know the correct motional model. On the other hand, if one has a molecular dynamics trajectory, one may calculate the corresponding detector responses, allowing direct comparison to experimental NMR dynamics analysis. We describe how to construct a set of optimized detectors for a given set of relaxation measurements. We then investigate the properties of detectors for a number of different data sets, thus gaining an insight into the actual information content of the NMR data. Finally, we show an example analysis of ubiquitin dynamics data using detectors, using the DIFRATE software.
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Affiliation(s)
- Albert A Smith
- ETH Zurich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Matthias Ernst
- ETH Zurich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Beat H Meier
- ETH Zurich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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27
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Hellwagner J, Wili N, Ibáñez LF, Wittmann JJ, Meier BH, Ernst M. Transient effects in π-pulse sequences in MAS solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 287:65-73. [PMID: 29289819 DOI: 10.1016/j.jmr.2017.12.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/12/2017] [Accepted: 12/19/2017] [Indexed: 06/07/2023]
Abstract
Dipolar recoupling techniques that use isolated rotor-synchronized π pulses are commonly used in solid-state NMR spectroscopy to gain insight into the structure of biological molecules. These sequences excel through their simplicity, stability towards radio-frequency (rf) inhomogeneity, and low rf requirements. For a theoretical understanding of such sequences, we present a Floquet treatment based on an interaction-frame transformation including the chemical-shift offset dependence. This approach is applied to the homonuclear dipolar-recoupling sequence Radio-Frequency Driven Recoupling (RFDR) and the heteronuclear recoupling sequence Rotational Echo Double Resonance (REDOR). Based on the Floquet approach, we show the influence of effective fields caused by pulse transients and discuss the advantages of pulse-transient compensation. We demonstrate experimentally that the transfer efficiency for homonuclear recoupling can be doubled in some cases in model compounds as well as in simple peptides if pulse-transient compensation is applied to the π pulses. Additionally, we discuss the influence of various phase cycles on the recoupling efficiency in order to reduce the magnitude of effective fields. Based on the findings from RFDR, we are able to explain why the REDOR sequence does not suffer in the recoupling efficiency despite the presence of effective fields.
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Affiliation(s)
- Johannes Hellwagner
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Nino Wili
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | | | - Johannes J Wittmann
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Matthias Ernst
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
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28
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Asami S, Reif B. Comparative Study of REDOR and CPPI Derived Order Parameters by 1H-Detected MAS NMR and MD Simulations. J Phys Chem B 2017; 121:8719-8730. [DOI: 10.1021/acs.jpcb.7b06812] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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, Ingolstädter
Landstr. 1, 85764 Neuherberg, Germany
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29
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Jain MG, Rajalakshmi G, Equbal A, Mote KR, Agarwal V, Madhu PK. Sine-squared shifted pulses for recoupling interactions in solid-state NMR. J Chem Phys 2017; 146:244201. [PMID: 28668030 DOI: 10.1063/1.4986791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Rotational-Echo DOuble-Resonance (REDOR) is a versatile experiment for measuring internuclear distance between two heteronuclear spins in solid-state NMR. At slow to intermediate magic-angle spinning (MAS) frequencies, the measurement of distances between strongly coupled spins is challenging due to rapid dephasing of magnetisation. This problem can be remedied by employing the pulse-shifted version of REDOR known as Shifted-REDOR (S-REDOR) that scales down the recoupled dipolar coupling. In this study, we propose a new variant of the REDOR sequence where the positions of the π pulses are determined by a sine-squared function. This new variant has scaling properties similar to S-REDOR. We use theory, numerical simulations, and experiments to compare the dipolar recoupling efficiencies and the experimental robustness of the three REDOR schemes. The proposed variant has advantages in terms of radiofrequency field requirements at fast MAS frequencies.
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Affiliation(s)
- Mukul G Jain
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - G Rajalakshmi
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - Asif Equbal
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - Kaustubh R Mote
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - Vipin Agarwal
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - P K Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
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30
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Saurel O, Iordanov I, Nars G, Demange P, Le Marchand T, Andreas LB, Pintacuda G, Milon A. Local and Global Dynamics in Klebsiella pneumoniae Outer Membrane Protein a in Lipid Bilayers Probed at Atomic Resolution. J Am Chem Soc 2017; 139:1590-1597. [DOI: 10.1021/jacs.6b11565] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Olivier Saurel
- Institut de Pharmacologie
et de Biologie Structurale (CNRS/Université Paul Sabatier),
Université de Toulouse, 31077 Toulouse, France
| | - Iordan Iordanov
- Institut de Pharmacologie
et de Biologie Structurale (CNRS/Université Paul Sabatier),
Université de Toulouse, 31077 Toulouse, France
| | - Guillaume Nars
- Institut de Pharmacologie
et de Biologie Structurale (CNRS/Université Paul Sabatier),
Université de Toulouse, 31077 Toulouse, France
| | - Pascal Demange
- Institut de Pharmacologie
et de Biologie Structurale (CNRS/Université Paul Sabatier),
Université de Toulouse, 31077 Toulouse, France
| | - Tanguy Le Marchand
- Institut de Sciences
Analytiques (UMR 5280 CNRS/ENS-Lyon/UCB Lyon 1), Université
de Lyon, 69007 Lyon, France
| | - Loren B. Andreas
- Institut de Sciences
Analytiques (UMR 5280 CNRS/ENS-Lyon/UCB Lyon 1), Université
de Lyon, 69007 Lyon, France
| | - Guido Pintacuda
- Institut de Sciences
Analytiques (UMR 5280 CNRS/ENS-Lyon/UCB Lyon 1), Université
de Lyon, 69007 Lyon, France
| | - Alain Milon
- Institut de Pharmacologie
et de Biologie Structurale (CNRS/Université Paul Sabatier),
Université de Toulouse, 31077 Toulouse, France
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31
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Schanda P, Ernst M. Studying Dynamics by Magic-Angle Spinning Solid-State NMR Spectroscopy: Principles and Applications to Biomolecules. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 96:1-46. [PMID: 27110043 PMCID: PMC4836562 DOI: 10.1016/j.pnmrs.2016.02.001] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Magic-angle spinning solid-state NMR spectroscopy is an important technique to study molecular structure, dynamics and interactions, and is rapidly gaining importance in biomolecular sciences. Here we provide an overview of experimental approaches to study molecular dynamics by MAS solid-state NMR, with an emphasis on the underlying theoretical concepts and differences of MAS solid-state NMR compared to solution-state NMR. The theoretical foundations of nuclear spin relaxation are revisited, focusing on the particularities of spin relaxation in solid samples under magic-angle spinning. We discuss the range of validity of Redfield theory, as well as the inherent multi-exponential behavior of relaxation in solids. Experimental challenges for measuring relaxation parameters in MAS solid-state NMR and a few recently proposed relaxation approaches are discussed, which provide information about time scales and amplitudes of motions ranging from picoseconds to milliseconds. We also discuss the theoretical basis and experimental measurements of anisotropic interactions (chemical-shift anisotropies, dipolar and quadrupolar couplings), which give direct information about the amplitude of motions. The potential of combining relaxation data with such measurements of dynamically-averaged anisotropic interactions is discussed. Although the focus of this review is on the theoretical foundations of dynamics studies rather than their application, we close by discussing a small number of recent dynamics studies, where the dynamic properties of proteins in crystals are compared to those in solution.
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Affiliation(s)
- Paul Schanda
- CEA, Institut de Biologie Structurale (IBS), 38027 Grenoble, France ; CNRS, Institut de Biologie Structurale (IBS), 38027 Grenoble, France ; Université Grenoble Alpes, IBS, 38027 Grenoble, France
| | - Matthias Ernst
- ETH Zürich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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32
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Smith AA, Testori E, Cadalbert R, Meier BH, Ernst M. Characterization of fibril dynamics on three timescales by solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2016; 65:171-191. [PMID: 27423891 DOI: 10.1007/s10858-016-0047-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 07/08/2016] [Indexed: 05/26/2023]
Abstract
A multi-timescale analysis of the backbone dynamics of HET-s (218-289) fibrils is described based on multiple site-specific R 1 and R 1ρ data sets and S (2) measurements via REDOR for most backbone (15)N and (13)Cα nuclei. (15)N and (13)Cα data are fitted with motions at three timescales. Slow motion is found, indicating a global fibril motion. We further investigate the effect of (13)C-(13)C transfer in measurement of (13)Cα R 1. Finally, we show that it is necessary to go beyond the Redfield approximation for slow motions in order to obtain accurate numerical values for R 1ρ.
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Affiliation(s)
- Albert A Smith
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Emilie Testori
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Riccardo Cadalbert
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Matthias Ernst
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
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33
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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: 40] [Impact Index Per Article: 5.0] [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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34
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Lu X, Zhang H, Lu M, Vega AJ, Hou G, Polenova T. Improving dipolar recoupling for site-specific structural and dynamics studies in biosolids NMR: windowed RN-symmetry sequences. Phys Chem Chem Phys 2016; 18:4035-44. [PMID: 26776070 DOI: 10.1039/c5cp07818k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Experimental characterization of one-bond heteronuclear dipolar couplings is essential for structural and dynamics characterization of molecules by solid-state NMR. Accurate measurement of heteronuclear dipolar tensor parameters in magic-angle spinning NMR requires that the recoupling sequences efficiently reintroduce the desired heteronuclear dipolar coupling term, fully suppress other interactions (such as chemical shift anisotropy and homonuclear dipolar couplings), and be insensitive to experimental imperfections, such as radio frequency (rf) field mismatch. In this study, we demonstrate that the introduction of window delays into the basic elements of a phase-alternating R-symmetry (PARS) sequence results in a greatly improved protocol, termed windowed PARS (wPARS), which yields clean dipolar lineshapes that are unaffected by other spin interactions and are largely insensitive to experimental imperfections. Higher dipolar scaling factors can be attained in this technique with respect to PARS, which is particularly useful for the measurement of relatively small dipolar couplings. The advantages of wPARS are verified experimentally on model molecules N-acetyl-valine (NAV) and a tripeptide Met-Leu-Phe (MLF). The incorporation of wPARS into 3D heteronuclear or homonuclear correlation experiments permits accurate site-specific determination of dipolar tensors in proteins, as demonstrated on dynein light chain 8 (LC8). Through 3D wPARS recoupling based spectroscopy we have determined both backbone and side chain dipolar tensors in LC8 in a residue-resolved manner. We discuss these in the context of conformational dynamics of LC8. We have addressed the effect of paramagnetic relaxant Cu(ii)-EDTA doping on the dipolar coupling parameters in LC8 and observed no significant differences with respect to the neat sample permitting fast data collection. Our results indicate that wPARS is advantageous with respect to the windowless version of the sequence and is applicable to a broad range of systems including but not limited to biomolecules.
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Affiliation(s)
- Xingyu Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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35
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Paluch P, Pawlak T, Jeziorna A, Trébosc J, Hou G, Vega AJ, Amoureux JP, Dracinsky M, Polenova T, Potrzebowski MJ. Analysis of local molecular motions of aromatic sidechains in proteins by 2D and 3D fast MAS NMR spectroscopy and quantum mechanical calculations. Phys Chem Chem Phys 2015; 17:28789-801. [PMID: 26451400 PMCID: PMC4890705 DOI: 10.1039/c5cp04475h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We report a new multidimensional magic angle spinning NMR methodology, which provides an accurate and detailed probe of molecular motions occurring on timescales of nano- to microseconds, in sidechains of proteins. The approach is based on a 3D CPVC-RFDR correlation experiment recorded under fast MAS conditions (ν(R) = 62 kHz), where (13)C-(1)H CPVC dipolar lineshapes are recorded in a chemical shift resolved manner. The power of the technique is demonstrated in model tripeptide Tyr-(d)Ala-Phe and two nanocrystalline proteins, GB1 and LC8. We demonstrate that, through numerical simulations of dipolar lineshapes of aromatic sidechains, their detailed dynamic profile, i.e., the motional modes, is obtained. In GB1 and LC8 the results unequivocally indicate that a number of aromatic residues are dynamic, and using quantum mechanical calculations, we correlate the molecular motions of aromatic groups to their local environment in the crystal lattice. The approach presented here is general and can be readily extended to other biological systems.
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Affiliation(s)
- Piotr Paluch
- Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Sienkiewicza 112, PL-90-363 Łodz, Poland.
| | - Tomasz Pawlak
- Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Sienkiewicza 112, PL-90-363 Łodz, Poland.
| | - Agata Jeziorna
- Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Sienkiewicza 112, PL-90-363 Łodz, Poland.
| | - Julien Trébosc
- Unit of Catalysis and Chemistry of Solids (UCCS), CNRS-8181, University Lille North of France, 59652 Villeneuve d'Ascq, France
| | - Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA.
| | - Alexander J Vega
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA.
| | - Jean-Paul Amoureux
- Unit of Catalysis and Chemistry of Solids (UCCS), CNRS-8181, University Lille North of France, 59652 Villeneuve d'Ascq, France and Physics Department & Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062, China
| | - Martin Dracinsky
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo nam. 2, Prague, Czech Republic.
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA.
| | - Marek J Potrzebowski
- Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Sienkiewicza 112, PL-90-363 Łodz, Poland.
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36
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Hou G, Lu X, Vega AJ, Polenova T. Accurate measurement of heteronuclear dipolar couplings by phase-alternating R-symmetry (PARS) sequences in magic angle spinning NMR spectroscopy. J Chem Phys 2015; 141:104202. [PMID: 25217909 DOI: 10.1063/1.4894226] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We report a Phase-Alternating R-Symmetry (PARS) dipolar recoupling scheme for accurate measurement of heteronuclear (1)H-X (X = (13)C, (15)N, (31)P, etc.) dipolar couplings in MAS NMR experiments. It is an improvement of conventional C- and R-symmetry type DIPSHIFT experiments where, in addition to the dipolar interaction, the (1)H CSA interaction persists and thereby introduces considerable errors in the dipolar measurements. In PARS, phase-shifted RN symmetry pulse blocks applied on the (1)H spins combined with π pulses applied on the X spins at the end of each RN block efficiently suppress the effect from (1)H chemical shift anisotropy, while keeping the (1)H-X dipolar couplings intact. Another advantage over conventional DIPSHIFT experiments, which require the signal to be detected in the form of a reduced-intensity Hahn echo, is that the series of π pulses refocuses the X chemical shift and avoids the necessity of echo formation. PARS permits determination of accurate dipolar couplings in a single experiment; it is suitable for a wide range of MAS conditions including both slow and fast MAS frequencies; and it assures dipolar truncation from the remote protons. The performance of PARS is tested on two model systems, [(15)N]-N-acetyl-valine and [U-(13)C,(15)N]-N-formyl-Met-Leu-Phe tripeptide. The application of PARS for site-resolved measurement of accurate (1)H-(15)N dipolar couplings in the context of 3D experiments is presented on U-(13)C,(15)N-enriched dynein light chain protein LC8.
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Affiliation(s)
- Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA and Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, Pennsylvania 15261, USA
| | - Xingyu Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA and Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, Pennsylvania 15261, USA
| | - Alexander J Vega
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA and Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, Pennsylvania 15261, USA
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA and Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, Pennsylvania 15261, USA
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37
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Observing the overall rocking motion of a protein in a crystal. Nat Commun 2015; 6:8361. [PMID: 26436197 PMCID: PMC4600728 DOI: 10.1038/ncomms9361] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 08/13/2015] [Indexed: 12/25/2022] Open
Abstract
The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall ‘rocking' motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments. Small-amplitude overall motion of molecules in crystals limits the achievable resolution in X-ray diffraction, yet little is known about its exact nature. Here, the authors obtain NMR, XRD and MD data from three different crystal forms of a protein (ubiquitin) to gain insight into amplitude and timescale of such motions.
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Torchia DA. NMR studies of dynamic biomolecular conformational ensembles. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 84-85:14-32. [PMID: 25669739 PMCID: PMC4325279 DOI: 10.1016/j.pnmrs.2014.11.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 11/19/2014] [Accepted: 11/19/2014] [Indexed: 05/06/2023]
Abstract
Multidimensional heteronuclear NMR approaches can provide nearly complete sequential signal assignments of isotopically enriched biomolecules. The availability of assignments together with measurements of spin relaxation rates, residual spin interactions, J-couplings and chemical shifts provides information at atomic resolution about internal dynamics on timescales ranging from ps to ms, both in solution and in the solid state. However, due to the complexity of biomolecules, it is not possible to extract a unique atomic-resolution description of biomolecular motions even from extensive NMR data when many conformations are sampled on multiple timescales. For this reason, powerful computational approaches are increasingly applied to large NMR data sets to elucidate conformational ensembles sampled by biomolecules. In the past decade, considerable attention has been directed at an important class of biomolecules that function by binding to a wide variety of target molecules. Questions of current interest are: "Does the free biomolecule sample a conformational ensemble that encompasses the conformations found when it binds to various targets; and if so, on what time scale is the ensemble sampled?" This article reviews recent efforts to answer these questions, with a focus on comparing ensembles obtained for the same biomolecules by different investigators. A detailed comparison of results obtained is provided for three biomolecules: ubiquitin, calmodulin and the HIV-1 trans-activation response RNA.
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Affiliation(s)
- Dennis A Torchia
- National Institutes of Health (NIH), 5 Memorial Drive, Bethesda, MD 20892, USA.
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Das BB, Park SH, Opella SJ. Membrane protein structure from rotational diffusion. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1848:229-45. [PMID: 24747039 PMCID: PMC4201901 DOI: 10.1016/j.bbamem.2014.04.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 04/02/2014] [Indexed: 02/02/2023]
Abstract
The motional averaging of powder pattern line shapes is one of the most fundamental aspects of sold-state NMR. Since membrane proteins in liquid crystalline phospholipid bilayers undergo fast rotational diffusion, all of the signals reflect the angles of the principal axes of their dipole-dipole and chemical shift tensors with respect to the axis defined by the bilayer normal. The frequency span and sign of the axially symmetric powder patterns that result from motional averaging about a common axis provide sufficient structural restraints for the calculation of the three-dimensional structure of a membrane protein in a phospholipid bilayer environment. The method is referred to as rotationally aligned (RA) solid-state NMR and demonstrated with results on full-length, unmodified membrane proteins with one, two, and seven trans-membrane helices. RA solid-state NMR is complementary to other solid-state NMR methods, in particular oriented sample (OS) solid-state NMR of stationary, aligned samples. Structural distortions of membrane proteins from the truncations of terminal residues and other sequence modifications, and the use of detergent micelles instead of phospholipid bilayers have also been demonstrated. Thus, it is highly advantageous to determine the structures of unmodified membrane proteins in liquid crystalline phospholipid bilayers under physiological conditions. RA solid-state NMR provides a general method for obtaining accurate and precise structures of membrane proteins under near-native conditions.
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Affiliation(s)
- Bibhuti B Das
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0307 USA
| | - Sang Ho Park
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0307 USA
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0307 USA.
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Abstract
We describe a more broad-banded version of the DREAM double-quantum dipolar-recoupling sequence, which is devised by superimposing a phase-alternating RF irradiation scheme, that is, XiX pulses, on top of the original DREAM sequence. We call this sequence XiX(CW) DREAM. The recoupling conditions and the corresponding first-order effective Hamiltonian are analyzed using triple-mode Floquet theory. The performance of the XiX(CW) DREAM sequence is compared to the original DREAM sequence by numerical simulations and experiments on small model substances and the model protein ubiquitin. The results confirm that XiX(CW) DREAM shows a wider recoupling bandwidth compared to that of DREAM, therefore making the choice for the position of the carrier frequency less critical.
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Affiliation(s)
- Kong Ooi Tan
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Anders B Nielsen
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Matthias Ernst
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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del Amo JML, Agarwal V, Sarkar R, Porter J, Asami S, Rübbelke M, Fink U, Xue Y, Lange OF, Reif B. Site-specific analysis of heteronuclear Overhauser effects in microcrystalline proteins. JOURNAL OF BIOMOLECULAR NMR 2014; 59:241-9. [PMID: 24989039 DOI: 10.1007/s10858-014-9843-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 06/20/2014] [Indexed: 05/14/2023]
Abstract
Relaxation parameters such as longitudinal relaxation are susceptible to artifacts such as spin diffusion, and can be affected by paramagnetic impurities as e.g. oxygen, which make a quantitative interpretation difficult. We present here the site-specific measurement of [(1)H](13)C and [(1)H](15)N heteronuclear rates in an immobilized protein. For methyls, a strong effect is expected due to the three-fold rotation of the methyl group. Quantification of the [(1)H](13)C heteronuclear NOE in combination with (13)C-R 1 can yield a more accurate analysis of side chain motional parameters. The observation of significant [(1)H](15)N heteronuclear NOEs for certain backbone amides, as well as for specific asparagine/glutamine sidechain amides is consistent with MD simulations. The measurement of site-specific heteronuclear NOEs is enabled by the use of highly deuterated microcrystalline protein samples in which spin diffusion is reduced in comparison to protonated samples.
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Affiliation(s)
- Juan Miguel Lopez del Amo
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
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42
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Pawlak T, Potrzebowski MJ. Fine refinement of solid-state molecular structures of Leu- and Met-enkephalins by NMR crystallography. J Phys Chem B 2014; 118:3298-309. [PMID: 24605867 DOI: 10.1021/jp500379e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
This paper presents a methodology that allows the fine refinement of the crystal and molecular structure for compounds for which the data deposited in the crystallographic bases are of poor quality. Such species belong to the group of samples with molecular disorder. In the Cambridge Crystallographic Data Center (CCDC), there are approximately 22,000 deposited structures with an R-factor over 10. The powerful methodology we present employs crystal data for Leu-enkephalin (two crystallographic forms) with R-factor values of 14.0 and 8.9 and for Met-enkephalin (one form) with an R-factor of 10.5. NMR crystallography was employed in testing the X-ray data and the quality of the structure refinement. The GIPAW (gauge invariant projector augmented wave) method was used to optimize the coordinates of the enkephalins and to compute NMR parameters. As we reveal, this complementary approach makes it possible to generate a reasonable set of new coordinates that better correlate to real samples. This methodology is general and can be employed in the study of each compound possessing magnetically active nuclei.
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Affiliation(s)
- Tomasz Pawlak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences , Sienkiewicza 112, 90-363 Lodz, Poland
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43
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Haller JD, Schanda P. Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. JOURNAL OF BIOMOLECULAR NMR 2013; 57:263-80. [PMID: 24105432 PMCID: PMC3840295 DOI: 10.1007/s10858-013-9787-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 09/23/2013] [Indexed: 05/21/2023]
Abstract
Solid-state NMR provides insight into protein motion over time scales ranging from picoseconds to seconds. While in solution state the methodology to measure protein dynamics is well established, there is currently no such consensus protocol for measuring dynamics in solids. In this article, we perform a detailed investigation of measurement protocols for fast motions, i.e. motions ranging from picoseconds to a few microseconds, which is the range covered by dipolar coupling and relaxation experiments. We perform a detailed theoretical investigation how dipolar couplings and relaxation data can provide information about amplitudes and time scales of local motion. We show that the measurement of dipolar couplings is crucial for obtaining accurate motional parameters, while systematic errors are found when only relaxation data are used. Based on this realization, we investigate how the REDOR experiment can provide such data in a very accurate manner. We identify that with accurate rf calibration, and explicit consideration of rf field inhomogeneities, one can obtain highly accurate absolute order parameters. We then perform joint model-free analyses of 6 relaxation data sets and dipolar couplings, based on previously existing, as well as new data sets on microcrystalline ubiquitin. We show that nanosecond motion can be detected primarily in loop regions, and compare solid-state data to solution-state relaxation and RDC analyses. The protocols investigated here will serve as a useful basis towards the establishment of a routine protocol for the characterization of ps-μs motions in proteins by solid-state NMR.
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Affiliation(s)
- Jens D. Haller
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), 38027 Grenoble, France
- CEA, DSV, IBS, 38027 Grenoble, France
- CNRS, IBS, 38027 Grenoble, France
| | - Paul Schanda
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), 38027 Grenoble, France
- CEA, DSV, IBS, 38027 Grenoble, France
- CNRS, IBS, 38027 Grenoble, France
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44
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Das BB, Lin EC, Opella SJ. Experiments optimized for magic angle spinning and oriented sample solid-state NMR of proteins. J Phys Chem B 2013; 117:12422-31. [PMID: 24044695 DOI: 10.1021/jp407154h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Structure determination by solid-state NMR of proteins is rapidly advancing as a result of recent developments of samples, experimental methods, and calculations. There are a number of different solid-state NMR approaches that utilize stationary samples, aligned samples, or magic angle spinning of unoriented "powder" samples, and depending on the sample and the experimental method they can emphasize the measurement of distances or angles, ideally both, as sources of structural constraints. Multidimensional correlation spectroscopy of low-gamma nuclei such as (15)N and (13)C is an important step for making resonance assignments and measurements of angular restraints in membrane proteins. However, the efficiency of coherence transfer predominantly depends upon the strength of the dipole-dipole interaction, and this can vary from site to site and between sample alignments, for example, during the mixing of (13)C and (15)N magnetization in stationary aligned and in magic angle spinning samples. Here, we demonstrate that the efficiency of polarization transfer can be improved by using adiabatic demagnetization and remagnetization techniques on stationary aligned samples, and proton assisted insensitive nuclei cross-polarization in magic angle sample spinning samples. The adiabatic cross-polarization technique provides an alternative mechanism for spin-diffusion experiments correlating (15)N/(15)N and (15)N/(13)C chemical shifts over large distances. Improved efficiency in cross-polarization with 40-100% sensitivity enhancements is observed in proteins and single crystals, respectively. We describe solid-state NMR experimental techniques that are optimal for membrane proteins in liquid crystalline phospholipid bilayers under physiological conditions. The techniques are illustrated with data from single crystals both of peptides and of membrane proteins in phospholipid bilayers.
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Affiliation(s)
- Bibhuti B Das
- University of California, San Diego , 9500 Gilman Drive, 0307 La Jolla, California 92093-0307, United States
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45
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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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46
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Gansmüller A, Simorre JP, Hediger S. Windowed R-PDLF recoupling: a flexible and reliable tool to characterize molecular dynamics. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 234:154-64. [PMID: 23880256 DOI: 10.1016/j.jmr.2013.06.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 06/21/2013] [Accepted: 06/24/2013] [Indexed: 05/14/2023]
Abstract
This work focuses on the improvement of the R-PDLF heteronuclear recoupling scheme, a method that allows quantification of molecular dynamics up to the microsecond timescale in heterogeneous materials. We show how the stability of the sequence towards rf-imperfections, one of the main sources of error of this technique, can be improved by the insertion of windows without irradiation into the basic elements of the symmetry-based recoupling sequence. The impact of this modification on the overall performance of the sequence in terms of scaling factor and homonuclear decoupling efficiency is evaluated. This study indicates the experimental conditions for which precise and reliable measurement of dipolar couplings can be obtained using the popular R18(1)(7) recoupling sequence, as well as alternative symmetry-based R sequences suited for fast MAS conditions. An analytical expression for the recoupled dipolar modulation has been derived that applies to a whole class of sequences with similar recoupling properties as R18(1)(7). This analytical expression provides an efficient and precise way to extract dipolar couplings from the experimental dipolar modulation curves. We hereby provide helpful tools and information for tailoring R-PDLF recoupling schemes to specific sample properties and hardware capabilities. This approach is particularly well suited for the study of materials with strong and heterogeneous molecular dynamics where a precise measurement of dipolar couplings is crucial.
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Affiliation(s)
- Axel Gansmüller
- Institut de Biologie Structurale, UMR5075 (CEA/CNRS/UJF), 38027 Grenoble, France.
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Paluch P, Pawlak T, Amoureux JP, Potrzebowski MJ. Simple and accurate determination of X-H distances under ultra-fast MAS NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 233:56-63. [PMID: 23727588 DOI: 10.1016/j.jmr.2013.05.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 04/30/2013] [Accepted: 05/06/2013] [Indexed: 05/14/2023]
Abstract
We demonstrate that a very simple experiment, Cross-Polarization with Variable Contact-time (CP-VC), is very efficient at ultra-fast MAS (νR ≥ 60 kHz) to measure accurately the C-H and N-H distances, and to analyze the dynamics of bio-molecules. This experiment can be performed with samples that are either (13)C or (15)N labeled or without any labeling. The method is very robust experimentally with respect to imperfect Hartman-Hahn setting, and presents a large scaling factor allowing a better dipolar determination, especially for long C-H or N-H distances, or for CH3 or NH3 moieties with three-site hopping. At ultra-fast MAS, it can be used quantitatively in a 2D way, because its scaling factor is then little dependent on the offsets. This robustness with respect to offset is related to the ultra-fast spinning speed, and hence to the related small rotor diameter. Indeed, these two specifications lead to efficient n = ±1 zero-quantum Hartman-Hahn CP-transfers with large RF-fields on proton and carbon or nitrogen channels, and large dipolar scaling factor.
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Affiliation(s)
- Piotr Paluch
- Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Sienkiewicza 112, PL-90-363 Lodz, Poland
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48
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Hou G, Paramasivam S, Yan S, Polenova T, Vega AJ. Multidimensional magic angle spinning NMR spectroscopy for site-resolved measurement of proton chemical shift anisotropy in biological solids. J Am Chem Soc 2013; 135:1358-68. [PMID: 23286322 PMCID: PMC3586542 DOI: 10.1021/ja3084972] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The proton chemical shift (CS) tensor is a sensitive probe of structure and hydrogen bonding. Highly accurate quantum-chemical protocols exist for computation of (1)H magnetic shieldings in the various contexts, making proton chemical shifts potentially a powerful predictor of structural and electronic properties. However, (1)H CS tensors are not yet widely used in protein structure calculation due to scarcity of experimental data. While isotropic proton shifts can be readily measured in proteins even in the solid state, determination of the (1)H chemical shift anisotropy (CSA) tensors remains challenging, particularly in molecules containing multiple proton sites. We present a method for site-resolved measurement of amide proton CSAs in fully protonated solids under magic angle spinning. The approach consists of three concomitant 3D experiments yielding spectra determined by either mainly (1)H CSA, mainly (1)H–(15)N dipolar, or combined (1)H CSA and (1)H–(15)N dipolar interactions. The anisotropic interactions are recoupled using RN-sequences of appropriate symmetry, such as R12(1)(4), and (15)N/(13)C isotropic CS dimensions are introduced via a short selective (1)H–(15)N cross-polarization step. Accurate (1)H chemical shift tensor parameters are extracted by simultaneous fit of the lineshapes recorded in the three spectra. An application of this method is presented for an 89-residue protein, U-(13)C,(15)N-CAP-Gly domain of dynactin. The CSA parameters determined from the triple fits correlate with the hydrogen-bonding distances, and the trends are in excellent agreement with the prior solution NMR results. This approach is generally suited for recording proton CSA parameters in various biological and organic systems, including protein assemblies and nucleic acids.
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Affiliation(s)
- Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
| | | | - Si Yan
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
| | - Alexander J. Vega
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
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Ferreira TM, Coreta-Gomes F, Ollila OHS, Moreno MJ, Vaz WLC, Topgaard D. Cholesterol and POPC segmental order parameters in lipid membranes: solid state 1H-13C NMR and MD simulation studies. Phys Chem Chem Phys 2012; 15:1976-89. [PMID: 23258433 DOI: 10.1039/c2cp42738a] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The concentration of cholesterol in cell membranes affects membrane fluidity and thickness, and might regulate different processes such as the formation of lipid rafts. Since interpreting experimental data from biological membranes is rather intricate, investigations on simple models with biological relevance are necessary to understand the natural systems. We study the effect of cholesterol on the molecular structure of multi-lamellar vesicles (MLVs) composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), a phospholipid ubiquitous in cell membranes, with compositions in the range 0-60 mol% cholesterol. Order parameters, |S(CH)|, are experimentally determined by using (1)H-(13)C solid-state nuclear magnetic resonance (NMR) spectroscopy with segmental detail for all parts of both the cholesterol and POPC molecules, namely the ring system and alkyl chain of the sterol, as well as the glycerol backbone, choline headgroup and the sn-1 and sn-2 acyl chains of POPC. With increasing cholesterol concentration the acyl chains gradually adopt a more extended conformation while the orientation and dynamics of the polar groups are rather unaffected. Additionally, we perform classical molecular dynamics simulations on virtual bilayers mimicking the POPC-cholesterol MLVs investigated by NMR. Good agreement between experiments and simulations is found for the cholesterol alignment in the bilayer and for the |S(CH)| profiles of acyl chains below 15 mol% cholesterol. Deviations occur for the choline headgroup and glycerol backbone parts of POPC, as well as for the phospholipid and cholesterol alkyl chains at higher cholesterol concentrations. The unprecedented detail of the NMR data enables a more complete comparison between simulations and experiments on POPC-cholesterol bilayers and may aid in developing more realistic model descriptions of biological membranes.
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50
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Mollica L, Baias M, Lewandowski JR, Wylie BJ, Sperling LJ, Rienstra CM, Emsley L, Blackledge M. Atomic-Resolution Structural Dynamics in Crystalline Proteins from NMR and Molecular Simulation. J Phys Chem Lett 2012; 3:3657-62. [PMID: 26291002 DOI: 10.1021/jz3016233] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Solid-state NMR can provide atomic-resolution information about protein motions occurring on a vast range of time scales under similar conditions to those of X-ray diffraction studies and therefore offers a highly complementary approach to characterizing the dynamic fluctuations occurring in the crystal. We compare experimentally determined dynamic parameters, spin relaxation, chemical shifts, and dipolar couplings, to values calculated from a 200 ns MD simulation of protein GB1 in its crystalline form, providing insight into the nature of structural dynamics occurring within the crystalline lattice. This simulation allows us to test the accuracy of commonly applied procedures for the interpretation of experimental solid-state relaxation data in terms of dynamic modes and time scales. We discover that the potential complexity of relaxation-active motion can lead to significant under- or overestimation of dynamic amplitudes if different components are not taken into consideration.
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Affiliation(s)
- Luca Mollica
- †Protein Dynamics and Flexibility, Institut de Biologie Structurale, CEA, CNRS, UJF-Grenoble 1, 41 Rue Jules Horowitz, Grenoble 38027, France
| | - Maria Baias
- ‡CNRS/ENS-Lyon/UCB-Lyon 1, Centre de RMN à Très Hauts Champs, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Józef R Lewandowski
- §Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Benjamin J Wylie
- ⊥Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| | - Lindsay J Sperling
- #Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Chad M Rienstra
- ∥Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Lyndon Emsley
- ‡CNRS/ENS-Lyon/UCB-Lyon 1, Centre de RMN à Très Hauts Champs, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Martin Blackledge
- †Protein Dynamics and Flexibility, Institut de Biologie Structurale, CEA, CNRS, UJF-Grenoble 1, 41 Rue Jules Horowitz, Grenoble 38027, France
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