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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Xu J, Karra V, Large DE, Auguste DT, Hung FR. Understanding the Mechanical Properties of Ultradeformable Liposomes Using Molecular Dynamics Simulations. J Phys Chem B 2023; 127:9496-9512. [PMID: 37879075 PMCID: PMC10641833 DOI: 10.1021/acs.jpcb.3c04386] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/19/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023]
Abstract
Improving drug delivery efficiency to solid tumor sites is a central challenge in anticancer therapeutic research. Our previous experimental study (Guo et al., Nat. Commun. 2018, 9, 130) showed that soft, elastic liposomes had increased uptake and accumulation in cancer cells and tumors in vitro and in vivo respectively, relative to rigid particles. As a first step toward understanding how liposomes' molecular structure and composition modulates their elasticity, we performed all-atom and coarse-grained classical molecular dynamics (MD) simulations of lipid bilayers formed by mixing a long-tailed unsaturated phospholipid with a short-tailed saturated lipid with the same headgroup. The former types of phospholipids considered were 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-dipalmitoleoyl-sn-glycero-3-phosphocholine (termed here DPMPC). The shorter saturated lipids examined were 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC), 1,2-didecanoyl-sn-glycero-3-phosphocholine (DDPC), 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). Several lipid concentrations and surface tensions were considered. Our results show that DOPC or DPMPC systems having 25-35 mol % of the shortest lipids DHPC or DDPC are the least rigid, having area compressibility moduli KA that are ∼10% smaller than the values observed in pure DOPC or DPMPC bilayers. These results agree with experimental measurements of the stretching modulus and lysis tension in liposomes with the same compositions. These mixed systems also have lower areas per lipid and form more uneven x-y interfaces with water, the tails of both primary and secondary lipids are more disordered, and the terminal methyl groups in the tails of the long lipid DOPC or DPMPC wriggle more in the vertical direction, compared to pure DOPC or DPMPC bilayers or their mixtures with the longer saturated lipid DLPC or DMPC. These observations confirm our hypothesis that adding increasing concentrations of the short unsaturated lipid DHPC or DDPC to DOPC or DPMPC bilayers alters lipid packing and thus makes the resulting liposomes more elastic and less rigid. No formation of lipid nanodomains was noted in our simulations, and no clear trends were observed in the lateral diffusivities of the lipids as the concentration, type of secondary lipid, and surface tension were varied.
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Affiliation(s)
- Jiaming Xu
- Department
of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Vyshnavi Karra
- Department
of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Danielle E. Large
- Department
of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Debra T. Auguste
- Department
of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
- Department
of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Francisco R. Hung
- Department
of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
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3
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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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4
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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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5
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Ahlawat S, Mote KR, Lakomek NA, Agarwal V. Solid-State NMR: Methods for Biological Solids. Chem Rev 2022; 122:9643-9737. [PMID: 35238547 DOI: 10.1021/acs.chemrev.1c00852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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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6
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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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7
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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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8
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Pawlak T, Oszajca M, Szczesio M, Potrzebowski MJ. Solid-State Study of the Structure, Dynamics, and Thermal Processes of Safinamide Mesylate─A New Generation Drug for the Treatment of Neurodegenerative Diseases. Mol Pharm 2021; 19:287-302. [PMID: 34856803 PMCID: PMC8728732 DOI: 10.1021/acs.molpharmaceut.1c00779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Safinamide mesylate
(SM), the pure active pharmaceutical
ingredient (API) recently used in Parkinson disease treatment, recrystallized
employing water–ethanol mixture of solvents (vol/vol 1:9) gives
a different crystallographic form compared to SM in Xadago
tablets. Pure SM crystallizes as a hemihydrate in the
monoclinic system with the P21 space group.
Its crystal and molecular structure were determined by means of cryo
X-ray crystallography at 100 K. SM in the Xadago tablet
exists in anhydrous form in the orthorhombic crystallographic system
with the P212121 space group. The water migration and thermal processes in the crystal
lattice were monitored by solid-state NMR spectroscopy, differential
scanning calorimetry, and thermogravimetric analysis. SM in Xadago in the high-humidity environment undergoes phase transformation
to the P21 form which can be easily reversed
just by heating up to 80 °C. For the commercial form of the API,
there is also a reversible thermal transformation observed between Z′ = 1 ↔ Z′ = 3 crystallographic
forms in the 0–20 °C temperature range. Analysis of molecular
motion in the crystal lattice proves that the observed conformational
polymorphism is forced by intramolecular dynamics. All above-mentioned
processes were analyzed and described employing the NMR crystallography
approach with the support of advanced theoretical calculations.
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Affiliation(s)
- Tomasz Pawlak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Marcin Oszajca
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Małgorzata Szczesio
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland
| | - Marek J Potrzebowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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9
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Pawlak T, Sudgen I, Bujacz G, Iuga D, Brown SP, Potrzebowski MJ. Synergy of Solid-State NMR, Single-Crystal X-ray Diffraction, and Crystal Structure Prediction Methods: A Case Study of Teriflunomide (TFM). CRYSTAL GROWTH & DESIGN 2021; 21:3328-3343. [PMID: 34267599 PMCID: PMC8273857 DOI: 10.1021/acs.cgd.1c00123] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/27/2021] [Indexed: 06/13/2023]
Abstract
In this work, for the first time, we present the X-ray diffraction crystal structure and spectral properties of a new, room-temperature polymorph of teriflunomide (TFM), CSD code 1969989. As revealed by DSC, the low-temperature TFM polymorph recently reported by Gunnam et al. undergoes a reversible thermal transition at -40 °C. This reversible process is related to a change in Z' value, from 2 to 1, as observed by variable-temperature 1H-13C cross-polarization (CP) magic-angle spinning (MAS) solid-state NMR, while the crystallographic system is preserved (triclinic). Two-dimensional 13C-1H and 1H-1H double-quantum MAS NMR spectra are consistent with the new room-temperature structure, including comparison with GIPAW (gauge-including projector augmented waves) calculated NMR chemical shifts. A crystal structure prediction procedure found both experimental teriflunomide polymorphs in the energetic global minimum region. Differences between the polymorphs are seen for the torsional angle describing the orientation of the phenyl ring relative to the planarity of the TFM molecule. In the low-temperature structure, there are two torsion angles of 4.5 and 31.9° for the two Z' = 2 molecules, while in the room-temperature structure, there is disorder that is modeled with ∼50% occupancy between torsion angles of -7.8 and 28.6°. These observations are consistent with a broad energy minimum as revealed by DFT calculations. PISEMA solid-state NMR experiments show a reduction in the C-H dipolar coupling in comparison to the static limit for the aromatic CH moieties of 75% and 51% at 20 and 40 °C, respectively, that is indicative of ring flips at the higher temperature. Our study shows the power of combining experiments, namely DSC, X-ray diffraction, and MAS NMR, with DFT calculations and CSP to probe and understand the solid-state landscape, and in particular the role of dynamics, for pharmaceutical molecules.
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Affiliation(s)
- Tomasz Pawlak
- Centre
of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Isaac Sudgen
- Molecular
Systems Engineering Group, Centre for Process Systems Engineering,
Department of Chemical Engineering, Imperial
College London, London SW7 2AZ, U.K.
| | - Grzegorz Bujacz
- Institute
of Molecular and Industrial Biotechnology, Lodz University of Technology, Stefanowskiego 4/10, 90-924, Lodz, Poland
| | - Dinu Iuga
- Department
of Physics, University of Warwick, Coventry CV4 7AL, U.K.
| | - Steven P. Brown
- Department
of Physics, University of Warwick, Coventry CV4 7AL, U.K.
| | - Marek J. Potrzebowski
- Centre
of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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10
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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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11
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Dagys L, Klimkevičius V, Klimavicius V, Balčiūnas S, Banys J, Balevicius V. Cross‐polarization with magic‐angle spinning kinetics and impedance spectroscopy study of proton mobility, local disorder, and thermal equilibration in
hydrogen‐bonded
poly(methacrylic acid). JOURNAL OF POLYMER SCIENCE 2020. [DOI: 10.1002/pol.20200592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Laurynas Dagys
- Institute of Chemical Physics Vilnius University Vilnius Lithuania
- Department of Chemistry University of Southampton Southampton UK
| | | | - Vytautas Klimavicius
- Institute of Chemical Physics Vilnius University Vilnius Lithuania
- Eduard‐Zintl Institute for Inorganic and Physical Chemistry University of Technology Darmstadt Darmstadt Germany
| | - Sergejus Balčiūnas
- Institute of Applied Electrodynamics and Telecommunications Vilnius University Vilnius Lithuania
| | - Jūras Banys
- Institute of Applied Electrodynamics and Telecommunications Vilnius University Vilnius Lithuania
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12
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Guan H, Li J, Zhou T, Pang Z, Fu Y, Cornelio J, Wang Q, Telfer SG, Kong X. Probing Nonuniform Adsorption in Multicomponent Metal-Organic Frameworks via Segmental Dynamics by Solid-State Nuclear Magnetic Resonance. J Phys Chem Lett 2020; 11:7167-7176. [PMID: 32787305 DOI: 10.1021/acs.jpclett.0c01593] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The guest adsorption phenomena in multicomponent metal-organic frameworks (MOFs) are intricate due to their structural complexities. In this work, we studied two members of the isostructural series of MUF-77 frameworks that consist of long or short alkyl groups. The adsorption of methanol, N,N-dimethylaniline (DMA) and acridine orange (AO) in two structures of MUF-77 has been investigated. 2H solid-state nuclear magnetic resonance (SSNMR) and two-dimensional 1H-13C NMR spectroscopy were used to probe the dynamics of various compartments of MUF-77. Through the analyses of dynamic behavior by SSNMR and molecular dynamics simulations, we elucidate the spatial distribution of guest molecules are nonuniform around different chemical components, in different pore structures, and across different parts of MOF lattice. In addition, we reveal that the framework flexibility of MUF-77 with short alkyl groups is reduced upon guest adsorption yet the framework flexibility of MUF-77 with long alkyl groups increases upon loading with methanol.
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Affiliation(s)
- Hanxi Guan
- Center for Chemistry of High-Performance & Novel Materials, Department of Chemistry, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Jiachen Li
- Department of Chemistry, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Tianyou Zhou
- MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Zhenfeng Pang
- Center for Chemistry of High-Performance & Novel Materials, Department of Chemistry, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Yao Fu
- Center for Chemistry of High-Performance & Novel Materials, Department of Chemistry, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Joel Cornelio
- MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Qi Wang
- Department of Chemistry, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Shane G Telfer
- MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Xueqian Kong
- Center for Chemistry of High-Performance & Novel Materials, Department of Chemistry, Zhejiang University, Hangzhou 310027, People's Republic of China
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13
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Dagys L, Klimkevičius V, Klimavicius V, Aidas K, Makuška R, Balevicius V. CP MAS kinetics in soft matter: Spin diffusion, local disorder and thermal equilibration in poly(2-hydroxyethyl methacrylate). SOLID STATE NUCLEAR MAGNETIC RESONANCE 2020; 105:101641. [PMID: 31887667 DOI: 10.1016/j.ssnmr.2019.101641] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 12/02/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
The 1H-13C cross-polarization magic angle spinning kinetics was studied in poly(2-hydroxyethyl methacrylate) (pHEMA), i.e. a soft material with high degrees of internal freedom and molecular disorder, having the purpose to track the influence of increasing local incoherent contributions to the effects of coherent nature in the open quantum spin systems. The experimental CP MAS kinetic curves were analyzed in the frame of the models of isotropic and anisotropic spin diffusion with thermal equilibration. The rates of spin diffusion and spin-lattice relaxation as well as the profiles of distribution of dipolar coupling, the parameters accounting the effective size of spin clusters and the local order parameters were determined. The intensities of the peaks of periodic quasi-equilibrium origin gradually decrease with increasing disorder, i.e. going from most ordered to more disordered sites in the polymer. Assuming that the thermal motion induced by the temperature gradients is much faster than the equilibration driven by spin diffusion due the difference in spin temperatures, it was deduced that the thermal equilibration in pHEMA occurs in the time scale of 10-4 s. This is one order of magnitude faster than the spectral spin diffusion, which occurs between spins having different resonance frequencies. The thermal equilibration in the case of remote spin clusters was described by the 'stretched exponent' decay. This led to the fractal dimension Dp ≈ 1.65 for both carbon sites (quaternary and carbonyl). The obtained Dp value corresponds to the aggregates, which images are very similar to those for pHEMA and some other related polymer structures are usually conceived.
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Affiliation(s)
- Laurynas Dagys
- Institute of Chemical Physics, Vilnius University, LT-10257, Vilnius, Lithuania; Department of Chemistry, University of Southampton, SO17 1BJ, Southampton, UK
| | | | - Vytautas Klimavicius
- Institute of Chemical Physics, Vilnius University, LT-10257, Vilnius, Lithuania; Eduard-Zintl Institute for Inorganic and Physical Chemistry, University of Technology Darmstadt, D-64287, Darmstadt, Germany
| | - Kęstutis Aidas
- Institute of Chemical Physics, Vilnius University, LT-10257, Vilnius, Lithuania
| | - Ričardas Makuška
- Institute of Chemistry, Vilnius University, LT-03225, Vilnius, Lithuania
| | - Vytautas Balevicius
- Institute of Chemical Physics, Vilnius University, LT-10257, Vilnius, Lithuania.
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14
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Phan VC, Fry EA, Zilm KW. Accounting for the temperature dependence of 13C spin-lattice relaxation of methyl groups in the glycyl-alanyl-leucine model system under MAS with spin diffusion. JOURNAL OF BIOMOLECULAR NMR 2019; 73:411-421. [PMID: 31407207 PMCID: PMC6817761 DOI: 10.1007/s10858-019-00261-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 06/19/2019] [Indexed: 06/10/2023]
Abstract
The difficulties in quantitatively modeling the temperature dependence of spin-lattice relaxation in a model isotope-enriched peptide are explored as a prelude to obtaining dynamics parameters for motions in proteins from such measurements. The degree to which this can be handled by adding spin diffusion to a bath in standard rate matrix relaxation theory is studied using a small tri-peptide model system, glycyl-alanyl-leucine (GAL). We observe in this molecule that the relaxation of backbone carbons CO and Cα is not dominated by local fluctuations of the 13C-1H dipolar couplings, but rather by 13C-13C spin diffusion to nearby methyl relaxation sinks. A treatment of the methyl relaxation itself, which ignores 13C-13C spin diffusion effects back to the otherwise slowly relaxing bath, provides poor agreement between theory and experimental data obtained for the temperature dependence of the methyl relaxation rates. Closed form approximate spectral densities and relaxation rates for a methyl group during magic angle spinning are obtained to compute the needed transition rates. These average computed rates, in conjunction with an extended form of the Solomon equations, are found to adequately model the temperature dependence of the methyl relaxation rates when spin diffusion is included. The barrier to rotation for the alanine methyl in GAL is determined to be 3.5 kcal mol-1.
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Affiliation(s)
- Van C Phan
- Natural Science Department, Hostos Community College, 500 Grand Concourse, The Bronx, NY, 10451, USA
| | - Elizabeth A Fry
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA
| | - Kurt W Zilm
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA.
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15
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Dagys L, Klimavicius V, Gutmann T, Buntkowsky G, Balevicius V. Quasi-Equilibria and Polarization Transfer Between Adjacent and Remote Spins: 1H- 13C CP MAS Kinetics in Glycine. J Phys Chem A 2018; 122:8938-8947. [PMID: 30354129 DOI: 10.1021/acs.jpca.8b09036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The 1H-13C CP MAS kinetic curves were measured in glycine powder sample at the MAS rates of 7, 10, and 12 kHz. Each experimental curve contained up to 1000 equidistant points over the whole contact time range of 10 μs - 10 ms. The CP kinetic data for CH2 group, i.e., for the system containing adjacent 1H-13C spin pairs with a definite dominant dipolar coupling can be described in the frame of the isotropic spin-diffusion approach. The local order parameter ⟨ S⟩ ≈ 1.0, determined as the ratio of the measured dipolar 1H-13C coupling constant and the calculated static dipolar coupling constant, is very close to the values deduced in series of other amino acids. The strong narrow peaks observed in the spin coupling spectrum at multiples of the MAS frequency can be considered as the confirmation that the periodic quasi-equilibrium state can appear also in the powder samples. The anisotropic spin-diffusion approach improved by the introducing of the thermal equilibration in the proton bath is the most proper model to describe the CP kinetics in the system containing remote spins. Very realistic values of the spin-cluster size ( N) have been obtained without any constraint on the flow of the nonlinear curve fitting. The finite values of N ≤ 4 means that CP transfer is located within one glycine molecule.
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Affiliation(s)
- Laurynas Dagys
- Institute of Chemical Physics , Vilnius University , Sauletekio av. 3 , LT-10257 Vilnius , Lithuania
| | - Vytautas Klimavicius
- Institute of Chemical Physics , Vilnius University , Sauletekio av. 3 , LT-10257 Vilnius , Lithuania.,Eduard-Zintl Institute for Inorganic and Physical Chemistry , University of Technology Darmstadt , Alarich-Weiss-Strasse 8 , D-64287 Darmstadt , Germany
| | - Torsten Gutmann
- Eduard-Zintl Institute for Inorganic and Physical Chemistry , University of Technology Darmstadt , Alarich-Weiss-Strasse 8 , D-64287 Darmstadt , Germany
| | - Gerd Buntkowsky
- Eduard-Zintl Institute for Inorganic and Physical Chemistry , University of Technology Darmstadt , Alarich-Weiss-Strasse 8 , D-64287 Darmstadt , Germany
| | - Vytautas Balevicius
- Institute of Chemical Physics , Vilnius University , Sauletekio av. 3 , LT-10257 Vilnius , Lithuania
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16
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Matlahov I, van der Wel PCA. Hidden motions and motion-induced invisibility: Dynamics-based spectral editing in solid-state NMR. Methods 2018; 148:123-135. [PMID: 29702226 DOI: 10.1016/j.ymeth.2018.04.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/05/2018] [Accepted: 04/16/2018] [Indexed: 10/17/2022] Open
Abstract
Solid-state nuclear magnetic resonance (ssNMR) spectroscopy enables the structural characterization of a diverse array of biological assemblies that include amyloid fibrils, non-amyloid aggregates, membrane-associated proteins and viral capsids. Such biological samples feature functionally relevant molecular dynamics, which often affect different parts of the sample in different ways. Solid-state NMR experiments' sensitivity to dynamics represents a double-edged sword. On the one hand, it offers a chance to measure dynamics in great detail. On the other hand, certain types of motion lead to signal loss and experimental inefficiencies that at first glance interfere with the application of ssNMR to overly dynamic proteins. Dynamics-based spectral editing (DYSE) ssNMR methods leverage motion-dependent signal losses to simplify spectra and enable the study of sub-structures with particular motional properties.
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Affiliation(s)
- Irina Matlahov
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15213, USA
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15213, USA; Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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17
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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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18
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Ivanir-Dabora H, Nimerovsky E, Madhu PK, Goldbourt A. Site-Resolved Backbone and Side-Chain Intermediate Dynamics in a Carbohydrate-Binding Module Protein Studied by Magic-Angle Spinning NMR Spectroscopy. Chemistry 2015; 21:10778-85. [DOI: 10.1002/chem.201500856] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Indexed: 12/12/2022]
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19
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Abramov G, Morag O, Goldbourt A. Magic-angle spinning NMR of intact bacteriophages: insights into the capsid, DNA and their interface. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:80-90. [PMID: 25797007 DOI: 10.1016/j.jmr.2015.01.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 01/05/2015] [Accepted: 01/18/2015] [Indexed: 06/04/2023]
Abstract
Bacteriophages are viruses that infect bacteria. They are complex macromolecular assemblies, which are composed of multiple protein subunits that protect genomic material and deliver it to specific hosts. Various biophysical techniques have been used to characterize their structure in order to unravel phage morphogenesis. Yet, most bacteriophages are non-crystalline and have very high molecular weights, in the order of tens of MegaDaltons. Therefore, complete atomic-resolution characterization on such systems that encompass both capsid and DNA is scarce. In this perspective article we demonstrate how magic-angle spinning solid-state NMR has and is used to characterize in detail bacteriophage viruses, including filamentous and icosahedral phage. We discuss the process of sample preparation, spectral assignment of both capsid and DNA and the use of chemical shifts and dipolar couplings to probe the capsid-DNA interface, describe capsid structure and dynamics and extract structural differences between viruses.
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Affiliation(s)
- Gili Abramov
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
| | - Omry Morag
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
| | - Amir Goldbourt
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel.
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20
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Paluch P, Trébosc J, Nishiyama Y, Potrzebowski MJ, Malon M, Amoureux JP. Theoretical study of CP-VC: a simple, robust and accurate MAS NMR method for analysis of dipolar C-H interactions under rotation speeds faster than ca. 60 kHz. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 252:67-77. [PMID: 25662360 DOI: 10.1016/j.jmr.2015.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 12/24/2014] [Accepted: 01/05/2015] [Indexed: 06/04/2023]
Abstract
We show that Cross-Polarization with Variable Contact-time (CP-VC) allows an accurate determination of C-H dipolar interactions, which permits an easy detailed analysis of bond lengths and local dynamics, e.g. in biomolecules. The method presents a large dipolar scaling factor of 1/√2, leading to a better determination of dipolar interactions, especially for long C-H distances, and it allows the observation of very small local details such as those related either to CH(2) three spin systems, or even to hydrogen bonds. CP-VC is very simple to set up and very robust with respect to most experimental parameters, such as: rf-offsets, chemical-shift anisotropies, imperfect Hartmann-Hahn setting, and rf-inhomogeneity. The only required condition is the use of a sufficiently fast MAS spinning speed of at least ca. 60 kHz.
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Affiliation(s)
- P Paluch
- Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Lodz 90-363, Poland
| | - J Trébosc
- UCCS, University Lille North of France, Villeneuve d'Ascq 59652, France
| | - Y Nishiyama
- JEOL RESONANCE Inc., Musashino, Akishima, Tokyo 196-8558, Japan; RIKEN CLST-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan
| | - M J Potrzebowski
- Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Lodz 90-363, Poland
| | - M Malon
- JEOL RESONANCE Inc., Musashino, Akishima, Tokyo 196-8558, Japan; RIKEN CLST-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan
| | - J P Amoureux
- UCCS, University Lille North of France, Villeneuve d'Ascq 59652, France; Physics Department, Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062, China.
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21
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Cobo MF, Reichert D, Saalwächter K, deAzevedo ER. A double-component Anderson-Weiss approach for describing NMR signals of mobile SIn units: application to constant-time DIPSHIFT experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 248:115-125. [PMID: 25442780 DOI: 10.1016/j.jmr.2014.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 09/11/2014] [Accepted: 09/15/2014] [Indexed: 06/04/2023]
Abstract
A composed Gaussian local field is proposed to describe the effect of molecular motions on NMR signals of SIn units (e.g., CHn or NHn), based upon the well-know Anderson-Weiss (AW) approximation. The approach is exemplified on constant-time recoupled dipolar chemical-shift correlation (tC-recDIPSHIFT) experiments, providing an analytical formula that can be used as a fitting function in studies of intermediate-regime motions. By comparison of analytical tC-recDIPSHIFT curves and dynamic spin dynamics simulations, we show that for heteronuclear spin pairs (SI system), the AW treatment assuming the usual Gaussian local field is accurate. However, the approximation fails for the case of SIn spin systems for motional rates higher than a few kHz. Based on earlier work of Terao et al., who proposed a decomposition of CHn dipolar powder patterns into to 2(n) spin-pair-type patterns, we propose an AW approach based upon a double-Gaussian local field. We derive an analytical formula for tC-recDIPSHIFT signals, and demonstrate its accuracy by comparison with simulations of several motional geometries and rates, and with experimental results for a model sample. The approach is not limited to the tC-recDIPSHIFT experiment and should be of general use in dipolar-coupling based experiments probing (partially) mobile SIn molecular moieties.
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Affiliation(s)
- Marcio Fernando Cobo
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, CEP, 13560-970 São Carlos, São Paulo, Brazil.
| | - Detlef Reichert
- Institut für Physik - NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 7, D-06120 Halle, Germany
| | - Kay Saalwächter
- Institut für Physik - NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 7, D-06120 Halle, Germany.
| | - Eduardo Ribeiro deAzevedo
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, CEP, 13560-970 São Carlos, São Paulo, Brazil.
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22
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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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23
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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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24
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Reif B. Ultra-high resolution in MAS solid-state NMR of perdeuterated proteins: implications for structure and dynamics. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 216:1-12. [PMID: 22280934 DOI: 10.1016/j.jmr.2011.12.017] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 12/20/2011] [Accepted: 12/22/2011] [Indexed: 05/14/2023]
Abstract
High resolution proton spectra are obtained in MAS solid-state NMR in case samples are prepared using perdeuterated protein and D(2)O in the recrystallization buffer. Deuteration reduces drastically (1)H, (1)H dipolar interactions and allows to obtain amide proton line widths on the order of 20 Hz. Similarly, high-resolution proton spectra of aliphatic groups can be obtained if specifically labeled precursors for biosynthesis of methyl containing side chains are used, or if limited amounts of H(2)O in the bacterial growth medium is employed. This review summarizes recent spectroscopic developments to access structure and dynamics of biomacromolecules in the solid-state, and shows a number of applications to amyloid fibrils and membrane proteins.
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Affiliation(s)
- Bernd Reif
- Munich Center for Integrated Protein Science (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany.
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25
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Walczak M, Ciesielski W, Galeski A, Potrzebowski MJ, Regnier G, Hiltner A, Baer E. Structure and molecular dynamics of multilayered polycarbonate/polystyrene films. J Appl Polym Sci 2012. [DOI: 10.1002/app.36567] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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26
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Veshtort M, Griffin RG. Proton-driven spin diffusion in rotating solids via reversible and irreversible quantum dynamics. J Chem Phys 2012; 135:134509. [PMID: 21992326 DOI: 10.1063/1.3635374] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Proton-driven spin diffusion (PDSD) experiments in rotating solids have received a great deal of attention as a potential source of distance constraints in large biomolecules. However, the quantitative relationship between the molecular structure and observed spin diffusion has remained obscure due to the lack of an accurate theoretical description of the spin dynamics in these experiments. We start with presenting a detailed relaxation theory of PDSD in rotating solids that provides such a description. The theory applies to both conventional and radio-frequency-assisted PDSD experiments and extends to the non-Markovian regime to include such phenomena as rotational resonance (R(2)). The basic kinetic equation of the theory in the non-Markovian regime has the form of a memory function equation, with the role of the memory function played by the correlation function. The key assumption used in the derivation of this equation expresses the intuitive notion of the irreversible dissipation of coherences in macroscopic systems. Accurate expressions for the correlation functions and for the spin diffusion constants are given. The theory predicts that the spin diffusion constants governing the multi-site PDSD can be approximated by the constants observed in the two-site diffusion. Direct numerical simulations of PDSD dynamics via reversible Liouville-von Neumann equation are presented to support and compliment the theory. Remarkably, an exponential decay of the difference magnetization can be observed in such simulations in systems consisting of only 12 spins. This is a unique example of a real physical system whose typically macroscopic and apparently irreversible behavior can be traced via reversible microscopic dynamics. An accurate value for the spin diffusion constant can be usually obtained through direct simulations of PDSD in systems consisting of two (13)C nuclei and about ten (1)H nuclei from their nearest environment. Spin diffusion constants computed by this method are in excellent agreement with the spin diffusion constants obtained through equations given by the relaxation theory of PDSD. The constants resulting from these two approaches were also in excellent agreement with the results of 2D rotary resonance recoupling proton-driven spin diffusion (R(3)-PDSD) experiments performed in three model compounds, where magnetization exchange occurred over distances up to 4.9 Å. With the methodology presented, highly accurate internuclear distances can be extracted from such data. Relayed transfer of magnetization between distant nuclei appears to be the main (and apparently resolvable) source of uncertainty in such measurements. The non-Markovian kinetic equation was applied to the analysis of the R(2) spin dynamics. The conventional semi-phenomenological treatment of relxation in R(2) has been shown to be equivalent to the assumption of the Lorentzian spectral density function in the relaxatoin theory of PDSD. As this assumption is a poor approximation in real physical systems, the conventional R(2) treatment is likely to carry a significant model error that has not been recognized previously. The relaxation theory of PDSD appears to provide an accurate, parameter-free alternative. Predictions of this theory agreed well with the full quantum mechanical simulations of the R(2) dynamics in the few simple model systems we considered.
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Affiliation(s)
- Mikhail Veshtort
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Pawlak T, Trzeciak-Karlikowska K, Czernek J, Ciesielski W, Potrzebowski MJ. Computed and Experimental Chemical Shift Parameters for Rigid and Flexible YAF Peptides in the Solid State. J Phys Chem B 2012; 116:1974-83. [DOI: 10.1021/jp2111567] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tomasz Pawlak
- Centre of Molecular
and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, PL-90-363 Lodz, Poland
| | | | - Jiri Czernek
- Institute of Macromolecular
Chemistry, Academy of Sciences of the Czech Republic, Heyrovsky Square 2, CZ-16206 Praha 6, Czech
Republic
| | - Wlodzimierz Ciesielski
- Centre of Molecular
and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, PL-90-363 Lodz, Poland
| | - Marek J. Potrzebowski
- Centre of Molecular
and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, PL-90-363 Lodz, Poland
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28
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Czernek J, Pawlak T, Potrzebowski MJ. Benchmarks for the 13C NMR chemical shielding tensors in peptides in the solid state. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.01.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Reif B. Deuterated peptides and proteins: structure and dynamics studies by MAS solid-state NMR. Methods Mol Biol 2012; 831:279-301. [PMID: 22167680 DOI: 10.1007/978-1-61779-480-3_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Perdeuteration and back substitution of exchangeable protons in microcrystalline proteins, in combination with recrystallization from D(2)O-containing buffers, significantly reduce (1)H, (1)H dipolar interactions. This way, amide proton line widths on the order of 20 Hz are obtained. Aliphatic protons are accessible either via specifically protonated precursors or by using low amounts of H(2)O in the bacterial growth medium. The labeling scheme enables characterization of structure and dynamics in the solid-state without dipolar truncation artifacts.
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Affiliation(s)
- Bernd Reif
- Munich Center for Integrated Protein Science (CIPSM) at Department Chemie, Technische Universität München, Garching, Germany.
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30
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Torchia DA. Dynamics of biomolecules from picoseconds to seconds at atomic resolution. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 212:1-10. [PMID: 21840740 DOI: 10.1016/j.jmr.2011.07.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 07/14/2011] [Indexed: 05/31/2023]
Abstract
Although biomolecular dynamics has been investigated using NMR for at least 40 years, only in the past 20 years have internal motions been characterized at atomic resolution throughout proteins and nucleic acids. This development was made possible by multidimensional heteronuclear NMR approaches that provide near complete sequential signal assignments of uniformly labeled biomolecules. Recent methodological advances have enabled characterization of internal dynamics on timescales ranging from picoseconds to seconds, both in solution and in the solid state. The size, complexity and functional significance of biomolecules investigated by NMR continue to grow, as do the insights that have been obtained about function. In this article I review a number of recent advances that have made such studies possible, and provide a few examples of where NMR either by itself or in combination with other approaches has paved the way to a better understanding of the complex relationship between dynamics and biomolecular function. Finally, I discuss prospects for further advances in this field.
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Trzeciak-Karlikowska K, Bujacz A, Ciesielski W, Bujacz GD, Potrzebowski MJ. The Influence of the Stereochemistry of Alanine Residue on the Solid State Conformation and Crystal Packing of Opioid Peptides Containing d-Ala or l-Ala in Message Domain – XRD and NMR Study. J Phys Chem B 2011; 115:9910-9. [DOI: 10.1021/jp205570y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Anna Bujacz
- Institute of Technical Biochemistry, Technical University of Lodz, Stefanowskiego 4/10, 90-924 Lodz, Poland
| | - Włodzimierz Ciesielski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Grzegorz D. Bujacz
- Institute of Technical Biochemistry, Technical University of Lodz, Stefanowskiego 4/10, 90-924 Lodz, Poland
| | - Marek J. Potrzebowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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Schanda P, Meier BH, Ernst M. Accurate measurement of one-bond H-X heteronuclear dipolar couplings in MAS solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 210:246-59. [PMID: 21482161 DOI: 10.1016/j.jmr.2011.03.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 03/08/2011] [Accepted: 03/14/2011] [Indexed: 05/13/2023]
Abstract
The accurate experimental determination of dipolar-coupling constants for one-bond heteronuclear dipolar couplings in solids is a key for the quantification of the amplitudes of motional processes. Averaging of the dipolar coupling reports on motions on time scales up to the inverse of the coupling constant, in our case tens of microseconds. Combining dipolar-coupling derived order parameters that characterize the amplitudes of the motion with relaxation data leads to a more precise characterization of the dynamical parameters and helps to disentangle the amplitudes and the time scales of the motional processes, which impact relaxation rates in a highly correlated way. Here. we describe and characterize an improved experimental protocol--based on REDOR--to measure these couplings in perdeuterated proteins with a reduced sensitivity to experimental missettings. Because such effects are presently the dominant source of systematic errors in experimental dipolar-coupling measurements, these compensated experiments should help to significantly improve the precision of such data. A detailed comparison with other commonly used pulse sequences (T-MREV, phase-inverted CP, R18(2)(5), and R18(1)(7)) is provided.
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Affiliation(s)
- Paul Schanda
- Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
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Park SH, Das BB, De Angelis AA, Scrima M, Opella SJ. Mechanically, magnetically, and "rotationally aligned" membrane proteins in phospholipid bilayers give equivalent angular constraints for NMR structure determination. J Phys Chem B 2011; 114:13995-4003. [PMID: 20961141 DOI: 10.1021/jp106043w] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The native environment for membrane proteins is the highly asymmetric phospholipid bilayer, and this has a large effect on both their structure and dynamics. Reproducing this environment in samples suitable for spectroscopic and diffraction experiments is a key issue, and flexibility in sample preparation is essential to accommodate the diverse size, shape, and other physical properties of membrane proteins. In most cases, to ensure that the biological activities are maintained, this means reconstituting the proteins in fully hydrated planar phospholipid bilayers. The asymmetric character of protein-containing bilayers means that it is possible to prepare either oriented or unoriented (powder) samples. Here we demonstrate the equivalence of mechanical, magnetic, and what we refer to as "rotational alignment" of membrane proteins in phospholipid bilayer samples for solid-state NMR spectroscopy. The trans-membrane domain of virus protein "u" (Vpu) from human immunodeficiency virus (HIV-1) and the full-length membrane-bound form of fd bacteriophage coat protein in phospholipid bilayers are used as examples. The equivalence of structural constraints from oriented and unoriented (powder) samples of membrane proteins is based on two concepts: (1) their alignment is defined by the direction of the bilayer normal relative to the magnetic field and (2) they undergo rapid rotational diffusion about the same bilayer normal in liquid crystalline membranes. The measurement of angular constraints relative to a common external axis system defined by the bilayer normal for all sites in the protein is an essential element of oriented sample (OS) solid-state NMR.
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Affiliation(s)
- Sang Ho Park
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0307, USA
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Schanda P, Meier BH, Ernst M. Quantitative Analysis of Protein Backbone Dynamics in Microcrystalline Ubiquitin by Solid-State NMR Spectroscopy. J Am Chem Soc 2010; 132:15957-67. [PMID: 20977205 DOI: 10.1021/ja100726a] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Paul Schanda
- ETH Zürich, Physical Chemistry, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Beat H. Meier
- ETH Zürich, Physical Chemistry, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Matthias Ernst
- ETH Zürich, Physical Chemistry, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
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Wu CH, Das BB, Opella SJ. (1)H-(13)C Hetero-nuclear dipole-dipole couplings of methyl groups in stationary and magic angle spinning solid-state NMR experiments of peptides and proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 202:127-34. [PMID: 19896874 PMCID: PMC2888030 DOI: 10.1016/j.jmr.2009.10.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Revised: 10/16/2009] [Accepted: 10/16/2009] [Indexed: 05/16/2023]
Abstract
(13)C NMR of isotopically labeled methyl groups has the potential to combine spectroscopic simplicity with ease of labeling for protein NMR studies. However, in most high resolution separated local field experiments, such as polarization inversion spin exchange at the magic angle (PISEMA), that are used to measure (1)H-(13)C hetero-nuclear dipolar couplings, the four-spin system of the methyl group presents complications. In this study, the properties of the (1)H-(13)C hetero-nuclear dipolar interactions of (13)C-labeled methyl groups are revealed through solid-state NMR experiments on a range of samples, including single crystals, stationary powders, and magic angle spinning of powders, of (13)C(3) labeled alanine alone and incorporated into a protein. The spectral simplifications resulting from proton detected local field (PDLF) experiments are shown to enhance resolution and simplify the interpretation of results on single crystals, magnetically aligned samples, and powders. The complementarity of stationary sample and magic angle spinning (MAS) measurements of dipolar couplings is demonstrated by applying polarization inversion spin exchange at the magic angle and magic angle spinning (PISEMAMAS) to unoriented samples.
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Chevelkov V, Fink U, Reif B. Accurate determination of order parameters from 1H,15N dipolar couplings in MAS solid-state NMR experiments. J Am Chem Soc 2009; 131:14018-22. [PMID: 19743845 DOI: 10.1021/ja902649u] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A reliable site-specific estimate of the individual N-H bond lengths in the protein backbone is the fundamental basis of any relaxation experiment in solution and in the solid-state NMR. The N-H bond length can in principle be influenced by hydrogen bonding, which would result in an increased N-H distance. At the same time, dynamics in the backbone induces a reduction of the experimental dipolar coupling due to motional averaging. We present a 3D dipolar recoupling experiment in which the (1)H,(15)N dipolar coupling is reintroduced in the indirect dimension using phase-inverted CP to eliminate effects from rf inhomogeneity. We find no variation of the N-H dipolar coupling as a function of hydrogen bonding. Instead, variations in the (1)H,(15)N dipolar coupling seem to be due to dynamics of the protein backbone. This is supported by the observed correlation between the H(N)-N dipolar coupling and the amide proton chemical shift. The experiment is demonstrated for a perdeuterated sample of the alpha-spectrin SH3 domain. Perdeuteration is a prerequisite to achieve high accuracy. The average error in the analysis of the H-N dipolar couplings is on the order of +/-370 Hz (+/-0.012 A) and can be as small as 150 Hz, corresponding to a variation of the bond length of +/-0.005 A.
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Affiliation(s)
- Veniamin Chevelkov
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, D-13125 Berlin, Germany
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37
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McDermott A. Structure and dynamics of membrane proteins by magic angle spinning solid-state NMR. Annu Rev Biophys 2009; 38:385-403. [PMID: 19245337 DOI: 10.1146/annurev.biophys.050708.133719] [Citation(s) in RCA: 288] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Membrane proteins remain difficult to study by traditional methods. Magic angle spinning solid-state NMR (MAS SSNMR) methods present an important approach for studying membrane proteins of moderate size. Emerging MAS SSNMR methods are based on extensive assignments of the nuclei as a basis for structure determination and characterization of function. These methods have already been used to characterize fibrils and globular proteins and are being increasingly used to study membrane proteins embedded in lipids. This review highlights recent applications to intrinsic membrane proteins and summarizes recent technical advances that will enable these methods to be utilized for more complex membrane protein systems in the near future.
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Affiliation(s)
- Ann McDermott
- Department of Chemistry, Columbia University, New York, NY 10027, USA.
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38
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Tang M, Waring AJ, Hong M. Arginine dynamics in a membrane-bound cationic beta-hairpin peptide from solid-state NMR. Chembiochem 2008; 9:1487-92. [PMID: 18442147 DOI: 10.1002/cbic.200800005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The site-specific motion of Arg residues in a membrane-bound disulfide-linked antimicrobial peptide, protegrin-1 (PG-1), was investigated by using magic-angle-spinning solid-state NMR spectroscopy to better understand the membrane insertion and lipid interaction of this cationic membrane-disruptive peptide. The C-H and N-H dipolar couplings and 13C chemical shift anisotropies were measured in the anionic POPE/POPG membrane, and were found to be reduced from the rigid-limit values by varying extents; this indicates the presence of segmental motion. An Arg residue at the beta-turn region of the peptide showed much weaker spin interactions, which indicates larger amplitudes of motion than an Arg residue in the beta-strand region of the peptide. This is consistent with the exposure of the beta turn to the membrane surface and the immersion of the beta strand in the hydrophobic middle of the membrane, and supports the previously proposed oligomerization of the peptide into beta barrels in the anionic membrane. The 13C T2 and 1H T(1rho) relaxation times indicate that the beta-turn backbone undergoes large-amplitude intermediate-timescale motion in the fluid phase of the membrane; this causes significant line broadening and loss of spectral intensity. This study illustrates the strong correlation between the dynamics and structure of membrane proteins, and the capability of solid-state NMR spectroscopy to provide detailed information on site-specific dynamics in complex membrane-protein assemblies.
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Affiliation(s)
- Ming Tang
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA.
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39
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Conformational dynamics of an intact virus: order parameters for the coat protein of Pf1 bacteriophage. Proc Natl Acad Sci U S A 2008; 105:10366-71. [PMID: 18653759 DOI: 10.1073/pnas.0800405105] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
This study has examined the atomic-level dynamics of the protein in the capsid of filamentous phage Pf1. This capsid consists of approximately 7,300 small subunits of only 46 aa in a helical array around a highly extended, circular single-stranded DNA molecule of 7,349 nt. Measurements were made of site-specific, solid-state NMR order parameters, S, the values which are dimensionless quantities between 0 (mobile) and 1 (static) that characterize the amplitudes of molecular bond angular motions that are faster than microseconds. It was found that the protein subunit backbone is very static, and of particular interest, it appears to be static at residues glycine 15 and glutamine 16 where it had been previously thought to be mobile. In contrast to the backbone, several side chains display large-amplitude angular motions. Side chains on the virion exterior that interact with solvent are highly mobile, but surprisingly, the side chains of residues arginine 44 and lysine 45 near the DNA deep in the interior of the virion are also highly mobile. The large-amplitude dynamic motion of these positively charged side chains in their interactions with the DNA were not previously expected. The results reveal a highly dynamic aspect of a DNA-protein interface within a virus.
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Blanc F, Basset JM, Copéret C, Sinha A, Tonzetich ZJ, Schrock RR, Solans-Monfort X, Clot E, Eisenstein O, Lesage A, Emsley L. Dynamics of Silica-Supported Catalysts Determined by Combining Solid-State NMR Spectroscopy and DFT Calculations. J Am Chem Soc 2008; 130:5886-900. [DOI: 10.1021/ja077749v] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Frédéric Blanc
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Jean-Marie Basset
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Christophe Copéret
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Amritanshu Sinha
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Zachary J. Tonzetich
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Richard R. Schrock
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Xavier Solans-Monfort
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Eric Clot
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Odile Eisenstein
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Anne Lesage
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
| | - Lyndon Emsley
- Laboratoire de Chimie, Catalyse, Polymères et Procédés (UMR 5265), Chimie Organométallique de Surface, ESCPE Lyon, Université de Lyon, 43 Bd du 11 Novembre 1918, F-69616 Villeurbanne, France, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachussets 02139, Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Institut Charles Gerhardt Montpellier (UMR 5253, CNRS, UM2, UM1, ENSCM), Université Montpellier 2, cc 1501, Place E. Bataillon, F-34095
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Chevelkov V, Diehl A, Reif B. Measurement of N15-T1 relaxation rates in a perdeuterated protein by magic angle spinning solid-state nuclear magnetic resonance spectroscopy. J Chem Phys 2008; 128:052316. [DOI: 10.1063/1.2819311] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Chevelkov V, Diehl A, Reif B. Quantitative measurement of differential 15N-H(alpha/beta)T2 relaxation rates in a perdeuterated protein by MAS solid-state NMR spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S156-60. [PMID: 18157805 DOI: 10.1002/mrc.2129] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Dynamic parameters become more and more accessible in the study of uniformly isotopically enriched proteins by MAS solid-state NMR. We demonstrate that T(2)-related relaxation properties can quantitatively be determined in a sample of a perdeuterated microcrystalline protein by the measurement of (15)N,(1)H dipole, (15)N CSA cross-correlated relaxation rates. We find that the measured cross-correlated relaxation rates are independent of the MAS rotation frequency, and therefore reflect local dynamic fluctuations of the protein structure.
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Böckmann A. High-resolution solid-state MAS NMR of proteins-Crh as an example. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S24-S31. [PMID: 18081212 DOI: 10.1002/mrc.2106] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Revised: 09/04/2007] [Accepted: 09/12/2007] [Indexed: 05/25/2023]
Abstract
Solid-state NMR spectroscopy provides unique possibilities for the structural investigation of insoluble molecules at the atomic level. Recent efforts aim at solving the complete structures of biological macromolecules using high-resolution magic angle spinning NMR. Structurally homogenous samples of [(13)C,(15)N]-labeled proteins have to be used in this type of studies. Microcrystalline model proteins present valuable tools for the developments of methods towards this goal. This review discusses recent progress in the field, using the Crh protein as an illustrative example. We discuss strategies for resonance assignments and for the determination of structure and dynamics, as well as techniques for the detection of protein interaction partners and folding mechanisms by solid-state NMR methods.
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Affiliation(s)
- Anja Böckmann
- IFR 128 BioSciences Lyon-Gerland, IBCP UMR 5086 CNRS/Université de Lyon Claude Bernard, 7 passage du Vercors, 69367 Lyon, France.
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Lorieau JL, McDermott AE. Conformational Flexibility of a Microcrystalline Globular Protein: Order Parameters by Solid-State NMR Spectroscopy. J Am Chem Soc 2006; 128:11505-12. [PMID: 16939274 DOI: 10.1021/ja062443u] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The majority of protein structures are determined in the crystalline state, yet few methods exist for the characterization of dynamics for crystalline biomolecules. Solid-state NMR can be used to probe detailed dynamic information in crystalline biomolecules. Recent advances in high-resolution solid-state NMR have enabled the site-specific assignment of (13)C and (15)N nuclei in proteins. With the use of multidimensional separated-local-field experiments, we report the backbone and side chain conformational dynamics of ubiquitin, a globular microcrystalline protein. The measurements of molecular conformational order parameters are based on heteronuclear dipolar couplings, and they are correlated to assigned chemical shifts, to obtain a global perspective on the sub-microsecond dynamics in microcrystalline ubiquitin. A total of 38 Calpha, 35 Cbeta and multiple side chain unique order parameters are collected, and they reveal the high mobility of ubiquitin in the microcrystalline state. In general the side chains show elevated motion in comparison with the backbone sites. The data are compared to solution NMR order parameter measurements on ubiquitin. The SSNMR measurements are sensitive to motions on a broader time scale (low microsecond and faster) than solution NMR measurements (low nanosecond and faster), and the SSNMR order parameters are generally lower than the corresponding solution values. Unlike solution NMR relaxation-based order parameters, order parameters for (13)C(1)H(2) spin systems are readily measured from the powder line shape data. These results illustrate the potential for detailed, extensive, and site-specific dynamic studies of biopolymers by solid-state NMR.
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Affiliation(s)
- Justin L Lorieau
- Department of Chemistry, Columbia University, Havemeyer Hall, 3000 Broadway, New York, New York 10027, USA
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