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Sardo M, Morais T, Soares M, Vieira R, Ilkaeva M, Lourenço MAO, Marín-Montesinos I, Mafra L. Unravelling the structure of CO 2 in silica adsorbents: an NMR and computational perspective. Chem Commun (Camb) 2024; 60:4015-4035. [PMID: 38525497 PMCID: PMC11003455 DOI: 10.1039/d3cc05942a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/08/2024] [Indexed: 03/26/2024]
Abstract
This comprehensive review describes recent advancements in the use of solid-state NMR-assisted methods and computational modeling strategies to unravel gas adsorption mechanisms and CO2 speciation in porous CO2-adsorbent silica materials at the atomic scale. This work provides new perspectives for the innovative modifications of these materials rendering them more amenable to the use of advanced NMR methods.
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Affiliation(s)
- Mariana Sardo
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Tiago Morais
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
- Department of Chemistry, University of Iceland, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland
| | - Márcio Soares
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Ricardo Vieira
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Marina Ilkaeva
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
- Department of Chemical and Environmental Engineering, University of Oviedo, Av. Julián Clavería 8, 33006 Oviedo, Spain
| | - Mirtha A O Lourenço
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Ildefonso Marín-Montesinos
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Luís Mafra
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
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2
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Fonseca R, Vieira R, Sardo M, Marin-Montesinos I, Mafra L. Exploring Molecular Dynamics of Adsorbed CO 2 Species in Amine-Modified Porous Silica by Solid-State NMR Relaxation. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2022; 126:12582-12591. [PMID: 35968194 PMCID: PMC9358655 DOI: 10.1021/acs.jpcc.2c02656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Previous studies on CO2 adsorbents have mainly addressed the identification and quantification of adsorbed CO2 species in amine-modified porous materials. Investigation of molecular motion of CO2 species in confinement has not been explored in depth yet. This work entails a comprehensive study of molecular dynamics of the different CO2 species chemi- and physisorbed at amine-modified silica materials through the determination of the rotating frame spin-lattice relaxation times (T 1ρ) by solid-state NMR. Rotational correlation times (τC) were also estimated using spin relaxation models based on the Bloch, Wangsness, and Redfield and the Bloembergen-Purcell-Pound theories. As expected, the τC values for the two physisorbed CO2 species are considerably shorter (32 and 20 μs) than for the three identified chemisorbed CO2 species (162, 62, and 123 μs). The differences in molecular dynamics between the different chemisorbed species correlate well with the structures previously proposed. In the case of the physisorbed CO2 species, the τC values of the CO2 species displaying faster molecular dynamics falls in the range of viscous liquids, whereas the species presenting slower dynamics exhibit T 1ρ and τC values compatible with a CO2 layer of weakly interacting molecules with the silica surface. The values for chemical shift anisotropy (CSA) and 1H-13C heteronuclear dipolar couplings have also been estimated from T 1ρ measurements, for each adsorbed CO2 species. The CSA tensor parameters obtained from fitting the relaxation data agree with the experimentally measured CSA values, thus showing that the theories are well suited to study CO2 dynamics in silica surfaces.
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3
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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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4
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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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5
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Malär AA, Callon M, Smith AA, Wang S, Lecoq L, Pérez-Segura C, Hadden-Perilla JA, Böckmann A, Meier BH. Experimental Characterization of the Hepatitis B Virus Capsid Dynamics by Solid-State NMR. Front Mol Biosci 2022; 8:807577. [PMID: 35047563 PMCID: PMC8762115 DOI: 10.3389/fmolb.2021.807577] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/06/2021] [Indexed: 01/14/2023] Open
Abstract
Protein plasticity and dynamics are important aspects of their function. Here we use solid-state NMR to experimentally characterize the dynamics of the 3.5 MDa hepatitis B virus (HBV) capsid, assembled from 240 copies of the Cp149 core protein. We measure both T1 and T1ρ relaxation times, which we use to establish detectors on the nanosecond and microsecond timescale. We compare our results to those from a 1 microsecond all-atom Molecular Dynamics (MD) simulation trajectory for the capsid. We show that, for the constituent residues, nanosecond dynamics are faithfully captured by the MD simulation. The calculated values can be used in good approximation for the NMR-non-detected residues, as well as to extrapolate into the range between the nanosecond and microsecond dynamics, where NMR has a blind spot at the current state of technology. Slower motions on the microsecond timescale are difficult to characterize by all-atom MD simulations owing to computational expense, but are readily accessed by NMR. The two methods are, thus, complementary, and a combination thereof can reliably characterize motions covering correlation times up to a few microseconds.
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Affiliation(s)
| | | | - Albert A Smith
- Institute of Medical Physics and Biophysics, Universität Leipzig, Leipzig, Germany
| | - Shishan Wang
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS-Université de Lyon, Labex Ecofect, Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS-Université de Lyon, Labex Ecofect, Lyon, France
| | - Carolina Pérez-Segura
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Jodi A Hadden-Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS-Université de Lyon, Labex Ecofect, Lyon, France
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Zürich, Switzerland
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6
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Bonaccorsi M, Knight MJ, Le Marchand T, Dannatt HRW, Schubeis T, Salmon L, Felli IC, Emsley L, Pierattelli R, Pintacuda G. Multimodal Response to Copper Binding in Superoxide Dismutase Dynamics. J Am Chem Soc 2020; 142:19660-19667. [PMID: 33166153 DOI: 10.1021/jacs.0c09242] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Copper/zinc superoxide dismutase (SOD) is a homodimeric metalloenzyme that has been extensively studied as a benchmark for structure-function relationships in proteins, in particular because of its implication in the familial form of the neurodegenerative disease amyotrophic lateral sclerosis. Here, we investigate microcrystalline preparations of two differently metalated forms of SOD, namely, the fully mature functional Cu,Zn state and the E,Zn-SOD state in which the Cu site is empty. By using solid-state NMR with fast magic-angle spinning (MAS) at high magnetic fields (1H Larmor frequency of 800-1000 MHz), we quantify motions spanning a dynamic range from ns to ms. We determine that metal ion uptake does not act as a rigidification element but as a switch redistributing motional processes on different time scales, with coupling of the dynamics of histidine side chains and those of remote key backbone elements of the protein.
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Affiliation(s)
- Marta Bonaccorsi
- Centre de RMN à Très Hauts Champs, FRE 2034 (CNRS/Université Claude Bernard Lyon 1/Ecole Normale Supérieure de Lyon), University of Lyon, 69100 Villeurbanne, France
| | - Michael J Knight
- Centre de RMN à Très Hauts Champs, FRE 2034 (CNRS/Université Claude Bernard Lyon 1/Ecole Normale Supérieure de Lyon), University of Lyon, 69100 Villeurbanne, France
| | - Tanguy Le Marchand
- Centre de RMN à Très Hauts Champs, FRE 2034 (CNRS/Université Claude Bernard Lyon 1/Ecole Normale Supérieure de Lyon), University of Lyon, 69100 Villeurbanne, France
| | - Hugh R W Dannatt
- Centre de RMN à Très Hauts Champs, FRE 2034 (CNRS/Université Claude Bernard Lyon 1/Ecole Normale Supérieure de Lyon), University of Lyon, 69100 Villeurbanne, France
| | - Tobias Schubeis
- Centre de RMN à Très Hauts Champs, FRE 2034 (CNRS/Université Claude Bernard Lyon 1/Ecole Normale Supérieure de Lyon), University of Lyon, 69100 Villeurbanne, France
| | - Loïc Salmon
- Centre de RMN à Très Hauts Champs, FRE 2034 (CNRS/Université Claude Bernard Lyon 1/Ecole Normale Supérieure de Lyon), University of Lyon, 69100 Villeurbanne, France
| | - Isabella C Felli
- Department of Chemistry "Ugo Schiff" and CERM, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Lyndon Emsley
- Laboratory of Magnetic Resonance, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Roberta Pierattelli
- Department of Chemistry "Ugo Schiff" and CERM, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs, FRE 2034 (CNRS/Université Claude Bernard Lyon 1/Ecole Normale Supérieure de Lyon), University of Lyon, 69100 Villeurbanne, France
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7
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Rovó P. Recent advances in solid-state relaxation dispersion techniques. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2020; 108:101665. [PMID: 32574905 DOI: 10.1016/j.ssnmr.2020.101665] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/11/2020] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
This review describes two rotating-frame (R1ρ) relaxation dispersion methods, namely the Bloch-McConnell Relaxation Dispersion and the Near-rotary Resonance Relaxation Dispersion, which enable the study of microsecond time-scale conformational fluctuations in the solid state using magic-angle-spinning nuclear magnetic resonance spectroscopy. The goal is to provide the reader with key ideas, experimental descriptions, and practical considerations associated with R1ρ measurements that are needed for analyzing relaxation dispersion and quantifying conformational exchange. While the focus is on protein motion, many presented concepts can be equally well adapted to study the microsecond time-scale dynamics of other bio- (e.g. lipids, polysaccharides, nucleic acids), organic (e.g. pharmaceutical compounds), or inorganic molecules (e.g., metal organic frameworks). This article summarizes the essential contributions made by recent theoretical and experimental solid-state NMR studies to our understanding of protein motion. Here we discuss recent advances in fast MAS applications that enable the observation and atomic level characterization of sparsely populated conformational states which are otherwise inaccessible for other experimental methods. Such high-energy states are often associated with protein functions such as molecular recognition, ligand binding, or enzymatic catalysis, as well as with disease-related properties such as misfolding and amyloid formation.
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Affiliation(s)
- Petra Rovó
- Department of Chemistry, Ludwig Maximilian University Munich, Butenandtstr. 5-13, 81377, Munich, Germany; Center for NanoScience (CeNS), Schellingstr. 4, 80799, Munich, Germany.
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8
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Kashefi M, Malik N, Struppe JO, Thompson LK. Carbon-nitrogen REDOR to identify ms-timescale mobility in proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 305:5-15. [PMID: 31158793 PMCID: PMC6656615 DOI: 10.1016/j.jmr.2019.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 06/09/2023]
Abstract
Protein dynamics play key mechanistic roles but are difficult to measure in large proteins and protein complexes. INEPT and CP solid-state NMR experiments have often been used to obtain spectra of protein regions that are mobile and rigid, respectively, on the nanosecond timescale. To complement this approach, we have implemented 13C{15N} REDOR to detect protein regions with backbone dynamics on the millisecond time scale that average the ≈1 kHz carbon-nitrogen dipolar coupling. REDOR-filtering of carbon correlation spectra removes signals from rigid backbone carbons and retains signals from backbone carbons with ms-timescale dynamics that would be missing in dipolar-driven NCA/NCO spectra. We use these experiments to investigate functionally important dynamics within the E coli Asp receptor cytoplasmic fragment (U-13C, 15N-CF) in native-like complexes with CheA and CheW. The CF backbone carbons exhibit only 60-75% of the expected REDOR dephasing, suggesting that 40-25% of the backbone experiences significant mobility that averages the 13C15N dipolar couplings to zero. Furthermore, the extent of this mobility changes with signaling state.
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Affiliation(s)
- Maryam Kashefi
- Department of Chemistry, University of Massachusetts Amherst, 710 N Pleasant St, Amherst, MA 01003, USA
| | - Nikita Malik
- Department of Chemistry, University of Massachusetts Amherst, 710 N Pleasant St, Amherst, MA 01003, USA
| | - Jochem O Struppe
- Bruker BioSpin Corporation, 15 Fortune Drive, Billerica, MA 01821, USA
| | - Lynmarie K Thompson
- Department of Chemistry, University of Massachusetts Amherst, 710 N Pleasant St, Amherst, MA 01003, USA.
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9
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Gauto DF, Macek P, Barducci A, Fraga H, Hessel A, Terauchi T, Gajan D, Miyanoiri Y, Boisbouvier J, Lichtenecker R, Kainosho M, Schanda P. Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 kDa Enzyme by Specific 1H- 13C Labeling and Fast Magic-Angle Spinning NMR. J Am Chem Soc 2019; 141:11183-11195. [PMID: 31199882 DOI: 10.1021/jacs.9b04219] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Aromatic residues are located at structurally important sites of many proteins. Probing their interactions and dynamics can provide important functional insight but is challenging in large proteins. Here, we introduce approaches to characterize the dynamics of phenylalanine residues using 1H-detected fast magic-angle spinning (MAS) NMR combined with a tailored isotope-labeling scheme. Our approach yields isolated two-spin systems that are ideally suited for artifact-free dynamics measurements, and allows probing motions effectively without molecular weight limitations. The application to the TET2 enzyme assembly of ∼0.5 MDa size, the currently largest protein assigned by MAS NMR, provides insights into motions occurring on a wide range of time scales (picoseconds to milliseconds). We quantitatively probe ring-flip motions and show the temperature dependence by MAS NMR measurements down to 100 K. Interestingly, favorable line widths are observed down to 100 K, with potential implications for DNP NMR. Furthermore, we report the first 13C R1ρ MAS NMR relaxation-dispersion measurements and detect structural excursions occurring on a microsecond time scale in the entry pore to the catalytic chamber and at a trimer interface that was proposed as the exit pore. We show that the labeling scheme with deuteration at ca. 50 kHz MAS provides superior resolution compared to 100 kHz MAS experiments with protonated, uniformly 13C-labeled samples.
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Affiliation(s)
- Diego F Gauto
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
| | - Pavel Macek
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
| | - Alessandro Barducci
- Centre de Biochimie Structurale (CBS) , INSERM, CNRS, Université de Montpellier , Montpellier , France
| | - Hugo Fraga
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France.,Departamento de Biomedicina , Faculdade de Medicina da Universidade do Porto , Porto , Portugal.,i3S, Instituto de Investigação e Inovação em Saúde , Universidade do Porto , Porto , Portugal
| | - Audrey Hessel
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
| | - Tsutomu Terauchi
- Graduate School of Science , Tokyo Metropolitan University , 1-1 Minami-ohsawa , Hachioji , Tokyo 192-0397 , Japan.,SI Innovation Center , Taiyo Nippon Sanso Corp. , 2008-2 Wada , Tama-city , Tokyo 206-0001 , Japan
| | - David Gajan
- Université de Lyon , Centre de RMN à Hauts Champs de Lyon CRMN, FRE 2034, Université de Lyon, CNRS, ENS Lyon, UCB Lyon 1 , 69100 Villeurbanne , France
| | - Yohei Miyanoiri
- Institute of Protein Research , Osaka University , 3-2 Yamadaoka , Suita , Osaka 565-0871 , Japan.,Structural Biology Research Center, Graduate School of Sciences , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602 , Japan
| | - Jerome Boisbouvier
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
| | - Roman Lichtenecker
- Institute of Organic Chemistry , University of Vienna , Währinger Str. 38 , 1090 Vienna , Austria
| | - Masatsune Kainosho
- Graduate School of Science , Tokyo Metropolitan University , 1-1 Minami-ohsawa , Hachioji , Tokyo 192-0397 , Japan.,Structural Biology Research Center, Graduate School of Sciences , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602 , Japan
| | - Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
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10
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Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R 1p Relaxation-Dispersion MAS NMR. Chemphyschem 2019; 20:276-284. [PMID: 30444575 PMCID: PMC6354937 DOI: 10.1002/cphc.201800935] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/15/2018] [Indexed: 12/14/2022]
Abstract
Studying protein dynamics on microsecond-to-millisecond (μs-ms) time scales can provide important insight into protein function. In magic-angle-spinning (MAS) NMR, μs dynamics can be visualized by R 1 ρ rotating-frame relaxation dispersion experiments in different regimes of radio-frequency field strengths: at low RF field strength, isotropic-chemical-shift fluctuation leads to "Bloch-McConnell-type" relaxation dispersion, while when the RF field approaches rotary resonance conditions bond angle fluctuations manifest as increased R 1 ρ rate constants ("Near-Rotary-Resonance Relaxation Dispersion", NERRD). Here we explore the joint analysis of both regimes to gain comprehensive insight into motion in terms of geometric amplitudes, chemical-shift changes, populations and exchange kinetics. We use a numerical simulation procedure to illustrate these effects and the potential of extracting exchange parameters, and apply the methodology to the study of a previously described conformational exchange process in microcrystalline ubiquitin.
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Affiliation(s)
- Dominique Marion
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71 avenue des martyrs, 38000 Grenoble (France)
| | - Diego F. Gauto
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71 avenue des martyrs, 38000 Grenoble (France)
| | - Isabel Ayala
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71 avenue des martyrs, 38000 Grenoble (France)
| | - Karine Giandoreggio-Barranco
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71 avenue des martyrs, 38000 Grenoble (France)
| | - Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71 avenue des martyrs, 38000 Grenoble (France)
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11
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Keeler EG, Fritzsching KJ, McDermott AE. Refocusing CSA during magic angle spinning rotating-frame relaxation experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 296:130-137. [PMID: 30253322 PMCID: PMC6512962 DOI: 10.1016/j.jmr.2018.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/10/2018] [Accepted: 09/12/2018] [Indexed: 05/27/2023]
Abstract
We examine coherent evolution of spin-locked magnetization during magic-angle spinning (MAS), in the context of relaxation experiments designed to probe chemical exchange (rotating-frame relaxation (R1ρ)). Coherent evolution is expected in MAS based rotating-frame relaxation decay experiments if matching conditions are met (such as, ω1 = nωr) and if the chemical shielding anisotropy (CSA) is substantial. We show here using numerical simulations and experiments that even when such matching requirements are avoided (e.g., ω1 < 0.5ωr, ∼1.5ωr, >2.5ωr), coherent evolution of spin-locked magnetization with large CSA is still considerable. The coherent evolution has important consequences on the analysis of relaxation decay and the ability to extract accurate information of interest about dynamics. We present a pulse sequence that employs rotary echoes and refocuses CSA contributions, allowing for more sensitive measurement of rotating-frame relaxation with less interference from coherent evolution. In practice, the proposed pulse sequence, REfocused CSA Rotating-frame Relaxation (RECRR) is robust to carrier frequency offset, B1-field inhomogeneity, and slight miscalibrations of the refocusing pulses.
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Affiliation(s)
- Eric G Keeler
- Department of Chemistry, Columbia University, New York, NY 10027, United States
| | - Keith J Fritzsching
- Department of Chemistry, Columbia University, New York, NY 10027, United States
| | - Ann E McDermott
- Department of Chemistry, Columbia University, New York, NY 10027, United States.
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12
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Bougault C, Ayala I, Vollmer W, Simorre JP, Schanda P. Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. J Struct Biol 2018; 206:66-72. [PMID: 30031884 DOI: 10.1016/j.jsb.2018.07.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/19/2018] [Accepted: 07/12/2018] [Indexed: 12/19/2022]
Abstract
The bacterial cell wall is composed of the peptidoglycan (PG), a large polymer that maintains the integrity of the bacterial cell. Due to its multi-gigadalton size, heterogeneity, and dynamics, atomic-resolution studies are inherently complex. Solid-state NMR is an important technique to gain insight into its structure, dynamics and interactions. Here, we explore the possibilities to study the PG with ultra-fast (100 kHz) magic-angle spinning NMR. We demonstrate that highly resolved spectra can be obtained, and show strategies to obtain site-specific resonance assignments and distance information. We also explore the use of proton-proton correlation experiments, thus opening the way for NMR studies of intact cell walls without the need for isotope labeling.
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Affiliation(s)
- Catherine Bougault
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, 38044 Grenoble, France
| | - Isabel Ayala
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, 38044 Grenoble, France
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, United Kingdom
| | - Jean-Pierre Simorre
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, 38044 Grenoble, France.
| | - Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, 38044 Grenoble, France.
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13
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Krushelnitsky A, Gauto D, Rodriguez Camargo DC, Schanda P, Saalwächter K. Microsecond motions probed by near-rotary-resonance R 1ρ15N MAS NMR experiments: the model case of protein overall-rocking in crystals. JOURNAL OF BIOMOLECULAR NMR 2018; 71:53-67. [PMID: 29845494 PMCID: PMC5986846 DOI: 10.1007/s10858-018-0191-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/26/2018] [Indexed: 05/27/2023]
Abstract
Solid-state near-rotary-resonance measurements of the spin-lattice relaxation rate in the rotating frame (R1ρ) is a powerful NMR technique for studying molecular dynamics in the microsecond time scale. The small difference between the spin-lock (SL) and magic-angle-spinning (MAS) frequencies allows sampling very slow motions, at the same time it brings up some methodological challenges. In this work, several issues affecting correct measurements and analysis of 15N R1ρ data are considered in detail. Among them are signal amplitude as a function of the difference between SL and MAS frequencies, "dead time" in the initial part of the relaxation decay caused by transient spin-dynamic oscillations, measurements under HORROR condition and proper treatment of the multi-exponential relaxation decays. The multiple 15N R1ρ measurements at different SL fields and temperatures have been conducted in 1D mode (i.e. without site-specific resolution) for a set of four different microcrystalline protein samples (GB1, SH3, MPD-ubiquitin and cubic-PEG-ubiquitin) to study the overall protein rocking in a crystal. While the amplitude of this motion varies very significantly, its correlation time for all four sample is practically the same, 30-50 μs. The amplitude of the rocking motion correlates with the packing density of a protein crystal. It has been suggested that the rocking motion is not diffusive but likely a jump-like dynamic process.
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Affiliation(s)
| | - Diego Gauto
- Institut de Biologie Structurale (IBS), Grenoble Cedex 9, France
| | | | - Paul Schanda
- Institut de Biologie Structurale (IBS), Grenoble Cedex 9, France
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14
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Le Marchand T, de Rosa M, Salvi N, Sala BM, Andreas LB, Barbet-Massin E, Sormanni P, Barbiroli A, Porcari R, Sousa Mota C, de Sanctis D, Bolognesi M, Emsley L, Bellotti V, Blackledge M, Camilloni C, Pintacuda G, Ricagno S. Conformational dynamics in crystals reveal the molecular bases for D76N beta-2 microglobulin aggregation propensity. Nat Commun 2018; 9:1658. [PMID: 29695721 PMCID: PMC5916882 DOI: 10.1038/s41467-018-04078-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 03/29/2018] [Indexed: 11/09/2022] Open
Abstract
Spontaneous aggregation of folded and soluble native proteins in vivo is still a poorly understood process. A prototypic example is the D76N mutant of beta-2 microglobulin (β2m) that displays an aggressive aggregation propensity. Here we investigate the dynamics of β2m by X-ray crystallography, solid-state NMR, and molecular dynamics simulations to unveil the effects of the D76N mutation. Taken together, our data highlight the presence of minor disordered substates in crystalline β2m. The destabilization of the outer strands of D76N β2m accounts for the increased aggregation propensity. Furthermore, the computational modeling reveals a network of interactions with residue D76 as a keystone: this model allows predicting the stability of several point mutants. Overall, our study shows how the study of intrinsic dynamics in crystallo can provide crucial answers on protein stability and aggregation propensity. The comprehensive approach here presented may well be suited for the study of other folded amyloidogenic proteins. The aggregation prone D76N beta-2 microglobulin mutant causes systemic amyloidosis. Here the authors combine crystallography, solid-state NMR, and computational studies and show that the D76N mutation increases protein dynamics and destabilizes the outer strands, which leads to an exposure of amyloidogenic parts explaining its aggregation propensity.
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Affiliation(s)
- Tanguy Le Marchand
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France
| | - Matteo de Rosa
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy
| | - Nicola Salvi
- Institut de Biologie Structurale, CNRS, CEA, UGA, 30044, Grenoble, France
| | - Benedetta Maria Sala
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy
| | - Loren B Andreas
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France
| | - Emeline Barbet-Massin
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France
| | - Pietro Sormanni
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Alberto Barbiroli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, 20133, Milano, Italy
| | - Riccardo Porcari
- Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, University College London, London, NW3 2PF, UK
| | | | | | - Martino Bolognesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy.,Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, 20133, Milano, Italy
| | - Lyndon Emsley
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France
| | - Vittorio Bellotti
- Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, University College London, London, NW3 2PF, UK
| | - Martin Blackledge
- Institut de Biologie Structurale, CNRS, CEA, UGA, 30044, Grenoble, France
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy.
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France.
| | - Stefano Ricagno
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy.
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15
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Gauto DF, Hessel A, Rovó P, Kurauskas V, Linser R, Schanda P. Protein conformational dynamics studied by 15N and 1H R 1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 87:86-95. [PMID: 28438365 PMCID: PMC5531261 DOI: 10.1016/j.ssnmr.2017.04.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/01/2017] [Accepted: 04/12/2017] [Indexed: 05/12/2023]
Abstract
Solid-state NMR spectroscopy can provide site-resolved information about protein dynamics over many time scales. Here we combine protein deuteration, fast magic-angle spinning (~45-60kHz) and proton detection to study dynamics of ubiquitin in microcrystals, and in particular a mutant in a region that undergoes microsecond motions in a β-turn region in the wild-type protein. We use 15N R1ρ relaxation measurements as a function of the radio-frequency (RF) field strength, i.e. relaxation dispersion, to probe how the G53A mutation alters these dynamics. We report a population-inversion of conformational states: the conformation that in the wild-type protein is populated only sparsely becomes the predominant state. We furthermore explore the potential to use amide-1H R1ρ relaxation to obtain insight into dynamics. We show that while quantitative interpretation of 1H relaxation remains beyond reach under the experimental conditions, due to coherent contributions to decay, one may extract qualitative information about flexibility.
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Affiliation(s)
- Diego F Gauto
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CEA, Institut de Biologie Structurale, F-38044 Grenoble, France; CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Audrey Hessel
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CEA, Institut de Biologie Structurale, F-38044 Grenoble, France; CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Petra Rovó
- Ludwig-Maximilians-Universität, Department Chemie, D-81377 München, Germany
| | - Vilius Kurauskas
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CEA, Institut de Biologie Structurale, F-38044 Grenoble, France; CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Rasmus Linser
- Ludwig-Maximilians-Universität, Department Chemie, D-81377 München, Germany
| | - Paul Schanda
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CEA, Institut de Biologie Structurale, F-38044 Grenoble, France; CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France.
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16
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Öster C, Kosol S, Hartlmüller C, Lamley JM, Iuga D, Oss A, Org ML, Vanatalu K, Samoson A, Madl T, Lewandowski JR. Characterization of Protein-Protein Interfaces in Large Complexes by Solid-State NMR Solvent Paramagnetic Relaxation Enhancements. J Am Chem Soc 2017; 139:12165-12174. [PMID: 28780861 PMCID: PMC5590091 DOI: 10.1021/jacs.7b03875] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Solid-state NMR is becoming a viable
alternative for obtaining
information about structures and dynamics of large biomolecular complexes,
including ones that are not accessible to other high-resolution biophysical
techniques. In this context, methods for probing protein–protein
interfaces at atomic resolution are highly desirable. Solvent paramagnetic
relaxation enhancements (sPREs) proved to be a powerful method for
probing protein–protein interfaces in large complexes in solution
but have not been employed toward this goal in the solid state. We
demonstrate that 1H and 15N relaxation-based
sPREs provide a powerful tool for characterizing intermolecular interactions
in large assemblies in the solid state. We present approaches for
measuring sPREs in practically the entire range of magic angle spinning
frequencies used for biomolecular studies and discuss their benefits
and limitations. We validate the approach on crystalline GB1, with
our experimental results in good agreement with theoretical predictions.
Finally, we use sPREs to characterize protein–protein interfaces
in the GB1 complex with immunoglobulin G (IgG). Our results suggest
the potential existence of an additional binding site and provide
new insights into GB1:IgG complex structure that amend and revise
the current model available from studies with IgG fragments. We demonstrate
sPREs as a practical, widely applicable, robust, and very sensitive
technique for determining intermolecular interaction interfaces in
large biomolecular complexes in the solid state.
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Affiliation(s)
- Carl Öster
- Department of Chemistry, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Simone Kosol
- Department of Chemistry, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Christoph Hartlmüller
- Center for Integrated Protein Science, Department of Chemistry, Munich Technische Universität München , Lichtenbergstrasse 4, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München , Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Jonathan M Lamley
- Department of Chemistry, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Dinu Iuga
- Department of Physics, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Andres Oss
- Institute of Health Technologies, Tallinn University of Technology , Akadeemia tee 15a, 19086 Tallinn, Estonia
| | - Mai-Liis Org
- Institute of Health Technologies, Tallinn University of Technology , Akadeemia tee 15a, 19086 Tallinn, Estonia
| | - Kalju Vanatalu
- Institute of Health Technologies, Tallinn University of Technology , Akadeemia tee 15a, 19086 Tallinn, Estonia
| | - Ago Samoson
- Institute of Health Technologies, Tallinn University of Technology , Akadeemia tee 15a, 19086 Tallinn, Estonia
| | - Tobias Madl
- Center for Integrated Protein Science, Department of Chemistry, Munich Technische Universität München , Lichtenbergstrasse 4, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München , Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.,Institute of Molecular Biology and Biochemistry, Center of Molecular Medicine, Medical University of Graz , Harrachgasse 21, 8010 Graz, Austria
| | - Józef R Lewandowski
- Department of Chemistry, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, U.K
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17
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Good D, Pham C, Jagas J, Lewandowski JR, Ladizhansky V. Solid-State NMR Provides Evidence for Small-Amplitude Slow Domain Motions in a Multispanning Transmembrane α-Helical Protein. J Am Chem Soc 2017; 139:9246-9258. [PMID: 28613900 PMCID: PMC5510093 DOI: 10.1021/jacs.7b03974] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Indexed: 02/06/2023]
Abstract
Proteins are dynamic entities and populate ensembles of conformations. Transitions between states within a conformational ensemble occur over a broad spectrum of amplitude and time scales, and are often related to biological function. Whereas solid-state NMR (SSNMR) spectroscopy has recently been used to characterize conformational ensembles of proteins in the microcrystalline states, its applications to membrane proteins remain limited. Here we use SSNMR to study conformational dynamics of a seven-helical transmembrane (TM) protein, Anabaena Sensory Rhodopsin (ASR) reconstituted in lipids. We report on site-specific measurements of the 15N longitudinal R1 and rotating frame R1ρ relaxation rates at two fields of 600 and 800 MHz and at two temperatures of 7 and 30 °C. Quantitative analysis of the R1 and R1ρ values and of their field and temperature dependencies provides evidence of motions on at least two time scales. We modeled these motions as fast local motions and slower collective motions of TM helices and of structured loops, and used the simple model-free and extended model-free analyses to fit the data and estimate the amplitudes, time scales and activation energies. Faster picosecond (tens to hundreds of picoseconds) local motions occur throughout the protein and are dominant in the middle portions of the TM helices. In contrast, the amplitudes of the slower collective motions occurring on the nanosecond (tens to hundreds of nanoseconds) time scales, are smaller in the central parts of helices, but increase toward their cytoplasmic sides as well as in the interhelical loops. ASR interacts with a soluble transducer protein on its cytoplasmic surface, and its binding affinity is modulated by light. The larger amplitude of motions on the cytoplasmic side of the TM helices correlates with the ability of ASR to undergo large conformational changes in the process of binding/unbinding the transducer.
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Affiliation(s)
- Daryl Good
- Department
of Physics and Biophysics Interdepartmental Group, University
of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Charlie Pham
- Department
of Physics and Biophysics Interdepartmental Group, University
of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Jacob Jagas
- Department
of Physics and Biophysics Interdepartmental Group, University
of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Józef R. Lewandowski
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Vladimir Ladizhansky
- Department
of Physics and Biophysics Interdepartmental Group, University
of Guelph, Guelph, Ontario N1G 2W1, Canada
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18
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Lakomek NA, Penzel S, Lends A, Cadalbert R, Ernst M, Meier BH. Microsecond Dynamics in Ubiquitin Probed by Solid-State 15
N NMR Spectroscopy R
1ρ
Relaxation Experiments under Fast MAS (60-110 kHz). Chemistry 2017; 23:9425-9433. [DOI: 10.1002/chem.201701738] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Nils-Alexander Lakomek
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Susanne Penzel
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Alons Lends
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Riccardo Cadalbert
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Matthias Ernst
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Beat H. Meier
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
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19
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Rovó P, Linser R. Microsecond Time Scale Proton Rotating-Frame Relaxation under Magic Angle Spinning. J Phys Chem B 2017; 121:6117-6130. [PMID: 28534618 DOI: 10.1021/acs.jpcb.7b03333] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This paper deals with the theoretical foundation of proton magic angle spinning rotating-frame relaxation (R1ρ) and establishes the range of validity and accuracy of the presented approach to describe low-amplitude microsecond time scale motion in the solid state. Beside heteronuclear dipolar and chemical shift anisotropy interactions, a major source of relaxation for protons is the homonuclear dipolar interaction. For this latter relaxation process, no general analytical equation has been published until now, which would describe the R1ρ relaxation at any spinning speed, spin-lock field, or tilt angle. To validate the derived equations, we compared the analytical relaxation rates, obtained by solving the master equation within the framework of Redfield theory, with numerically simulated relaxation rates. We found that for small opening angles (∼10°), the relaxation rates obtained with stochastic Liouville simulations agree well with the analytical Redfield relaxation rates for a large range of motional correlation times. However, deviations around the rotary-resonance conditions highlight the fact that Redfield treatment of the solid-state relaxation rates can only provide qualitative insights into the microsecond time scale motion.
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Affiliation(s)
- Petra Rovó
- Department Chemie und Pharmazie, Ludwig-Maximilians-Universität München , 81377 München, Germany
| | - Rasmus Linser
- Department Chemie und Pharmazie, Ludwig-Maximilians-Universität München , 81377 München, Germany
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20
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Saurel O, Iordanov I, Nars G, Demange P, Le Marchand T, Andreas LB, Pintacuda G, Milon A. Local and Global Dynamics in Klebsiella pneumoniae Outer Membrane Protein a in Lipid Bilayers Probed at Atomic Resolution. J Am Chem Soc 2017; 139:1590-1597. [DOI: 10.1021/jacs.6b11565] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Olivier Saurel
- Institut de Pharmacologie
et de Biologie Structurale (CNRS/Université Paul Sabatier),
Université de Toulouse, 31077 Toulouse, France
| | - Iordan Iordanov
- Institut de Pharmacologie
et de Biologie Structurale (CNRS/Université Paul Sabatier),
Université de Toulouse, 31077 Toulouse, France
| | - Guillaume Nars
- Institut de Pharmacologie
et de Biologie Structurale (CNRS/Université Paul Sabatier),
Université de Toulouse, 31077 Toulouse, France
| | - Pascal Demange
- Institut de Pharmacologie
et de Biologie Structurale (CNRS/Université Paul Sabatier),
Université de Toulouse, 31077 Toulouse, France
| | - Tanguy Le Marchand
- Institut de Sciences
Analytiques (UMR 5280 CNRS/ENS-Lyon/UCB Lyon 1), Université
de Lyon, 69007 Lyon, France
| | - Loren B. Andreas
- Institut de Sciences
Analytiques (UMR 5280 CNRS/ENS-Lyon/UCB Lyon 1), Université
de Lyon, 69007 Lyon, France
| | - Guido Pintacuda
- Institut de Sciences
Analytiques (UMR 5280 CNRS/ENS-Lyon/UCB Lyon 1), Université
de Lyon, 69007 Lyon, France
| | - Alain Milon
- Institut de Pharmacologie
et de Biologie Structurale (CNRS/Université Paul Sabatier),
Université de Toulouse, 31077 Toulouse, France
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21
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Kurauskas V, Weber E, Hessel A, Ayala I, Marion D, Schanda P. Cross-Correlated Relaxation of Dipolar Coupling and Chemical-Shift Anisotropy in Magic-Angle Spinning R1ρ NMR Measurements: Application to Protein Backbone Dynamics Measurements. J Phys Chem B 2016; 120:8905-13. [PMID: 27500976 DOI: 10.1021/acs.jpcb.6b06129] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transverse relaxation rate measurements in magic-angle spinning solid-state nuclear magnetic resonance provide information about molecular motions occurring on nanosecond-to-millisecond (ns-ms) time scales. The measurement of heteronuclear ((13)C, (15)N) relaxation rate constants in the presence of a spin-lock radiofrequency field (R1ρ relaxation) provides access to such motions, and an increasing number of studies involving R1ρ relaxation in proteins have been reported. However, two factors that influence the observed relaxation rate constants have so far been neglected, namely, (1) the role of CSA/dipolar cross-correlated relaxation (CCR) and (2) the impact of fast proton spin flips (i.e., proton spin diffusion and relaxation). We show that CSA/D CCR in R1ρ experiments is measurable and that the CCR rate constant depends on ns-ms motions; it can thus provide insight into dynamics. We find that proton spin diffusion attenuates this CCR due to its decoupling effect on the doublet components. For measurements of dynamics, the use of R1ρ rate constants has practical advantages over the use of CCR rates, and this article reveals factors that have so far been disregarded and which are important for accurate measurements and interpretation.
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Affiliation(s)
- Vilius Kurauskas
- CEA, CNRS, Université Grenoble Alpes, Institut de Biologie Structurale (IBS) , 38027 Grenoble, France
| | - Emmanuelle Weber
- CEA, CNRS, Université Grenoble Alpes, Institut de Biologie Structurale (IBS) , 38027 Grenoble, France
| | - Audrey Hessel
- CEA, CNRS, Université Grenoble Alpes, Institut de Biologie Structurale (IBS) , 38027 Grenoble, France
| | - Isabel Ayala
- CEA, CNRS, Université Grenoble Alpes, Institut de Biologie Structurale (IBS) , 38027 Grenoble, France
| | - Dominique Marion
- CEA, CNRS, Université Grenoble Alpes, Institut de Biologie Structurale (IBS) , 38027 Grenoble, France
| | - Paul Schanda
- CEA, CNRS, Université Grenoble Alpes, Institut de Biologie Structurale (IBS) , 38027 Grenoble, France
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22
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Schanda P, Ernst M. Studying Dynamics by Magic-Angle Spinning Solid-State NMR Spectroscopy: Principles and Applications to Biomolecules. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 96:1-46. [PMID: 27110043 PMCID: PMC4836562 DOI: 10.1016/j.pnmrs.2016.02.001] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Magic-angle spinning solid-state NMR spectroscopy is an important technique to study molecular structure, dynamics and interactions, and is rapidly gaining importance in biomolecular sciences. Here we provide an overview of experimental approaches to study molecular dynamics by MAS solid-state NMR, with an emphasis on the underlying theoretical concepts and differences of MAS solid-state NMR compared to solution-state NMR. The theoretical foundations of nuclear spin relaxation are revisited, focusing on the particularities of spin relaxation in solid samples under magic-angle spinning. We discuss the range of validity of Redfield theory, as well as the inherent multi-exponential behavior of relaxation in solids. Experimental challenges for measuring relaxation parameters in MAS solid-state NMR and a few recently proposed relaxation approaches are discussed, which provide information about time scales and amplitudes of motions ranging from picoseconds to milliseconds. We also discuss the theoretical basis and experimental measurements of anisotropic interactions (chemical-shift anisotropies, dipolar and quadrupolar couplings), which give direct information about the amplitude of motions. The potential of combining relaxation data with such measurements of dynamically-averaged anisotropic interactions is discussed. Although the focus of this review is on the theoretical foundations of dynamics studies rather than their application, we close by discussing a small number of recent dynamics studies, where the dynamic properties of proteins in crystals are compared to those in solution.
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Affiliation(s)
- Paul Schanda
- CEA, Institut de Biologie Structurale (IBS), 38027 Grenoble, France ; CNRS, Institut de Biologie Structurale (IBS), 38027 Grenoble, France ; Université Grenoble Alpes, IBS, 38027 Grenoble, France
| | - Matthias Ernst
- ETH Zürich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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23
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Smith AA, Testori E, Cadalbert R, Meier BH, Ernst M. Characterization of fibril dynamics on three timescales by solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2016; 65:171-191. [PMID: 27423891 DOI: 10.1007/s10858-016-0047-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 07/08/2016] [Indexed: 05/26/2023]
Abstract
A multi-timescale analysis of the backbone dynamics of HET-s (218-289) fibrils is described based on multiple site-specific R 1 and R 1ρ data sets and S (2) measurements via REDOR for most backbone (15)N and (13)Cα nuclei. (15)N and (13)Cα data are fitted with motions at three timescales. Slow motion is found, indicating a global fibril motion. We further investigate the effect of (13)C-(13)C transfer in measurement of (13)Cα R 1. Finally, we show that it is necessary to go beyond the Redfield approximation for slow motions in order to obtain accurate numerical values for R 1ρ.
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Affiliation(s)
- Albert A Smith
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Emilie Testori
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Riccardo Cadalbert
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Matthias Ernst
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
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24
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Habenstein B, Loquet A. Solid-state NMR: An emerging technique in structural biology of self-assemblies. Biophys Chem 2016; 210:14-26. [DOI: 10.1016/j.bpc.2015.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 07/08/2015] [Indexed: 12/13/2022]
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25
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Lamley JM, Öster C, Stevens RA, Lewandowski JR. Intermolecular Interactions and Protein Dynamics by Solid-State NMR Spectroscopy. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 127:15594-15598. [PMID: 27478273 PMCID: PMC4954056 DOI: 10.1002/ange.201509168] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Indexed: 11/21/2022]
Abstract
Understanding the dynamics of interacting proteins is a crucial step toward describing many biophysical processes. Here we investigate the backbone dynamics for protein GB1 in two different assemblies: crystalline GB1 and the precipitated GB1-antibody complex with a molecular weight of more than 300 kDa. We perform these measurements on samples containing as little as eight nanomoles of GB1. From measurements of site-specific 15N relaxation rates including relaxation dispersion we obtain snapshots of dynamics spanning nine orders of magnitude in terms of the time scale. A comparison of measurements for GB1 in either environment reveals that while many of the dynamic features of the protein are conserved between them (in particular for the fast picosecond-nanosecond motions), much greater differences occur for slow motions with motions in the >500 ns range being more prevalent in the complex. The data suggest that GB1 can potentially undergo a small-amplitude overall anisotropic motion sampling the interaction interface in the complex.
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Affiliation(s)
- Jonathan M. Lamley
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL (UK)
| | - Carl Öster
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL (UK)
| | - Rebecca A. Stevens
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL (UK)
| | - Józef R. Lewandowski
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL (UK)
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26
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Lamley JM, Öster C, Stevens RA, Lewandowski JR. Intermolecular Interactions and Protein Dynamics by Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2015; 54:15374-8. [PMID: 26537742 PMCID: PMC4736466 DOI: 10.1002/anie.201509168] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Indexed: 11/23/2022]
Abstract
Understanding the dynamics of interacting proteins is a crucial step toward describing many biophysical processes. Here we investigate the backbone dynamics for protein GB1 in two different assemblies: crystalline GB1 and the precipitated GB1-antibody complex with a molecular weight of more than 300 kDa. We perform these measurements on samples containing as little as eight nanomoles of GB1. From measurements of site-specific (15) N relaxation rates including relaxation dispersion we obtain snapshots of dynamics spanning nine orders of magnitude in terms of the time scale. A comparison of measurements for GB1 in either environment reveals that while many of the dynamic features of the protein are conserved between them (in particular for the fast picosecond-nanosecond motions), much greater differences occur for slow motions with motions in the >500 ns range being more prevalent in the complex. The data suggest that GB1 can potentially undergo a small-amplitude overall anisotropic motion sampling the interaction interface in the complex.
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Affiliation(s)
- Jonathan M Lamley
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL (UK)
| | - Carl Öster
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL (UK)
| | - Rebecca A Stevens
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL (UK)
| | - Józef R Lewandowski
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL (UK).
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27
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Rovó P, Grohe K, Giller K, Becker S, Linser R. Proton Transverse Relaxation as a Sensitive Probe for Structure Determination in Solid Proteins. Chemphyschem 2015; 16:3791-6. [PMID: 26359781 DOI: 10.1002/cphc.201500799] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Indexed: 11/11/2022]
Abstract
Solid-state nuclear magnetic resonance (NMR) spectroscopy has been successfully applied to elucidate the atomic-resolution structures of insoluble proteins. The major bottleneck is the difficulty to obtain valuable long-distance structural information. Here, we propose the use of distance restraints as long as 32 Å, obtained from the quantification of transverse proton relaxation induced by a methanethiosulfonate spin label (MTSL). Combined with dipolar proton-proton distance restraints, this method allows us to obtain protein structures with excellent precision from single spin-labeled 1 mg protein samples using fast magic angle spinning.
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Affiliation(s)
- Petra Rovó
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Kristof Grohe
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Karin Giller
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefan Becker
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Rasmus Linser
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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28
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Lamley JM, Lougher MJ, Sass HJ, Rogowski M, Grzesiek S, Lewandowski JR. Unraveling the complexity of protein backbone dynamics with combined (13)C and (15)N solid-state NMR relaxation measurements. Phys Chem Chem Phys 2015; 17:21997-2008. [PMID: 26234369 DOI: 10.1039/c5cp03484a] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Typically, protein dynamics involve a complex hierarchy of motions occurring on different time scales between conformations separated by a range of different energy barriers. NMR relaxation can in principle provide a site-specific picture of both the time scales and amplitudes of these motions, but independent relaxation rates sensitive to fluctuations in different time scale ranges are required to obtain a faithful representation of the underlying dynamic complexity. This is especially pertinent for relaxation measurements in the solid state, which report on dynamics in a broader window of time scales by more than 3 orders of magnitudes compared to solution NMR relaxation. To aid in unraveling the intricacies of biomolecular dynamics we introduce (13)C spin-lattice relaxation in the rotating frame (R1ρ) as a probe of backbone nanosecond-microsecond motions in proteins in the solid state. We present measurements of (13)C'R1ρ rates in fully protonated crystalline protein GB1 at 600 and 850 MHz (1)H Larmor frequencies and compare them to (13)C'R1, (15)N R1 and R1ρ measured under the same conditions. The addition of carbon relaxation data to the model free analysis of nitrogen relaxation data leads to greatly improved characterization of time scales of protein backbone motions, minimizing the occurrence of fitting artifacts that may be present when (15)N data is used alone. We also discuss how internal motions characterized by different time scales contribute to (15)N and (13)C relaxation rates in the solid state and solution state, leading to fundamental differences between them, as well as phenomena such as underestimation of picosecond-range motions in the solid state and nanosecond-range motions in solution.
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Affiliation(s)
- Jonathan M Lamley
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK.
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29
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Ward ME, Brown LS, Ladizhansky V. Advanced solid-state NMR techniques for characterization of membrane protein structure and dynamics: application to Anabaena Sensory Rhodopsin. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:119-128. [PMID: 25637099 DOI: 10.1016/j.jmr.2014.11.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 11/30/2014] [Indexed: 06/04/2023]
Abstract
Studies of the structure, dynamics, and function of membrane proteins (MPs) have long been considered one of the main applications of solid-state NMR (SSNMR). Advances in instrumentation, and the plethora of new SSNMR methodologies developed over the past decade have resulted in a number of high-resolution structures and structural models of both bitopic and polytopic α-helical MPs. The necessity to retain lipids in the sample, the high proportion of one type of secondary structure, differential dynamics, and the possibility of local disorder in the loop regions all create challenges for structure determination. In this Perspective article we describe our recent efforts directed at determining the structure and functional dynamics of Anabaena Sensory Rhodopsin, a heptahelical transmembrane (7TM) protein. We review some of the established and emerging methods which can be utilized for SSNMR-based structure determination, with a particular focus on those used for ASR, a bacterial protein which shares its 7TM architecture with G-protein coupled receptors.
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Affiliation(s)
- Meaghan E Ward
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Vladimir Ladizhansky
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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30
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Schanda P, Triboulet S, Laguri C, Bougault CM, Ayala I, Callon M, Arthur M, Simorre JP. Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. J Am Chem Soc 2014; 136:17852-60. [PMID: 25429710 PMCID: PMC4544747 DOI: 10.1021/ja5105987] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The maintenance of bacterial cell shape and integrity is largely attributed to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform this cross-linking are important targets for antibiotics. Despite this biomedical importance, to date no structure of a protein in complex with an intact bacterial peptidoglycan has been resolved, primarily due to the large size and flexibility of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly, the model obtained from protein chemical shift perturbation data shows that both domains-the catalytic domain as well as the proposed peptidoglycan recognition domain-are important for the interaction and reveals a novel binding motif that involves residues outside of the classical enzymatic pocket. Experiments on mutants and truncated protein constructs independently confirm the binding site and the implication of both domains. Through measurements of dipolar-coupling derived order parameters of bond motion we show that protein binding reduces the flexibility of peptidoglycan. This first report of an atomic model of a protein-peptidoglycan complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases. The strategy developed here can be extended to the study of a large variety of enzymes involved in peptidoglycan morphogenesis.
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Affiliation(s)
- Paul Schanda
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Sébastien Triboulet
- Centre de Recherche des Cordeliers, LRMA, Equipe 12, Univ. Pierre et Marie Curie-Paris 6, UMR S 1138, 75006 Paris (France)
- Université Paris Descartes, Sorbonne, UMR S 1138, 75006 Paris (France); INSERM, U1138, 75006 Paris (France)
| | - Cédric Laguri
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Catherine M. Bougault
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Isabel Ayala
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Morgane Callon
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Michel Arthur
- Centre de Recherche des Cordeliers, LRMA, Equipe 12, Univ. Pierre et Marie Curie-Paris 6, UMR S 1138, 75006 Paris (France)
- Université Paris Descartes, Sorbonne, UMR S 1138, 75006 Paris (France); INSERM, U1138, 75006 Paris (France)
| | - Jean-Pierre Simorre
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
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31
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Krushelnitsky A, Zinkevich T, Reif B, Saalwächter K. Slow motions in microcrystalline proteins as observed by MAS-dependent 15N rotating-frame NMR relaxation. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 248:8-12. [PMID: 25282442 DOI: 10.1016/j.jmr.2014.09.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/04/2014] [Accepted: 09/09/2014] [Indexed: 05/14/2023]
Abstract
(15)N NMR relaxation rate R1ρ measurements reveal that a substantial fraction of residues in the microcrystalline chicken alpha-spectrin SH3 domain protein undergoes dynamics in the μs-ms timescale range. On the basis of a comparison of 2D site-resolved with 1D integrated (15)N spectral intensities, we demonstrate that the significant fraction of broad signals in the 2D spectrum exhibits the most pronounced slow mobility. We show that (15)N R1ρ's in proton-diluted protein samples are practically free from the coherent spin-spin contribution even at low MAS rates, and thus can be analysed quantitatively. Moderate MAS rates (10-30 kHz) can be more advantageous in comparison with the rates >50-60 kHz when slow dynamics are to be identified and quantified by means of R1ρ experiments.
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Affiliation(s)
- Alexey Krushelnitsky
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str.7, D-06120 Halle, Germany.
| | - Tatiana Zinkevich
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str.7, D-06120 Halle, Germany
| | - Bernd Reif
- Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Kay Saalwächter
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str.7, D-06120 Halle, Germany
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32
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del Amo JML, Agarwal V, Sarkar R, Porter J, Asami S, Rübbelke M, Fink U, Xue Y, Lange OF, Reif B. Site-specific analysis of heteronuclear Overhauser effects in microcrystalline proteins. JOURNAL OF BIOMOLECULAR NMR 2014; 59:241-9. [PMID: 24989039 DOI: 10.1007/s10858-014-9843-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 06/20/2014] [Indexed: 05/14/2023]
Abstract
Relaxation parameters such as longitudinal relaxation are susceptible to artifacts such as spin diffusion, and can be affected by paramagnetic impurities as e.g. oxygen, which make a quantitative interpretation difficult. We present here the site-specific measurement of [(1)H](13)C and [(1)H](15)N heteronuclear rates in an immobilized protein. For methyls, a strong effect is expected due to the three-fold rotation of the methyl group. Quantification of the [(1)H](13)C heteronuclear NOE in combination with (13)C-R 1 can yield a more accurate analysis of side chain motional parameters. The observation of significant [(1)H](15)N heteronuclear NOEs for certain backbone amides, as well as for specific asparagine/glutamine sidechain amides is consistent with MD simulations. The measurement of site-specific heteronuclear NOEs is enabled by the use of highly deuterated microcrystalline protein samples in which spin diffusion is reduced in comparison to protonated samples.
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Affiliation(s)
- Juan Miguel Lopez del Amo
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
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33
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Linser R, Sarkar R, Krushelnitzky A, Mainz A, Reif B. Dynamics in the solid-state: perspectives for the investigation of amyloid aggregates, membrane proteins and soluble protein complexes. JOURNAL OF BIOMOLECULAR NMR 2014; 59:1-14. [PMID: 24595988 DOI: 10.1007/s10858-014-9822-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/26/2014] [Indexed: 06/03/2023]
Abstract
Aggregates formed by amyloidogenic peptides and proteins and reconstituted membrane protein preparations differ significantly in terms of the spectral quality that they display in solid-state NMR experiments. Structural heterogeneity and dynamics can both in principle account for that observation. This perspectives article aims to point out challenges and limitations, but also potential opportunities in the investigation of these systems.
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Affiliation(s)
- Rasmus Linser
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA, 02115, USA
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34
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Good DB, Wang S, Ward ME, Struppe J, Brown LS, Lewandowski JR, Ladizhansky V. Conformational Dynamics of a Seven Transmembrane Helical Protein Anabaena Sensory Rhodopsin Probed by Solid-State NMR. J Am Chem Soc 2014; 136:2833-42. [DOI: 10.1021/ja411633w] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | | | | | - Jochem Struppe
- Bruker Biospin Ltd., Billerica, Massachusetts 01821, United States
| | | | - Józef R. Lewandowski
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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35
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Zinkevich T, Chevelkov V, Reif B, Saalwächter K, Krushelnitsky A. Internal protein dynamics on ps to μs timescales as studied by multi-frequency (15)N solid-state NMR relaxation. JOURNAL OF BIOMOLECULAR NMR 2013; 57:219-35. [PMID: 24048638 DOI: 10.1007/s10858-013-9782-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 09/06/2013] [Indexed: 05/14/2023]
Abstract
A comprehensive analysis of the dynamics of the SH3 domain of chicken alpha-spectrin is presented, based upon (15)N T1 and on- and off-resonance T1ρ relaxation times obtained on deuterated samples with a partial back-exchange of labile protons under a variety of the experimental conditions, taking explicitly into account the dipolar order parameters calculated from (15)N-(1)H dipole-dipole couplings. It is demonstrated that such a multi-frequency approach enables access to motional correlation times spanning about 6 orders of magnitude. We asses the validity of different motional models based upon orientation autocorrelation functions with a different number of motional components. We find that for many residues a "two components" model is not sufficient for a good description of the data and more complicated fitting models must be considered. We show that slow motions with correlation times on the order of 1-10 μs can be determined reliably in spite of rather low apparent amplitudes (below 1 %), and demonstrate that the distribution of the protein backbone mobility along the time scale axis is pronouncedly non-uniform and non-monotonic: two domains of fast (τ < 10(-10) s) and intermediate (10(-9) s < τ < 10(-7) s) motions are separated by a gap of one order of magnitude in time with almost no motions. For slower motions (τ > 10(-6) s) we observe a sharp ~1 order of magnitude decrease of the apparent motional amplitudes. Such a distribution obviously reflects different nature of backbone motions on different time scales, where the slow end may be attributed to weakly populated "excited states." Surprisingly, our data reveal no clearly evident correlations between secondary structure of the protein and motional parameters. We also could not notice any unambiguous correlations between motions in different time scales along the protein backbone emphasizing the importance of the inter-residue interactions and the cooperative nature of protein dynamics.
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Affiliation(s)
- Tatiana Zinkevich
- NMRGroup, Faculty of Natural Sciences II, Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 7, Saale, 06120, Halle, Germany
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36
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Haller JD, Schanda P. Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin. JOURNAL OF BIOMOLECULAR NMR 2013; 57:263-80. [PMID: 24105432 PMCID: PMC3840295 DOI: 10.1007/s10858-013-9787-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 09/23/2013] [Indexed: 05/21/2023]
Abstract
Solid-state NMR provides insight into protein motion over time scales ranging from picoseconds to seconds. While in solution state the methodology to measure protein dynamics is well established, there is currently no such consensus protocol for measuring dynamics in solids. In this article, we perform a detailed investigation of measurement protocols for fast motions, i.e. motions ranging from picoseconds to a few microseconds, which is the range covered by dipolar coupling and relaxation experiments. We perform a detailed theoretical investigation how dipolar couplings and relaxation data can provide information about amplitudes and time scales of local motion. We show that the measurement of dipolar couplings is crucial for obtaining accurate motional parameters, while systematic errors are found when only relaxation data are used. Based on this realization, we investigate how the REDOR experiment can provide such data in a very accurate manner. We identify that with accurate rf calibration, and explicit consideration of rf field inhomogeneities, one can obtain highly accurate absolute order parameters. We then perform joint model-free analyses of 6 relaxation data sets and dipolar couplings, based on previously existing, as well as new data sets on microcrystalline ubiquitin. We show that nanosecond motion can be detected primarily in loop regions, and compare solid-state data to solution-state relaxation and RDC analyses. The protocols investigated here will serve as a useful basis towards the establishment of a routine protocol for the characterization of ps-μs motions in proteins by solid-state NMR.
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Affiliation(s)
- Jens D. Haller
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), 38027 Grenoble, France
- CEA, DSV, IBS, 38027 Grenoble, France
- CNRS, IBS, 38027 Grenoble, France
| | - Paul Schanda
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), 38027 Grenoble, France
- CEA, DSV, IBS, 38027 Grenoble, France
- CNRS, IBS, 38027 Grenoble, France
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37
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Knight MJ, Felli IC, Pierattelli R, Emsley L, Pintacuda G. Magic angle spinning NMR of paramagnetic proteins. Acc Chem Res 2013; 46:2108-16. [PMID: 23506094 DOI: 10.1021/ar300349y] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Metal ions are ubiquitous in biochemical and cellular processes. Since many metal ions are paramagnetic due to the presence of unpaired electrons, paramagnetic molecules are an important class of targets for research in structural biology and related fields. Today, NMR spectroscopy plays a central role in the investigation of the structure and chemical properties of paramagnetic metalloproteins, linking the observed paramagnetic phenomena directly to electronic and molecular structure. A major step forward in the study of proteins by solid-state NMR came with the advent of ultrafast magic angle spinning (MAS) and the ability to use (1)H detection. Combined, these techniques have allowed investigators to observe nuclei that previously were invisible in highly paramagnetic metalloproteins. In addition, these techniques have enabled quantitative site-specific measurement of a variety of long-range paramagnetic effects. Instead of limiting solid-state NMR studies of biological systems, paramagnetism provides an information-rich phenomenon that can be exploited in these studies. This Account emphasizes state-of-the-art methods and applications of solid-state NMR in paramagnetic systems in biological chemistry. In particular, we discuss the use of ultrafast MAS and (1)H-detection in perdeuterated paramagnetic metalloproteins. Current methodology allows us to determine the structure and dynamics of metalloenzymes, and, as an example, we describe solid-state NMR studies of microcrystalline superoxide dismutase, a 32 kDa dimer. Data were acquired with remarkably short times, and these experiments required only a few milligrams of sample.
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Affiliation(s)
- Michael J. Knight
- Université de Lyon, Institut de Sciences Analytiques (CNRS / ENS-Lyon / UCB Lyon 1), Centre de RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Isabella C. Felli
- Department of Chemistry “Ugo Schiff“ and Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6 − 50019 Sesto Fiorentino, FI, Italy
| | - Roberta Pierattelli
- Department of Chemistry “Ugo Schiff“ and Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6 − 50019 Sesto Fiorentino, FI, Italy
| | - Lyndon Emsley
- Université de Lyon, Institut de Sciences Analytiques (CNRS / ENS-Lyon / UCB Lyon 1), Centre de RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Guido Pintacuda
- Université de Lyon, Institut de Sciences Analytiques (CNRS / ENS-Lyon / UCB Lyon 1), Centre de RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France
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Krushelnitsky A, Reichert D, Saalwächter K. Solid-state NMR approaches to internal dynamics of proteins: from picoseconds to microseconds and seconds. Acc Chem Res 2013; 46:2028-36. [PMID: 23875699 DOI: 10.1021/ar300292p] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Solid-state nuclear magnetic resonance (NMR) spectroscopy has matured to the point that it is possible to determine the structure of proteins in immobilized states, such as within microcrystals or embedded in membranes. Currently, researchers continue to develop and apply NMR techniques that can deliver site-resolved dynamic information toward the goal of understanding protein function at the atomic scale. As a widely-used, natural approach, researchers have mostly measured longitudinal (T1) relaxation times, which, like in solution-state NMR, are sensitive to picosecond and nanosecond motions, and motionally averaged dipolar couplings, which provide an integral amplitude of all motions with a correlation time of up to a few microseconds. While overall Brownian tumbling in solution mostly precludes access to slower internal dynamics, dedicated solid-state NMR approaches are now emerging as powerful new options. In this Account, we give an overview of the classes of solid-state NMR experiments that have expanded the accessible range correlation times from microseconds to many milliseconds. The measurement of relaxation times in the rotating frame, T1ρ, now allows researchers to access the microsecond range. Using our recent theoretical work, researchers can now quantitatively analyze this data to distinguish relaxation due to chemical-shift anisotropy (CSA) from that due to dipole-dipole couplings. Off-resonance irradiation allows researchers to extend the frequency range of such experiments. We have built multidimensional analogues of T2-type or line shape experiments using variants of the dipolar-chemical shift correlation (DIPSHIFT) experiment that are particularly suited to extract intermediate time scale motions in the millisecond range. In addition, we have continuously improved variants of exchange experiments, mostly relying on the recoupling of anisotropic interactions to address ultraslow motions in the ms to s ranges. The NH dipolar coupling offers a useful probe of local dynamics, especially with proton-depleted samples that suppress the adverse effect of strong proton dipolar couplings. We demonstrate how these techniques have provided a concise picture of the internal dynamics in a popular model system, the SH3 domain of α-spectrin. T1-based methods have shown that large-amplitude bond orientation fluctuations in the picosecond range and slower 10 ns low-amplitude motions coexist in these structures. When we include T1ρ data, we observe that many residues undergo low amplitude motions slower than 100 ns. On the millisecond to second scale, mostly localized but potentially cooperative motions occur. Comparing different exchange experiments, we found that terminal NH2 groups in side chains can even undergo a combination of ultraslow large-angle two-site jumps accompanied by small-angle fluctuations that occur 10 times more quickly.
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Affiliation(s)
- Alexey Krushelnitsky
- Institut für Physik − NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 7, D-06120 Halle (Saale), Germany
| | - Detlef Reichert
- Institut für Physik − NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 7, D-06120 Halle (Saale), Germany
| | - Kay Saalwächter
- Institut für Physik − NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 7, D-06120 Halle (Saale), Germany
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Asami S, Reif B. Proton-detected solid-state NMR spectroscopy at aliphatic sites: application to crystalline systems. Acc Chem Res 2013; 46:2089-97. [PMID: 23745638 DOI: 10.1021/ar400063y] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
When applied to biomolecules, solid-state NMR suffers from low sensitivity and resolution. The major obstacle to applying proton detection in the solid state is the proton dipolar network, and deuteration can help avoid this problem. In the past, researchers had primarily focused on the investigation of exchangeable protons in these systems. In this Account, we review NMR spectroscopic strategies that allow researchers to observe aliphatic non-exchangeable proton resonances in proteins with high sensitivity and resolution. Our labeling scheme is based on u-[(2)H,(13)C]-glucose and 5-25% H2O (95-75% D2O) in the M9 bacterial growth medium, known as RAP (reduced adjoining protonation). We highlight spectroscopic approaches for obtaining resonance assignments, a prerequisite for any study of structure and dynamics of a protein by NMR spectroscopy. Because of the dilution of the proton spin system in the solid state, solution-state NMR (1)HCC(1)H type strategies cannot easily be transferred to these experiments. Instead, we needed to pursue ((1)H)CC(1)H, CC(1)H, (1)HCC or ((2)H)CC(1)H type experiments. In protonated samples, we obtained distance restraints for structure calculations from samples grown in bacteria in media containing [1,3]-(13)C-glycerol, [2]-(13)C-glycerol, or selectively enriched glucose to dilute the (13)C spin system. In RAP-labeled samples, we obtained a similar dilution effect by randomly introducing protons into an otherwise deuterated matrix. This isotopic labeling scheme allows us to measure the long-range contacts among aliphatic protons, which can then serve as restraints for the three-dimensional structure calculation of a protein. Due to the high gyromagnetic ratio of protons, longer range contacts are more easily accessible for these nuclei than for carbon nuclei in homologous experiments. Finally, the RAP labeling scheme allows access to dynamic parameters, such as longitudinal relaxation times T1, and order parameters S(2) for backbone and side chain carbon resonances. We expect that these measurements will open up new opportunities to obtain a more detailed description of protein backbone and side chain dynamics.
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Affiliation(s)
- Sam Asami
- Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU), Helmholtz-Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Bernd Reif
- Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU), Helmholtz-Zentrum München, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
- Munich Center for Integrated Protein Science (CIPSM) at Department of Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, D-85747 Garching, Germany
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Mollica L, Baias M, Lewandowski JR, Wylie BJ, Sperling LJ, Rienstra CM, Emsley L, Blackledge M. Atomic-Resolution Structural Dynamics in Crystalline Proteins from NMR and Molecular Simulation. J Phys Chem Lett 2012; 3:3657-62. [PMID: 26291002 DOI: 10.1021/jz3016233] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Solid-state NMR can provide atomic-resolution information about protein motions occurring on a vast range of time scales under similar conditions to those of X-ray diffraction studies and therefore offers a highly complementary approach to characterizing the dynamic fluctuations occurring in the crystal. We compare experimentally determined dynamic parameters, spin relaxation, chemical shifts, and dipolar couplings, to values calculated from a 200 ns MD simulation of protein GB1 in its crystalline form, providing insight into the nature of structural dynamics occurring within the crystalline lattice. This simulation allows us to test the accuracy of commonly applied procedures for the interpretation of experimental solid-state relaxation data in terms of dynamic modes and time scales. We discover that the potential complexity of relaxation-active motion can lead to significant under- or overestimation of dynamic amplitudes if different components are not taken into consideration.
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Affiliation(s)
- Luca Mollica
- †Protein Dynamics and Flexibility, Institut de Biologie Structurale, CEA, CNRS, UJF-Grenoble 1, 41 Rue Jules Horowitz, Grenoble 38027, France
| | - Maria Baias
- ‡CNRS/ENS-Lyon/UCB-Lyon 1, Centre de RMN à Très Hauts Champs, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Józef R Lewandowski
- §Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Benjamin J Wylie
- ⊥Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| | - Lindsay J Sperling
- #Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Chad M Rienstra
- ∥Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Lyndon Emsley
- ‡CNRS/ENS-Lyon/UCB-Lyon 1, Centre de RMN à Très Hauts Champs, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Martin Blackledge
- †Protein Dynamics and Flexibility, Institut de Biologie Structurale, CEA, CNRS, UJF-Grenoble 1, 41 Rue Jules Horowitz, Grenoble 38027, France
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Tollinger M, Sivertsen A, Meier BH, Ernst M, Schanda P. Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy. J Am Chem Soc 2012; 134:14800-7. [PMID: 22908968 PMCID: PMC3557925 DOI: 10.1021/ja303591y] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Indexed: 02/04/2023]
Abstract
We demonstrate that conformational exchange processes in proteins on microsecond-to-millisecond time scales can be detected and quantified by solid-state NMR spectroscopy. We show two independent approaches that measure the effect of conformational exchange on transverse relaxation parameters, namely Carr-Purcell-Meiboom-Gill relaxation-dispersion experiments and measurement of differential multiple-quantum coherence decay. Long coherence lifetimes, as required for these experiments, are achieved by the use of highly deuterated samples and fast magic-angle spinning. The usefulness of the approaches is demonstrated by application to microcrystalline ubiquitin. We detect a conformational exchange process in a region of the protein for which dynamics have also been observed in solution. Interestingly, quantitative analysis of the data reveals that the exchange process is more than 1 order of magnitude slower than in solution, and this points to the impact of the crystalline environment on free energy barriers.
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Affiliation(s)
- Martin Tollinger
- Institut für Organische
Chemie, Universität Innsbruck, 6020
Innsbruck, Austria
| | - Astrid
C. Sivertsen
- CEA, Institut de Biologie Structurale
Jean-Pierre Ebel, 41 rue Jules
Horowitz, 38027 Grenoble Cedex 1, France
- CNRS, Institut
de Biologie Structurale Jean-Pierre Ebel, Grenoble, 41 rue Jules Horowitz,
38027 Grenoble Cedex 1, France
- Université
Joseph Fourier−Grenoble 1, Institut de Biologie
Structurale Jean-Pierre Ebel, Grenoble, 41 rue Jules Horowitz, 38027
Grenoble Cedex 1, France
| | - Beat H. Meier
- Physical
Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse
10, 8093
Zürich, Switzerland
| | - Matthias Ernst
- Physical
Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse
10, 8093
Zürich, Switzerland
| | - Paul Schanda
- CEA, Institut de Biologie Structurale
Jean-Pierre Ebel, 41 rue Jules
Horowitz, 38027 Grenoble Cedex 1, France
- CNRS, Institut
de Biologie Structurale Jean-Pierre Ebel, Grenoble, 41 rue Jules Horowitz,
38027 Grenoble Cedex 1, France
- Université
Joseph Fourier−Grenoble 1, Institut de Biologie
Structurale Jean-Pierre Ebel, Grenoble, 41 rue Jules Horowitz, 38027
Grenoble Cedex 1, France
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Quinn CM, McDermott AE. Quantifying conformational dynamics using solid-state R₁ρ experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 222:1-7. [PMID: 22820004 PMCID: PMC3572234 DOI: 10.1016/j.jmr.2012.05.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 05/14/2012] [Accepted: 05/20/2012] [Indexed: 05/14/2023]
Abstract
We demonstrate the determination of quantitative rates of molecular reorientation in the solid state with rotating frame (R(1ρ)) relaxation measurements. Reorientation of the carbon chemical shift anisotropy (CSA) tensor was used to probe site-specific conformational exchange in a model system, d(6)-dimethyl sulfone (d(6)-DMS). The CSA as a probe of exchange has the advantage that it can still be utilized when there is no dipolar mechanism (i.e. no protons attached to the site of interest). Other works have presented R(1ρ) measurements as a general indicator of dynamics, but this study extracts quantitative rates of molecular reorientation from the R(1ρ) values. Some challenges of this technique include precise knowledge of sample temperature and determining the R(2)(0) contribution to the observed relaxation rate from interactions other than molecular reorientation, such as residual dipolar couplings or fast timescale dynamics; determination of this term is necessary in order to quantify the exchange rate due to covariance between the 2 terms. Low-temperature experiments measured an R(2)(0) value of 1.8±0.2s(-1) Allowing for an additional relaxation term (R(2)(0)), which was modeled as both temperature-dependent and temperature-independent, rates of molecular reorientation were extracted from field strength-dependent R(1ρ) measurements at four different temperatures and the activation energy was determined from these exchange rates. The activation energies determined were 74.7±4.3kJ/mol and 71.7±2.9kJ/mol for the temperature-independent and temperature-dependent R(2)(0) models respectively, in excellent agreement with literature values. The results of this study suggest important methodological considerations for the application of the method to more complicated systems such as proteins, such as the importance of deuterating samples and the need to make assumptions regarding the R(2)(0) contribution to relaxation.
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Reichert D, Zinkevich T, Saalwächter K, Krushelnitsky A. The relation of the X-ray B-factor to protein dynamics: insights from recent dynamic solid-state NMR data. J Biomol Struct Dyn 2012; 30:617-27. [PMID: 22746382 DOI: 10.1080/07391102.2012.689695] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In addressing the potential use of B-factors derived from X-ray scattering data of proteins for the understanding the (functional) dynamics of proteins, we present a comparison of B-factors of five different proteins (SH3 domain, Crh, GB1, ubiquitin and thioredoxin) with data from recent solid-state nuclear magnetic resonance experiments reflecting true (rotational) dynamics on well-defined timescales. Apart from trivial correlations involving mobile loop regions and chain termini, we find no significant correlation of B-factors with the dynamic data on any of the investigated timescales, concluding that there is no unique and general correlation of B-factors with the internal reorientational dynamics of proteins.
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Affiliation(s)
- Detlef Reichert
- Institut für Physik - NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 7, Halle, 06120, Germany.
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Structure and backbone dynamics of a microcrystalline metalloprotein by solid-state NMR. Proc Natl Acad Sci U S A 2012; 109:11095-100. [PMID: 22723345 DOI: 10.1073/pnas.1204515109] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We introduce a new approach to improve structural and dynamical determination of large metalloproteins using solid-state nuclear magnetic resonance (NMR) with (1)H detection under ultrafast magic angle spinning (MAS). The approach is based on the rapid and sensitive acquisition of an extensive set of (15)N and (13)C nuclear relaxation rates. The system on which we demonstrate these methods is the enzyme Cu, Zn superoxide dismutase (SOD), which coordinates a Cu ion available either in Cu(+) (diamagnetic) or Cu(2+) (paramagnetic) form. Paramagnetic relaxation enhancements are obtained from the difference in rates measured in the two forms and are employed as structural constraints for the determination of the protein structure. When added to (1)H-(1)H distance restraints, they are shown to yield a twofold improvement of the precision of the structure. Site-specific order parameters and timescales of motion are obtained by a gaussian axial fluctuation (GAF) analysis of the relaxation rates of the diamagnetic molecule, and interpreted in relation to backbone structure and metal binding. Timescales for motion are found to be in the range of the overall correlation time in solution, where internal motions characterized here would not be observable.
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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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Hackel C, Zinkevich T, Belton P, Achilles A, Reichert D, Krushelnitsky A. The trehalose coating effect on the internal protein dynamics. Phys Chem Chem Phys 2012; 14:2727-34. [DOI: 10.1039/c2cp23098d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kurbanov R, Zinkevich T, Krushelnitsky A. The nuclear magnetic resonance relaxation data analysis in solids: General R1/R1ρ equations and the model-free approach. J Chem Phys 2011; 135:184104. [DOI: 10.1063/1.3658383] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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