51
|
Jayanthi S, Chatterjee B, Raghothama S. Natural abundant solid state NMR studies in designed tripeptides for differentiation of multiple conformers. Biopolymers 2009; 91:851-60. [DOI: 10.1002/bip.21270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
52
|
Expression and purification of a recombinant amyloidogenic peptide from transthyretin for solid-state NMR spectroscopy. Protein Expr Purif 2009; 70:101-8. [PMID: 19796687 DOI: 10.1016/j.pep.2009.09.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2009] [Revised: 09/22/2009] [Accepted: 09/23/2009] [Indexed: 11/17/2022]
Abstract
We describe the expression and purification of a model amyloidogenic peptide comprising residues 105-115 of human transthyretin (TTR105-115). Recombinant TTR105-115, which does not contain any non-native residues, was prepared as part of a fusion protein construct with a highly soluble B1 immunoglobulin binding domain of protein G (GB1), with typical yields of approximately 4 mg/L of uniformly (13)C,(15)N-enriched HPLC-purified peptide per liter of minimal media culture. Amyloid fibrils formed by recombinant TTR105-115 were characterized by transmission electron microscopy and solid-state NMR spectroscopy, and found to be comparable to synthetic TTR105-115 fibrils. These results establish recombinant TTR105-115 as a valuable model system for the development of new solid-state NMR techniques for the atomic-level characterization of amyloid architecture.
Collapse
|
53
|
Vijayan V, Demers JP, Biernat J, Mandelkow E, Becker S, Lange A. Low-Power Solid-State NMR Experiments for Resonance Assignment under Fast Magic-Angle Spinning. Chemphyschem 2009; 10:2205-8. [DOI: 10.1002/cphc.200900439] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
54
|
Tian Y, Chen L, Niks D, Kaiser JM, Lai J, Rienstra CM, Dunn MF, Mueller LJ. J-Based 3D sidechain correlation in solid-state proteins. Phys Chem Chem Phys 2009; 11:7078-86. [PMID: 19652843 PMCID: PMC2798598 DOI: 10.1039/b911570f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Scalar-based three-dimensional homonuclear correlation experiments are reported for (13)C sidechain correlation in solid-state proteins. These experiments are based on a sensitive constant-time format, in which homonuclear scalar couplings are utilized for polarization transfer, but decoupled during chemical shift evolution, to yield highly resolved indirect dimensions and band selectivity as desired. The methods therefore yield spectra of high quality that give unique sets of sidechain correlations for small proteins even at 9.4 Tesla (400 MHz (1)H frequency). We demonstrate versions of the pulse sequence that enable correlation from the sidechain to the backbone carbonyl as well as purely sidechain correlation sets; together these two data sets provide the majority of (13)C-(13)C correlations for assignment. The polarization transfer efficiency is approximately 30% over two bonds. In the protein GB1 (56 residues), we find essentially all cross peaks uniquely resolved. We find similar efficiency of transfer (approximately 30%) in the 140 kDa tryptophan synthase (TS), since the relaxation rates of immobilized solid proteins are not sensitive to global molecular tumbling, as long as the correlation time is much longer than the magic-angle spinning rotor period. In 3D data sets of TS at 400 MHz, some peaks are resolved and, in combination with higher field data sets, we anticipate that assignments will be possible; in this vein, we demonstrate 2D (13)C-(13)C spectra of TS at 900 MHz that are well resolved. These results together provide optimism about the prospects for assigning the spectra of such large enzymes in the solid state.
Collapse
Affiliation(s)
- Ye Tian
- Department of Chemistry, University of California, Riverside, California 92521
| | - Lingling Chen
- Department of Chemistry, University of California, Riverside, California 92521
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, California 92521
| | - J. Michael Kaiser
- Department of Chemistry, University of California, Riverside, California 92521
| | - Jinfeng Lai
- Department of Chemistry, University of California, Riverside, California 92521
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Michael F. Dunn
- Department of Biochemistry, University of California, Riverside, California 92521
| | - Leonard J. Mueller
- Department of Chemistry, University of California, Riverside, California 92521
| |
Collapse
|
55
|
Abstract
AbstractIn order to fulfill their function, membrane transport proteins have to cycle through a number of conformational and/or energetic states. Thus, understanding the role of conformational dynamics seems to be the key for elucidation of the functional mechanism of these proteins. However, membrane proteins in general are often difficult to express heterologously and in sufficient amounts for structural studies. It is especially challenging to trap a stable energy minimum, e.g., for crystallographic analysis. Furthermore, crystallization is often only possible by subjecting the protein to conditions that do not resemble its native environment and crystals can only be snapshots of selected conformational states. Nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy are complementary methods that offer unique possibilities for studying membrane proteins in their natural membrane environment and for investigating functional conformational changes, lipid interactions, substrate-lipid and substrate-protein interactions, oligomerization states and overall dynamics of membrane transporters. Here, we review recent progress in the field including studies from primary and secondary active transporters.
Collapse
|
56
|
Butler MC, Dumez JN, Emsley L. Dynamics of large nuclear-spin systems from low-order correlations in Liouville space. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.07.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
57
|
Laage S, Lesage A, Emsley L, Bertini I, Felli IC, Pierattelli R, Pintacuda G. Transverse-Dephasing Optimized Homonuclear J-Decoupling in Solid-State NMR Spectroscopy of Uniformly 13C-Labeled Proteins. J Am Chem Soc 2009; 131:10816-7. [DOI: 10.1021/ja903542h] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ségolène Laage
- Université de Lyon, CNRS/ ENS Lyon/ UCB-Lyon 1, Centre RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France, and Department of Chemistry and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Anne Lesage
- Université de Lyon, CNRS/ ENS Lyon/ UCB-Lyon 1, Centre RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France, and Department of Chemistry and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Lyndon Emsley
- Université de Lyon, CNRS/ ENS Lyon/ UCB-Lyon 1, Centre RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France, and Department of Chemistry and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Ivano Bertini
- Université de Lyon, CNRS/ ENS Lyon/ UCB-Lyon 1, Centre RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France, and Department of Chemistry and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Isabella C. Felli
- Université de Lyon, CNRS/ ENS Lyon/ UCB-Lyon 1, Centre RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France, and Department of Chemistry and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Roberta Pierattelli
- Université de Lyon, CNRS/ ENS Lyon/ UCB-Lyon 1, Centre RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France, and Department of Chemistry and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Guido Pintacuda
- Université de Lyon, CNRS/ ENS Lyon/ UCB-Lyon 1, Centre RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France, and Department of Chemistry and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| |
Collapse
|
58
|
Brown MF, Martínez-Mayorga K, Nakanishi K, Salgado GFJ, Struts AV. Retinal conformation and dynamics in activation of rhodopsin illuminated by solid-state H NMR spectroscopy. Photochem Photobiol 2009; 85:442-53. [PMID: 19267870 DOI: 10.1111/j.1751-1097.2008.00510.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Solid-state NMR spectroscopy gives a powerful avenue for investigating G protein-coupled receptors and other integral membrane proteins in a native-like environment. This article reviews the use of solid-state (2)H NMR to study the retinal cofactor of rhodopsin in the dark state as well as the meta I and meta II photointermediates. Site-specific (2)H NMR labels have been introduced into three regions (methyl groups) of retinal that are crucially important for the photochemical function of rhodopsin. Despite its phenomenal stability (2)H NMR spectroscopy indicates retinal undergoes rapid fluctuations within the protein binding cavity. The spectral lineshapes reveal the methyl groups spin rapidly about their three-fold (C(3)) axes with an order parameter for the off-axial motion of SC(3) approximately 0.9. For the dark state, the (2)H NMR structure of 11-cis-retinal manifests torsional twisting of both the polyene chain and the beta-ionone ring due to steric interactions of the ligand and the protein. Retinal is accommodated within the rhodopsin binding pocket with a negative pretwist about the C11=C12 double bond. Conformational distortion explains its rapid photochemistry and reveals the trajectory of the 11-cis to trans isomerization. In addition, (2)H NMR has been applied to study the retinylidene dynamics in the dark and light-activated states. Upon isomerization there are drastic changes in the mobility of all three methyl groups. The relaxation data support an activation mechanism whereby the beta-ionone ring of retinal stays in nearly the same environment, without a large displacement of the ligand. Interactions of the beta-ionone ring and the retinylidene Schiff base with the protein transmit the force of the retinal isomerization. Solid-state (2)H NMR thus provides information about the flow of energy that triggers changes in hydrogen-bonding networks and helix movements in the activation mechanism of the photoreceptor.
Collapse
Affiliation(s)
- Michael F Brown
- Department of Chemistry, University of Arizona, Tucson, AZ, USA.
| | | | | | | | | |
Collapse
|
59
|
Nadaud PS, Helmus JJ, Kall SL, Jaroniec CP. Paramagnetic Ions Enable Tuning of Nuclear Relaxation Rates and Provide Long-Range Structural Restraints in Solid-State NMR of Proteins. J Am Chem Soc 2009; 131:8108-20. [DOI: 10.1021/ja900224z] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Philippe S. Nadaud
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Jonathan J. Helmus
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Stefanie L. Kall
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | | |
Collapse
|
60
|
Robustelli P, Cavalli A, Vendruscolo M. Determination of protein structures in the solid state from NMR chemical shifts. Structure 2009; 16:1764-9. [PMID: 19081052 DOI: 10.1016/j.str.2008.10.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 09/26/2008] [Accepted: 10/29/2008] [Indexed: 11/29/2022]
Abstract
Solid-state NMR spectroscopy does not require proteins to form crystalline or soluble samples and can thus be applied under a variety of conditions, including precipitates, gels, and microcrystals. It has recently been shown that NMR chemical shifts can be used to determine the structures of the native states of proteins in solution. By considering the cases of two proteins, GB1 and SH3, we provide an initial demonstration here that this type of approach can be extended to the use of solid-state NMR chemical shifts to obtain protein structures in the solid state without the need for measuring interatomic distances.
Collapse
Affiliation(s)
- Paul Robustelli
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | | | | |
Collapse
|
61
|
Laage S, Sachleben JR, Steuernagel S, Pierattelli R, Pintacuda G, Emsley L. Fast acquisition of multi-dimensional spectra in solid-state NMR enabled by ultra-fast MAS. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 196:133-41. [PMID: 19028122 DOI: 10.1016/j.jmr.2008.10.019] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Revised: 10/29/2008] [Accepted: 10/29/2008] [Indexed: 05/10/2023]
Abstract
The advantages offered by ultra-fast (>60 kHz) magic angle spinning (MAS) rotation for the study of biological samples, notably containing paramagnetic centers are explored. It is shown that optimal conditions for performing solid-state (13)C NMR under 60 kHz MAS are obtained with low-power CW (1)H decoupling, as well as after a low-power (1)H,(13)C cross-polarization step at a double-quantum matching condition. Acquisition with low-power decoupling highlights the existence of rotational decoupling sidebands. The sideband intensities and the existence of first and second rotary conditions are explained in the framework of the Floquet-van Vleck theory. As a result, optimal (13)C spectra of the oxidized, paramagnetic form of human copper zinc superoxide dismutase (SOD) can be obtained employing rf-fields which do not exceed 40 kHz during the whole experiment. This enables the removal of unwanted heating which can lead to deterioration of the sample. Furthermore, combined with the short (1)H T(1)s, this allows the repetition rate of the experiments to be shortened from 3 s to 500 ms, thus compensating for the sensitivity loss due to the smaller sample volume in a 1.3 mm rotor. The result is that 2D (13)C-(13)C correlation could be acquired in about 24 h on less than 1 mg of SOD sample.
Collapse
Affiliation(s)
- Ségolène Laage
- Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, Centre RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France
| | | | | | | | | | | |
Collapse
|
62
|
Agarwal V, Xue Y, Reif B, Skrynnikov NR. Protein Side-Chain Dynamics As Observed by Solution- and Solid-State NMR Spectroscopy: A Similarity Revealed. J Am Chem Soc 2008; 130:16611-21. [PMID: 19049457 DOI: 10.1021/ja804275p] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vipin Agarwal
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany, and Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084
| | - Yi Xue
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany, and Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084
| | - Bernd Reif
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany, and Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084
| | - Nikolai R. Skrynnikov
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany, and Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084
| |
Collapse
|
63
|
Paramagnetic shifts in solid-state NMR of proteins to elicit structural information. Proc Natl Acad Sci U S A 2008; 105:17284-9. [PMID: 18988744 DOI: 10.1073/pnas.0708460105] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The recent observation of pseudocontact shifts (pcs) in (13)C high-resolution solid-state NMR of paramagnetic proteins opens the way to their application as structural restraints. Here, by investigating a microcrystalline sample of cobalt(II)-substituted matrix metalloproteinase 12 [CoMMP-12 (159 AA, 17.5 kDa)], it is shown that a combined strategy of protein labeling and dilution of the paramagnetic species (i.e., (13)C-,(15)N-labeled CoMMP-12 diluted in unlabeled ZnMMP-12, and (13)C-,(15)N-labeled ZnMMP-12 diluted in unlabeled CoMMP-12) allows one to easily separate the pcs contributions originated from the protein internal metal (intramolecular pcs) from those due to the metals in neighboring proteins in the crystal lattice (intermolecular pcs) and that both can be used for structural purposes. It is demonstrated that intramolecular pcs are significant structural restraints helpful in increasing both precision and accuracy of the structure, which is a need in solid-state structural biology nowadays. Furthermore, intermolecular pcs provide unique information on positions and orientations of neighboring protein molecules in the solid phase.
Collapse
|
64
|
Breitung ST, Lopez JJ, Dürner G, Glaubitz C, Göbel MW, Suhartono M. A practical synthesis of the 16C/15N-labelled tripeptide N-formyl-Met-Leu-Phe, useful as a reference in solid-state NMR spectroscopy. Beilstein J Org Chem 2008; 4:35. [PMID: 18982075 PMCID: PMC2577282 DOI: 10.3762/bjoc.4.35] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Accepted: 10/01/2008] [Indexed: 11/29/2022] Open
Abstract
A mild synthetic method for N-formyl-Met-Leu-Phe-OH (1) is described. After Fmoc solid phase peptide synthesis, on-bead formylation and HPLC purification, more than 30 mg of the fully 13C/15N-labelled tripeptide 1 could be isolated in a typical batch. This peptide can be easily crystallised and is therefore well suited as a standard sample for setting up solid-state NMR experiments.
Collapse
Affiliation(s)
- Sven T Breitung
- Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Jakob J Lopez
- Institute of Biophysical Chemistry, Johann Wolfgang Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Gerd Dürner
- Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Clemens Glaubitz
- Institute of Biophysical Chemistry, Johann Wolfgang Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Michael W Göbel
- Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Marcel Suhartono
- Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| |
Collapse
|
65
|
Biocatalyst activity in nonaqueous environments correlates with centisecond-range protein motions. Proc Natl Acad Sci U S A 2008; 105:15672-7. [PMID: 18840689 DOI: 10.1073/pnas.0804566105] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent studies exploring the relationship between enzymatic catalysis and protein dynamics in the aqueous phase have yielded evidence that dynamics and enzyme activity are strongly correlated. Given that protein dynamics are significantly attenuated in organic solvents and that proteins exhibit a wide range of motions depending on the specific solvent environment, the nonaqueous milieu provides a unique opportunity to examine the role of protein dynamics in enzyme activity. Variable-temperature kinetic measurements, X-band electron spin resonance spectroscopy, (1)H NMR relaxation, and (19)F NMR spectroscopy experiments were performed on subtilisin Carlsberg colyophilized with several inorganic salts and suspended in organic solvents. The results indicate that salt activation induces a greater degree of transition-state flexibility, reflected by a more positive DeltaDeltaS(dagger), for the more active biocatalyst preparations in organic solvents. In contrast, DeltaDeltaH(dagger) was negligible regardless of salt type or salt content. Electron spin resonance spectroscopy and (1)H NMR relaxation measurements, including spin-lattice relaxation, spin-lattice relaxation in the rotating frame, and longitudinal magnetization exchange, revealed that the enzyme's turnover number (k(cat)) was strongly correlated with protein motions in the centisecond time regime, weakly correlated with protein motions in the millisecond regime, and uncorrelated with protein motions on the piconanosecond timescale. In addition, (19)F chemical shift measurements and hyperfine tensor measurements of biocatalyst formulations inhibited with 4-fluorobenzenesulfonyl fluoride and 4-ethoxyfluorophosphinyl-oxy-TEMPO, respectively, suggest that enzyme activation was only weakly affected by changes in active-site polarity.
Collapse
|
66
|
Loquet A, Laage S, Gardiennet C, Elena B, Emsley L, Böckmann A, Lesage A. Methyl Proton Contacts Obtained Using Heteronuclear Through-Bond Transfers in Solid-State NMR Spectroscopy. J Am Chem Soc 2008; 130:10625-32. [DOI: 10.1021/ja801464g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Antoine Loquet
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Ségolène Laage
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Carole Gardiennet
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Bénédicte Elena
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Lyndon Emsley
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Anne Lesage
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7 passage du Vercors, 69367 Lyon, France, and Centre RMN à Très Hauts Champs, Université de Lyon, CNRS/ENS Lyon/UCB-Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| |
Collapse
|
67
|
Molecular conformation and dynamics of the Y145Stop variant of human prion protein in amyloid fibrils. Proc Natl Acad Sci U S A 2008; 105:6284-9. [PMID: 18436646 DOI: 10.1073/pnas.0711716105] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A C-terminally truncated Y145Stop variant of the human prion protein (huPrP23-144) is associated with a hereditary amyloid disease known as PrP cerebral amyloid angiopathy. Previous studies have shown that recombinant huPrP23-144 can be efficiently converted in vitro to the fibrillar amyloid state, and that residues 138 and 139 play a critical role in the amyloidogenic properties of this protein. Here, we have used magic-angle spinning solid-state NMR spectroscopy to provide high-resolution insight into the protein backbone conformation and dynamics in fibrils formed by (13)C,(15)N-labeled huPrP23-144. Surprisingly, we find that signals from approximately 100 residues (i.e., approximately 80% of the sequence) are not detected above approximately -20 degrees C in conventional solid-state NMR spectra. Sequential resonance assignments revealed that signals, which are observed, arise exclusively from residues in the region 112-141. These resonances are remarkably narrow, exhibiting average (13)C and (15)N linewidths of approximately 0.6 and 1 ppm, respectively. Altogether, the present findings indicate the existence of a compact, highly ordered core of huPrP23-144 amyloid encompassing residues 112-141. Analysis of (13)C secondary chemical shifts identified likely beta-strand segments within this core region, including beta-strand 130-139 containing critical residues 138 and 139. In contrast to this relatively rigid, beta-sheet-rich amyloid core, the remaining residues in huPrP23-144 amyloid fibrils under physiologically relevant conditions are largely unordered, displaying significant conformational dynamics.
Collapse
|
68
|
Xu J, Struppe J, Ramamoorthy A. Two-dimensional homonuclear chemical shift correlation established by the cross-relaxation driven spin diffusion in solids. J Chem Phys 2008; 128:052308. [PMID: 18266425 DOI: 10.1063/1.2826323] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A new type of spin diffusion, cross-relaxation driven spin diffusion (CRDSD), is investigated using (15)N NMR on a N-acetyl-L-valyl-L-leucine (NAVL) single crystal under stationary condition. A two-dimensional (2D) pulse sequence that correlates the chemical shifts of (15)N nuclei, with a radio-frequency spin lock on the (15)N channel during the mixing time, is used to observe CRDSD. Experimental results obtained using CRDSD, rf-driven spin diffusion, and proton driven spin diffusion approaches on the NAVL single crystal are compared. Our experimental results suggest that the (15)N spin diffusion rate can be enhanced by about 1000 times using CRDSD than by the normal proton driven spin diffusion. Interestingly, the required spin-locking rf field strength for CRDSD is much lower than that used for the rf-driven spin diffusion experiments. The cross-peak patterns observed in 2D (15)N-(15)N correlation spectra using CRDSD and RFDSD are very different as they arise from different spin-spin interactions. A detailed theory describing CRDSD and RFDSD processes is also presented using a thermodynamic model. The speedy spin diffusion process rendered by the CRDSD approach will be useful to assign resonances from a uniformly (15)N or (13)C labeled proteins and peptides, particularly in aligned samples.
Collapse
Affiliation(s)
- Jiadi Xu
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
| | | | | |
Collapse
|
69
|
Helmus JJ, Nadaud PS, Höfer N, Jaroniec CP. Determination of methyl 13C-15N dipolar couplings in peptides and proteins by three-dimensional and four-dimensional magic-angle spinning solid-state NMR spectroscopy. J Chem Phys 2008; 128:052314. [PMID: 18266431 DOI: 10.1063/1.2817638] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We describe three- and four-dimensional semiconstant-time transferred echo double resonance (SCT-TEDOR) magic-angle spinning solid-state nuclear magnetic resonance (NMR) experiments for the simultaneous measurement of multiple long-range (15)N-(13)C(methyl) dipolar couplings in uniformly (13)C, (15)N-enriched peptides and proteins with high resolution and sensitivity. The methods take advantage of (13)C spin topologies characteristic of the side-chain methyl groups in amino acids alanine, isoleucine, leucine, methionine, threonine, and valine to encode up to three distinct frequencies ((15)N-(13)C(methyl) dipolar coupling, (15)N chemical shift, and (13)C(methyl) chemical shift) within a single SCT evolution period of initial duration approximately 1(1)J(CC) (where (1)J(CC) approximately 35 Hz, is the one-bond (13)C(methyl)-(13)C J-coupling) while concurrently suppressing the modulation of NMR coherences due to (13)C-(13)C and (15)N-(13)C J-couplings and transverse relaxation. The SCT-TEDOR schemes offer several important advantages over previous methods of this type. First, significant (approximately twofold to threefold) gains in experimental sensitivity can be realized for weak (15)N-(13)C(methyl) dipolar couplings (corresponding to structurally interesting, approximately 3.5 A or longer, distances) and typical (13)C(methyl) transverse relaxation rates. Second, the entire SCT evolution period can be used for (13)C(methyl) and/or (15)N frequency encoding, leading to increased spectral resolution with minimal additional coherence decay. Third, the experiments are inherently "methyl selective," which results in simplified NMR spectra and obviates the use of frequency-selective pulses or other spectral filtering techniques. Finally, the (15)N-(13)C cross-peak buildup trajectories are purely dipolar in nature (i.e., not influenced by J-couplings or relaxation), which enables the straightforward extraction of (15)N-(13)C(methyl) distances using an analytical model. The SCT-TEDOR experiments are demonstrated on a uniformly (13)C, (15)N-labeled peptide, N-acetyl-valine, and a 56 amino acid protein, B1 immunoglobulin-binding domain of protein G (GB1), where the measured (15)N-(13)C(methyl) dipolar couplings provide site-specific information about side-chain dihedral angles and the packing of protein molecules in the crystal lattice.
Collapse
Affiliation(s)
- Jonathan J Helmus
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | | | | |
Collapse
|
70
|
Affiliation(s)
- Henrike Heise
- Institute for Physical Biology, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany.
| |
Collapse
|
71
|
Loquet A, Bardiaux B, Gardiennet C, Blanchet C, Baldus M, Nilges M, Malliavin T, Böckmann A. 3D Structure Determination of the Crh Protein from Highly Ambiguous Solid-State NMR Restraints. J Am Chem Soc 2008; 130:3579-89. [DOI: 10.1021/ja078014t] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Antoine Loquet
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS Université Lyon 1, IFR128 BioSciences Lyon-Gerland, 7, passage du Vercors, 69367 Lyon, France, Unité de Bio-Informatique Structurale, URA 2185 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, F-75015 Paris, France, and Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Benjamin Bardiaux
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS Université Lyon 1, IFR128 BioSciences Lyon-Gerland, 7, passage du Vercors, 69367 Lyon, France, Unité de Bio-Informatique Structurale, URA 2185 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, F-75015 Paris, France, and Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Carole Gardiennet
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS Université Lyon 1, IFR128 BioSciences Lyon-Gerland, 7, passage du Vercors, 69367 Lyon, France, Unité de Bio-Informatique Structurale, URA 2185 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, F-75015 Paris, France, and Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christophe Blanchet
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS Université Lyon 1, IFR128 BioSciences Lyon-Gerland, 7, passage du Vercors, 69367 Lyon, France, Unité de Bio-Informatique Structurale, URA 2185 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, F-75015 Paris, France, and Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Marc Baldus
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS Université Lyon 1, IFR128 BioSciences Lyon-Gerland, 7, passage du Vercors, 69367 Lyon, France, Unité de Bio-Informatique Structurale, URA 2185 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, F-75015 Paris, France, and Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Michael Nilges
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS Université Lyon 1, IFR128 BioSciences Lyon-Gerland, 7, passage du Vercors, 69367 Lyon, France, Unité de Bio-Informatique Structurale, URA 2185 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, F-75015 Paris, France, and Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Thérèse Malliavin
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS Université Lyon 1, IFR128 BioSciences Lyon-Gerland, 7, passage du Vercors, 69367 Lyon, France, Unité de Bio-Informatique Structurale, URA 2185 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, F-75015 Paris, France, and Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS Université Lyon 1, IFR128 BioSciences Lyon-Gerland, 7, passage du Vercors, 69367 Lyon, France, Unité de Bio-Informatique Structurale, URA 2185 CNRS, Institut Pasteur, 25-28 rue du docteur Roux, F-75015 Paris, France, and Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| |
Collapse
|
72
|
Li Y, Berthold DA, Gennis RB, Rienstra CM. Chemical shift assignment of the transmembrane helices of DsbB, a 20-kDa integral membrane enzyme, by 3D magic-angle spinning NMR spectroscopy. Protein Sci 2008; 17:199-204. [PMID: 18227427 PMCID: PMC2222720 DOI: 10.1110/ps.073225008] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Revised: 11/06/2007] [Accepted: 11/10/2007] [Indexed: 10/22/2022]
Abstract
The Escherichia coli inner membrane enzyme DsbB catalyzes disulfide bond formation in periplasmic proteins, by transferring electrons to ubiquinone from DsbA, which in turn directly oxidizes cysteines in substrate proteins. We have previously shown that DsbB can be prepared in a state that gives highly resolved magic-angle spinning (MAS) NMR spectra. Here we report sequential 13C and 15N chemical shift assignments for the majority of the residues in the transmembrane helices, achieved by three-dimensional (3D) correlation experiments on a uniformly 13C, 15N-labeled sample at 750-MHz 1H frequency. We also present a four-dimensional (4D) correlation spectrum, which confirms assignments in some highly congested regions of the 3D spectra. Overall, our results show the potential to assign larger membrane proteins using 3D and 4D correlation experiments and form the basis of further structural and dynamical studies of DsbB by MAS NMR.
Collapse
Affiliation(s)
- Ying Li
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | | | | | | |
Collapse
|
73
|
Peng X, Libich D, Janik R, Harauz G, Ladizhansky V. Dipolar Chemical Shift Correlation Spectroscopy for Homonuclear Carbon Distance Measurements in Proteins in the Solid State: Application to Structure Determination and Refinement. J Am Chem Soc 2007; 130:359-69. [DOI: 10.1021/ja076658v] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaohu Peng
- Department of Physics, Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
| | - David Libich
- Department of Physics, Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
| | - Rafal Janik
- Department of Physics, Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
| | - George Harauz
- Department of Physics, Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
| | - Vladimir Ladizhansky
- Department of Physics, Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
| |
Collapse
|
74
|
Brown MF, Heyn MP, Job C, Kim S, Moltke S, Nakanishi K, Nevzorov AA, Struts AV, Salgado GFJ, Wallat I. Solid-state 2H NMR spectroscopy of retinal proteins in aligned membranes. BIOCHIMICA ET BIOPHYSICA ACTA 2007; 1768:2979-3000. [PMID: 18021739 PMCID: PMC5233718 DOI: 10.1016/j.bbamem.2007.10.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 10/10/2007] [Accepted: 10/10/2007] [Indexed: 11/21/2022]
Abstract
Solid-state 2H NMR spectroscopy gives a powerful avenue to investigating the structures of ligands and cofactors bound to integral membrane proteins. For bacteriorhodopsin (bR) and rhodopsin, retinal was site-specifically labeled by deuteration of the methyl groups followed by regeneration of the apoprotein. 2H NMR studies of aligned membrane samples were conducted under conditions where rotational and translational diffusion of the protein were absent on the NMR time scale. The theoretical lineshape treatment involved a static axial distribution of rotating C-C2H3 groups about the local membrane frame, together with the static axial distribution of the local normal relative to the average normal. Simulation of solid-state 2H NMR lineshapes gave both the methyl group orientations and the alignment disorder (mosaic spread) of the membrane stack. The methyl bond orientations provided the angular restraints for structural analysis. In the case of bR the retinal chromophore is nearly planar in the dark- and all-trans light-adapted states, as well upon isomerization to 13-cis in the M state. The C13-methyl group at the "business end" of the chromophore changes its orientation to the membrane upon photon absorption, moving towards W182 and thus driving the proton pump in energy conservation. Moreover, rhodopsin was studied as a prototype for G protein-coupled receptors (GPCRs) implicated in many biological responses in humans. In contrast to bR, the retinal chromophore of rhodopsin has an 11-cis conformation and is highly twisted in the dark state. Three sites of interaction affect the torsional deformation of retinal, viz. the protonated Schiff base with its carboxylate counterion; the C9-methyl group of the polyene; and the beta-ionone ring within its hydrophobic pocket. For rhodopsin, the strain energy and dynamics of retinal as established by 2H NMR are implicated in substituent control of activation. Retinal is locked in a conformation that is twisted in the direction of the photoisomerization, which explains the dark stability of rhodopsin and allows for ultra-fast isomerization upon absorption of a photon. Torsional strain is relaxed in the meta I state that precedes subsequent receptor activation. Comparison of the two retinal proteins using solid-state 2H NMR is thus illuminating in terms of their different biological functions.
Collapse
Affiliation(s)
- Michael F Brown
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
75
|
Skrynnikov NR. Asymmetric doublets in MAS NMR: coherent and incoherent mechanisms. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S161-73. [PMID: 18157846 DOI: 10.1002/mrc.2162] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
It has been long noted that J-resolved doublets observed in solid-state MAS experiments are asymmetric. The asymmetry has been attributed to a coherent interference effect involving dipolar and CSA interactions. Recently, Bernd Reif and co-workers suggested that under fast MAS conditions the coherent portion of the effect is suppressed and it becomes possible to observe an incoherent mechanism reminiscent of TROSY. The researchers were able to observe the characteristic TROSY-type patterns in (15)N-(1)H(N) spectra of heavily deuterated protein samples (Chevlekov, Diehl, and Reif, previous article in this issue). In the present computer simulation study, we seek to obtain a unified picture of this phenomenon, including both coherent and incoherent aspects. The chosen model focuses on the (15)N-(1)H(N) pair from a polycrystalline sample subject to magic angle spinning. To mimic local dynamics, we assume that the corresponding peptide plane jumps between two orientations. The simulations demonstrate that this simple model reproduces both coherent and incoherent behavior, depending on the MAS speed and the time scale of local dynamics. Furthermore, semianalytical expressions can be derived for both coherent and incoherent (Redfield) limits. Of particular interest is the possibility to use solution-style Redfield results to probe internal protein motions, especially slower motions on the nanosecond time scale. Our simulations show that the differential relaxation measurement permits accurate determination of (15)N dipolar-CSA cross correlations already at moderately high MAS speed (ca 15 kHz).
Collapse
Affiliation(s)
- N R Skrynnikov
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA.
| |
Collapse
|
76
|
A high resolution structure of the putative hinge region in M2 channel-lining segments of the nicotinic acetylcholine receptor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:2961-70. [DOI: 10.1016/j.bbamem.2007.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Revised: 10/12/2007] [Accepted: 10/15/2007] [Indexed: 02/07/2023]
|
77
|
Chen L, Kaiser JM, Lai J, Polenova T, Yang J, Rienstra CM, Mueller LJ. J-based 2D homonuclear and heteronuclear correlation in solid-state proteins. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S84-S92. [PMID: 18157839 DOI: 10.1002/mrc.2107] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Scalar-based two-dimensional heteronuclear experiments are reported for NCO and NCA chemical shift correlation in the solid state. In conjunction with homonuclear CACO correlation, these experiments form a useful set for tracing connectivities and assigning backbone resonances in solid-state proteins. The applicability of this approach is demonstrated on two proteins, the β 1 immunoglobulin binding domain of protein G at 9.4 T and reassembled thioredoxin at 14.1 T, using different decoupling conditions and MAS frequencies. These constant-time J-based correlation experiments exhibit increased resolution in the indirect dimension owing to homonuclear and heteronuclear decoupling, and because the indirect evolution and transfer periods are combined into a single constant time interval, this increased resolution is not obtained at the cost of sensitivity. These experiments are also shown to be compatible with in-phase anti-phase (IPAP) selection, giving increased resolution in the directly detected dimension.
Collapse
Affiliation(s)
- Lingling Chen
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | | | | | | | | | | | | |
Collapse
|
78
|
Dürr UH, Waskell L, Ramamoorthy A. The cytochromes P450 and b5 and their reductases—Promising targets for structural studies by advanced solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3235-59. [DOI: 10.1016/j.bbamem.2007.08.007] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 08/08/2007] [Indexed: 02/02/2023]
|
79
|
Böckmann A. High-resolution solid-state MAS NMR of proteins-Crh as an example. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S24-S31. [PMID: 18081212 DOI: 10.1002/mrc.2106] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Revised: 09/04/2007] [Accepted: 09/12/2007] [Indexed: 05/25/2023]
Abstract
Solid-state NMR spectroscopy provides unique possibilities for the structural investigation of insoluble molecules at the atomic level. Recent efforts aim at solving the complete structures of biological macromolecules using high-resolution magic angle spinning NMR. Structurally homogenous samples of [(13)C,(15)N]-labeled proteins have to be used in this type of studies. Microcrystalline model proteins present valuable tools for the developments of methods towards this goal. This review discusses recent progress in the field, using the Crh protein as an illustrative example. We discuss strategies for resonance assignments and for the determination of structure and dynamics, as well as techniques for the detection of protein interaction partners and folding mechanisms by solid-state NMR methods.
Collapse
Affiliation(s)
- Anja Böckmann
- IFR 128 BioSciences Lyon-Gerland, IBCP UMR 5086 CNRS/Université de Lyon Claude Bernard, 7 passage du Vercors, 69367 Lyon, France.
| |
Collapse
|
80
|
Kijac AZ, Li Y, Sligar SG, Rienstra CM. Magic-angle spinning solid-state NMR spectroscopy of nanodisc-embedded human CYP3A4. Biochemistry 2007; 46:13696-703. [PMID: 17985934 DOI: 10.1021/bi701411g] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome P450 (CYP) 3A4 contributes to the metabolism of approximately 50% of commercial drugs by oxidizing a large number of structurally diverse substrates. Like other endoplasmic reticulum-localized P450s, CYP3A4 contains a membrane-anchoring N-terminal helix and a significant number of hydrophobic domains, important for the interaction between CYP3A4 and the membrane. Although the membrane affects specificity of CYP3A4 ligand binding, the structural details of the interaction have not been revealed so far because X-ray crystallography studies are available only for the soluble domain of CYP3A4. Here we report sample preparation and initial magic-angle spinning (MAS) solid-state NMR (SSNMR) of CYP3A4 (Delta3-12) embedded in a nanoscale membrane bilayer, or Nanodisc. The growth protocol yields approximately 2.5 mg of the enzymatically active, uniformly 13C,15N-enriched CYP3A4 from 1 L of growth medium. Polyethylene glycol 3350-precipitated CYP3A4 in Nanodiscs yields spectra of high resolution and sensitivity, consistent with a folded, homogeneous protein. CYP3A4 in Nanodiscs remains enzymatically active throughout the precipitation protocol as monitored by bromocriptine binding. The 13C line widths measured from 13C-13C 2D chemical shift correlation spectra are approximately 0.5 ppm. The secondary structure distribution within several amino acid types determined from 13C chemical shifts is consistent with the ligand-free X-ray structures. These results demonstrate that MAS SSNMR can be performed on Nanodisc-embedded membrane proteins in a folded, active state. The combination of SSNMR and Nanodisc methodologies opens up new possibilities for obtaining structural information on CYP3A4 and other integral membrane proteins with full retention of functionality.
Collapse
Affiliation(s)
- Aleksandra Z Kijac
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 618001, USA
| | | | | | | |
Collapse
|
81
|
Wylie BJ, Sperling LJ, Rienstra CM. Isotropic chemical shifts in magic-angle spinning NMR spectra of proteins. Phys Chem Chem Phys 2007; 10:405-13. [PMID: 18174982 DOI: 10.1039/b710736f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we examine the effect of magic-angle spinning (MAS) rate upon lineshape and observed peak position for backbone carbonyl (C') peaks in NMR spectra of uniformly-(13)C,15N-labeled (U-(13)C,15N) solid proteins. 2D N-C' spectra of U-(13)C,15N microcrystalline protein GB1 were acquired at six MAS rates, and the site-resolved C' lineshapes were analyzed by numerical simulations and comparison to spectra from a sparsely labeled sample (derived from 1,3-(13)C-glycerol). Spectra of the U-(13)C,15N sample demonstrate large variations in the signal-to-noise ratio and peak positions, which are absent in spectra of the sparsely labeled sample, in which most 13C' sites do not possess a directly bonded 13CA. These effects therefore are a consequence of rotational resonance, which is a well-known phenomenon. Yet the magnitude of this effect pertaining to chemical shift assignment has not previously been examined. To quantify these effects in high-resolution protein spectra, we performed exact numerical two- and four-spin simulations of the C' lineshapes, which reproduced the experimentally observed features. Observed peak positions differ from the isotropic shift by up to 1.0 ppm, even for MAS rates relatively far (a few ppm) from rotational resonance. Although under these circumstances the correct isotropic chemical shift values may be determined through simulation, systematic errors are minimized when the MAS rate is equivalent to approximately 85 ppm for 13C. This moderate MAS condition simplifies spectral assignment and enables data sets from different labeling patterns and spinning rates to be used most efficiently for structure determination.
Collapse
Affiliation(s)
- Benjamin J Wylie
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | | | | |
Collapse
|
82
|
Huang W, Vega AJ, Gullion T, Polenova T. Internuclear (31)P-(51)V distance measurements in polyoxoanionic solids using rotational echo adiabatic passage double resonance NMR spectroscopy. J Am Chem Soc 2007; 129:13027-34. [PMID: 17918932 PMCID: PMC3985602 DOI: 10.1021/ja073170l] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the first results establishing rotational echo adiabatic passage double resonance (REAPDOR) experiments for distance measurements between a spin-1/2 (31P) and spin-7/2 (51V) pair in a series of vanadium-substituted polyoxoanionic solids from the Keggin and Wells-Dawson families. We have quantitatively measured 31P-51V distances in monovanadium substituted K4PVW11O40, 1-K7P2VW17O62, and 4-K7P2VW17O62. Numerical simulations of the experimental data yield very good agreement with the averaged P-W/P-V distances determined from the X-ray diffraction measurements in the same or related compounds. REAPDOR is therefore a very sensitive P-V distance probe anticipated to be especially useful in the absence of long-range order. Our results suggest that REAPDOR spectroscopy could be broadly applicable for interatomic distance measurements in other spin-7/2-spin-1/2 nuclear pairs.
Collapse
Affiliation(s)
- Wenlin Huang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
| | - Alexander J. Vega
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
| | - Terry Gullion
- Department of Chemistry, West Virginia University, Morgantown, WV 26506
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716
| |
Collapse
|
83
|
Magic-angle-spinning NMR spectroscopy applied to small molecules and peptides in lipid bilayers. Biochem Soc Trans 2007; 35:991-5. [DOI: 10.1042/bst0350991] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
ssNMR (solid-state NMR) spectroscopy provides increasing possibilities to study the structural and dynamic aspects of biological membranes. Here, we review recent ssNMR experiments that are based on MAS (magic angle spinning) and that provide insight into the structure and dynamics of membrane systems at the atomic level. Such methods can be used to study membrane architecture, domain formation or molecular complexation in a way that is highly complementary to other biophysical methods such as imaging or calorimetry.
Collapse
|
84
|
Rupasinghe SG, Duan H, Frericks Schmidt HL, Berthold DA, Rienstra CM, Schuler MA. High-yield expression and purification of isotopically labeled cytochrome P450 monooxygenases for solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3061-70. [PMID: 18005930 DOI: 10.1016/j.bbamem.2007.09.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2007] [Revised: 09/11/2007] [Accepted: 09/13/2007] [Indexed: 10/22/2022]
Abstract
Cytochrome P450 monooxygenases (P450s), which represent the major group of drug metabolizing enzymes in humans, also catalyze important synthetic and detoxicative reactions in insects, plants and many microbes. Flexibilities in their catalytic sites and membrane associations are thought to play central roles in substrate binding and catalytic specificity. To date, Escherichia coli expression strategies for structural analysis of eukaryotic membrane-bound P450s by X-ray crystallography have necessitated full or partial removal of their N-terminal signal anchor domain and, often, replacement of residues more peripherally associated with the membrane (such as the F-G loop region). Even with these modifications, investigations of P450 structural flexibility remain challenging with multiple single crystal conditions needed to identify spatial variations between substrate-free and different substrate-bound forms. To overcome these limitations, we have developed methods for the efficient expression of 13C- and 15N-labeled P450s and analysis of their structures by magic-angle spinning solid-state NMR (SSNMR) spectroscopy. In the presence of co-expressed GroEL and GroES chaperones, full-length (53 kDa) Arabidopsis 13C,15N-labeled His4CYP98A3 is expressed at yields of 2-4 mg per liter of minimal media without the necessity of generating side chain modifications or N-terminal deletions. Precipitated His4CYP98A3 generates high quality SSNMR spectra consistent with a homogeneous, folded protein. These data highlight the potential of these methodologies to contribute to the structural analysis of membrane-bound proteins.
Collapse
Affiliation(s)
- Sanjeewa G Rupasinghe
- Department of Cell and Developmental Biology, University of Illinois, Urbana, IL 61801, USA
| | | | | | | | | | | |
Collapse
|
85
|
Baldus M. ICMRBS founder's medal 2006: biological solid-state NMR, methods and applications. JOURNAL OF BIOMOLECULAR NMR 2007; 39:73-86. [PMID: 17657566 DOI: 10.1007/s10858-007-9177-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Accepted: 06/26/2007] [Indexed: 05/16/2023]
Abstract
Solid-state NMR (ssNMR) provides increasing possibilities to study structure and dynamics of biomolecular systems. Our group has been interested in developing ssNMR-based approaches that are applicable to biomolecules of increasing molecular size and complexity without the need of specific isotope-labelling. Methodological aspects ranging from spectral assignments to the indirect detection of proton-proton contacts in multi-dimensional ssNMR are discussed and applied to (membrane) protein complexes.
Collapse
Affiliation(s)
- Marc Baldus
- Research Group Solid-state NMR, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany.
| |
Collapse
|
86
|
Chen L, Kaiser JM, Polenova T, Yang J, Rienstra CM, Mueller LJ. Backbone Assignments in Solid-State Proteins Using J-Based 3D Heteronuclear Correlation Spectroscopy. J Am Chem Soc 2007; 129:10650-1. [PMID: 17691789 DOI: 10.1021/ja073498e] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lingling Chen
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | | | | | | | | | | |
Collapse
|
87
|
Hong M. Structure, topology, and dynamics of membrane peptides and proteins from solid-state NMR spectroscopy. J Phys Chem B 2007; 111:10340-51. [PMID: 17685648 DOI: 10.1021/jp073652j] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The high-resolution structure of membrane proteins is notoriously difficult to determine due to the hydrophobic nature of the protein-membrane complexes. Solid-state NMR spectroscopy is a unique and powerful atomic-resolution probe of the structure and dynamics of these important biological molecules. A number of new solid-state NMR methods for determining the depth of insertion, orientation, oligomeric structure, and long-range (10-15 A) distances of membrane proteins are summarized. Membrane protein depths can now be determined using several complementary techniques with varying site-specificity, distance precision, and mobility requirement on the protein. Membrane protein orientation can now be determined with or without macroscopic alignment, the latter providing a novel alternative for orientation determination of intrinsically curvature-inducing proteins. The novel analyses of beta-sheet membrane protein orientation are described. The quaternary structure of membrane peptide assemblies can now be elucidated using a 19F spin diffusion technique that simultaneously yields the oligomeric number and intermolecular distances up to 15 A. Finally, long-range distances up to approximately 10 A can now be measured using 1H spins with an accuracy of better than 1 A. These methods are demonstrated on several beta-sheet membrane peptides with antimicrobial activities and on two alpha-helical ion-channel proteins. Finally, we show that the nearly ubiquitous dynamics of membrane proteins can be readily examined using 2D correlation experiments. An intimate appreciation of molecular motion in these systems not only leads to important insights into the specific function of these membrane proteins but also may be exploited for other purposes such as orientation determination.
Collapse
Affiliation(s)
- Mei Hong
- Department of Chemistry, Iowa State University, Ames, Iowa, USA.
| |
Collapse
|
88
|
Minor DL. The neurobiologist's guide to structural biology: a primer on why macromolecular structure matters and how to evaluate structural data. Neuron 2007; 54:511-33. [PMID: 17521566 PMCID: PMC3011226 DOI: 10.1016/j.neuron.2007.04.026] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Structural biology now plays a prominent role in addressing questions central to understanding how excitable cells function. Although interest in the insights gained from the definition and dissection of macromolecular anatomy is high, many neurobiologists remain unfamiliar with the methods employed. This primer aims to help neurobiologists understand approaches for probing macromolecular structure and where the limits and challenges remain. Using examples of macromolecules with neurobiological importance, the review covers X-ray crystallography, electron microscopy (EM), small-angle X-ray scattering (SAXS), and nuclear magnetic resonance (NMR) and biophysical methods with which these approaches are often paired: isothermal titration calorimetry (ITC), equilibrium analytical ultracentifugation, and molecular dynamics (MD).
Collapse
Affiliation(s)
- Daniel L Minor
- Cardiovascular Research Institute, Department of Biochemistry and Biophysics, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158-2330, USA.
| |
Collapse
|
89
|
Nadaud PS, Helmus JJ, Jaroniec CP. 13C and 15N chemical shift assignments and secondary structure of the B3 immunoglobulin-binding domain of streptococcal protein G by magic-angle spinning solid-state NMR spectroscopy. BIOMOLECULAR NMR ASSIGNMENTS 2007; 1:117-120. [PMID: 19636843 DOI: 10.1007/s12104-007-9041-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2007] [Accepted: 06/29/2007] [Indexed: 05/28/2023]
Abstract
Complete 13C and 15N assignments of the B3 IgG-binding domain of protein G (GB3) in the microcrystalline solid phase, obtained using 2D and 3D MAS NMR, are presented. The chemical shifts are used to predict the protein backbone conformation and compared with solution-state shifts.
Collapse
Affiliation(s)
- Philippe S Nadaud
- Department of Chemistry, The Ohio State University, 1035 Evans Laboratory, 100 West 18th Avenue, Columbus, OH 43210, USA
| | | | | |
Collapse
|
90
|
Li Y, Williams TD, Schowen RL, Topp EM. Characterizing protein structure in amorphous solids using hydrogen/deuterium exchange with mass spectrometry. Anal Biochem 2007; 366:18-28. [PMID: 17490599 DOI: 10.1016/j.ab.2007.03.041] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2006] [Revised: 03/28/2007] [Accepted: 03/29/2007] [Indexed: 10/23/2022]
Abstract
Elucidating protein structure in amorphous solids is central to the rational design of stable lyophilized protein drugs. Hydrogen/deuterium (H/D) exchange with electrospray ionization mass spectrometry was applied to lyophilized powders containing calmodulin (17 kDa) and exposed to D(2)O vapor at controlled relative humidity (RH) and temperature. H/D exchange was influenced by RH and by the inclusion of calcium chloride and/or trehalose in the solid. The effects were not exhibited uniformly along the protein backbone but occurred in a site-specific manner, with calcium primarily influencing the calcium-binding loops and trehalose primarily influencing the alpha-helices. The results demonstrate that the method can provide quantitative and site-specific structural information on proteins in amorphous solids and on changes in structure induced by protein cofactors and formulation excipients. Such information is not readily available with other techniques used to characterize proteins in the solid state, such as Fourier transform infrared, Raman, and near-infrared spectroscopy.
Collapse
Affiliation(s)
- Yunsong Li
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | | | | | | |
Collapse
|
91
|
Baldus M. Magnetic resonance in the solid state: applications to protein folding, amyloid fibrils and membrane proteins. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36 Suppl 1:S37-48. [PMID: 17541576 DOI: 10.1007/s00249-007-0174-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2007] [Accepted: 05/08/2007] [Indexed: 11/25/2022]
Abstract
Solid-state nuclear magnetic resonance (ssNMR) represents a spectroscopic method to study non-crystalline molecules at atomic resolution. Advancements in spectroscopy and biochemistry provide increasing possibilities to study structure and dynamics of complex biomolecular systems by ssNMR. Here, methodological aspects and applications in the context of protein folding and aggregation are discussed. In addition, studies involving membrane proteins are considered.
Collapse
Affiliation(s)
- Marc Baldus
- Solid-state NMR, Max-Planck-Institut für Biophysikalische Chemie, 37077 Göttingen, Germany.
| |
Collapse
|
92
|
Nadaud PS, Helmus JJ, Höfer N, Jaroniec CP. Long-range structural restraints in spin-labeled proteins probed by solid-state nuclear magnetic resonance spectroscopy. J Am Chem Soc 2007; 129:7502-3. [PMID: 17530852 DOI: 10.1021/ja072349t] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Philippe S Nadaud
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | | | | |
Collapse
|
93
|
Sein J, Giraud N, Blackledge M, Emsley L. The role of (15)N CSA and CSA/dipole cross-correlation in (15)N relaxation in solid proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 186:26-33. [PMID: 17280844 DOI: 10.1016/j.jmr.2007.01.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Revised: 01/15/2007] [Accepted: 01/16/2007] [Indexed: 05/13/2023]
Abstract
The influence of the (15)N CSA on (15)N longitudinal relaxation is investigated for an amide group in solid proteins in powder form under MAS. This contribution is determined to be typically 20-33% of the overall longitudinal relaxation rate, at 11.74 and 16.45 T, respectively. The improved treatment is used to analyze the internal dynamics in the protein Crh, in the frame of a motional model of diffusion in a cone, using the explicit average sum approach. Significant variations with respect to the determined dynamics parameters are observed when properly accounting for the contribution of (15)N CSA fluctuations. In general, the fit of experimental data including CSA led to the determination of diffusion times (tau(w)) which are longer than when considering only an (15)N-(1)H dipolar relaxation mechanism. CSA-Dipole cross-correlation is shown to play little or no role in protonated solids, in direct contrast to the liquid state case.
Collapse
Affiliation(s)
- Julien Sein
- Laboratoire de Chimie (UMR 5182 CNRS/ENS Lyon), Ecole Normale Supérieure de Lyon, 69364 Lyon, France
| | | | | | | |
Collapse
|
94
|
Etzkorn M, Böckmann A, Penin F, Riedel D, Baldus M. Characterization of folding intermediates of a domain-swapped protein by solid-state NMR spectroscopy. J Am Chem Soc 2007; 129:169-75. [PMID: 17199296 DOI: 10.1021/ja066469x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have employed two-dimensional solid-state NMR to study structure and dynamics of insoluble folding states of the domain-swapped protein Crh. Starting from the protein precipitated at its pI, conformational changes due to a modest temperature increase were investigated at the level of individual residues and in real-time. As compared to the crystalline state, Crh pI-precipitates exhibited a higher degree of molecular mobility for several regions of the protein. A rigidly intact center was observed including a subset of residues of the hydrophobic core. Raising the temperature by 13 K to 282 K created a partially unfolded intermediate state that was converted into beta-sheet-rich aggregates that are mostly of spherical character according to electron microscopy. Residue-by-residue analysis indicated that two out of three alpha-helices in aggregated Crh underwent major structural rearrangements while the third helix was preserved. Residues in the hinge region exhibited major chemical-shift changes, indicating that the domain swap was not conserved in the aggregated form. Our study provides direct evidence that protein aggregates of a domain-swapped protein retain a significant fraction of native secondary structure and demonstrates that solid-state NMR can be used to directly monitor slow molecular folding events.
Collapse
Affiliation(s)
- Manuel Etzkorn
- Department of NMR-Based Structural Biology and Electron Microscopy, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | | | | | | |
Collapse
|
95
|
Riedel K, Herbst C, Leppert J, Ohlenschläger O, Görlach M, Ramachandran R. Broadband homonuclear chemical shift correlation at high MAS frequencies: a study of tanh/tan adiabatic RF pulse schemes without 1H decoupling during mixing. JOURNAL OF BIOMOLECULAR NMR 2007; 37:277-86. [PMID: 17288003 DOI: 10.1007/s10858-006-9137-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2006] [Accepted: 12/11/2006] [Indexed: 05/13/2023]
Abstract
At high magic angle spinning (MAS) frequencies the potential of tanh/tan adiabatic RF pulse schemes for 13C chemical shift correlation without 1H decoupling during mixing has been evaluated. It is shown via numerical simulations that a continuous train of adiabatic 13C inversion pulses applied at high RF field strengths leads to efficient broadband heteronuclear decoupling. It is demonstrated that this can be exploited effectively for generating through-bond and through-space, including double-quantum, correlation spectra of biological systems at high magnetic fields and spinning speeds with no 1H decoupling applied during the mixing period. Experiments carried out on a polycrystalline sample of histidine clearly suggest that an improved signal to noise ratio can be realised by eliminating 1H decoupling during mixing.
Collapse
Affiliation(s)
- Kerstin Riedel
- Research Group Molecular Biophysics/NMR Spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, 07745 Jena, Germany
| | | | | | | | | | | |
Collapse
|
96
|
Goldbourt A, Gross BJ, Day LA, McDermott AE. Filamentous Phage Studied by Magic-Angle Spinning NMR: Resonance Assignment and Secondary Structure of the Coat Protein in Pf1. J Am Chem Soc 2007; 129:2338-44. [PMID: 17279748 DOI: 10.1021/ja066928u] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Assignments are presented for resonances in the magic-angle spinning solid-state NMR spectra of the major coat protein subunit of the filamentous bacteriophage Pf1. NMR spectra were collected on uniformly 13C and 15N isotopically enriched, polyethylene glycol precipitated samples of fully infectious and hydrated phage. Site-specific assignments were achieved for 231 of the 251 labeled atoms (92%) of the 46-residue-long coat protein, including 136 of the 138 backbone atoms, by means of two- and three-dimensional 15N and 13C correlation experiments. A single chemical shift was observed for the vast majority of atoms, suggesting a single conformation for the 7300 subunits in the 36 MDa virion in its high-temperature form. On the other hand, multiple chemical shifts were observed for the Calpha, Cbeta, and Cgamma atoms of T5 in the helix terminus and the Calpha and Cbeta atoms of M42 in the DNA interaction domain. The chemical shifts of the backbone atoms indicate that the coat protein conformation involves a 40-residue continuous alpha-helix extending from residue 6 to the C-terminus.
Collapse
Affiliation(s)
- Amir Goldbourt
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | | | | | | |
Collapse
|
97
|
Pintacuda G, Giraud N, Pierattelli R, Böckmann A, Bertini I, Emsley L. Solid-State NMR Spectroscopy of a Paramagnetic Protein: Assignment and Study of Human Dimeric Oxidized CuII–ZnII Superoxide Dismutase (SOD). Angew Chem Int Ed Engl 2007; 46:1079-82. [PMID: 17191298 DOI: 10.1002/anie.200603093] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Guido Pintacuda
- Laboratoire de Chimie, UMR 5182 CNRS-ENS Lyon, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon, France
| | | | | | | | | | | |
Collapse
|
98
|
Pintacuda G, Giraud N, Pierattelli R, Böckmann A, Bertini I, Emsley L. Solid-State NMR Spectroscopy of a Paramagnetic Protein: Assignment and Study of Human Dimeric Oxidized CuII–ZnII Superoxide Dismutase (SOD). Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200603093] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
99
|
Oligomeric structure, dynamics, and orientation of membrane proteins from solid-state NMR. Structure 2007; 14:1731-40. [PMID: 17161364 DOI: 10.1016/j.str.2006.10.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2006] [Revised: 10/01/2006] [Accepted: 10/03/2006] [Indexed: 11/27/2022]
Abstract
Solid-state NMR is a versatile and powerful tool for determining the dynamic structure of membrane proteins at atomic resolution. I review the recent progress in determining the orientation, the internal and global protein dynamics, the oligomeric structure, and the ligand-bound structure of membrane proteins with both alpha-helical and beta sheet conformations. Examples are given that illustrate the insights into protein function that can be gained from the NMR structural information.
Collapse
|
100
|
Kervern G, Pintacuda G, Emsley L. Fast adiabatic pulses for solid-state NMR of paramagnetic systems. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2006.12.056] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|