151
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Sperling LJ, Tang M, Berthold DA, Nesbitt AE, Gennis RB, Rienstra CM. Solid-state NMR study of a 41 kDa membrane protein complex DsbA/DsbB. J Phys Chem B 2013; 117:6052-60. [PMID: 23527473 DOI: 10.1021/jp400795d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The disulfide bond generation system in E. coli is led by a periplasmic protein, DsbA, and an integral membrane protein, DsbB. Here we present a solid-state NMR (SSNMR) study of a 41 kDa membrane protein complex DsbA/DsbB precipitated in the presence of native lipids to investigate conformational changes and dynamics that occur upon transient complex formation within the electron transfer pathway. Chemical shift changes in the periplasmic enzyme DsbA in three states (wild type, C33S mutant, and in complex with DsbB) reveal structural and/or dynamic information. We report a 4.9 ppm (15)N chemical shift change observed for Pro31 in the active site between the wild type and C33S mutant of DsbA. Additionally, the Pro31 residue remains elusive in the DsbA/DsbB complex, indicating that the dynamics change drastically in the active site between the three states of DsbA. Using three-dimensional SSNMR spectra, partial (13)C and (15)N de novo chemical shift assignments throughout DsbA in the DsbA/DsbB complex were compared with the shifts from DsbA alone to map site-specific chemical shift perturbations. These results demonstrate that there are further structural and dynamic changes of DsbA in the native membrane observed by SSNMR, beyond the differences between the crystal structures of DsbA and the DsbA/DsbB complex.
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Affiliation(s)
- Lindsay J Sperling
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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152
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Chevelkov V, Giller K, Becker S, Lange A. Efficient CO-CA transfer in highly deuterated proteins by band-selective homonuclear cross-polarization. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 230:205-11. [PMID: 23558259 DOI: 10.1016/j.jmr.2013.02.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 02/08/2013] [Accepted: 02/17/2013] [Indexed: 05/10/2023]
Abstract
Robust and efficient band-selective magnetization transfer between CO and CA spins can be achieved in highly deuterated solid proteins by dipolar-based homonuclear cross polarization. The approach is designed for moderate magic-angle spinning rates and high external magnetic fields where the isotropic chemical shift difference of CO and CA considerably exceeds the spinning rate. The most efficient recoupling is achieved when the sum of effective radio-frequency fields on CO and CA resonances equals two times the spinning rate. This method can be directly implemented in proton-detected versions of inter-residual correlation experiments as needed for resonance assignment in protein solid-state NMR spectroscopy.
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153
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Barbet-Massin E, Pell AJ, Knight MJ, Webber AL, Felli IC, Pierattelli R, Emsley L, Lesage A, Pintacuda G. 13C-Detected Through-Bond Correlation Experiments for Protein Resonance Assignment by Ultra-Fast MAS Solid-State NMR. Chemphyschem 2013; 14:3131-7. [DOI: 10.1002/cphc.201201097] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/02/2013] [Indexed: 11/11/2022]
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154
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Cheng CY, Han S. Dynamic Nuclear Polarization Methods in Solids and Solutions to Explore Membrane Proteins and Membrane Systems. Annu Rev Phys Chem 2013; 64:507-32. [DOI: 10.1146/annurev-physchem-040412-110028] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Membrane proteins regulate vital cellular processes, including signaling, ion transport, and vesicular trafficking. Obtaining experimental access to their structures, conformational fluctuations, orientations, locations, and hydration in membrane environments, as well as the lipid membrane properties, is critical to understanding their functions. Dynamic nuclear polarization (DNP) of frozen solids can dramatically boost the sensitivity of current solid-state nuclear magnetic resonance tools to enhance access to membrane protein structures in native membrane environments. Overhauser DNP in the solution state can map out the local and site-specific hydration dynamics landscape of membrane proteins and lipid membranes, critically complementing the structural and dynamics information obtained by electron paramagnetic resonance spectroscopy. Here, we provide an overview of how DNP methods in solids and solutions can significantly increase our understanding of membrane protein structures, dynamics, functions, and hydration in complex biological membrane environments.
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Affiliation(s)
- Chi-Yuan Cheng
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
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155
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Banigan JR, Gayen A, Traaseth NJ. Combination of ¹⁵N reverse labeling and afterglow spectroscopy for assigning membrane protein spectra by magic-angle-spinning solid-state NMR: application to the multidrug resistance protein EmrE. JOURNAL OF BIOMOLECULAR NMR 2013; 55:391-9. [PMID: 23539118 PMCID: PMC3747971 DOI: 10.1007/s10858-013-9724-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 03/15/2013] [Indexed: 05/20/2023]
Abstract
Magic-angle-spinning (MAS) solid-state NMR spectroscopy has emerged as a viable method to characterize membrane protein structure and dynamics. Nevertheless, the spectral resolution for uniformly labeled samples is often compromised by redundancy of the primary sequence and the presence of helical secondary structure that results in substantial resonance overlap. The ability to simplify the spectrum in order to obtain unambiguous site-specific assignments is a major bottleneck for structure determination. To address this problem, we used a combination of (15)N reverse labeling, afterglow spectroscopic techniques, and frequency-selective dephasing experiments that dramatically improved the ability to resolve peaks in crowded spectra. This was demonstrated using the polytopic membrane protein EmrE, an efflux pump involved in multidrug resistance. Residues preceding the (15)N reverse labeled amino acid were imaged using a 3D NCOCX afterglow experiment and those following were recorded using a frequency-selective dephasing experiment. Our approach reduced the spectral congestion and provided a sensitive way to obtain chemical shift assignments for a membrane protein where no high-resolution structure is available. This MAS methodology is widely applicable to the study of other polytopic membrane proteins in functional lipid bilayer environments.
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Affiliation(s)
| | | | - Nathaniel J. Traaseth
- Author for correspondence: Nathaniel J. Traaseth 100 Washington Square East New York, NY 10003 Phone: (212) 992-9784
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156
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Schneider R, Odronitz F, Hammesfahr B, Hellkamp M, Kollmar M. Peakr: simulating solid-state NMR spectra of proteins. ACTA ACUST UNITED AC 2013; 29:1134-40. [PMID: 23493322 DOI: 10.1093/bioinformatics/btt125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
MOTIVATION When analyzing solid-state nuclear magnetic resonance (NMR) spectra of proteins, assignment of resonances to nuclei and derivation of restraints for 3D structure calculations are challenging and time-consuming processes. Simulated spectra that have been calculated based on, for example, chemical shift predictions and structural models can be of considerable help. Existing solutions are typically limited in the type of experiment they can consider and difficult to adapt to different settings. RESULTS Here, we present Peakr, a software to simulate solid-state NMR spectra of proteins. It can generate simulated spectra based on numerous common types of internuclear correlations relevant for assignment and structure elucidation, can compare simulated and experimental spectra and produces lists and visualizations useful for analyzing measured spectra. Compared with other solutions, it is fast, versatile and user friendly. AVAILABILITY AND IMPLEMENTATION Peakr is maintained under the GPL license and can be accessed at http://www.peakr.org. The source code can be obtained on request from the authors.
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Affiliation(s)
- Robert Schneider
- Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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157
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Su Y, Li S, Hong M. Cationic membrane peptides: atomic-level insight of structure-activity relationships from solid-state NMR. Amino Acids 2013; 44:821-33. [PMID: 23108593 PMCID: PMC3570695 DOI: 10.1007/s00726-012-1421-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 10/11/2012] [Indexed: 12/24/2022]
Abstract
Many membrane-active peptides, such as cationic cell-penetrating peptides (CPPs) and antimicrobial peptides (AMPs), conduct their biological functions by interacting with the cell membrane. The interactions of charged residues with lipids and water facilitate membrane insertion, translocation or disruption of these highly hydrophobic species. In this review, we will summarize high-resolution structural and dynamic findings towards the understanding of the structure-activity relationship of lipid membrane-bound CPPs and AMPs, as examples of the current development of solid-state NMR (SSNMR) techniques for studying membrane peptides. We will present the most recent atomic-resolution structure of the guanidinium-phosphate complex, as constrained from experimentally measured site-specific distances. These SSNMR results will be valuable specifically for understanding the intracellular translocation pathway of CPPs and antimicrobial mechanism of AMPs, and more generally broaden our insight into how cationic macromolecules interact with and cross the lipid membrane.
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Affiliation(s)
- Yongchao Su
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA.
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158
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Emami S, Fan Y, Munro R, Ladizhansky V, Brown LS. Yeast-expressed human membrane protein aquaporin-1 yields excellent resolution of solid-state MAS NMR spectra. JOURNAL OF BIOMOLECULAR NMR 2013; 55:147-155. [PMID: 23344971 DOI: 10.1007/s10858-013-9710-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 01/15/2013] [Indexed: 06/01/2023]
Abstract
One of the biggest challenges in solid-state NMR studies of membrane proteins is to obtain a homogeneous natively folded sample giving high spectral resolution sufficient for structural studies. Eukaryotic membrane proteins are especially difficult and expensive targets in this respect. Methylotrophic yeast Pichia pastoris is a reliable producer of eukaryotic membrane proteins for crystallography and a promising economical source of isotopically labeled proteins for NMR. We show that eukaryotic membrane protein human aquaporin 1 can be doubly ((13)C/(15)N) isotopically labeled in this system and functionally reconstituted into phospholipids, giving excellent resolution of solid-state magic angle spinning NMR spectra.
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Affiliation(s)
- Sanaz Emami
- Departments of Physics, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
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159
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Pandey MK, Ramamoorthy A. Quantum chemical calculations of amide-15N chemical shift anisotropy tensors for a membrane-bound cytochrome-b5. J Phys Chem B 2013; 117:859-67. [PMID: 23268659 PMCID: PMC3564578 DOI: 10.1021/jp311116p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
There is considerable interest in determining amide-(15)N chemical shift anisotropy (CSA) tensors from biomolecules and understanding their variation for structural and dynamics studies using solution and solid-state NMR spectroscopy and also by quantum chemical calculations. Due to the difficulties associated with the measurement of CSA tensors from membrane proteins, NMR-based structural studies heavily relied on the CSA tensors determined from model systems, typically single crystals of model peptides. In the present study, the principal components of backbone amide-(15)N CSA tensors have been determined using density functional theory for a 16.7 kDa membrane-bound paramagnetic heme containing protein, cytochrome-b(5) (cytb(5)). All the calculations were performed by taking residues within 5 Å distance from the backbone amide-(15)N nucleus of interest. The calculated amide-(15)N CSA spans agree less well with our solution NMR data determined for an effective internuclear distance r(N-H) = 1.023 Å and a constant angle β = 18° that the least shielded component (δ(11)) makes with the N-H bond. The variation of amide-(15)N CSA span obtained using quantum chemical calculations is found to be smaller than that obtained from solution NMR measurements, whereas the trends of the variations are found to be in close agreement. We believe that the results reported in this study will be useful in studying the structure and dynamics of membrane proteins and heme-containing proteins, and also membrane-bound protein-protein complexes such as cytochromes-b5-P450.
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Affiliation(s)
- Manoj Kumar Pandey
- Biophysics and Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055
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160
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Hussain S, Franck JM, Han S. Transmembrane Protein Activation Refined by Site-Specific Hydration Dynamics. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201206147] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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161
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Mithu VS, Bakthavatsalam S, Madhu PK. (13)C-(13)c homonuclear recoupling in solid-state nuclear magnetic resonance at a moderately high magic-angle-spinning frequency. PLoS One 2013; 8:e50504. [PMID: 23326308 PMCID: PMC3542364 DOI: 10.1371/journal.pone.0050504] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 10/22/2012] [Indexed: 11/18/2022] Open
Abstract
Two-dimensional (13)C-(13)C correlation experiments are widely employed in structure determination of protein assemblies using solid-state nuclear magnetic resonance. Here, we investigate the process of (13)C-(13)C magnetisation transfer at a moderate magic-angle-spinning frequency of 30 kHz using some of the prominent second-order dipolar recoupling schemes. The effect of isotropic chemical-shift difference and spatial distance between two carbons and amplitude of radio frequency on (1)H channel on the magnetisation transfer efficiency of these schemes is discussed in detail.
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Affiliation(s)
- Venus Singh Mithu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India
| | - Subha Bakthavatsalam
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India
| | - Perunthiruthy K. Madhu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, India
- * E-mail:
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162
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Hussain S, Franck JM, Han S. Transmembrane protein activation refined by site-specific hydration dynamics. Angew Chem Int Ed Engl 2013; 52:1953-8. [PMID: 23307344 DOI: 10.1002/anie.201206147] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/18/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Sunyia Hussain
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93016, USA
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163
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Yao Y, Ding Y, Tian Y, Opella SJ, Marassi FM. Membrane protein structure determination: back to the membrane. Methods Mol Biol 2013; 1063:145-58. [PMID: 23975776 DOI: 10.1007/978-1-62703-583-5_8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
NMR spectroscopy enables the structures of membrane proteins to be determined in the native-like environment of the phospholipid bilayer membrane. This chapter outlines the methods for membrane protein structural studies using solid-state NMR spectroscopy with samples of membrane proteins incorporated in proteoliposomes or planar lipid bilayers. The methods for protein expression and purification, sample preparation, and NMR experiments are described and illustrated with examples from OmpX and Ail, two bacterial outer membrane proteins that function in bacterial virulence.
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Affiliation(s)
- Yong Yao
- Sanford Burnham Medical Research Institute, La Jolla, CA, USA
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164
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Xie L, Ghosh U, Schmick SD, Weliky DP. Residue-specific membrane location of peptides and proteins using specifically and extensively deuterated lipids and ¹³C-²H rotational-echo double-resonance solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2013; 55:11-7. [PMID: 23225071 PMCID: PMC3557618 DOI: 10.1007/s10858-012-9692-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 11/28/2012] [Indexed: 05/12/2023]
Abstract
Residue-specific location of peptides in the hydrophobic core of membranes was examined using (13)C-(2)H REDOR and samples in which the lipids were selectively deuterated. The transmembrane topology of the KALP peptide was validated with this approach with substantial dephasing observed for deuteration in the bilayer center and reduced or no dephasing for deuteration closer to the headgroups. Insertion of β sheet HIV and helical and β sheet influenza virus fusion peptides into the hydrophobic core of the membrane was validated in samples with extensively deuterated lipids.
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Affiliation(s)
- Li Xie
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| | - Ujjayini Ghosh
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| | - Scott D. Schmick
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| | - David P. Weliky
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
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165
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Goncalves J, Eilers M, South K, Opefi CA, Laissue P, Reeves PJ, Smith SO. Magic angle spinning nuclear magnetic resonance spectroscopy of G protein-coupled receptors. Methods Enzymol 2013; 522:365-89. [PMID: 23374193 DOI: 10.1016/b978-0-12-407865-9.00017-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
G protein-coupled receptors (GPCRs) represent the largest family of membrane receptors and mediate a diversity of cellular processes. These receptors have a common seven-transmembrane helix structure, yet have evolved to respond to literally thousands of different ligands. In this chapter, we describe the use of magic angle spinning solid-state NMR spectroscopy for characterizing the structure and dynamics of GPCRs. Solid-state NMR spectroscopy is well suited for structural measurements in both detergent micelles and membrane bilayer environments. We first outline the methods for large-scale production of stable, functional receptors containing (13)C- and (15)N-labeled amino acids. The expression methods make use of eukaryotic HEK293S cell lines that produce correctly folded, fully functional receptors. We subsequently describe the basic methods used for magic angle spinning solid-state NMR measurements of chemical shifts and dipolar couplings, which reveal detailed information on GPCR structure and dynamics.
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Affiliation(s)
- Joseph Goncalves
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
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166
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Abstract
Solid-state NMR spectroscopy proved to be a versatile tool for characterization of structure and dynamics of complex biochemical systems. In particular, magic angle spinning (MAS) solid-state NMR came to maturity for application towards structural elucidation of biological macromolecules. Current challenges in applying solid-state NMR as well as progress achieved recently will be discussed in the following chapter focusing on conceptual aspects important for structural elucidation of proteins.
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Affiliation(s)
- Henrik Müller
- Institute of Physical Biology, Heinrich-Heine-University of Düsseldorf, 40225, Düsseldorf, Germany
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167
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Sun S, Yan S, Guo C, Li M, Hoch JC, Williams JC, Polenova T. A time-saving strategy for MAS NMR spectroscopy by combining nonuniform sampling and paramagnetic relaxation assisted condensed data collection. J Phys Chem B 2012; 116:13585-96. [PMID: 23094591 DOI: 10.1021/jp3005794] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We present a time-saving strategy for acquiring 3D magic angle spinning NMR spectra for chemical shift assignments in proteins and protein assemblies in the solid state. By simultaneous application of nonuniform sampling (NUS) and paramagnetic-relaxation-assisted condensed data collection (PACC), we can attain 16-fold time reduction in the 3D experiments without sacrificing the signal-to-noise ratio or the resolution. We demonstrate that with appropriate concentration of paramagnetic dopant introduced into the sample the overwhelming majority of chemical shifts are not perturbed, with the exception of a limited number of shifts corresponding to residues located at the surface of the protein, which exhibit small perturbations. This approach enables multidimensional MAS spectroscopy in samples of intrinsically low sensitivity and/or high spectral congestion where traditional experiments fail, and is especially beneficial for structural and dynamics studies of large proteins and protein assemblies.
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Affiliation(s)
- Shangjin Sun
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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168
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Membrane-protein structure determination by solid-state NMR spectroscopy of microcrystals. Nat Methods 2012; 9:1212-7. [DOI: 10.1038/nmeth.2248] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 10/10/2012] [Indexed: 11/08/2022]
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169
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Structure of the chemokine receptor CXCR1 in phospholipid bilayers. Nature 2012; 491:779-83. [PMID: 23086146 PMCID: PMC3700570 DOI: 10.1038/nature11580] [Citation(s) in RCA: 317] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 09/12/2012] [Indexed: 01/04/2023]
Abstract
CXCR1 is one of two high-affinity receptors for the CXC chemokine interleukin-8 (IL-8), a major mediator of immune and inflammatory responses implicated in many disorders, including tumor growth1-3. IL-8, released in response to inflammatory stimuli, binds to the extracellular side of CXCR1. The ligand-activated intracellular signaling pathways result in neutrophil migration to the site of inflammation2. CXCR1 is a class-A, rhodopsin-like G-protein-coupled receptor (GPCR), the largest class of integral membrane proteins responsible for cellular signal transduction and targeted as drug receptors4-7. Despite its importance, its molecular mechanism is poorly understood due to the limited structural information available. Recently, structure determination of GPCRs has advanced by tailoring the receptors with stabilizing mutations, insertion of the protein T4 lysozyme and truncations of their amino acid sequences8, as well as addition of stabilizing antibodies and small molecules9 that facilitate crystallization in cubic phase monoolein mixtures10. The intracellular loops of GPCRs are critical for G-protein interactions11 and activation of CXCR1 involves both N-terminal residues and extracellular loops2,12,13. Our previous NMR studies indicate that IL-8 binding to the N-terminal residues is mediated by the membrane, underscoring the importance of the phospholipid bilayer for physiological activity14. Here we report the three-dimensional structure of human CXCR1 determined by NMR spectroscopy. The receptor is in liquid crystalline phospholipid bilayers, without modification of its amino acid sequence and under physiological conditions. Features important for intracellular G-protein activation and signal transduction are revealed.
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170
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Hong M, DeGrado WF. Structural basis for proton conduction and inhibition by the influenza M2 protein. Protein Sci 2012; 21:1620-33. [PMID: 23001990 DOI: 10.1002/pro.2158] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 09/10/2012] [Accepted: 09/11/2012] [Indexed: 12/20/2022]
Abstract
The influenza M2 protein forms an acid-activated and drug-sensitive proton channel in the virus envelope that is important for the virus lifecycle. The functional properties and high-resolution structures of this proton channel have been extensively studied to understand the mechanisms of proton conduction and drug inhibition. We review biochemical and electrophysiological studies of M2 and discuss how high-resolution structures have transformed our understanding of this proton channel. Comparison of structures obtained in different membrane-mimetic solvents and under different pH using X-ray crystallography, solution NMR, and solid-state NMR spectroscopy revealed how the M2 structure depends on the environment and showed that the pharmacologically relevant drug-binding site lies in the transmembrane (TM) pore. Competing models of proton conduction have been evaluated using biochemical experiments, high-resolution structural methods, and computational modeling. These results are converging to a model in which a histidine residue in the TM domain mediates proton relay with water, aided by microsecond conformational dynamics of the imidazole ring. These mechanistic insights are guiding the design of new inhibitors that target drug-resistant M2 variants and may be relevant for other proton channels.
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Affiliation(s)
- Mei Hong
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA.
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171
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Wang S, Munro RA, Kim SY, Jung KH, Brown LS, Ladizhansky V. Paramagnetic Relaxation Enhancement Reveals Oligomerization Interface of a Membrane Protein. J Am Chem Soc 2012; 134:16995-8. [DOI: 10.1021/ja308310z] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | | | - So Young Kim
- Department of Life Science and
Institute of Biological Interfaces, Sogang University, Seoul, Korea
| | - Kwang-Hwan Jung
- Department of Life Science and
Institute of Biological Interfaces, Sogang University, Seoul, Korea
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172
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Huang W, Bardaro MF, Varani G, Drobny GP. Preparation of RNA samples with narrow line widths for solid state NMR investigations. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 223:51-54. [PMID: 22967888 DOI: 10.1016/j.jmr.2012.07.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Revised: 07/19/2012] [Accepted: 07/22/2012] [Indexed: 06/01/2023]
Abstract
Solid state NMR can provide detailed structural and dynamic information on biological systems that cannot be studied under solution conditions, and can investigate motions which occur with rates that cannot be fully studied by solution NMR. This approach has successfully been used to study proteins, but the application of multidimensional solid state NMR to RNA has been limited because reported line widths have been too broad to execute most multidimensional experiments successfully. A reliable method to generate spectra with narrow line widths is necessary to apply the full range of solid state NMR spectroscopic approaches to RNA. Using the HIV-1 transactivation response (TAR) RNA as a model, we present an approach based on precipitation with polyethylene glycol that improves the line width of (13)C signals in TAR from >6 ppm to about 1 ppm, making solid state 2D NMR studies of selectively enriched RNAs feasible at ambient temperature.
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Affiliation(s)
- Wei Huang
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195, USA
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173
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Marchetti A, Jehle S, Felletti M, Knight MJ, Wang Y, Xu ZQ, Park AY, Otting G, Lesage A, Emsley L, Dixon NE, Pintacuda G. Backbone assignment of fully protonated solid proteins by 1H detection and ultrafast magic-angle-spinning NMR spectroscopy. Angew Chem Int Ed Engl 2012; 51:10756-9. [PMID: 23023570 DOI: 10.1002/anie.201203124] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 06/20/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Alessandro Marchetti
- Centre de RMN à Très Hauts Champs, UMR 5280 CNRS/Ecole Normale Supérieure de Lyon, University of Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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174
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Marchetti A, Jehle S, Felletti M, Knight MJ, Wang Y, Xu ZQ, Park AY, Otting G, Lesage A, Emsley L, Dixon NE, Pintacuda G. Backbone Assignment of Fully Protonated Solid Proteins by1H Detection and Ultrafast Magic-Angle-Spinning NMR Spectroscopy. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203124] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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175
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Hall Z, Politis A, Robinson C. Structural Modeling of Heteromeric Protein Complexes from Disassembly Pathways and Ion Mobility-Mass Spectrometry. Structure 2012; 20:1596-609. [DOI: 10.1016/j.str.2012.07.001] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 06/29/2012] [Accepted: 07/02/2012] [Indexed: 12/30/2022]
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176
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Iordanov I, Renault M, Réat V, Bosshart PD, Engel A, Saurel O, Milon A. Dynamics of Klebsiella pneumoniae OmpA transmembrane domain: The four extracellular loops display restricted motion behavior in micelles and in lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2344-53. [DOI: 10.1016/j.bbamem.2012.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 05/02/2012] [Accepted: 05/03/2012] [Indexed: 10/28/2022]
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177
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Knight MJ, Felli IC, Pierattelli R, Bertini I, Emsley L, Herrmann T, Pintacuda G. Rapid Measurement of Pseudocontact Shifts in Metalloproteins by Proton-Detected Solid-State NMR Spectroscopy. J Am Chem Soc 2012; 134:14730-3. [DOI: 10.1021/ja306813j] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael J. Knight
- Centre de RMN à Très
Hauts Champs, UMR 5280 CNRS/ENS Lyon/UCB Lyon 1, Université de Lyon, 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, Italy
| | - Roberta Pierattelli
- Department of Chemistry “Ugo
Schiff“ and Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, 50019
Sesto Fiorentino, Italy
| | - Ivano Bertini
- Department of Chemistry “Ugo
Schiff“ and Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, 50019
Sesto Fiorentino, Italy
| | - Lyndon Emsley
- Centre de RMN à Très
Hauts Champs, UMR 5280 CNRS/ENS Lyon/UCB Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Torsten Herrmann
- Centre de RMN à Très
Hauts Champs, UMR 5280 CNRS/ENS Lyon/UCB Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Guido Pintacuda
- Centre de RMN à Très
Hauts Champs, UMR 5280 CNRS/ENS Lyon/UCB Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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178
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Dick-Perez M, Wang T, Salazar A, Zabotina OA, Hong M. Multidimensional solid-state NMR studies of the structure and dynamics of pectic polysaccharides in uniformly 13C-labeled Arabidopsis primary cell walls. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50:539-50. [PMID: 22777793 DOI: 10.1002/mrc.3836] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Revised: 05/22/2012] [Accepted: 05/24/2012] [Indexed: 05/14/2023]
Abstract
Plant cell wall (CW) polysaccharides are responsible for the mechanical strength and growth of plant cells; however, the high-resolution structure and dynamics of the CW polysaccharides are still poorly understood because of the insoluble nature of these molecules. Here, we use 2D and 3D magic-angle-spinning (MAS) solid-state NMR (SSNMR) to investigate the structural role of pectins in the plant CW. Intact and partially depectinated primary CWs of Arabidopsis thaliana were uniformly labeled with (13)C and their NMR spectra were compared. Recent (13)C resonance assignment of the major polysaccharides in Arabidopsis thaliana CWs allowed us to determine the effects of depectination on the intermolecular packing and dynamics of the remaining wall polysaccharides. 2D and 3D correlation spectra show the suppression of pectin signals, confirming partial pectin removal by chelating agents and sodium carbonate. Importantly, higher cross peaks are observed in 2D and 3D (13)C spectra of the depectinated CW, suggesting higher rigidity and denser packing of the remaining wall polysaccharides compared with the intact CW. (13)C spin-lattice relaxation times and (1)H rotating-frame spin-lattice relaxation times indicate that the polysaccharides are more rigid on both the nanosecond and microsecond timescales in the depectinated CW. Taken together, these results indicate that pectic polysaccharides are highly dynamic and endow the polysaccharide network of the primary CW with mobility and flexibility, which may be important for pectin functions. This study demonstrates the capability of multidimensional SSNMR to determine the intermolecular interactions and dynamic structures of complex plant materials under near-native conditions.
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Affiliation(s)
- Marilu Dick-Perez
- Department of Chemistry and the Ames Laboratory, Iowa State University, Ames, IA 50011, USA
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179
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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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180
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Lamley JM, Lewandowski JR. Simultaneous acquisition of homonuclear and heteronuclear long-distance contacts with time-shared third spin assisted recoupling. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 218:30-34. [PMID: 22578552 DOI: 10.1016/j.jmr.2012.03.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Revised: 03/13/2012] [Accepted: 03/17/2012] [Indexed: 05/31/2023]
Abstract
We present a time-shared Third Spin Assisted Recoupling (TSTSAR) experiment that allows for simultaneous acquisition of homonuclear ((13)C-(13)C) and heteronuclear ((15)N-(13)C) long-distance contacts in biomolecular solids under magic angle spinning. TSTSAR leads to substantial time savings and increases the information content of 2D correlation spectra.
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Affiliation(s)
- Jonathan M Lamley
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
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181
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Webber AL, Pell AJ, Barbet-Massin E, Knight MJ, Bertini I, Felli IC, Pierattelli R, Emsley L, Lesage A, Pintacuda G. Combination of DQ and ZQ coherences for sensitive through-bond NMR correlation experiments in biosolids under ultra-fast MAS. Chemphyschem 2012; 13:2405-11. [PMID: 22528552 DOI: 10.1002/cphc.201200099] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 04/02/2012] [Indexed: 11/08/2022]
Abstract
A double-zero quantum (DZQ)-refocused INADEQUATE experiment is introduced for J-based NMR correlations under ultra-fast (60 kHz) magic angle spinning (MAS). The experiment records two spectra in the same dataset, a double quantum-single quantum (DQ-SQ) and zero quantum-single quantum (ZQ-SQ) spectrum, whereby the corresponding signals appear at different chemical shifts in ω(1). Furthermore, the spin-state selective excitation (S(3)E) J-decoupling block is incorporated in place of the second refocusing echo of the INADEQUATE scheme, providing an additional gain in sensitivity and resolution. The two sub-spectra acquired in this way can be treated separately by a shearing transformation, producing two diagonal-free single quantum (SQ-SQ)-type spectra, which are subsequently recombined to give an additional sensitivity enhancement, thus offering an improvement greater than a factor of two as compared to the original refocused INADEQUATE experiment. The combined DZQ scheme retains transverse magnetization on the initially polarized (I) spin, which typically exhibits a longer transverse dephasing time (T(2)') than its through-bond neighbour (S). By doing so, less magnetization is lost during the refocusing periods in the sequence to give even further gains in sensitivity for the J correlations. The experiment is demonstrated for the correlation between the carbonyl (CO) and alpha (CA) carbons in a microcrystalline sample of fully protonated, [(15)N,(13)C]-labelled Cu(II),Zn(II) superoxide dismutase, and its efficiency is discussed with respect to other J-based schemes.
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Affiliation(s)
- Amy L Webber
- Centre de RMN à Très Hauts Champs, UMR 5280 CNRS/Ecole Normale Supérieure de Lyon, University of Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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182
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Bechinger B, Salnikov ES. The membrane interactions of antimicrobial peptides revealed by solid-state NMR spectroscopy. Chem Phys Lipids 2012; 165:282-301. [DOI: 10.1016/j.chemphyslip.2012.01.009] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 01/25/2012] [Accepted: 01/27/2012] [Indexed: 01/29/2023]
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183
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Gopinath T, Veglia G. Dual acquisition magic-angle spinning solid-state NMR-spectroscopy: simultaneous acquisition of multidimensional spectra of biomacromolecules. Angew Chem Int Ed Engl 2012; 51:2731-5. [PMID: 22311700 PMCID: PMC3513283 DOI: 10.1002/anie.201108132] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Indexed: 11/05/2022]
Abstract
Fast data collection: a general method for dual data acquisition of multidimensional magic-angle spinning solid-state NMR experiments is presented. The method uses a simultaneous Hartmann-Hahn cross-polarization from (1)H to (13)C and (15)N nuclei and exploits the long-living (15)N polarization for parallel acquisition of two multidimensional experiments.
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Affiliation(s)
- T. Gopinath
- Department of Chemistry and Department of Biochemistry, Molecular Biology and Biophysics, 321 Church St. SE, Minneapolis, MN 55455 USA
| | - Gianluigi Veglia
- Department of Chemistry and Department of Biochemistry, Molecular Biology and Biophysics, 321 Church St. SE, Minneapolis, MN 55455 USA
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184
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Pandit A, de Groot HJM. Solid-state NMR applied to photosynthetic light-harvesting complexes. PHOTOSYNTHESIS RESEARCH 2012; 111:219-226. [PMID: 21842288 PMCID: PMC3295999 DOI: 10.1007/s11120-011-9674-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 07/12/2011] [Indexed: 05/29/2023]
Abstract
This short review describes how solid-state NMR has provided a mechanistic and electronic picture of pigment-protein and pigment-pigment interactions in photosynthetic antenna complexes. NMR results on purple bacterial antenna complexes show how the packing of the protein and the pigments inside the light-harvesting oligomers induces mutual conformational stress. The protein scaffold produces deformation and electrostatic polarization of the BChl macrocycles and leads to a partial electronic charge transfer between the BChls and their coordinating histidines, which can tune the light-harvesting function. In chlorosome antennae assemblies, the NMR template structure reveals how the chromophores can direct their self-assembly into higher macrostructures which, in turn, tune the light-harvesting properties of the individual molecules by controlling their disorder, structural deformation, and electronic polarization without the need for a protein scaffold. These results pave the way for addressing the next challenge, which is to resolve the functional conformational dynamics of the lhc antennae of oxygenic species that allows them to switch between light-emitting and light-energy dissipating states.
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Affiliation(s)
- Anjali Pandit
- Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Huub J. M. de Groot
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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185
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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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186
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Gopinath T, Veglia G. Dual Acquisition Magic-Angle Spinning Solid-State NMR-Spectroscopy: Simultaneous Acquisition of Multidimensional Spectra of Biomacromolecules. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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187
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Wang S, Ishii Y. Revealing protein structures in solid-phase peptide synthesis by 13C solid-state NMR: evidence of excessive misfolding for Alzheimer's β. J Am Chem Soc 2012; 134:2848-51. [PMID: 22280020 DOI: 10.1021/ja212190z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Solid-phase peptide synthesis (SPPS) is a widely used technique in biology and chemistry. However, the synthesis yield in SPPS often drops drastically for longer amino acid sequences, presumably because of the occurrence of incomplete coupling reactions. The underlying cause for this problem is hypothesized to be a sequence-dependent propensity to form secondary structures through protein aggregation. However, few methods are available to study the site-specific structure of proteins or long peptides that are anchored to the solid support used in SPPS. This study presents a novel solid-state NMR (SSNMR) approach to examine protein structure in the course of SPPS. As a useful benchmark, we describe the site-specific SSNMR structural characterization of the 40-residue Alzheimer's β-amyloid (Aβ) peptide during SPPS. Our 2D (13)C/(13)C correlation SSNMR data on Aβ(1-40) bound to a resin support demonstrated that Aβ underwent excessive misfolding into a highly ordered β-strand structure across the entire amino acid sequence during SPPS. This approach is likely to be applicable to a wide range of peptides/proteins bound to the solid support that are synthesized through SPPS.
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Affiliation(s)
- Songlin Wang
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, USA
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188
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Aliev AE, Mia ZA, Khaneja HS, King FD. Structures in Solutions from Joint Experimental-Computational Analysis: Applications to Cyclic Molecules and Studies of Noncovalent Interactions. J Phys Chem A 2012; 116:1093-109. [DOI: 10.1021/jp211083f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Abil E. Aliev
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Zakirin A. Mia
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Harmeet S. Khaneja
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Frank D. King
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
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189
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Hoop CL, Sivanandam VN, Kodali R, Srnec MN, van der Wel PCA. Structural characterization of the caveolin scaffolding domain in association with cholesterol-rich membranes. Biochemistry 2012; 51:90-9. [PMID: 22142403 PMCID: PMC3290515 DOI: 10.1021/bi201356v] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 12/01/2011] [Indexed: 01/16/2023]
Abstract
Members of the caveolin protein family are implicated in the formation of caveolae and play important roles in a number of signaling pathways and in the regulation of various proteins. We employ complementary spectroscopic methods to study the structure of the caveolin scaffolding domain (CSD) in caveolin-1 fragments, while bound to cholesterol-rich membranes. This key domain is thought to be involved in multiple critical functions that include protein recognition, oligomerization, and cholesterol binding. In our membrane-bound peptides, residues within the flanking intramembrane domain (IMD) are found to adopt an α-helical structure, consistent with its commonly believed helical hairpin conformation. Intriguingly, in these same peptides, we observe a β-stranded conformation for residues in the CSD, contrasting with earlier reports, which commonly do not reflect β-structure. Our experimental data based on solid-state NMR, CD, and FTIR are found to be consistent with computational analyses of the secondary structure preference of the primary sequence. We discuss how our structural data of membrane binding Cav fragments may match certain general features of cholesterol-binding domains and could be consistent with the role for CSD in protein recognition and homo-oligomerization.
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Affiliation(s)
| | | | - Ravindra Kodali
- Department
of Structural Biology, University
of Pittsburgh School of Medicine, Biomedical Science
Tower 3, 3501 Fifth Ave., Pittsburgh, Pennsylvania 15260, United States
| | - Matthew N. Srnec
- Department
of Structural Biology, University
of Pittsburgh School of Medicine, Biomedical Science
Tower 3, 3501 Fifth Ave., Pittsburgh, Pennsylvania 15260, United States
| | - Patrick C. A. van der Wel
- Department
of Structural Biology, University
of Pittsburgh School of Medicine, Biomedical Science
Tower 3, 3501 Fifth Ave., Pittsburgh, Pennsylvania 15260, United States
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190
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Reif B. Deuterated peptides and proteins: structure and dynamics studies by MAS solid-state NMR. Methods Mol Biol 2012; 831:279-301. [PMID: 22167680 DOI: 10.1007/978-1-61779-480-3_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Perdeuteration and back substitution of exchangeable protons in microcrystalline proteins, in combination with recrystallization from D(2)O-containing buffers, significantly reduce (1)H, (1)H dipolar interactions. This way, amide proton line widths on the order of 20 Hz are obtained. Aliphatic protons are accessible either via specifically protonated precursors or by using low amounts of H(2)O in the bacterial growth medium. The labeling scheme enables characterization of structure and dynamics in the solid-state without dipolar truncation artifacts.
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Affiliation(s)
- Bernd Reif
- Munich Center for Integrated Protein Science (CIPSM) at Department Chemie, Technische Universität München, Garching, Germany.
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191
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192
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Itaya M, Brett IC, Smith SO. Synthesis, purification, and characterization of single helix membrane peptides and proteins for NMR spectroscopy. Methods Mol Biol 2012; 831:333-57. [PMID: 22167682 DOI: 10.1007/978-1-61779-480-3_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Membrane proteins function as receptors, channels, transporters, and enzymes. These proteins are generally difficult to express and purify in a functional form due to the hydrophobic nature of their membrane spanning sequences. Studies on membrane proteins with a single membrane spanning helix have been particularly challenging. Single-pass membrane proteins will often form dimers or higher order oligomers in cell membranes as a result of sequence motifs that mediate specific transmembrane helix interactions. Understanding the structural basis for helix association provides insights into how these proteins function. Nevertheless, nonspecific association or aggregation of hydrophobic membrane spanning sequences can occur when isolated transmembrane domains are reconstituted into membrane bilayers or solubilized into detergent micelles for structural studies by solid-state or solution NMR spectroscopy. Here, we outline the methods used to synthesize, purify, and characterize single transmembrane segments for structural studies. Two synthetic strategies are discussed. The first strategy is to express hydrophobic peptides as protein chimera attached to the maltose binding protein. The second strategy is by direct chemical synthesis. Purification is carried out by several complementary chromatography methods. The peptides are solubilized in detergent for solution NMR studies or reconstituted into model membranes for solid-state NMR studies. We describe the methods used to characterize the reconstitution of these systems prior to NMR structural studies to establish if there is nonspecific aggregation.
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Affiliation(s)
- Miki Itaya
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
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193
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Verardi R, Traaseth NJ, Masterson LR, Vostrikov VV, Veglia G. Isotope labeling for solution and solid-state NMR spectroscopy of membrane proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 992:35-62. [PMID: 23076578 PMCID: PMC3555569 DOI: 10.1007/978-94-007-4954-2_3] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this chapter, we summarize the isotopic labeling strategies used to obtain high-quality solution and solid-state NMR spectra of biological samples, with emphasis on integral membrane proteins (IMPs). While solution NMR is used to study IMPs under fast tumbling conditions, such as in the presence of detergent micelles or isotropic bicelles, solid-state NMR is used to study the structure and orientation of IMPs in lipid vesicles and bilayers. In spite of the tremendous progress in biomolecular NMR spectroscopy, the homogeneity and overall quality of the sample is still a substantial obstacle to overcome. Isotopic labeling is a major avenue to simplify overlapped spectra by either diluting the NMR active nuclei or allowing the resonances to be separated in multiple dimensions. In the following we will discuss isotopic labeling approaches that have been successfully used in the study of IMPs by solution and solid-state NMR spectroscopy.
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Affiliation(s)
- Raffaello Verardi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
| | | | | | | | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455
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194
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Qiang W. Signal enhancement for the sensitivity-limited solid state NMR experiments using a continuous, non-uniform acquisition scheme. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 213:171-5. [PMID: 21930405 PMCID: PMC3206163 DOI: 10.1016/j.jmr.2011.08.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2011] [Revised: 08/17/2011] [Accepted: 08/23/2011] [Indexed: 05/12/2023]
Abstract
We describe a sampling scheme for the two-dimensional (2D) solid state NMR experiments, which can be readily applied to the sensitivity-limited samples. The sampling scheme utilizes continuous, non-uniform sampling profile for the indirect dimension, i.e. the acquisition number decreases as a function of the evolution time (t1) in the indirect dimension. For a beta amyloid (Aβ) fibril sample, we observed overall 40-50% signal enhancement by measuring the cross peak volume, while the cross peak linewidths remained comparable to the linewidths obtained by regular sampling and processing strategies. Both the linear and Gaussian decay functions for the acquisition numbers result in similar percentage of increment in signal. In addition, we demonstrated that this sampling approach can be applied with different dipolar recoupling approaches such as radiofrequency assisted diffusion (RAD) and finite-pulse radio-frequency-driven recoupling (fpRFDR). This sampling scheme is especially suitable for the sensitivity-limited samples which require long signal averaging for each t1 point, for instance the biological membrane proteins where only a small fraction of the sample is isotopically labeled.
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Affiliation(s)
- Wei Qiang
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 406, Bethesda, MD 20892-0520, United States.
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195
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Wang S, Shi L, Kawamura I, Brown LS, Ladizhansky V. Site-specific solid-state NMR detection of hydrogen-deuterium exchange reveals conformational changes in a 7-helical transmembrane protein. Biophys J 2011; 101:L23-5. [PMID: 21806918 DOI: 10.1016/j.bpj.2011.06.035] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 05/18/2011] [Accepted: 06/23/2011] [Indexed: 10/17/2022] Open
Abstract
Solid-state NMR spectroscopy is an efficient tool for following conformational dynamics of membrane proteins at atomic resolution. We used this technique for the site-specific detection of light-induced hydrogen-deuterium exchange in the lipid-embedded heptahelical transmembrane photosensor Anabaena sensory rhodopsin to pinpoint the location of its conformational changes upon activation. We show that the light-induced conformational changes result in a dramatic, but localized, increase in the exchange in the transmembrane regions. Most notably, the cytoplasmic half of helix G and the cytoplasmic ends of helices B and C exchange more extensively, probably as a result of their relative displacement in the activated state, allowing water to penetrate into the core of the protein. These light-induced rearrangements must provide the structural basis for the photosensory function of Anabaena sensory rhodopsin.
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Affiliation(s)
- Shenlin Wang
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
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196
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Abstract
We review the current state of membrane protein structure determination using solid-state nuclear magnetic resonance (NMR) spectroscopy. Multidimensional magic-angle-spinning correlation NMR combined with oriented-sample experiments has made it possible to measure a full panel of structural constraints of membrane proteins directly in lipid bilayers. These constraints include torsion angles, interatomic distances, oligomeric structure, protein dynamics, ligand structure and dynamics, and protein orientation and depth of insertion in the lipid bilayer. Using solid-state NMR, researchers have studied potassium channels, proton channels, Ca(2+) pumps, G protein-coupled receptors, bacterial outer membrane proteins, and viral fusion proteins to elucidate their mechanisms of action. Many of these membrane proteins have also been investigated in detergent micelles using solution NMR. Comparison of the solid-state and solution NMR structures provides important insights into the effects of the solubilizing environment on membrane protein structure and dynamics.
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Affiliation(s)
- Mei Hong
- Department of Chemistry, Iowa State University, Ames, 50011, USA.
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197
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Vogel EP, Curtis-Fisk J, Young KM, Weliky DP. Solid-state nuclear magnetic resonance (NMR) spectroscopy of human immunodeficiency virus gp41 protein that includes the fusion peptide: NMR detection of recombinant Fgp41 in inclusion bodies in whole bacterial cells and structural characterization of purified and membrane-associated Fgp41. Biochemistry 2011; 50:10013-26. [PMID: 21985645 PMCID: PMC3220598 DOI: 10.1021/bi201292e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Human immunodeficiency virus (HIV) infection of a host cell begins with fusion of the HIV and host cell membranes and is mediated by the gp41 protein, a single-pass integral membrane protein of HIV. The 175 N-terminal residues make up the ectodomain that lies outside the virus. This work describes the production and characterization of an ectodomain construct containing the 154 N-terminal gp41 residues, including the fusion peptide (FP) that binds to target cell membranes. The Fgp41 sequence was derived from one of the African clade A strains of HIV-1 that have been less studied than European/North American clade B strains. Fgp41 expression at a level of ~100 mg/L of culture was evidenced by an approach that included amino acid type (13)CO and (15)N labeling of recombinant protein and solid-state NMR (SSNMR) spectroscopy of lyophilized whole cells. The approach did not require any protein solubilization or purification and may be a general approach for detection of recombinant protein. The purified Fgp41 yield was ~5 mg/L of culture. SSNMR spectra of membrane-associated Fgp41 showed high helicity for the residues C-terminal of the FP. This was consistent with a "six-helix bundle" (SHB) structure that is the final gp41 state during membrane fusion. This observation and negligible Fgp41-induced vesicle fusion supported a function for SHB gp41 of membrane stabilization and fusion arrest. SSNMR spectra of residues in the membrane-associated FP provided evidence of a mixture of molecular populations with either helical or β-sheet FP conformation. These and earlier SSNMR data strongly support the existence of these populations in the SHB state of membrane-associated gp41.
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Affiliation(s)
- Erica P. Vogel
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824
| | - Jaime Curtis-Fisk
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824
| | - Kaitlin M. Young
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824
| | - David P. Weliky
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824
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198
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Tang M, Sperling LJ, Berthold DA, Schwieters CD, Nesbitt AE, Nieuwkoop AJ, Gennis RB, Rienstra CM. High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data. JOURNAL OF BIOMOLECULAR NMR 2011; 51:227-33. [PMID: 21938394 PMCID: PMC3204959 DOI: 10.1007/s10858-011-9565-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 08/29/2011] [Indexed: 05/12/2023]
Abstract
X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside of X-ray reflections to the conventional model building and refinement steps of structure calculations. Using the 3.7 Å crystal structure of the integral membrane protein complex DsbB-DsbA as a test case yielded a significantly improved backbone precision of 0.92 Å in the transmembrane region, a 58% enhancement from using X-ray reflections alone. Furthermore, addition of solid-state NMR restraints greatly improved the overall quality of the structure by promoting 22% of DsbB transmembrane residues into the most favored regions of Ramachandran space in comparison to the crystal structure. This method is widely applicable to any protein system where X-ray data are available, and is particularly useful for the study of weakly diffracting crystals.
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Affiliation(s)
- Ming Tang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 USA
| | - Lindsay J. Sperling
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 USA
| | - Deborah A. Berthold
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 USA
| | - Charles D. Schwieters
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anna E. Nesbitt
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 USA
| | - Andrew J. Nieuwkoop
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 USA
| | - Robert B. Gennis
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 USA
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 USA
- CORRESPONDING AUTHOR:
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199
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Nadaud PS, Sengupta I, Helmus JJ, Jaroniec CP. Evaluation of the influence of intermolecular electron-nucleus couplings and intrinsic metal binding sites on the measurement of 15N longitudinal paramagnetic relaxation enhancements in proteins by solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2011; 51:293-302. [PMID: 21826518 DOI: 10.1007/s10858-011-9536-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 07/25/2011] [Indexed: 05/31/2023]
Abstract
Magic-angle spinning solid-state NMR measurements of (15)N longitudinal paramagnetic relaxation enhancements (PREs) in (13)C,(15)N-labeled proteins modified with Cu(2+)-chelating tags can yield multiple long-range electron-nucleus distance restraints up to ~20 Å (Nadaud et al. in J Am Chem Soc 131:8108-8120, 2009). Using the EDTA-Cu(2+) K28C mutant of B1 immunoglobulin binding domain of protein G (GB1) as a model, we investigate the effects on such measurements of intermolecular electron-nucleus couplings and intrinsic metal binding sites, both of which may potentially complicate the interpretation of PRE data in terms of the intramolecular protein fold. To quantitatively assess the influence of intermolecular (15)N-Cu(2+) interactions we have determined a nearly complete set of longitudinal (15)N PREs for a series of microcrystalline samples containing ~10, 15 and 25 mol percent of the (13)C,(15)N-labeled EDTA-Cu(2+)-tagged protein diluted in a matrix of diamagnetic natural abundance GB1. The residual intermolecular interactions were found to be minor on the whole and account for only a fraction of the relatively small but systematic deviations observed between the experimental (15)N PREs and corresponding values calculated using protein structural models for residues furthest removed from the EDTA-Cu(2+) tag. This suggests that these deviations are also caused in part by other factors not related to the protein structure, such as the presence in the protein of intrinsic secondary sites capable of binding Cu(2+) ions. To probe this issue we performed a Cu(2+) titration study for K28C-EDTA GB1 monitored by 2D (15)N-(1)H solution-state NMR, which revealed that while for Cu(2+):protein molar ratios of ≤ 1.0 Cu(2+) binds primarily to the high-affinity EDTA tag, as anticipated, at even slightly super-stoichiometric ratios the Cu(2+) ions can also associate with side-chains of aspartate and glutamate residues. This in turn is expected to lead to enhanced PREs for residues located in the vicinity of the secondary Cu(2+) binding sites, and indeed many of these residues were ones found to display the elevated longitudinal (15)N PREs in the solid phase.
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Affiliation(s)
- Philippe S Nadaud
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
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200
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Bosse M, Thomas L, Hassert R, Beck-Sickinger AG, Huster D, Schmidt P. Assessment of a fully active class A G protein-coupled receptor isolated from in vitro folding. Biochemistry 2011; 50:9817-25. [PMID: 21999704 DOI: 10.1021/bi201320e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We provide a protocol for the preparation of fully active Y2 G protein-coupled receptors (GPCRs). Although a valuable target for pharmaceutical research, information about the structure and dynamics of these molecules remains limited due to the difficulty in obtaining sufficient amounts of homogeneous and fully active receptors for in vitro studies. Recombinant expression of GPCRs as inclusion bodies provides the highest protein yields at lowest costs. But this strategy can only successfully be applied if the subsequent in vitro folding results in a high yield of active receptors and if this fraction can be isolated from the nonactive receptors in a homogeneous form. Here, we followed that strategy to provide large quantities of the human neuropeptide Y receptor type 2 and determined the folding yield before and after ligand affinity chromatography using a radioligand binding assay. Directly after folding, we achieved a proportion of ~25% active receptor. This value could be increased to ~96% using ligand affinity chromatography. Thus, a very homogeneous sample of the Y2 receptor could be prepared that exhibited a K(D) value of 0.1 ± 0.05 nM for the binding of polypeptide Y, which represents one of the natural ligands of the Y2 receptor.
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Affiliation(s)
- Mathias Bosse
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany
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