101
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Kloepper KD, Zhou DH, Li Y, Winter KA, George JM, Rienstra CM. Temperature-dependent sensitivity enhancement of solid-state NMR spectra of alpha-synuclein fibrils. JOURNAL OF BIOMOLECULAR NMR 2007; 39:197-211. [PMID: 17899395 DOI: 10.1007/s10858-007-9189-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Accepted: 08/09/2007] [Indexed: 05/11/2023]
Abstract
The protein alpha-synuclein (AS) is the primary fibrillar component of Lewy bodies, the pathological hallmark of Parkinson's disease. Wild-type human AS and the three mutant forms linked to Parkinson's disease (A53T, A30P, and E46K) all form fibrils through a nucleation-dependent pathway; however, the biophysical details of these fibrillation events are not yet well understood. Atomic-level structural insight is required in order to elucidate the potential role of AS fibrils in Parkinson's disease. Here we show that low temperature acquisition of magic-angle spinning NMR spectra of wild type AS fibrils-greatly enhances spectral sensitivity, enabling the detection of a substantially larger number of spin systems. At 0 +/- 3 degrees C sample temperature, cross polarization (CP) experiments yield weak signals. Lower temperature spectra (-40 +/- 3 degrees C) demonstrated several times greater signal intensity, an effect further amplified in 3D 15N-13C-13C experiments, which are required to perform backbone assignments on this sample. Thus 3D experiments enabled assignments of most amino acids in the rigid part of the fibril (approximately residues 64 to 94), as well as tentative site-specific assignments for T22, V26, A27, Y39, G41, S42, H50, V52, A53, T54, V55, V63, A107, I112, and S129. Most of these signals were not observed in 2D or 3D spectra at 0 +/- 3 degrees C. Spectra acquired at low temperatures therefore permitted more complete chemical shift assignments. Observation of the majority of residues in AS fibrils represents an important step towards solving the 3D structure.
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Affiliation(s)
- Kathryn D Kloepper
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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102
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Franks WT, Kloepper KD, Wylie BJ, Rienstra CM. Four-dimensional heteronuclear correlation experiments for chemical shift assignment of solid proteins. JOURNAL OF BIOMOLECULAR NMR 2007; 39:107-31. [PMID: 17687624 DOI: 10.1007/s10858-007-9179-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Revised: 07/05/2007] [Accepted: 07/10/2007] [Indexed: 05/16/2023]
Abstract
Chemical shift assignment is the first step in all established protocols for structure determination of uniformly labeled proteins by NMR. The explosive growth in recent years of magic-angle spinning (MAS) solid-state NMR (SSNMR) applications is largely attributable to improved methods for backbone and side-chain chemical shift correlation spectroscopy. However, the techniques developed so far have been applied primarily to proteins in the size range of 5-10 kDa, despite the fact that SSNMR has no inherent molecular weight limits. Rather, the degeneracy inherent to many 2D and 3D SSNMR spectra of larger proteins has prevented complete unambiguous chemical shift assignment. Here we demonstrate the implementation of 4D backbone chemical shift correlation experiments for assignment of solid proteins. The experiments greatly reduce spectral degeneracy at a modest cost in sensitivity, which is accurately described by theory. We consider several possible implementations and investigate the CANCOCX pulse sequence in detail. This experiment involves three cross polarization steps, from H to CA[i], CA[i] to N[i], and N[i] to C'[i-1], followed by a final homonuclear mixing period. With short homonuclear mixing times (<20 ms), backbone correlations are observed with high sensitivity; with longer mixing times (>200 ms), long-range correlations are revealed. For example, a single 4D experiment with 225 ms homonuclear mixing time reveals approximately 200 uniquely resolved medium and long-range correlations in the 56-residue protein GB1. In addition to experimental demonstrations in the 56-residue protein GB1, we present a theoretical analysis of anticipated improvements in resolution for much larger proteins and compare these results in detail with the experiments, finding good agreement between experiment and theory under conditions of stable instrumental performance.
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Affiliation(s)
- W Trent Franks
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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103
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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: 13] [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.
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Affiliation(s)
- Sanjeewa G Rupasinghe
- Department of Cell and Developmental Biology, University of Illinois, Urbana, IL 61801, USA
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104
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Varga K, Tian L, McDermott AE. Solid-state NMR study and assignments of the KcsA potassium ion channel of S. lividans. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:1604-13. [PMID: 17974509 DOI: 10.1016/j.bbapap.2007.08.029] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Revised: 08/15/2007] [Accepted: 08/29/2007] [Indexed: 10/22/2022]
Abstract
The extraordinary efficiency and selectivity of potassium channels have made them ideal systems for biophysical and functional studies of ion conduction. We carried out solid-state NMR studies of the selectivity filter region of the protein. Partial site-specific assignments of the NMR signals were obtained based on high field multidimensional solid-state NMR spectra of uniformly (13)C, (15)N enriched KcsA potassium channel from Streptomyces lividans. Both backbone and sidechain atoms were assigned for residues V76-D80 and P83-L90, in and near the selectivity filter region of the protein; this region exhibits good dispersion and useful chemical shift fingerprints. This study will enable structure, dynamic and mechanistic studies of ion conduction by NMR.
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Affiliation(s)
- Krisztina Varga
- Department of Chemistry, Columbia University, 3000 Broadway MC 3113, New York, NY 10027, USA
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105
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Marulanda D, Tasayco ML, Cataldi M, Arriaran V, Polenova T. Resonance assignments and secondary structure analysis of E. coli thioredoxin by magic angle spinning solid-state NMR spectroscopy. J Phys Chem B 2007; 109:18135-45. [PMID: 16853329 DOI: 10.1021/jp052774d] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
De novo site-specific 13C and 15N backbone and sidechain resonance assignments are presented for uniformly enriched E. coli thioredoxin, established using two-dimensional homo- and heteronuclear solid-state magic angle spinning NMR correlation spectroscopy. Backbone dihedral angles and secondary structure were derived from the statistical analysis of the secondary chemical shifts, and are in good agreement with solution values for the intact full-length thioredoxin, with the exception of a small number of residues located at the termini of the individual secondary structure elements. A large number of cross-peaks observed in the DARR spectra with long mixing times correspond to the pairs of carbon atoms separated by 4-6 angstroms, suggesting that DARR could be efficiently employed for observation of medium- and long-range correlations. The 108 amino acid residue E. coli thioredoxin is the largest uniformly enriched protein assigned to this degree of completeness by solid-state NMR spectroscopy to date. It is anticipated that with a combination of two-dimensional correlation experiments and high magnetic fields, resonance assignments and secondary structure can be generally derived for other noncrystalline proteins.
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Affiliation(s)
- Dabeiba Marulanda
- Department of Chemistry and Biochemistry, Brown Laboratories, University of Delaware, Newark, Delaware 19716, USA
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106
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Li Y, Berthold DA, Frericks HL, Gennis RB, Rienstra CM. Partial13C and15N Chemical-Shift Assignments of the Disulfide-Bond-Forming Enzyme DsbB by 3D Magic-Angle Spinning NMR Spectroscopy. Chembiochem 2007; 8:434-42. [PMID: 17285659 DOI: 10.1002/cbic.200600484] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DsbB is a 20 kDa Escherichia coli inner-membrane protein that catalyzes disulfide-bond formation in periplasmic proteins. We report highly resolved, multidimensional magic-angle spinning NMR spectra at 750 MHz (1)H frequency, which enable partial (13)C and (15)N chemical-shift assignments of the signals. The narrow line widths observed indicate excellent microscopic order of the protein sample, suitable for full structure determination by solid-state NMR. Experiments were performed exclusively on uniformly (13)C,(15)N-labeled DsbB. Chemical-shift-correlation experiments based on dipolar transfer yielded strong signals in the 3D spectra, many of which have been site-specifically assigned to the four transmembrane helices of DsbB. Significant numbers of additional residues have been assigned to stretches of amino acids, although not yet placed in the amino acid sequence. We also report the temperature dependence of signal intensities from -50 degrees C to 0 degrees C, a range over which samples of DsbB are highly stable. Structural and dynamic information derived from SSNMR studies can give insight into DsbB in a state that so far has not been successfully crystallized.
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Affiliation(s)
- Ying Li
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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107
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Forbes RT, Barry BW, Elkordy AA. Preparation and characterisation of spray-dried and crystallised trypsin: FT-Raman study to detect protein denaturation after thermal stress. Eur J Pharm Sci 2007; 30:315-23. [PMID: 17236751 DOI: 10.1016/j.ejps.2006.11.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2006] [Revised: 10/15/2006] [Accepted: 11/28/2006] [Indexed: 11/25/2022]
Abstract
The production of stable protein formulations is difficult due to unique properties of proteins. Accordingly, spray drying and crystallisation techniques were assessed for their effects on trypsin, a model protein. Samples were investigated using polarising microscopy, thermogravimetry, differential scanning calorimetry (DSC), FT-Raman spectroscopy and enzymatic assay. Unprocessed, spray-dried and crystallised trypsin were evaluated in solution for secondary structure in low and high protein concentrations using aqueous state FT-Raman spectroscopy and for folding reversibility employing high sensitivity differential scanning calorimetry. Spray-dried trypsin showed FT-Raman spectral changes and less biological activity, after rehydration, compared with unprocessed and crystallised trypsin. Crystals maintained activity better than did the spray-dried form and retained a higher folding reversibility compared to unprocessed and spray-dried protein. Proteins may denature with structural changes under thermal stress and lose their activities. Thus, this research studied the effect of heating solid unprocessed, spray-dried and crystallised trypsin samples on their secondary structures, using FT-Raman spectroscopy, to identify the influence of the initial solid form on its propensity for thermal denaturation and whether this can be correlated with catalytic activity. DSC heated protein samples to two temperatures, one before the apparent denaturation temperature (T(m)) and the other after the T(m). Samples heated below their T(m) showed some perturbations of the secondary structure and some activity, whilst materials rose to the higher temperature were insoluble with complete loss of activity.
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Affiliation(s)
- Robert T Forbes
- Drug Delivery Group, School of Pharmacy, University of Bradford, Bradford BD7 1DP, UK
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108
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Ader C, Spoerner M, Kalbitzer HR, Brunner E. Solid-state 31P NMR spectroscopy of precipitated guanine nucleotide-binding protein Ras in complexes with its effector molecules Raf kinase and RalGDS. J Phys Chem B 2007; 111:2752-7. [PMID: 17315921 DOI: 10.1021/jp067792p] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Liquid-state 31P NMR spectroscopy is a well-established method for the study of guanine nucleotide-binding proteins (GNB proteins) such as the proto-oncogene Ras. Solid-state 31P NMR spectroscopy could meanwhile also be used to study microcrystalline samples of Ras as well as its partial loss-of-function mutants Ras(T35S) and Ras(T35A). However, solid-state NMR studies of the latter mutants in complex with effector molecules such as RalGDS or Raf kinase were so far prevented, since it has been impossible to crystallize these complexes yet. The aim of the present contribution is to make such complexes accessible to solid-state 31P NMR spectroscopy by the application of precipitation methods. The complex formed by Ras(T35S) and Raf kinase is preserved during precipitation. In contrast, the weakly bound complex of Ras(T35S) with RalGDS is dissociated or at least perturbed by the precipitation procedure. Solid-state 31P NMR experiments on precipitates of these complexes deliver spectra of high resolution and signal-to-noise ratio which allows the application of two-dimensional techniques. Precipitates prepared using polyethylene glycol 6000 (PEG) as precipitant were found to exhibit spectra of maximum resolution and signal-to-noise ratio. Interestingly, the 31P signal due to the alpha-phosphate of GppNHp bound to Ras(T35S) in crystalline samples or aged precipitates has a significantly different isotropic chemical shift than in the liquid state or in freshly prepared precipitates. This directly indicates that the crystal structure differs from the equilibrium solution structure at least in the neighborhood of the alpha-phosphate group.
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Affiliation(s)
- Christian Ader
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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109
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Verel R, Manolikas T, Siemer AB, Meier BH. Improved resolution in (13)C solid-state spectra through spin-state-selection. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 184:322-9. [PMID: 17088090 DOI: 10.1016/j.jmr.2006.09.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Revised: 09/21/2006] [Accepted: 09/26/2006] [Indexed: 05/12/2023]
Abstract
The application of a spin-state-selective coherence transfer experiment (INADEQUATE-SSS) to solid-state NMR spectroscopy is described. Two-dimensional (13)C double-quantum/single-quantum spectra without J splittings in both dimensions lead to enhanced spectral resolution. The method is demonstrated to significantly improve the spectral resolution of the crowded C'-C(alpha) region of two proteins.
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Affiliation(s)
- René Verel
- Physical Chemistry, ETH Zurich, Wolfgang-Pauli-Strasse 10, CH-8093 Zurich, Switzerland
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110
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Wickramasinghe NP, Kotecha M, Samoson A, Past J, Ishii Y. Sensitivity enhancement in (13)C solid-state NMR of protein microcrystals by use of paramagnetic metal ions for optimizing (1)H T(1) relaxation. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 184:350-6. [PMID: 17126048 PMCID: PMC1839830 DOI: 10.1016/j.jmr.2006.10.012] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Revised: 10/21/2006] [Accepted: 10/24/2006] [Indexed: 05/04/2023]
Abstract
We discuss a simple approach to enhance sensitivity for (13)C high-resolution solid-state NMR for proteins in microcrystals by reducing (1)H T(1) relaxation times with paramagnetic relaxation reagents. It was shown that (1)H T(1) values can be reduced from 0.4-0.8s to 60-70 ms for ubiquitin and lysozyme in D(2)O in the presence of 10 mM Cu(II)Na(2)EDTA without substantial degradation of the resolution in (13)C CPMAS spectra. Faster signal accumulation using the shorter (1)H T(1) attained by paramagnetic doping provided sensitivity enhancements of 1.4-2.9 for these proteins, reducing the experimental time for a given signal-to-noise ratio by a factor of 2.0-8.4. This approach presented here is likely to be applicable to various other proteins in order to enhance sensitivity in (13)C high-resolution solid-state NMR spectroscopy.
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Affiliation(s)
- Nalinda P Wickramasinghe
- Department of Chemistry, University of Illinois at Chicago, 845 W Taylor St., Chicago, IL 60607, USA
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111
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Kobayashi M, Matsuki Y, Yumen I, Fujiwara T, Akutsu H. Signal assignment and secondary structure analysis of a uniformly [13C, 15N]-labeled membrane protein, H +-ATP synthase subunit c, by magic-angle spinning solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2006; 36:279-93. [PMID: 17080295 DOI: 10.1007/s10858-006-9094-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2006] [Revised: 09/09/2006] [Accepted: 09/19/2006] [Indexed: 05/12/2023]
Abstract
Signal assignment and secondary structural analysis of uniformly [13C, 15N] labeled H+-ATP synthase subunit c from E. coli (79 residues) in the solid state were carried out by two- and three-dimensional solid-state NMR under magic-angle spinning. The protein took on a unique structure even in the solid state from the 13C linewidths of about 1.7 ppm. On the basis of several inter- and intra-residue 13C-13C and 13C-15N chemical shift correlations, 78% of Calpha, 72% of Cbeta, 62% of C' and 61% of NH signals were assigned, which provided the secondary structure information for 84% of the 79 residues. Here, inter-residue correlations involving Gly, Ala, Pro and side-chains and a higher resolution in the 3D spectrum were significantly useful for the sequence specific assignment. On top of this, the 13C-13C correlation spectra of subunit c was analyzed by reproducing experimental cross peaks quantitatively with chemical shift prediction and signal-intensity calculation based on the structure. It revealed that the subunit c in the solid state could be specified by alpha-helices with a loop structure in the middle (at sequence 41-45) as in the case of the solution structure in spite of additional extended conformations at 76-79 at the C-terminus.
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Affiliation(s)
- Masatoshi Kobayashi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
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112
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Li Y, Kijac AZ, Sligar SG, Rienstra CM. Structural analysis of nanoscale self-assembled discoidal lipid bilayers by solid-state NMR spectroscopy. Biophys J 2006; 91:3819-28. [PMID: 16905610 PMCID: PMC1630456 DOI: 10.1529/biophysj.106.087072] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2006] [Accepted: 07/18/2006] [Indexed: 01/10/2023] Open
Abstract
Nanodiscs are an example of discoidal nanoscale self-assembled lipid/protein particles similar to nascent high-density lipoproteins, which reduce the risk of coronary artery disease. The major protein component of high-density lipoproteins is human apolipoprotein A-I, and the corresponding protein component of Nanodiscs is membrane scaffold protein 1 (MSP1), a 200-residue lipid-binding domain of human apolipoprotein A-I. Here we present magic-angle spinning (MAS) solid-state NMR studies of uniformly (13)C,(15)N-labeled MSP1 in polyethylene glycol precipitated Nanodiscs. Two-dimensional MAS (13)C-(13)C correlation spectra show excellent microscopic order of MSP1 in precipitated Nanodiscs. Secondary isotropic chemical shifts throughout the protein are consistent with a predominantly helical structure. Moreover, the backbone conformations of prolines derived from their (13)C chemical shifts are consistent with the molecular belt model but not the picket fence model of lipid-bound MSP1. Overall comparison of experimental spectra and (13)C chemical shifts predicted from several structural models also favors the belt model. Our study thus supports the belt model of Nanodisc structure and demonstrates the utility of MAS NMR to study the structure of high molecular weight lipid-protein complexes.
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Affiliation(s)
- Ying Li
- Center for Biophysics and Computational Biology, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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113
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Bu Z, Shi Y, Callaway DJE, Tycko R. Molecular alignment within beta-sheets in Abeta(14-23) fibrils: solid-state NMR experiments and theoretical predictions. Biophys J 2006; 92:594-602. [PMID: 17056725 PMCID: PMC1751388 DOI: 10.1529/biophysj.106.091017] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report investigations of the molecular structure of amyloid fibrils formed by residues 14-23 of the beta-amyloid peptide associated with Alzheimer's disease (Abeta(14-23)), using solid-state nuclear magnetic resonance (NMR) techniques in conjunction with electron microscopy and atomic force microscopy. The NMR measurements, which include two-dimensional proton-mediated (13)C-(13)C exchange and two-dimensional relayed proton-mediated (13)C-(13)C exchange spectra, show that Abeta(14-23) fibrils contain antiparallel beta-sheets with a registry of backbone hydrogen bonds that aligns residue 17+k of each peptide molecule with residue 22-k of neighboring molecules in the same beta-sheet. We compare these results, as well as previously reported experimental results for fibrils formed by other beta-amyloid fragments, with theoretical predictions of molecular alignment based on databases of residue-specific alignments in antiparallel beta-sheets in known protein structures. While the theoretical predictions are not in exact agreement with the experimental results, they facilitate the design of experiments by suggesting a small number of plausible alignments that are readily distinguished by solid-state NMR.
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Affiliation(s)
- Zimei Bu
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
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114
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Krushelnitsky A, Gogolev Y, Golbik R, Dahlquist F, Reichert D. Comparison of the internal dynamics of globular proteins in the microcrystalline and rehydrated lyophilized states. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1639-45. [PMID: 17027351 DOI: 10.1016/j.bbapap.2006.08.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2006] [Revised: 08/28/2006] [Accepted: 08/31/2006] [Indexed: 11/26/2022]
Abstract
Natural abundance solid-state 13C-NMR spin-lattice relaxation experiments in the laboratory (T1) and off-resonance rotating (T(1rho)) frames were applied for qualitative comparison of the internal molecular dynamics of barstar, hen egg white lysozyme and bacteriophage T4 lysozyme in both the microcrystalline and the rehydrated (water content is 50% of the protein mass) lyophilized states. The microcrystalline state of proteins provides a better spectral resolution; however, less is known about the local structure and dynamics in the different states. We found by visual comparison of both T1 and T(1rho) relaxation decays of various resonance bands of the CPMAS spectra that within the ns-mus range of correlation times there is no appreciable difference in the internal dynamics between rehydrated lyophilized and crystalline states for all three proteins tested. This suggests that the internal conformational dynamics depends weakly if at all on inter-protein interactions in the solid state. Hence, physical properties of globular proteins in a fully hydrated solid state seem to be similar to those in solution. This result at least partly removes concerns about biological relevance of studies of globular proteins in the solid state.
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115
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Frericks HL, Zhou DH, Yap LL, Gennis RB, Rienstra CM. Magic-angle spinning solid-state NMR of a 144 kDa membrane protein complex: E. coli cytochrome bo3 oxidase. JOURNAL OF BIOMOLECULAR NMR 2006; 36:55-71. [PMID: 16964530 DOI: 10.1007/s10858-006-9070-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Accepted: 07/24/2006] [Indexed: 05/11/2023]
Abstract
Recent progress in magic-angle spinning (MAS) solid-state NMR (SSNMR) has enabled multidimensional studies of large, macroscopically unoriented membrane proteins with associated lipids, without the requirement of solubility that limits other structural techniques. Here we present initial sample preparation and SSNMR studies of a 144 kDa integral membrane protein, E. coli cytochrome bo(3) oxidase. The optimized protocol for expression and purification yields approximately 5 mg of the enzymatically active, uniformly (13)C,(15)N-enriched membrane protein complex from each liter of growth medium. The preparation retains endogenous lipids and yields spectra of high sensitivity and resolution, consistent with a folded, homogenous protein. Line widths of isolated signals are less than 0.5 ppm, with a large number of individual resonances resolved in the 2D and 3D spectra. The (13)C chemical shifts, assigned by amino acid type, are consistent with the secondary structure previously observed by diffraction methods. Although the structure is predominantly helical, the percentage of non-helical signals varies among residue types; these percentages agree well between the NMR and diffraction data. Samples show minimal evidence of degradation after several weeks of NMR data acquisition. Use of a triple resonance scroll resonator probe further improves sample stability and enables higher power decoupling, higher duty cycles and more advanced 3D experiments to be performed. These initial results in cytochrome bo(3) oxidase demonstrate that multidimensional MAS SSNMR techniques have sufficient sensitivity and resolution to interrogate selected parts of a very large uniformly (13)C,(15)N-labeled membrane protein.
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Affiliation(s)
- Heather L Frericks
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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116
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Ohgo K, Kawase T, Ashida J, Asakura T. Solid-State NMR Analysis of a Peptide (Gly-Pro-Gly-Gly-Ala)6-Gly Derived from a Flagelliform Silk Sequence of Nephila clavipes. Biomacromolecules 2006; 7:1210-4. [PMID: 16602740 DOI: 10.1021/bm0600522] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solid-state NMR is especially useful when the structures of peptides and proteins should be analyzed by taking into account the structural distribution, that is, the distribution of the torsion angle of the individual residue. In this study, two-dimensional spin-diffusion solid-state NMR spectra of 13C-double-labeled model peptides (GPGGA)6G of flagelliform silk were observed for studying the local structure in the solid state. The spin-diffusion NMR spectra calculated by assuming the torsion angles of the beta-spiral structure exclusively could not reproduce the observed spectra. In contrast, the spectra calculated by taking into account the statistical distribution of the torsion angles of the individual central residues in the sequences Ala-Gly-Pro, Gly-Pro-Gly, Pro-Gly-Gly, Gly-Gly-Ala, and Gly-Ala-Gly from PDB data could reproduce the observed spectra well. This indicates that the statistical distribution of the torsion angles should be considered for the structural model of (GPGGA)6G similar to the case of the model peptide of elastin.
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Affiliation(s)
- Kosuke Ohgo
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
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117
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118
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Lorch M, Faham S, Kaiser C, Weber I, Mason AJ, Bowie JU, Glaubitz C. How to prepare membrane proteins for solid-state NMR: A case study on the alpha-helical integral membrane protein diacylglycerol kinase from E. coli. Chembiochem 2006; 6:1693-700. [PMID: 16138309 DOI: 10.1002/cbic.200500054] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Several studies have demonstrated that it is viable to use microcrystalline preparations of water-soluble proteins as samples in solid-state NMR experiments [1-5]. Here, we investigate whether this approach holds any potential for studying water-insoluble systems, namely membrane proteins. For this case study, we have prepared proteoliposomes and small crystals of the alpha-helical membrane-protein diacylglycerol kinase (DGK). Preparations were characterised by 13C- and 15N-cross-polarization magic-angle spinning (CPMAS) NMR. It was found that crystalline samples produce better-resolved spectra than proteoliposomes. This makes them more suitable for structural NMR experiments. However, reconstitution is the method of choice for biophysical studies by solid-state NMR. In addition, we discuss the identification of lipids bound to membrane-protein crystals by 31P-MAS NMR.
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Affiliation(s)
- Mark Lorch
- Centre for Biomolecular Magnetic Resonance and Institut für Biophysikalische Chemie, J. W. Goethe Universität, Marie-Curie-Strasse 9, 60439 Frankfurt, Germany
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119
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Hiller M, Krabben L, Vinothkumar KR, Castellani F, van Rossum BJ, Kühlbrandt W, Oschkinat H. Solid-State Magic-Angle Spinning NMR of Outer-Membrane Protein G from Escherichia coli. Chembiochem 2005; 6:1679-84. [PMID: 16138308 DOI: 10.1002/cbic.200500132] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Uniformly 13C-,15N-labelled outer-membrane protein G (OmpG) from Escherichia coli was expressed for structural studies by solid-state magic-angle spinning (MAS) NMR. Inclusion bodies of the recombinant, labelled protein were purified under denaturing conditions and refolded in detergent. OmpG was reconstituted into lipid bilayers and several milligrams of two-dimensional crystals were obtained. Solid-state MAS NMR spectra showed signals with an apparent line width of 80-120 Hz (including homonuclear scalar couplings). Signal patterns for several amino acids, including threonines, prolines and serines were resolved and identified in 2D proton-driven spin-diffusion (PDSD) spectra.
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Affiliation(s)
- Matthias Hiller
- Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
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120
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Wang J, Gülich S, Bradford C, Ramirez-Alvarado M, Regan L. A Twisted Four-Sheeted Model for an Amyloid Fibril. Structure 2005; 13:1279-88. [PMID: 16154085 DOI: 10.1016/j.str.2005.06.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2005] [Revised: 06/08/2005] [Accepted: 06/14/2005] [Indexed: 11/25/2022]
Abstract
The formation of amyloid fibers and their deposition in the body is a characteristic of a number of devastating human diseases. Here, we propose a structural model, based on X-ray diffraction data, for the basic structure of an amyloid fibril formed by using the variants of the B1 domain of IgG binding protein G of Streptococcus. The model for the fibril incorporates four beta sheets in a bundle with a diameter of 45 A. Its cross-section, or layer, consists of four strands, one strand from each sheet. Layers stack on top of each other to form the fibril, which has an overall helical twist with a periodicity of about 154 A. Each strand interacts in a parallel fashion with the strands in the layers above and below it, in an infinite beta sheet. Some geometric features of this model and the logic behind it may be applicable for constructing other related cross-beta amyloid fibrils.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CN 06520, USA.
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121
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Franks WT, Zhou DH, Wylie BJ, Money BG, Graesser DT, Frericks HL, Sahota G, Rienstra CM. Magic-Angle Spinning Solid-State NMR Spectroscopy of the β1 Immunoglobulin Binding Domain of Protein G (GB1): 15N and 13C Chemical Shift Assignments and Conformational Analysis. J Am Chem Soc 2005; 127:12291-305. [PMID: 16131207 DOI: 10.1021/ja044497e] [Citation(s) in RCA: 265] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Magic-angle spinning solid-state NMR (SSNMR) studies of the beta1 immunoglobulin binding domain of protein G (GB1) are presented. Chemical shift correlation spectra at 11.7 T (500 MHz 1H frequency) were employed to identify signals specific to each amino acid residue type and to establish backbone connectivities. High sensitivity and resolution facilitated the detection and assignment of every 15N and 13C site, including the N-terminal (M1) 15NH3, the C-terminal (E56) 13C', and side-chain resonances from residues exhibiting fast-limit conformational exchange near room temperature. The assigned spectra lend novel insight into the structure and dynamics of microcrystalline GB1. Secondary isotropic chemical shifts report on conformation, enabling a detailed comparison of the microcrystalline state with the conformation of single crystals and the protein in solution; the consistency of backbone conformation in these three preparations is the best among proteins studied so far. Signal intensities and line widths vary as a function of amino acid position and temperature. High-resolution spectra are observed near room temperature (280 K) and at <180 K, whereas resolution and sensitivity greatly degrade substantially near 210 K; the magnitude of this effect is greatest among the side chains of residues at the intermolecular interface of the microcrystal lattice, which we attribute to intermediate-rate translational diffusion of solvent molecules near the glass transition. These features of GB1 will enable its use as an excellent model protein not only for SSNMR methods development but also for fundamental studies of protein thermodynamics in the solid state.
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Affiliation(s)
- W Trent Franks
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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122
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Seidel K, Etzkorn M, Heise H, Becker S, Baldus M. High-Resolution Solid-State NMR Studies on Uniformly [13C,15N]-Labeled Ubiquitin. Chembiochem 2005; 6:1638-47. [PMID: 16094694 DOI: 10.1002/cbic.200500085] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Understanding of the effects of intermolecular interactions, molecular dynamics, and sample preparation on high-resolution magic-angle spinning NMR data is currently limited. Using the example of a uniformly [13C,15N]-labeled sample of ubiquitin, we discuss solid-state NMR methods tailored to the construction of 3D molecular structure and study the influence of solid-phase protein preparation on solid-state NMR spectra. A comparative analysis of 13C', 13Calpha, and 13Cbeta resonance frequencies suggests that 13C chemical-shift variations are most likely to occur in protein regions that exhibit an enhanced degree of molecular mobility. Our results can be refined by additional solid-state NMR techniques and serve as a reference for ongoing efforts to characterize the structure and dynamics of (membrane) proteins, protein complexes, and other biomolecules by high-resolution solid-state NMR.
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Affiliation(s)
- Karsten Seidel
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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123
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Zech SG, Wand AJ, McDermott AE. Protein structure determination by high-resolution solid-state NMR spectroscopy: application to microcrystalline ubiquitin. J Am Chem Soc 2005; 127:8618-26. [PMID: 15954766 DOI: 10.1021/ja0503128] [Citation(s) in RCA: 181] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High-resolution solid-state NMR spectroscopy has become a promising method for the determination of three-dimensional protein structures for systems which are difficult to crystallize or exhibit low solubility. Here we describe the structure determination of microcrystalline ubiquitin using 2D (13)C-(13)C correlation spectroscopy under magic angle spinning conditions. High-resolution (13)C spectra have been acquired from hydrated microcrystals of site-directed (13)C-enriched ubiquitin. Inter-residue carbon-carbon distance constraints defining the global protein structure have been evaluated from 'dipolar-assisted rotational resonance' experiments recorded at various mixing times. Additional constraints on the backbone torsion angles have been derived from chemical shift analysis. Using both distance and dihedral angle constraints, the structure of microcrystalline ubiquitin has been refined to a root-mean-square deviation of about 1 A. The structure determination strategies for solid samples described herein are likely to be generally applicable to many proteins that cannot be studied by X-ray crystallography or solution NMR spectroscopy.
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Affiliation(s)
- Stephan G Zech
- Department of Chemistry, Columbia University, 3000 Broadway Mail Code 3113, New York, New York 10027, USA.
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124
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Bang D, Makhatadze GI, Tereshko V, Kossiakoff AA, Kent SB. Total Chemical Synthesis and X-ray Crystal Structure of a Protein Diastereomer: [D-Gln 35]Ubiquitin. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200463040] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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125
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Bang D, Makhatadze GI, Tereshko V, Kossiakoff AA, Kent SB. Total Chemical Synthesis and X-ray Crystal Structure of a Protein Diastereomer: [D-Gln 35]Ubiquitin. Angew Chem Int Ed Engl 2005; 44:3852-6. [PMID: 15834850 DOI: 10.1002/anie.200463040] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Duhee Bang
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
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126
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Cvetkovic A, Picioreanu C, Straathof AJJ, Krishna R, van der Wielen LAM. Quantification of Binary Diffusion in Protein Crystals. J Phys Chem B 2005; 109:10561-6. [PMID: 16852280 DOI: 10.1021/jp050289c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The use of confocal laser scanning microscopy for visualization and quantification of binary diffusion within anisotropic porous material is described here for the first time. The dynamics of adsorption profiles of dianionic fluorescein, zwitterionic rhodamine B, and their mixture in the cationic native orthorhombic lysozyme crystal were subsequently analyzed. All data could be described by a classical pore diffusion model. There was no change in the adsorption characteristics, but diffusion decreased with the introduction of a second solute in the solution. It was found that diffusion is determined by the combination of steric and electrostatic interactions,while adsorption is dependent on electrostatic and hydrophobic interactions. Thus, it was established that the outcome of binary transport depends on the solute, protein, and crystal characteristics.
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Affiliation(s)
- Aleksandar Cvetkovic
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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127
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Luo W, Yao X, Hong M. Large Structure Rearrangement of Colicin Ia Channel Domain after Membrane Binding from 2D13C Spin Diffusion NMR. J Am Chem Soc 2005; 127:6402-8. [PMID: 15853348 DOI: 10.1021/ja0433121] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One of the main mechanisms of membrane protein folding is by spontaneous insertion into the lipid bilayer from the aqueous environment. The bacterial toxin, colicin Ia, is one such protein. To shed light on the conformational changes involved in this dramatic transfer from the polar to the hydrophobic milieu, we carried out 2D magic-angle spinning (13)C NMR experiments on the water-soluble and membrane-bound states of the channel-forming domain of colicin Ia. Proton-driven (13)C spin diffusion spectra of selectively (13)C-labeled protein show unequivocal attenuation of cross-peaks after membrane binding. This attenuation can be assigned to distance increases but not reduction of the diffusion coefficient. Analysis of the statistics of the interhelical and intrahelical (13)C-(13)C distances in the soluble protein structure indicates that the observed cross-peak reduction is well correlated with a high percentage of short interhelical contacts in the soluble protein. This suggests that colicin Ia channel domain becomes open and extended upon membrane binding, thus lengthening interhelical distances. In comparison, cross-peaks with similar intensities between the two states are dominated by intrahelical contacts in the soluble state. This suggests that the membrane-bound structure of colicin Ia channel domain may be described as a "molten globule", in which the helical secondary structure is retained while the tertiary structure is unfolded. This study demonstrates that (13)C spin diffusion NMR is a valuable tool for obtaining qualitative long-range distance constraints on membrane protein folding.
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Affiliation(s)
- Wenbin Luo
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
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128
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McDermott AE. Structural and dynamic studies of proteins by solid-state NMR spectroscopy: rapid movement forward. Curr Opin Struct Biol 2005; 14:554-61. [PMID: 15465315 DOI: 10.1016/j.sbi.2004.09.007] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2004] [Revised: 08/24/2004] [Accepted: 09/03/2004] [Indexed: 10/26/2022]
Abstract
Starting only a few years ago, many solid-state NMR spectroscopy laboratories have become engaged in solving the complete structures of biological macromolecules using high-resolution methods based on magic angle spinning. These efforts typically involve structurally homogeneous samples, and utilize recently developed pulse sequences for the sequential correlation of resonances, the detection of tertiary contacts and the characterization of torsion angles. Thereby, systems have been studied that evaded other, more established, structure determination methods.
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Affiliation(s)
- Ann E McDermott
- Columbia University, Department of Chemistry, MC 3113, 3000 Broadway, New York, New York 10027, USA.
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129
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Basu SK, Govardhan CP, Jung CW, Margolin AL. Protein crystals for the delivery of biopharmaceuticals. Expert Opin Biol Ther 2005; 4:301-17. [PMID: 15006725 DOI: 10.1517/14712598.4.3.301] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The year 2002 marked the 20th anniversary of the first successful product of modern biotechnology, the regulatory approval of recombinant insulin for biopharmaceutical applications. Insulin is also the first crystalline protein to be approved for therapeutic use. Over the past two decades, almost 150 biopharmaceuticals have gained marketing authorisation; however, insulin remains the only crystalline protein on the market. Significant research and development efforts have focused on the engineering of protein molecules, efficacy testing, model development, and protein production and characterisation. These advances have dramatically boosted the therapeutic applications of proteins, which now include treatments against acute conditions, such as cancer, cardiovascular disease and viral disease, and chronic conditions, such as diabetes, growth hormone deficiency, haemophilia, arthritis, psoriasis and Crohn's disease. Despite these successes, many challenges normally associated with biopharmaceuticals, such as poor stability and limited delivery options, remain. Protein crystals have shown significant benefits in the delivery of biopharmaceuticals to achieve high concentration, low viscosity formulation and controlled release protein delivery. This review will discuss challenges related to the broader utilisation of protein crystals in biopharmaceutical applications, as well as recent advances and valuable new directions that protein crystallisation-based technologies present.
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Affiliation(s)
- Sujit K Basu
- Altus Biologics Inc., 625 Putnam Avenue, Cambridge, MA 02139, USA
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130
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Stringer JA, Bronnimann CE, Mullen CG, Zhou DH, Stellfox SA, Li Y, Williams EH, Rienstra CM. Reduction of RF-induced sample heating with a scroll coil resonator structure for solid-state NMR probes. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2005; 173:40-8. [PMID: 15705511 DOI: 10.1016/j.jmr.2004.11.015] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2004] [Revised: 11/04/2004] [Indexed: 05/15/2023]
Abstract
Heating due to high power 1H decoupling limits the experimental lifetime of protein samples for solid-state NMR (SSNMR). Sample deterioration can be minimized by lowering the experimental salt concentration, temperature or decoupling fields; however, these approaches may compromise biological relevance and/or spectroscopic resolution and sensitivity. The desire to apply sophisticated multiple pulse experiments to proteins therefore motivates the development of probes that utilize the RF power more efficiently to generate a high ratio of magnetic to electric field in the sample. Here a novel scroll coil resonator structure is presented and compared to a traditional solenoid. The scroll coil is demonstrated to be more tolerant of high sample salt concentrations and cause less RF-induced sample heating. With it, the viable experimental lifetime of a microcrystalline ubiquitin sample has been extended by more than an order of magnitude. The higher B1 homogeneity and permissible decoupling fields enhance polarization transfer efficiency in 15N-13C correlation experiments employed for protein chemical shift assignments and structure determination.
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Affiliation(s)
- John A Stringer
- Varian, Inc., 2607 Midpoint Drive, Fort Collins, CO 80525, USA
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131
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Heise H, Seidel K, Etzkorn M, Becker S, Baldus M. 3D NMR spectroscopy for resonance assignment and structure elucidation of proteins under MAS: novel pulse schemes and sensitivity considerations. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2005; 173:64-74. [PMID: 15705514 DOI: 10.1016/j.jmr.2004.11.020] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2004] [Revised: 11/15/2004] [Indexed: 05/24/2023]
Abstract
Two types of 3D MAS NMR experiments are introduced, which combine standard (NC,CC) transfer schemes with (1H,1H) mixing to simultaneously detect connectivities and structural constraints of uniformly 15N,13C-labeled proteins with high spectral resolution. The homonuclear CCHHC and CCC experiments are recorded with one double-quantum evolution dimension in order to avoid a cubic diagonal in the spectrum. Depending on the second transfer step, spin systems or proton-proton contacts can be determined with reduced spectral overlap. The heteronuclear NHHCC experiment encodes NH-HC proton-proton interactions, which are indicative for the backbone conformation of the protein. The third dimension facilitates the identification of the amino acid spin system. Experimental results on U-[15N,13C]valine and U-[15N,13C]ubiquitin demonstrate their usefulness for resonance assignments and for the determination of structural constraints. Furthermore, we give a detailed analysis of alternative multidimensional sampling schemes and their effect on sensitivity and resolution.
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Affiliation(s)
- Henrike Heise
- Department for NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany.
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132
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Morcombe CR, Paulson EK, Gaponenko V, Byrd RA, Zilm KW. 1H-15N correlation spectroscopy of nanocrystalline proteins. JOURNAL OF BIOMOLECULAR NMR 2005; 31:217-230. [PMID: 15803395 DOI: 10.1007/s10858-005-0527-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2004] [Accepted: 12/20/2004] [Indexed: 05/24/2023]
Abstract
The limits of resolution that can be obtained in 1H-15N 2D NMR spectroscopy of isotopically enriched nanocrystalline proteins are explored. Combinations of frequency switched Lee-Goldburg (FSLG) decoupling, fast magic angle sample spinning (MAS), and isotopic dilution via deuteration are investigated as methods for narrowing the amide 1H resonances. Heteronuclear decoupling of 15N from the 1H resonances is also studied. Using human ubiquitin as a model system, the best resolution is most easily obtained with uniformly 2H and 15N enriched protein where the amides have been exchanged in normal water, MAS at approximately 20 kHz, and WALTZ-16 decoupling of the 15N nuclei. The combination of these techniques results in average 1H lines of only approximately 0.26 ppm full width at half maximum. Techniques for optimizing instrument stability and 15N decoupling are described for achieving the best possible performance in these experiments.
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Affiliation(s)
- Corey R Morcombe
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520-8107, USA
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133
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Cvetkovic A, Straathof AJJ, Krishna R, van der Wielen LAM. Adsorption of xanthene dyes by lysozyme crystals. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2005; 21:1475-1480. [PMID: 15697297 DOI: 10.1021/la0478090] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Adsorption characteristics of cross-linked lysozyme crystals of different morphologies (tetragonal, orthorhombic, triclinic and monoclinic) were examined using four anionic dyes (fluorescein, eosin, erythrosin, and rose bengal), one zwitterionic dye (rhodamine B), and one cationic dye (rhodamine 6G). The adsorption isotherms were of the Langmuir type for all examined systems with the exception of rhodamine B adsorption by monoclinic crystals. The weakest adsorption was observed for the cationic dye, rhodamine B, whereas dianionic dyes, eosin, rose bengal, and erythrosin were strongly adsorbed on the protein surface. The adsorption capacities of the crystals for the dyes were found to depend on both charge and hydrophobicity of the dye, reflecting the heterogeneous character of the lysozyme pore surface. The adsorption affinity of the crystals for the dyes was a function of the dyes' hydrophobicity. Furthermore, the crystal morphology was identified as an additional factor determining capacity and affinity for dye adsorption. Differences between crystals prepared in the presence of the same precipitant were lower than between morphologies prepared with different precipitants.
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Affiliation(s)
- Aleksandar Cvetkovic
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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134
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Cvetkovic A, Picioreanu C, Straathof AJJ, Krishna R, van der Wielen LAM. Relation between Pore Sizes of Protein Crystals and Anisotropic Solute Diffusivities. J Am Chem Soc 2004; 127:875-9. [PMID: 15656625 DOI: 10.1021/ja0440708] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The diffusion of a solute, fluorescein, into lysozyme protein crystals with different pore structures was investigated. To determine the diffusion coefficients, three-dimensional solute concentration fields acquired by confocal laser scanning microscopy (CLSM) during diffusion into the crystals were compared with the output of a time-dependent 3-D diffusion model. The diffusion process was found to be anisotropic, and the degree of anisotropy increased in the order: triclinic, tetragonal and orthorhombic crystal morphology. A linear correlation between the pore diffusion coefficients and the pore sizes was established. The maximum size of the solute, deduced from the established correlation of diffusion coefficients and pore size, was 0.73 +/- 0.06 nm, which was in the range of the average diameter of fluorescein (0.69 +/- 0.02 nm). This proves that size exclusion is the key mechanism for solute diffusion in protein crystals. Hence, the origin of solute diffusion anisotropy can be found in the packing of the protein molecules in the crystals, which determines the crystal pore organization.
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Affiliation(s)
- Aleksandar Cvetkovic
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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135
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Abstract
The fact that membrane proteins are notoriously difficult to analyse using standard protocols for atomic-resolution structure determination methods have motivated adaptation of these techniques to membrane protein studies as well as development of new technologies. With this motivation, liquid-state nuclear magnetic resonance (NMR) has recently been used with success for studies of peptides and membrane proteins in detergent micelles, and solid-state NMR has undergone a tremendous evolution towards characterization of membrane proteins in native membrane and oriented phospholipid bilayers. In this mini-review, we describe some of the technological challenges behind these efforts and provide examples on their use in membrane biology.
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Affiliation(s)
- Nielschr Nielsen
- Department of Chemistry, University of Aarhus, Aarhus C, Denmark.
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136
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Zech SG, Olejniczak E, Hajduk P, Mack J, McDermott AE. Characterization of Protein−Ligand Interactions by High-Resolution Solid-State NMR Spectroscopy. J Am Chem Soc 2004; 126:13948-53. [PMID: 15506755 DOI: 10.1021/ja040086m] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel approach for detection of ligand binding to a protein in solid samples is described. Hydrated precipitates of the anti-apoptotic protein Bcl-xL show well-resolved (13)C-(13)C 2D solid-state NMR spectra that allow site-specific assignment of resonances for many residues in uniformly (13)C-enriched samples. Binding of a small peptide or drug-like organic molecule leads to changes in the chemical shift of resonances from multiple residues in the protein that can be monitored to characterize binding. Differential chemical shifts can be used to distinguish between direct protein-ligand contacts and small conformational changes of the protein induced by ligand binding. The agreement with prior solution-state NMR results indicates that the binding pocket in solid and liquid samples is similar for this protein. Advantages of different labeling schemes involving selective (13)C enrichment of methyl groups of Ala, Val, Leu, and Ile (Cdelta1) for characterizing protein-ligand interactions are also discussed. It is demonstrated that high-resolution solid-state NMR spectroscopy on uniformly or extensively (13)C-enriched samples has the potential to screen proteins of moderate size ( approximately 20 kDa) for ligand binding as hydrated solids. The results presented here suggest the possibility of using solid-state NMR to study ligand binding in proteins not amenable to solution NMR.
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Affiliation(s)
- Stephan G Zech
- Department of Chemistry, Columbia University, New York, New York 10027, USA
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137
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Bernard GM, Miskolzie M, Kotovych G, Wasylishen RE. A solid-state NMR investigation of orexin-B. CAN J CHEM 2004. [DOI: 10.1139/v04-131] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Some key aspects of the secondary structure of solid orexin-B, a 28 amino-acid peptide, have been investigated by solid-state NMR spectroscopy. The 13C15N dipolar coupling between the carbonyl carbon of Leu11 and the nitrogen of Leu15, as determined by rotational echo double resonance (REDOR) experiments, is 35 Hz, indicating that these nuclei are separated by approximately 4.5 Å. This distance is consistent with the α-helical structure determined for this segment of orexin-B by solution NMR measurements. REDOR measurements of the dipolar coupling between the carbonyl carbon of Ala17 and the nitrogen of Ala22 support the contention in an earlier solution NMR study that a bend exists between the two α helices of orexin-B. However, in the solid state the internuclear distance (6.4 Å) is significantly greater than that observed for orexin-B in aqueous solution. In addition to the distance measurements, the principal components of the amide carbonyl carbon chemical shift (CS) tensors for Leu11 and Ala17 and of the amide nitrogen CS tensors for Leu15 and Ala22 are reported. There are only minor differences between the amide carbonyl carbon CS tensors for Leu11 and Ala17 and between the nitrogen CS tensors for Leu15 and Ala22.Key words: orexin-B, solid-state NMR, REDOR, chemical shift tensors.
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138
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Caldeira J, Figueirinhas JL, Santos C, Godinho MH. EPR spectroscopy of protein microcrystals oriented in a liquid crystalline polymer medium. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2004; 170:213-219. [PMID: 15388083 DOI: 10.1016/j.jmr.2004.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2004] [Revised: 06/14/2004] [Indexed: 05/24/2023]
Abstract
Correlation of the g-tensor of a paramagnetic active center of a protein with its structure provides a unique experimental information on the electronic structure of the metal site. To address this problem, we made solid films containing metalloprotein (Desulfovibrio gigas cytochrome c(3)) microcrystals. The microcrystals in a liquid crystalline polymer medium (water/hydroxypropylcellulose) were partially aligned by a shear flow. A strong orientation effect of the metalloprotein was observed by EPR spectroscopy and polarizing optical microscopy. The EPR spectra of partially oriented samples were simulated, allowing for molecular orientation distribution function determination. The observed effect results in enhanced sensitivity and resolution of the EPR spectra and provides a new approach towards the correlation of spectroscopic data, obtained by EPR or some other technique, with the three-dimensional structure of a protein or a model compound.
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Affiliation(s)
- Jorge Caldeira
- Requimte/Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
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139
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Giraud N, Böckmann A, Lesage A, Penin F, Blackledge M, Emsley L. Site-Specific Backbone Dynamics from a Crystalline Protein by Solid-State NMR Spectroscopy. J Am Chem Soc 2004; 126:11422-3. [PMID: 15366872 DOI: 10.1021/ja046578g] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Site-specific nitrogen-15 longitudinal relaxation rates are measured for the microcrystalline dimeric form of the protein Crh using multidimensional high-resolution solid-state NMR methods. The measured rates are used to provide a qualitative description of the site-specific internal mobility of the protein present in the solid state.
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Affiliation(s)
- Nicolas Giraud
- Laboratoire de Chimie, UMR 5182 CNRS/ENS, Laboratoire de Recherche Conventionné du CEA (no. 23V), Ecole Normale Supérieure de Lyon, 69364 Lyon, France
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140
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Martin RW, Zilm KW. Variable temperature system using vortex tube cooling and fiber optic temperature measurement for low temperature magic angle spinning NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2004; 168:202-209. [PMID: 15140428 DOI: 10.1016/j.jmr.2004.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2003] [Revised: 03/05/2004] [Indexed: 05/24/2023]
Abstract
We describe the construction and operation of a variable temperature (VT) system for a high field fast magic angle spinning (MAS) probe. The probe is used in NMR investigations of biological macromolecules, where stable setting and continuous measurement of the temperature over periods of several days are required in order to prevent sample overheating and degradation. The VT system described is used at and below room temperature. A vortex tube is used to provide cooling in the temperature range of -20 to 20 degrees C, while a liquid nitrogen-cooled heat exchanger is used below -20 degrees C. Using this arrangement, the lowest temperature that is practically achievable is -140 degrees C. Measurement of the air temperature near the spinning rotor is accomplished using a fiber optic thermometer that utilizes the temperature dependence of the absorption edge of GaAs. The absorption edge of GaAs also has a magnetic field dependence that we have measured and corrected for. This dependence was calibrated at several field strengths using the well-known temperature dependence of the (1)H chemical shift difference of the protons in methanol.
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Affiliation(s)
- Rachel W Martin
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520-8107, USA
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141
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Igumenova TI, McDermott AE, Zilm KW, Martin RW, Paulson EK, Wand AJ. Assignments of Carbon NMR Resonances for Microcrystalline Ubiquitin. J Am Chem Soc 2004; 126:6720-7. [PMID: 15161300 DOI: 10.1021/ja030547o] [Citation(s) in RCA: 168] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solid-state NMR 2D spectroscopy was used to correlate carbon backbone and side-chain chemical shifts for uniformly (13)C,(15)N-enriched microcrystalline ubiquitin. High applied field strengths, 800 MHz for protons, moderate proton decoupling fields, 80-100 kHz, and high magic angle sample spinning frequencies, 20 kHz, were used to narrow the most of the carbon line widths to 0.5-0.8 ppm. Homonuclear magnetization transfer was effected by matching the proton RF field to the spinning frequency, the so-called dipolar-assisted rotational resonance (DARR) (Takegoshi, K.; Nakamura, S.; Terao, T. Chem. Phys. Lett. 2001, 344, 631-637), and a mixing time of 20 ms was used to maximize the intensity of one-bond transfers between carbon atoms. This polarization transfer sequence resulted in roughly 14% transfer efficiencies for directly bonded carbon pairs and 4% transfer efficiencies for carbons separated by a third carbon. With this simple procedure, the majority of the one-bond correlations was observed with moderate transfer efficiencies, and many two-bond correlations were also observed with weaker intensities. Spin systems could be identified for more than half of the amino acid side chains, and site-specific assignments were readily possible via comparison with 400 MHz (15)N-(13)C-(13)C correlation spectroscopy (described separately).
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Affiliation(s)
- Tatyana I Igumenova
- Department of Chemistry, Columbia University, 3000 Broadway MC 3113, New York, New York 10027, USA
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142
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Krabben L, van Rossum BJ, Castellani F, Bocharov E, Schulga AA, Arseniev AS, Weise C, Hucho F, Oschkinat H. Towards structure determination of neurotoxin II bound to nicotinic acetylcholine receptor: a solid-state NMR approach. FEBS Lett 2004; 564:319-24. [PMID: 15111116 DOI: 10.1016/s0014-5793(04)00252-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2003] [Accepted: 02/23/2004] [Indexed: 11/19/2022]
Abstract
Solid-state magic-angle spinning nuclear magnetic resonance (NMR) has sufficient resolving power for full assignment of resonances and structure determination of immobilised biological samples as was recently shown for a small microcrystalline protein. In this work, we show that highly resolved spectra may be obtained from a system composed of a receptor-toxin complex. The NMR sample used for our studies consists of a membrane preparation of the nicotinic acetylcholine receptor from the electric organ of Torpedo californica which was incubated with uniformly 13C-,15N-labelled neurotoxin II. Despite the large size of the ligand-receptor complex ( > 290 kDa) and the high lipid content of the sample, we were able to detect and identify residues from the ligand. The comparison with solution NMR data of the free toxin indicates that its overall structure is very similar when bound to the receptor, but significant changes were observed for one isoleucine.
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Affiliation(s)
- Ludwig Krabben
- Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, D-13125 Berlin, Germany.
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143
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Paulson EK, Morcombe CR, Gaponenko V, Dancheck B, Byrd RA, Zilm KW. Sensitive high resolution inverse detection NMR spectroscopy of proteins in the solid state. J Am Chem Soc 2004; 125:15831-6. [PMID: 14677974 DOI: 10.1021/ja037315+] [Citation(s) in RCA: 182] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new indirect detection scheme for obtaining (15)N/(1)H shift correlation spectra in crystalline proteins is described. Excellent water suppression is achieved without the need for pulsed field gradients, and using only a 2-step phase cycle. Careful attention to overall NMR instrument stability was found critical for obtaining the best resolution and sensitivity. Magnetic dilution by deuteration of the protein in combination with high-speed magic angle spinning produces (1)H resonances averaging only 0.22 ppm in width, and in some cases lines as narrow as 0.17 ppm are obtained. In application to two different polymorphs of ubiquitin, structure dependent differences in both (15)N and (1)H amide chemical shifts are observed. In one case, distinct shifts for different molecules in the asymmetric unit are seen, and all differ substantially from solution NMR shifts. A gain of 7 in sensitivity makes the method competitive with solution NMR as long as nanocrystalline samples are available.
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Affiliation(s)
- Eric K Paulson
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, USA
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