1
|
Kamihara T, Takegoshi K. Rotational resonance for a heteronuclear spin pair under magic-angle spinning in solid-state NMR. J Chem Phys 2017; 146:154202. [PMID: 28433023 DOI: 10.1063/1.4980156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Rotational resonance (R2) is one of the widely applied techniques in solid-state NMR for recoupling a homonuclear dipolar interaction under magic-angle spinning (MAS). R2 occurs as the result of interference between the difference of the chemical shifts and MAS. In this work, we extend R2 to a heteronuclear dipolar interaction in the interaction frame of RF irradiation. Based on the average Hamiltonian theory, we show that the recoupling of the heteronuclear dipolar (I-S) interaction occurs at the recoupling conditions written as ΩI'±ΩS'=kωr (k=0,±1,±2), where ΩX' is the RF offset for spin-X (X = I or S) scaled by RF irradiation. The new recoupling sequence for a heteronuclear spin pair is referred to as offset-driven cross polarization along the z axis (OD-CPZ). With the robustness for RF inhomogeneity and ten recoupling conditions to choose, OD-CPZ can be a useful frequency-selective cross polarization method. Experiments and numerical simulations are shown with the results of the theoretical analysis.
Collapse
Affiliation(s)
- Takayuki Kamihara
- Division of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - K Takegoshi
- Division of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| |
Collapse
|
2
|
Traaseth NJ, Veglia G. Frequency-selective heteronuclear dephasing and selective carbonyl labeling to deconvolute crowded spectra of membrane proteins by magic angle spinning NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 211:18-24. [PMID: 21482162 PMCID: PMC3328402 DOI: 10.1016/j.jmr.2011.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/10/2011] [Accepted: 03/14/2011] [Indexed: 05/15/2023]
Abstract
We present a new method that combines carbonyl-selective labeling with frequency-selective heteronuclear recoupling to resolve the spectral overlap of magic angle spinning (MAS) NMR spectra of membrane proteins in fluid lipid membranes with broad lines and high redundancy in the primary sequence. We implemented this approach in both heteronuclear (15)N-(13)C(α) and homonuclear (13)C-(13)C dipolar assisted rotational resonance (DARR) correlation experiments. We demonstrate its efficacy for the membrane protein phospholamban reconstituted in fluid PC/PE/PA lipid bilayers. The main advantage of this method is to discriminate overlapped (13)C(α) resonances by strategically labeling the preceding residue. This method is highly complementary to (13)C(i-1)(')-(15)N(i)-(13)C(i)(α) and (13)C(i-1)(α)-(15)N(i-1)-(13)C(i)(') experiments to distinguish inter-residue spin systems at a minimal cost to signal-to-noise.
Collapse
Affiliation(s)
- Nathaniel J. Traaseth
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55445
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55445
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55445
| |
Collapse
|
3
|
Biophysical studies of the interactions between the phage varphiKZ gp144 lytic transglycosylase and model membranes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:263-76. [PMID: 19669132 DOI: 10.1007/s00249-009-0530-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Revised: 07/14/2009] [Accepted: 07/22/2009] [Indexed: 10/20/2022]
Abstract
The use of naturally occurring lytic bacteriophage proteins as specific antibacterial agents is a promising way to treat bacterial infections caused by antibiotic-resistant pathogens. The opportunity to develop bacterial resistance to these agents is minimized by their broad mechanism of action on bacterial membranes and peptidoglycan integrity. In the present study, we have investigated lipid interactions of the gp144 lytic transglycosylase from the Pseudomonas aeruginosa phage varphiKZ. Interactions with zwitterionic lipids characteristic of eukaryotic cells and with anionic lipids characteristic of bacterial cells were studied using fluorescence, solid-state nuclear magnetic resonance, Fourier transform infrared, circular dichroism, Langmuir monolayers, and Brewster angle microscopy (BAM). Gp144 interacted preferentially with anionic lipids, and the presence of gp144 in anionic model systems induced membrane disruption and lysis. Lipid domain formation in anionic membranes was observed by BAM. Gp144 did not induce disruption of zwitterionic membranes but caused an increase in rigidity of the lipid polar head group. However, gp144 interacted with zwitterionic and anionic lipids in a model membrane system containing both lipids. Finally, the gp144 secondary structure was not significantly modified upon lipid binding.
Collapse
|
4
|
Grage SL, Suleymanova AV, Afonin S, Wadhwani P, Ulrich AS. Solid state NMR analysis of the dipolar couplings within and between distant CF3-groups in a membrane-bound peptide. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2006; 183:77-86. [PMID: 16919983 DOI: 10.1016/j.jmr.2006.07.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2006] [Revised: 07/11/2006] [Accepted: 07/14/2006] [Indexed: 05/11/2023]
Abstract
Dipolar couplings contain information on internuclear distances as well as orientational constraints. To characterize the structure of the antimicrobial peptide gramicidin S when bound to model membranes, two rigid 4-CF3-phenylglycine labels were attached to the cyclic backbone such that they reflect the behavior of the entire peptide. By solid state 19F NMR we measured the homonuclear dipolar couplings of the two trifluoromethyl-groups in oriented membrane samples. Using the CPMG experiment, both the strong couplings within each CF3-group as well as the weak coupling between the two CF3-groups could be detected. An intra-CF3-group dipolar coupling of 86 Hz and a weak inter-group coupling of 20 Hz were obtained by lineshape simulation of the complex dipolar spectrum. It is thus possible to explore the large distance range provided by 19F-labels and to resolve weak dipolar couplings even in the presence of strong intra-CF3 couplings. We applied this approach to distinguish and assign two epimers of the labeled gramicidin S peptide on the basis of their distinct 19F dipolar coupling patterns.
Collapse
Affiliation(s)
- Stephan L Grage
- Institute of Biological Interfaces, Forschungszentrum Karlsruhe, P.O. Box 3640, 76021 Karlsruhe, Germany
| | | | | | | | | |
Collapse
|
5
|
Jehle S, Hiller M, Rehbein K, Diehl A, Oschkinat H, van Rossum BJ. Spectral editing: selection of methyl groups in multidimensional solid-state magic-angle spinning NMR. JOURNAL OF BIOMOLECULAR NMR 2006; 36:169-77. [PMID: 17031530 DOI: 10.1007/s10858-006-9078-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: 04/26/2006] [Accepted: 08/08/2006] [Indexed: 05/12/2023]
Abstract
A simple spectroscopic filtering technique is presented that may aid the assignment of (13)C and (15)N resonances of methyl-containing amino-acids in solid-state magic-angle spinning (MAS) NMR. A filtering block that selects methyl resonances is introduced in two-dimensional (2D) (13)C-homonuclear and (15)N-(13)C heteronuclear correlation experiments. The 2D (13)C-(13)C correlation spectra are recorded with the methyl filter implemented prior to a (13)C-(13)C mixing step. It is shown that these methyl-filtered (13)C-homonuclear correlation spectra are instrumental in the assignment of C(delta) resonances of leucines by suppression of C(gamma)-C(delta) cross peaks. Further, a methyl filter is implemented prior to a (15)N-(13)C transferred-echo double resonance (TEDOR) exchange scheme to obtain 2D (15)N-(13)C heteronuclear correlation spectra. These experiments provide correlations between methyl groups and backbone amides. Some of the observed sequential (15)N-(13)C correlations form the basis for initial sequence-specific assignments of backbone signals of the outer-membrane protein G.
Collapse
Affiliation(s)
- Stefan Jehle
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, D-13125, Berlin, Germany
| | | | | | | | | | | |
Collapse
|
6
|
Aussenac F, Lavigne B, Dufourc EJ. Toward bicelle stability with ether-linked phospholipids: temperature, composition, and hydration diagrams by 2H and 31P solid-state NMR. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2005; 21:7129-35. [PMID: 16042433 DOI: 10.1021/la050243a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Phosphorus and deuterium wide line NMR was used to determine diagrams of binary mixtures of 1,2-di-O-tetradecyl-sn-glycero-3-phosphocholine (DIOMPC) and 1,2-di-O-hexyl-sn-glycero-3-phosphocholine (DIOHPC) ether-phospholipids. By varying the hydration, h, the temperature, T, and the mole fraction, X, of long-chain ether-phospholipids, we delineated the conditions for which such systems are oriented by the magnetic field, in the presence of 100 mM KCl. The 3D domain is found for X = 62-90%, T = 27-50 degrees C, and h = 70-98%. At 80% hydration, the domain shape (X = 70-90% and T = 27-42 degrees C) is close to that already observed for ester-phospholipids mixtures (Raffard, G.; Steinbruckner, S.; Arnold, A.; Davis, J. H.; Dufourc, E. J. Langmuir 2000, 16, 7655-7662) where disc-shaped bicelles of 300-600 A have been found by electron microscopy (Arnold, A.; Labrot, T.; Oda, R.; Dufourc, E. J. Biophys. J. 2002, 83, 2667-2680). Systems made of ether-linked lipids are much more stable on time and acidic conditions than those made of ester lipids. Assuming that the disc-shaped species are also found with ether lipids, their diameter as determined from integration of phosphorus NMR lines ranges from 240 to 440 A +/- 10%; it is generally independent of hydration and temperature but decreases with decreasing long-chain lipid content, X. The structure and the dynamics of water in the DIOMPC-DIOHPC were characterized by (2)H NMR. Water exchanges between the membrane surface where it is bound and a bulk isotropic pool lead to an average ordered state for temperatures in the bicelle region and above, thus offering a larger thermal span for structural studies of dissolved molecules.
Collapse
Affiliation(s)
- Fabien Aussenac
- Bruker Biospin, Laboratoire d'applications, Wissembourg, France, and UMR5144 CNRS-UBx1, Institut Européen de Chimie et Biologie, Pessac, France
| | | | | |
Collapse
|
7
|
Grage SL, Wang J, Cross TA, Ulrich AS. Solid-state 19F-NMR analysis of 19F-labeled tryptophan in gramicidin A in oriented membranes. Biophys J 2002; 83:3336-50. [PMID: 12496101 PMCID: PMC1302409 DOI: 10.1016/s0006-3495(02)75334-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The response of membrane-associated peptides toward the lipid environment or other binding partners can be monitored by solid-state NMR of suitably labeled side chains. Tryptophan is a prominent amino acid in transmembrane helices, and its (19)F-labeled analogues are generally biocompatible and cause little structural perturbation. Hence, we use 5F-Trp as a highly sensitive NMR probe to monitor the conformation and dynamics of the indole ring. To establish this (19)F-NMR strategy, gramicidin A was labeled with 5F-Trp in position 13 or 15, whose chi(1)/chi(2) torsion angles are known from previous (2)H-NMR studies. First, the alignment of the (19)F chemical shift anisotropy tensor within the membrane was deduced by lineshape analysis of oriented samples. Next, the three principal axes of the (19)F chemical shift anisotropy tensor were assigned within the molecular frame of the indole ring. Finally, determination of chi(1)/chi(2) for 5F-Trp in the lipid gel phase showed that the side chain alignment differs by up to 20 degrees from its known conformation in the liquid crystalline state. The sensitivity gain of (19)F-NMR and the reduction in the amount of material was at least 10-fold compared with previous (2)H-NMR studies on the same system and 100-fold compared with (15)N-NMR.
Collapse
|
8
|
Venter H, Ashcroft AE, Keen JN, Henderson PJF, Herbert RB. Molecular dissection of membrane-transport proteins: mass spectrometry and sequence determination of the galactose-H+ symport protein, GalP, of Escherichia coli and quantitative assay of the incorporation of [ring-2-13C]histidine and (15)NH(3). Biochem J 2002; 363:243-52. [PMID: 11931651 PMCID: PMC1222472 DOI: 10.1042/0264-6021:3630243] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The molecular mass of the galactose-H(+) symport protein GalP, as its histidine-tagged derivative GalP(His)(6), has been determined by electrospray MS (ESI-MS) with an error of <0.02%. One methionine residue, predicted to be present from the DNA sequence, was deduced to be absent. This is a significant advance on the estimation of the molecular masses of membrane-transport proteins by SDS/PAGE, where there is a consistent under-estimation of the true molecular mass due to anomalous electrophoretic migration. Addition of a size-exclusion chromatography step after Ni(2+)-nitrilotriacetate affinity purification was essential to obtain GalP(His)(6) suitable for ESI-MS. Controlled trypsin, trypsin+chymotrypsin and CNBr digestion of the protein yielded peptide fragments suitable for ESI-MS and tandem MS analysis, and accurate mass determination of the derived fragments resulted in identification of 82% of the GalP(His)(6) protein. Tandem MS analysis of selected peptides then afforded 49% of the actual amino acid sequence of the protein; the absence of the N-terminal methionine was confirmed. Matrix-assisted laser-desorption ionization MS allowed identification of one peptide that was not detected by ESI-MS. All the protein/peptide mass and sequence determinations were in accord with the predictions of amino acid sequence deduced from the DNA sequence of the galP gene. [ring-2-(13)C]Histidine was incorporated into GalP(His)(6) in vivo, and ESI-MS analysis enabled the measurement of a high (80%) and specific incorporation of label into the histidine residues in the protein. MS could also be used to confirm the labelling of the protein by (15)NH(3) (93% enrichment) and [(19)F]tryptophan (83% enrichment). Such MS measurements will serve in the future analysis of the structures of membrane-transport proteins by NMR, and of their topology by indirect techniques.
Collapse
Affiliation(s)
- Henrietta Venter
- Astbury Centre for Structural Molecular Biology, School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | | | | | | | | |
Collapse
|
9
|
|
10
|
Appleyard AN, Herbert RB, Henderson PJ, Watts A, Spooner PJ. Selective NMR observation of inhibitor and sugar binding to the galactose-H(+) symport protein GalP, of Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1509:55-64. [PMID: 11118517 DOI: 10.1016/s0304-4157(00)00017-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The binding of the transport inhibitor forskolin, synthetically labelled with (13)C, to the galactose-H(+) symport protein GalP, overexpressed in its native inner membranes from Escherichia coli, was studied using cross-polarization magic angle spinning (13)C NMR. (13)C-Labelled D-galactose and D-glucose were displaced from GalP with the singly labelled [7-OCO(13)CH(3)]forskolin and were not bound to any alternative site within the protein, demonstrating that any multiple sugar binding sites are not simultaneously accessible to these sugars and the inhibitor within GalP. The observation of singly (13)C-labelled forskolin was hampered by interference from natural abundance (13)C in the membranes and so the effectiveness of double-quantum filtration was assessed for the exclusive detection of (13)C spin pairs in sugar (D-[1,2-(13)C(2)]glucose) and inhibitor ([7-O(13)CO(13)CH(3)]forskolin) bound to the GalP protein. The solid state NMR methodology was not effective in creating double-quantum selection of ligand bound with membranes in the 'fluid' state (approx. 2 degrees C) but could be applied in a straightforward way to systems that were kept frozen. At -35 degrees C, double-quantum filtration detected unbound sugar that was incorporated into ice structure within the sample, and was not distinguished from protein-bound sugar. However, the method detected doubly labelled forskolin that is selectively bound only to the transport system under these conditions and provided very effective suppression of interference from natural abundance (13)C background. These results indicate that solid state NMR methods can be used to resolve selectively the interactions of more hydrophobic ligands in the binding sites of target proteins.
Collapse
Affiliation(s)
- A N Appleyard
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, UK
| | | | | | | | | |
Collapse
|
11
|
Middleton DA, Rankin S, Esmann M, Watts A. Structural insights into the binding of cardiac glycosides to the digitalis receptor revealed by solid-state NMR. Proc Natl Acad Sci U S A 2000; 97:13602-7. [PMID: 11095733 PMCID: PMC17622 DOI: 10.1073/pnas.250471997] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2000] [Indexed: 11/18/2022] Open
Abstract
Several biologically active derivatives of the cardiotonic steroid ouabain have been made containing NMR isotopes ((13)C, (2)H, and (19)F) in the rhamnose sugar and steroid moieties, and examined at the digitalis receptor site of renal Na(+)/K(+)-ATPase by a combination of solid-state NMR methods. Deuterium NMR spectra of (2)H-labeled inhibitors revealed that the sugar group was only loosely associated with the binding site, whereas the steroid group was more constrained, probably because of hydrogen bonding to residues around the K(+)-channel region. Crosspolarization magic-angle spinning NMR showed that chemical shifts of inhibitors (13)C-labeled in the sugar group moved downfield by 0.5 ppm after binding to the digitalis site, suggesting that the sugar was close to aromatic side groups. A (19)F, (13)C- rotational-echo double-resonance NMR strategy was used to determine the structure of an inhibitor in the digitalis receptor site, and it showed that the ouabain derivatives adopt a conformation in which the sugar extends out of the plane of the steroid ring system. The combined structural and dynamic information favors a model for inhibition in which the ouabain analogues lie across the surface of the Na(+)/K(+)-ATPase alpha-subunit with the sugar group facing away from the surface of the membrane but free to move into contact with one or more aromatic residues.
Collapse
Affiliation(s)
- D A Middleton
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
| | | | | | | |
Collapse
|
12
|
Sanders CR, Oxenoid K. Customizing model membranes and samples for NMR spectroscopic studies of complex membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1508:129-45. [PMID: 11090822 DOI: 10.1016/s0005-2736(00)00308-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Both solution and solid state nuclear magnetic resonance (NMR) techniques for structural determination are advancing rapidly such that it is possible to contemplate bringing these techniques to bear upon integral membrane proteins having multiple transmembrane segments. This review outlines existing and emerging options for model membrane media for use in such studies and surveys the special considerations which must be taken into account when preparing larger membrane proteins for NMR spectroscopic studies.
Collapse
Affiliation(s)
- C R Sanders
- Department of Physiology and Biophysics, Case Western Reserve University, 44106-4970, Cleveland, OH, USA.
| | | |
Collapse
|
13
|
Abstract
Solid-state nmr spectroscopy provides a robust method for investigating polypeptides that have been prepared by chemical synthesis and that are immobilized by strong interactions with solid surfaces or large macroscopic complexes. Solid-state nmr spectroscopy has been widely used to investigate membrane polypeptides or peptide aggregates such as amyloid fibrils. Whereas magic angle spinning solid-state nmr spectroscopy allows one to measure distances and dihedral angles with high accuracy, static membrane samples that are aligned with respect to the magnetic field direction allow one to determine the secondary structure of bound polypeptides and their orientation with respect to the bilayer normal. Peptide dynamics and the effect of polypeptides on the macroscopic phase preference of phospholipid membranes have been investigated in nonoriented samples. Investigations of the structure and topology of membrane channels, peptide antibiotics, signal sequences as well as model systems that allow one to dissect the interaction contributions in phospholipid membranes will be presented in greater detail.
Collapse
Affiliation(s)
- B Bechinger
- Max-Planck-Institute for Biochemistry, Am Klopferspitz 18A, 82152 Marinsried, Germany.
| | | | | | | | | | | |
Collapse
|
14
|
Abstract
In the half-century since its discovery, nuclear magnetic resonance (NMR) has become the single most powerful form of spectroscopy in both chemistry and structural biology. The dramatic technical advances over the past 10-15 years, which continue apace, have markedly increased the range of applications for NMR in the study of protein-ligand interactions. These form the basis for its most exciting uses in the drug discovery process, which range from the simple identification of whether a compound (or a component of a mixture) binds to a given protein, through to the determination of the full three-dimensional structure of the complex, with all the information this yields for structure-based drug design.
Collapse
Affiliation(s)
- GC Roberts
- Centre for Mechanisms of Human Toxicity and Biological NMR Centre, University of Leicester, Hodgkin Building, PO Box 138, Lancaster Road, Leicester, UK LE1 9HN
| |
Collapse
|
15
|
Pauli J, van Rossum B, Förster H, de Groot HJ, Oschkinat H. Sample optimization and identification of signal patterns of amino acid side chains in 2D RFDR spectra of the alpha-spectrin SH3 domain. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2000; 143:411-6. [PMID: 10729269 DOI: 10.1006/jmre.2000.2029] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Future structural investigations of proteins by solid-state CPMAS NMR will rely on uniformly labeled protein samples showing spectra with an excellent resolution. NMR samples of the solid alpha-spectrin SH3 domain were generated in four different ways, and their (13)C CPMAS spectra were compared. The spectrum of a [u-(13)C, (15)N]-labeled sample generated by precipitation shows very narrow (13)C signals and resolved scalar carbon-carbon couplings. Linewidths of 16-19 Hz were found for the three alanine C(beta )signals of a selectively labeled [70% 3-(13)C]alanine-enriched SH3 sample. The signal pattern of the isoleucine, of all prolines, valines, alanines, and serines, and of three of the four threonines were identified in 2D (13)C-(13)C RFDR spectra of the [u-(13)C, (15)N]-labeled SH3 sample. A comparison of the (13)C chemical shifts of the found signal patterns with the (13)C assignment obtained in solution shows an intriguing match.
Collapse
Affiliation(s)
- J Pauli
- Forschungsinstitut für Molekulare Pharmakologie, Alfred-Kowalke-Strasse 4, Berlin, D-10315, Germany
| | | | | | | | | |
Collapse
|
16
|
Mathies R, Lugtenburg J. Chapter 2 The primary photoreaction of rhodopsin. HANDBOOK OF BIOLOGICAL PHYSICS 2000. [DOI: 10.1016/s1383-8121(00)80005-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
17
|
Degrip W, Rothschild K. Chapter 1 Structure and mechanism of vertebrate visual pigments. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1383-8121(00)80004-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
|
18
|
Gröbner G, Glaubitz C, Watts A. Probing membrane surfaces and the location of membrane-embedded peptides by (13)C MAS NMR using lanthanide ions. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1999; 141:335-339. [PMID: 10579957 DOI: 10.1006/jmre.1999.1894] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A simple but efficient (13)C MAS NMR method is presented for the determination of the location of embedded molecules such as peptides relative to biological membrane surfaces by exploiting the interaction with paramagnetic lanthanide ions. Using various aqueous Dy(3+) concentrations a distance-dependent differential paramagnetic quenching of NMR lipid resonance intensities for specific carbon sites was observed, with residues at the bilayer surface quenched effectively and hydrophobic sites unaffected by Dy(3+). Tested on the membrane-embedded 50 residue long M13 coat protein, (13)C labeled at its Val-29 and Val-31 residues, no paramagnetic quenching was observed for the peptide resonances by Dy(3+), suggesting that Val-29 and Val-31 are not in close proximity to the bilayer interface, but buried deeply inside the hydrophobic region of the lipid bilayer.
Collapse
Affiliation(s)
- G Gröbner
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.
| | | | | |
Collapse
|
19
|
Grage SL, Ulrich AS. Structural parameters from 19F homonuclear dipolar couplings, obtained by multipulse solid-state NMR on static and oriented systems. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1999; 138:98-106. [PMID: 10329231 DOI: 10.1006/jmre.1999.1726] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Local macromolecular structure can be determined by solid-state NMR measurements of weak dipolar couplings between selectively labeled groups. The nonperturbing use of 2H, 13C, or 15N in biological systems, however, faces drawbacks in terms of a low sensitivity and a comparatively short distance range relative to 1H. To extend these limitations, we illustrate the use of 19F as an alternative NMR probe. The Carr-Purcell-Meiboom-Gill (CPMG) multipulse sequence was adapted here to measure homonuclear dipolar couplings between two fluorine labels in static samples at 470 MHz. Two lipids (4, 4-DMPC-F2, and a difluorinated sterol), which are arranged in liquid crystalline bilayers, serve as models to assess the scope of the technique. In these 19F-background-free biological samples, weak couplings down to 100 Hz could be resolved directly from the splitting of the pure dipolar powder lineshape, and 1H-decoupling was not required. Order parameters were determined for the anisotropic motion of the lipids, consistent with their expected behavior in the membrane. Besides measuring the distance-dependent term of the dipolar coupling in powder samples, we have also used oriented membranes to extract additional angular information from the dipolar anisotropy. The strategy presented here thus has the potential to obtain not only the internuclear distance between two labels, but also their angular orientation in the sample, provided the molecules are aligned as a membrane or a fiber.
Collapse
Affiliation(s)
- S L Grage
- Institut für Molekularbiologie, Friedrich-Schiller-Universität Jena, Winzerlaer Str. 10, Jena, 07745, Germany
| | | |
Collapse
|
20
|
Hudson BS, Birge RR. Angular Orientation of the Retinyl Chromophore of Bacteriorhodopsin: Reconciliation of 2H NMR and Optical Measurements. J Phys Chem A 1999. [DOI: 10.1021/jp9836271] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bruce S. Hudson
- Department of Chemistry, Syracuse University, Syracuse, New York 13244-4100
| | - Robert R. Birge
- Department of Chemistry, Syracuse University, Syracuse, New York 13244-4100
| |
Collapse
|
21
|
|
22
|
Abstract
NMR methods are now able to give detailed structural, dynamic and electronic information about drugs and ligands while constrained at their site of action in membrane-embedded receptors, information which is essential for mechanistic descriptions of their action and design of new ligands. Using solid state NMR methods, a peptic ulcer drug analogue has been described at atomic resolution (to +/- 0.3 A between two atoms) at its site of action in the gastric H+/K+-ATPase, and the aromaticity of the agonist binding site of the nicotinic acetylcholine receptor has been demonstrated, with both targets in functionally competent membranes under conditions similar to those used in screening assays. G-protein-coupled receptor ligands and prosthetic groups are also being resolved using NMR methods.
Collapse
Affiliation(s)
- A Watts
- Biomembrane Structure Unit Biochemistry Department University of Oxford Oxford OX1 3QU UK.
| |
Collapse
|
23
|
Spooner PJ, O'Reilly WJ, Homans SW, Rutherford NG, Henderson PJ, Watts A. Weak substrate binding to transport proteins studied by NMR. Biophys J 1998; 75:2794-800. [PMID: 9826601 PMCID: PMC1299952 DOI: 10.1016/s0006-3495(98)77722-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The weak binding of sugar substrates fails to induce any quantifiable physical changes in the L-fucose-H+ symport protein, FucP, from Escherichia coli, and this protein lacks any strongly binding ligands for competitive binding assays. Access to substrate binding behavior is however possible using NMR methods which rely on substrate immobiliza-tion for detection. Cross-polarization from proton to carbon spins could detect the portion of 13C-labeled substrate associated with 0.2 micromol of the functional transport system overexpressed in the native membranes. The detected substrate was shown to be in the FucP binding site because its signal was diminished by the unlabeled substrates L-fucose and L-galactose but was unaffected by a three- to fivefold molar excess of the non-transportable stereoisomer D-fucose. FucP appeared to bind both anomers of its substrates equally well. An NMR method, designed to measure the rate of substrate exchange, could show that substrate exchanged slowly with the carrier center (>10(-1) s), although its dynamics are not necessarily coupled strongly to this site within the protein. Relaxation measurements support this view that fluctuations in the interaction with substrate would be confined to the binding site in this transport system.
Collapse
Affiliation(s)
- P J Spooner
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.
| | | | | | | | | | | |
Collapse
|
24
|
Watts A. Solid-state NMR approaches for studying the interaction of peptides and proteins with membranes. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1376:297-318. [PMID: 9804977 DOI: 10.1016/s0304-4157(98)00012-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- A Watts
- Biomembrane Structure Unit, Biochemistry Department, Oxford University, Oxford OX1 3QU, UK.
| |
Collapse
|
25
|
|
26
|
Warschawski DE, Traikia M, Devaux PF, Bodenhausen G. Solid-state NMR for the study of membrane systems: the use of anisotropic interactions. Biochimie 1998; 80:437-50. [PMID: 9782384 DOI: 10.1016/s0300-9084(00)80011-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The use of solid-state nuclear magnetic resonance (NMR) as a tool to determine the structure of membrane molecules is reviewed with a particular emphasis on techniques that provide information on orientation or order. Experiments reported here have been performed in membranes, rather than in micelles or organic solvents. Several ways to prepare and handle the samples are discussed, like sample orientation and magic-angle spinning (MAS). Results concerning lipids, membrane peptides and proteins are included, as well as a discussion regarding the potential of such methods and their pitfalls.
Collapse
|
27
|
Gröbner G, Choi G, Burnett IJ, Glaubitz C, Verdegem PJ, Lugtenburg J, Watts A. Photoreceptor rhodopsin: structural and conformational study of its chromophore 11-cis retinal in oriented membranes by deuterium solid state NMR. FEBS Lett 1998; 422:201-4. [PMID: 9490006 DOI: 10.1016/s0014-5793(97)01591-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Rhodopsin is the retinal photoreceptor responsible for visual signal transduction. To determine the orientation and conformation of retinal within the binding pocket of this membrane bound receptor, an ab initio solid state 2H NMR approach was used. Bovine rhodopsin containing 11-cis retinal, specifically deuterated at its methyl groups at the C19 or C20 position, was uniaxially oriented in DMPC bilayers. Integrity of the membranes and quality of alignment were monitored by 31P NMR. Analysis of the obtained 2H NMR spectra provided angles for the individual labelled chemical bond vectors leading to an overall picture for the three dimensional structure of the polyene chain of the chromophore in the protein binding pocket around the Schiff base attachment site.
Collapse
Affiliation(s)
- G Gröbner
- Department of Biochemistry, University of Oxford, UK
| | | | | | | | | | | | | |
Collapse
|
28
|
Gröbner G, Taylor A, Williamson PT, Choi G, Glaubitz C, Watts JA, de Grip WJ, Watts A. Macroscopic orientation of natural and model membranes for structural studies. Anal Biochem 1997; 254:132-8. [PMID: 9398355 DOI: 10.1006/abio.1997.2415] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
One approach for obtaining high-resolution structural and functional information for biomembranes and their proteins is by static solid-state NMR of oriented systems. Here, a general procedure to align fully functional biological membranes containing large membrane proteins (Mr >30,000) is described. The method, based on the isopotential spin-dry ultracentrifugation technique, relies on the centrifugation of membrane fragments onto a support with simultaneous, or subsequent, partial evaporation of the solvent which aids alignment. The quality of orientation, as shown by the mosaic spread of the samples, was monitored by static solid-state 31P NMR for the phospholipids and by 2H NMR for a deuterated retinal in bovine rhodopsin. The generality of this method is demonstrated with three different membranes containing bovine rhodopsin in reconstituted bilayers, natural membranes with the red cell anion exchange transport protein in erythrocytes, band 3, and the nicotinic acetylcholine receptor.
Collapse
Affiliation(s)
- G Gröbner
- Biomembrane Structure Unit, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | | | | | | | | | | | | | | |
Collapse
|
29
|
Abstract
The purpose of the present study is the investigation of the structure and dynamics of biological membranes using solid-state nuclear magnetic resonance (NMR) spectroscopy. Two approaches are used in our laboratory. The first involves the measurement of high-resolution 13C and 1H spectra obtained by the magic angle spinning (MAS) technique while the second approach involves the measurement of 31P and 2H powder spectra in static samples. This paper will present some recent results obtained by high-resolution solid-state 1H NMR on the conformation of gramicidin A incorporated in a phosphatidylcholine bilayers. More specifically, we were able to observe changes in the gramicidin spectra as a function of the cosolubilization solvent initially used to prepare the samples. The interaction between lipid bilayers and an anticancer drug derived from chloroethylurea was also investigated using proton NMR spectroscopy. Finally, we have studied the interaction between cardiotoxin, a toxic protein extracted from snake venom, and negatively charged lipid bilayers using 31P solid-state NMR spectroscopy.
Collapse
Affiliation(s)
- M Auger
- Département de Chimie, CERSIM, Université Laval, Québec, Canada.
| |
Collapse
|
30
|
Middleton DA, Robins R, Feng X, Levitt MH, Spiers ID, Schwalbe CH, Reid DG, Watts A. The conformation of an inhibitor bound to the gastric proton pump. FEBS Lett 1997; 410:269-74. [PMID: 9237643 DOI: 10.1016/s0014-5793(97)00525-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Substituted imidazo[1,2-a]pyridines are pharmaceutically important small molecule inhibitors of the gastric H+/K+-ATPase, the membrane-bound therapeutic target for peptic ulcer disease. A non-perturbing analytical technique, rotational resonance NMR spectroscopy, was used to measure a precise (to +/-0.2 A) distance between atomic sites in a substituted imidazo[1,2-a]pyridine, TMPIP, bound to H+/K+-ATPase at its high-affinity site in the intact, native membrane. The structural analysis of the enzyme-inhibitor complex revealed that the flexible moiety of TMPIP adopts a 'syn-type' conformation at its site of action. Hence, the conformation of an inhibitor has been resolved directly under near-physiological conditions, providing a sound experimental basis for rational design of many active compounds of pharmaceutical interest. Chemically restraining the flexible moiety of compounds like TMPIP in the syn-type binding conformation was found to increase activity by over 2 orders of magnitude. Such information is normally only available after extensive synthesis of related compounds and multiple screening approaches.
Collapse
Affiliation(s)
- D A Middleton
- Department of Biochemistry, University of Oxford, UK
| | | | | | | | | | | | | | | |
Collapse
|