Dipolar Correlation Spectroscopy Research Articles

Probing the spatial organization of bacteriochlorophyll C by solid-state nuclear magnetic resonance.

Green sulfur bacteria, which live in extremely low-light environments, use chlorosomes to harvest light. A chlorosome is the most efficient, and arguably the simplest, light-harvesting antenna complex, which contains hundreds of thousands of densely packed bacteriochlorophylls (BChls). To harvest light efficiently, BChls in a chlorosome form supramolecular aggregates; thus, it is of great interest to determine the organization of the BChls in a chlorosome. In this study, we conducted a (13)C solid-state nuclear magnetic resonance and Mg K-edge X-ray absorption analysis of chlorosomes from wild-type Chlorobaculum tepidum. The X-ray absorption results indicated that the coordination number of the Mg in the chlorosome must be >4, providing evidence that electrostatic interactions formed between the Mg of a BChl and the carbonyl group or the hydroxyl group of the neighboring BChl molecule. According to the intermolecular distance constraints obtained on the basis of (13)C homonuclear dipolar correlation spectroscopy, we determined that the molecular assembly of BChls is dimer-based and that the hydrogen bonds among the BChls are less extensive than commonly presumed because of the twist in the orientation of the BChl dimers. This paper also reports the first (13)C homonuclear correlation spectrum acquired for carotenoids and lipids-which are minor, but crucial, components of chlorosomes-extracted from wild-type Cba. tepidum.

Structure and Alignment of the Membrane-Associated Peptaibols Ampullosporin A and Alamethicin by Oriented 15N and 31P Solid-State NMR Spectroscopy

Ampullosporin A and alamethicin are two members of the peptaibol family of antimicrobial peptides. These compounds are produced by fungi and are characterized by a high content of hydrophobic amino acids, and in particular the α-tetrasubstituted amino acid residue α-amino isobutyric acid. Here ampullosporin A and alamethicin were uniformly labeled with 15N, purified and reconstituted into oriented phophatidylcholine lipid bilayers and investigated by proton-decoupled 15N and 31P solid-state NMR spectroscopy. Whereas alamethicin (20 amino acid residues) adopts transmembrane alignments in 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphocholine (POPC) or 1,2-dimyristoyl- sn-glycero-3-phosphocholine (DMPC) membranes the much shorter ampullosporin A (15 residues) exhibits comparable configurations only in thin membranes. In contrast the latter compound is oriented parallel to the membrane surface in 1,2-dimyristoleoyl- sn-glycero-3-phosphocholine and POPC bilayers indicating that hydrophobic mismatch has a decisive effect on the membrane topology of these peptides. Two-dimensional 15N chemical shift – 1H- 15N dipolar coupling solid-state NMR correlation spectroscopy suggests that in their transmembrane configuration both peptides adopt mixed α-/3 10-helical structures which can be explained by the restraints imposed by the membranes and the bulky α-amino isobutyric acid residues. The 15N solid-state NMR spectra also provide detailed information on the helical tilt angles. The results are discussed with regard to the antimicrobial activities of the peptides.

13C−1H heteronuclear dipolar correlation studies of the hydrogen bonding of the quinones inRhodobacter sphaeroides R26 reaction centers

The photosynthetic reaction center (RC) of the photosynthetic bacteriumRhodobacter sphaeroides R26 contains two quinones, QA and QB. Solid-state heteronuclear (1H−13C) dipolar correlation spectroscopy has been used to study the binding of the quinones in the ground state for RCs reconstituted with l-13C ubiquinone-10. Lee-Goldburg cross-polarization buildup curves are recorded to determine distancesrCH between the l-13C carbon labels and the protons involved in the polarization transfer. The l-13C of both QA and QB have intermolecular correlations with protons that resonate downfield, in the region of hydrogen-bonding protons. The distances between the carbon labels and the correlated protons are short, 0.21±0.01 nm. Hence the nuclear magnetic resonance provides evidence for strong hydrogen-bonding interactions at the l-C=O of both QA and QB for RCs in the ground state. The environment of the l-13C of the QB is structurally heterogeneous compared to that of the QA. The data can be reconciled with a strong H-bonding interaction of the l-C=O of QA with Ala M260 NH, and with complex hydrogen bonding involving NH of Ile-L224 and of Gly-L225, and possibly the Ser-L223 hydroxyl group of the l-C=O of the QB, in the proximal site.

Solid-State NMR Evidence for a Protonation Switch in the Binding Pocket of the H1 Receptor upon Binding of the Agonist Histamine

G protein coupled receptors (GPCRs) represent a major superfamily of transmembrane receptor proteins that are crucial in cellular signaling and are major pharmacological targets. While the activity of GPCRs can be modulated by agonist binding, the mechanisms that link agonist binding to G protein coupling are poorly understood. Here we present a method to accurately examine the activity of ligands in their bound state, even at low affinity, by solid-state NMR dipolar correlation spectroscopy and confront this method with the human H1 receptor. The analysis reveals two different charge states of the bound agonist, dicationic with a charged imidazole ring and monocationic with a neutral imidazole ring, with the same overall conformation. The combination of charge difference and pronounced heterogeneity agrees with converging evidence that the active and inactive states of the GPCR represent a dynamic equilibrium of substates and that proton transfer between agonist and protein side chains can shift this equilibrium by stabilizing the active receptor population relative to the inactive one. In fact, the data suggest a global functional analogy between H1 receptor activation and the meta I/meta II charge/discharge equilibrium in rhodopsin (GPCR). This corroborates current ideas on unifying principles in GPCR structure and function.

Water-protein interactions in microcrystalline crh measured by 1H-13C solid-state NMR spectroscopy.

Using solid-state NMR carbon-proton dipolar correlation spectroscopy, we observed hydrogen exchange on the millisecond time scale between water molecules and protein protons in a solid sample. These interactions are shown to be related to important structural features of the protein such as hydrogen-bonding or salt-bridge networks.

Determination of solid-state NMR structures of proteins by means of three-dimensional 15N-13C-13C dipolar correlation spectroscopy and chemical shift analysis.

In this paper, a three-dimensional (3D) NMR-based approach for the determination of the fold of moderately sized proteins by solid-state magic-angle spinning (MAS) NMR is presented and applied to the alpha-spectrin SH3 domain. This methodology includes the measurement of multiple (13)C-(13)C distance restraints on biosynthetically site-directed (13)C-enriched samples, obtained by growing bacteria on [2-(13)C]glycerol and [1,3-(13)C]glycerol. 3D (15)N-(13)C-(13)C dipolar correlation experiments were applied to resolve overlap of signals, in particular in the region where backbone carbon-carbon correlations of the C(alpha)-C(alpha), CO-CO, C(alpha)-CO, and CO-C(alpha) type appear. Additional restraints for confining the structure were obtained from phi and psi backbone torsion angles of 29 residues derived from C(alpha), C(beta), CO, NH, and H(alpha) chemical shifts. Using both distance and angular restraints, a refined structure was calculated with a backbone root-mean-square deviation of 0.7 A with respect to the average structure.

(1)H and (13)C MAS NMR evidence for pronounced ligand-protein interactions involving the ionone ring of the retinylidene chromophore in rhodopsin.

Rhodopsin is a member of the superfamily of G-protein-coupled receptors. This seven alpha-helix transmembrane protein is the visual pigment of the vertebrate rod photoreceptor cells that mediate dim light vision. In the active binding site of this protein the ligand or chromophore, 11-cis-retinal, is covalently bound via a protonated Schiff base to lysine residue 296. Here we present the complete (1)H and (13)C assignments of the 11-cis-retinylidene chromophore in its ligand-binding site determined with ultra high field magic angle spinning NMR. Native bovine opsin was regenerated with 99% enriched uniformly (13)C-labeled 11-cis-retinal. From the labeled pigment, (13)C carbon chemical shifts could be obtained by using two-dimensional radio frequency-driven dipolar recoupling in a solid-state magic angle spinning homonuclear correlation experiment. The (1)H chemical shifts were assigned by two-dimensional heteronuclear ((1)H-(13)C) dipolar correlation spectroscopy with phase-modulated Lee-Goldburg homonuclear (1)H decoupling applied during the t(1) period. The data indicate nonbonding interactions between the protons of the methyl groups of the retinylidene ionone ring and the protein. These nonbonding interactions are attributed to nearby aromatic acid residues Phe-208, Phe-212, and Trp-265 that are in close contact with, respectively, H-16/H-17 and H-18. Furthermore, binding of the chromophore involves a chiral selection of the ring conformation, resulting in equatorial and axial positions for CH(3)-16 and CH(3)-17.

A 3-D Structural Model of Solid Self-Assembled Chlorophyll a/H2O from Multispin Labeling and MAS NMR 2-D Dipolar Correlation Spectroscopy in High Magnetic Field

Magic angle spinning (MAS) NMR with Lee–Goldburg cross-polarization (LG-CP) is used to promote long-range heteronuclear transfer of magnetization and to constrain a structural model for uniformly labeled chlorophyll a/H2O. An effective maximum transfer range dmax can be determined experimentally from the detection of a gradually decreasing series of intramolecular correlations with the 13C along the molecular skeleton. To probe intermolecular contacts, dmax can be set to ∼4.2 Å by choosing an LG-CP contact time of 2 ms. Long-range 1H–13C correlations are used in conjunction with carbon and proton aggregation shifts to establish the stacking of the chlorophyll a (Chl a) molecules. First, high-field (14.1 T) 2-D MAS NMR homonuclear (13C–13C) dipolar correlation spectra provide a complete assignment of the carbon chemical shifts. Second, proton chemical shifts are obtained from 1H–13C heteronuclear dipolar correlation spectroscopy in high magnetic field. The shift constraints and long-range 1H–13C intermolecular correlations reveal a 2-D stacking homologous to the molecular arrangement in crystalline solid ethyl-chlorophyllide a. A doubling of a small subset of the carbon resonances, in the 7-methyl region of the molecule, provides evidence for two marginally different well-defined molecular environments. Evidence is found for the presence of neutral structural water molecules forming a hydrogen-bonded network to stabilize Chl a sheets. In line with the microcrystalline order observed for the rings, the long T1's, and absence of conformational shifts for the 13C in the phytyl tails, it is proposed that the Chl a form a rigid 3-D space-filling structure. Probably the only way this can be realized with the sheets is by forming bilayers with interpenetration of elongated tails. Such a 3-D space-filling organization of the aggregated Chl a from MAS NMR would match existing models inferred from electron microscopy and low-resolution X-ray powder diffraction, while a micellar model based on neutron diffraction and antiparallel stacking observed in solution can be discarded.

Sensitivity-enhanced static 15N NMR of solids by 1h indirect detection.

A method for enhancing the sensitivity of 15N spectra of nonspinning solids through 1H indirect detection is introduced. By sampling the 1H signals in the windows of a pulsed spin-lock sequence, high-sensitivity 1H spectra can be obtained in two-dimensional (2D) spectra whose indirect dimension yields the 15N chemical shift pattern. By sacrificing the 1H chemical shift information, sensitivity gains of 1.8 to 2.5 for the 15N spectra were achieved experimentally. A similar sensitivity enhancement was also obtained for 2D (15)N-(1)H dipolar and 15N chemical shift correlation spectroscopy, by means of a 3D 1H/15N-1H/15N correlation experiment. We demonstrate this technique, termed PRINS for proton indirectly detected nitrogen static NMR, on a crystalline model compound with long 1H T(1rho) and on a 25-kDa protein with short 1H T(1rho). This 1H indirect detection approach should be useful for enhancing the sensitivity of 15N NMR of oriented membrane peptides. It can also be used to facilitate the empirical optimization of 15N-detected experiments where the inherent sensitivity of the sample is low.

Ultrahigh field MAS NMR dipolar correlation spectroscopy of the histidine residues in light-harvesting complex II from photosynthetic bacteria reveals partial internal charge transfer in the B850/His complex.

Low-temperature 15N and 13C CP/MAS (cross-polarization/magic angle spinning) NMR has been used to analyze BChl-histidine interactions and the electronic structure of histidine residues in the light-harvesting complex II (LH2) of Rhodopseudomonas acidophila. The histidines were selectively labeled at both or one of the two nitrogen sites of the imidazole ring. The resonances of histidine nitrogens that are interacting with B850 BChl a have been assigned. Specific 15N labeling confirmed that it is the tau-nitrogen of histidines which is ligated to Mg2+ of B850 BChl molecules (beta-His30, alpha-His31). The pi-nitrogens of these Mg2+-bound histidines were found to be protonated and may be involved in hydrogen bond interactions. Comparison of the 2-D MAS NMR homonuclear (13C-13C) dipolar correlation spectrum of [13C6,15N3]-histidines in the LH2 complex with model systems in the solid state reveals two different classes of electronic structures from the histidines in the LH2. In terms of the 13C isotropic shifts, one corresponds to the neutral form of histidine and the other resembles a positively charged histidine species. 15N-13C double-CP/MAS NMR data provide evidence that the electronic structure of the histidines in the neutral BChl a/His complexes resembles the positive charge character form. While the Mg...15N isotropic shift confirms a partial positive charge transfer, its anisotropy is essentially of the lone pair type. This provides evidence that the hybridization structure corresponding to the neutral form of the imidazole is capable of "buffering" a significant amount of positive charge.

Ultra-high-field MAS NMR assay of a multispin labeled ligand bound to its G-protein receptor target in the natural membrane environment: electronic structure of the retinylidene chromophore in rhodopsin.

11-Z-[8,9,10,11,12,13,14,15,19,20-(13)C10]Retinal prepared by total synthesis is reconstituted with opsin to form rhodopsin in the natural lipid membrane environment. The 13C shifts are assigned with magic angle spinning NMR dipolar correlation spectroscopy in a single experiment and compared with data of singly labeled retinylidene ligands in detergent-solubilized rhodopsin. The use of multispin labeling in combination with 2-D correlation spectroscopy improves the relative accuracy of the shift measurements. We have used the chemical shift data to analyze the electronic structure of the retinylidene ligand at three levels of understanding: (i) by specifying interactions between the 13C-labeled ligand and the G-protein-coupled receptor target, (ii) by making a charge assessment of the protonation of the Schiff base in rhodopsin, and (iii) by evaluating the total charge on the carbons of the retinylidene chromophore. In this way it is shown that a conjugation defect is the predominant ground-state property governing the molecular electronics of the retinylidene chromophore in rhodopsin. The cumulative chemical shifts at the odd-numbered carbons (Delta(sigma)odd) of 11-Z-protonated Schiff base models relative to the unprotonated Schiff base can be used to measure the extent of delocalization of positive charge into the polyene. For a series of 11-Z-protonated Schiff base models and rhodopsin, Delta(sigma)odd appears to correlate linearly with the frequency of maximum visible absorption. Since rhodopsin has the largest value of Delta(sigma)odd, the data contribute to existing and converging spectroscopic evidence for a complex counterion stabilizing the protonated Schiff base in the binding pocket.

A refined model of the chlorosomal antennae of the green bacterium Chlorobium tepidum from proton chemical shift constraints obtained with high-field 2-D and 3-D MAS NMR dipolar correlation spectroscopy.

Heteronuclear 2-D and 3-D magic-angle spinning NMR dipolar correlation spectroscopy was applied to determine solid-state (1)H shifts for aggregated bacteriochlorophyll c (BChl c) in uniformly (13)C-enriched light harvesting chlorosomes of the green photosynthetic bacterium Chlorobium tepidum. A complete assignment of 29 different observable resonances of the 61 protons of the aggregated BChl c in the intact chlorosomes is obtained. Aggregation shifts relative to monomeric BChl c in solution are detected for protons attached to rings I, II, and III/V and to their side chains. The 2(1)-H(3), 3(2)-H(3), and 3(1)-H resonances are shifted upfield by -2.2, -1, and -3.3 ppm, respectively, relative to monomeric BChl c in solution. Although the resonances are inhomogeneously broadened and reveal considerable global structural heterogeneity, the 5-CH and the 7-Me responses are doubled, which provides evidence for the existence of at least two relatively well-defined structurally different arrangements. Ab initio quantum chemical modeling studies were performed to refine a model for the self-assembled BChl c with two different types of BChl stacks. The BChl in the stacks can adopt either anti- or syn-configuration of the coordinative bond, where anti and syn designate the relative orientation of the Mg-OH bond relative to the direction of the 17-17(1) bond. The analogy between aggregation shifts for BChl c in the chlorosome and for self-assembled chlorophyll a/H(2)O is explored, and a bilayer model for the tubular supra-structure of sheets of BChl c is proposed, from a homology modeling approach.

Multidimensional CP-MAS 13C NMR of uniformly enriched chlorophyll

The progress toward structure refinement of solid-type uniformly 13C enriched ([U- 13C]) chlorophyll-containing biological preparations is summarised. Solid state carbon chemical shifts of aggregated [U- 13C] bacteriochlorophyll (BChl) c in intact chlorosomes of Chlorobium tepidum and in [U- 13C] BChl c aggregates were determined by the application of homonuclear ( 13C 13C) magic angle spinning (MAS) NMR dipolar correlation spectroscopy. It was found that the arrangement of BChl c molecules in the chlorosomes and in the aggregates is highly similar, which provides convincing evidence that self-organisation of the BChl c is the main mechanism to support the structure of the chlorosomes. Additionally, high field 2-D ( 1H 13C) and 3-D ( 1H 13C 13C) dipolar correlation spectroscopy was applied to determine solid state proton chemical shifts of aggregated [U- 13C] BChl c in intact chlorosomes. From the high-field assignments, evidence is found for the existence of at least two well-defined interstack arrangements.

High Magnetic Field for Enhanced Proton Resolution in High-Speed CP/MAS Heteronuclear1H–13C Dipolar-Correlation Spectroscopy

We demonstrated that the heteronuclear correlation experiments between two quadrupolar nuclei, 23Na and 27Al, with close Larmor frequencies can be achieved via D-HMQC and D-RINEPT approaches by using a diplexer connected to a conventional probe in magic-angle-spinning solid-state NMR. Low-power heteronuclear dipolar recoupling schemes can be applied on 23Na or 27Al to establish polarization transfers between the central transitions of 23Na and 27Al for a model compound, NaAlO2. Further, we showed a practical implementation of the two dimensional 23Na-27Al dipolar-based heteronuclear correlation experiment on a heterogeneous catalyst, Na2CO3/γ-Al2O3. This allows to determine spatial proximities between different 23Na and 27Al sites, thus the surface Na species adjacent to octahedral-coordination Al can be clearly discriminated.

CP-MAS 13C-NMR Dipolar Correlation Spectroscopy of 13C-Enriched Chlorosomes and Isolated Bacteriochlorophyll c Aggregates of Chlorobium tepidum: The Self-Organization of Pigments Is the Main Structural Feature of Chlorosomes

Magic angle spinning (MAS) NMR dipolar correlation spectroscopy was applied for the first time to a biologically intact system, the light-harvesting chlorosomes of the green photosynthetic bacterium Chlorobium tepidum. The MAS spectra provide evidence that the self-organization of many thousands of bacteriochlorophyll c (BChl c) molecules is the predominant structural feature of the chlorosome. 13C-Enriched chlorosomes were prepared from nonuniformly labeled cultures grown with NaH13CO3 as the main carbon source and from a uniformly 13C-labeled culture grown with NaH13CO3 as the sole carbon source. For the nonuniformly labeled samples, the positions of the chlorin macrocycle originating from C-4 and C-5 of 5-aminolevulinic acid contained > 95% 13C while the remaining positions, which could have originated also from unlabeled acetate, were labeled to approximately 60% with 13C. The 1-D and 2-D MAS data of the labeled chlorosomes, when compared with data on the isolated labeled BChl c aggregated in n-hexane, show that the major component of the MAS signals in the chlorosomes is from BChl c, and only minor signal contributions arise from lipids and proteins. The 13C MAS signals of the BChl c aggregates were fully assigned by MAS 2-D dipolar correlation spectroscopy, using data on monomeric BChl c in CDCl3/CD3OD as reference. The 2(1)-, 3-, 3(2-), 5-, 12(1)-, 13-, and 13(1)-carbons are shifted by 2.5 ppm or more upfield with respect to the solution data.(ABSTRACT TRUNCATED AT 250 WORDS)

MAS NMR structure refinement of uniformly 13C enriched chlorophyll a/water aggregates with 2D dipolar correlation spectroscopy

2D MAS dipolar correlation spectroscopy of uniformly 13C enriched chlorophyll a/water aggregates was performed using broadband RFDR to promote exchange of coherence through homonuclear dipolar couplings. It is shown experimentally that incorporation of TPPI and coherence pathway selection in the RFDR pulse scheme yields virtually pure 2D absorption lineshapes. From a series of 2D correlation spectra collected at two spinning speeds with different mixing times of ∼ 1 and ∼ 10 ms all 13C resonances of the chlorophyll a molecule were assigned. The spectra with the longer mixing times reveal through-space intermolecular polarization transfer. This demonstrates that structural information can be obtained from uniformly 13C enriched samples, which paves the way for a full structural characterization of amorphous solids.

A pH-dependent Conformational Change of Staphylococcal Nuclease: Hydrogen-1 Two-Dimensional Nuclear Overhauser Spectroscopy Studies.

Two-dimensional nuclear magnetic resonance (2d-NMR) dipolar correlation spectroscopy (NOESY) for the calcium binding protein, staphylococcal nuclease, was used to study the conformations in solution as a function of pH. A series of 2d-NOESY spectra of the nuclease H124L-Ca(++)-thymidine 3'5'-bisphosphate ternary complex demonstrated significant pH dependent changes: NOE cross peaks between 46His delta H and an aliphatic proton at 2.66 ppm appeared at pH 10.2, but not at pH 5.5. Some other NOE cross peaks between aromatic and aliphatic protons displayed chemical shift changes in omega 2 or both dimensions (omega 1, omega 2). These results indicated that a local rearrangement accompanies the ionization of the functional groups and has a role in enzyme function.

Applications of zero field and 2-dimensional n.m.r. methods to fossil fuels

Three new two-dimensional (2D) solid-state n.m.r. methods are described which have much potential for increasing our knowledge of coal structure. A version of carbon-13/proton chemical shift correlation spectroscopy adapted for solids is outlined and results for one coal examined. A variant of dipolar shift correlation spectroscopy is described which is very convenient for determining the relative amounts of methylene, methine and methyl or non-protonated carbons in a complex mixture such as coal. The results for one hvA coal are presented and shown to be in agreement with its ultimate analysis. The principles underlying zero field n.m.r. are also presented, with an emphasis on deuterium ZF-n.m.r. This technique is assessed as a potentially powerful method in coal structure analysis for the future.