Determination of the backbone torsion psi angle by tensor correlation of chemical shift anisotropy and heteronuclear dipole-dipole interaction

We demonstrate that the backbone torsion psi angle of a uniformly labeled residue can be determined accurately by correlating the chemical shift anisotropy of the carbonyl carbon and the 13C-1H heteronuclear dipole-dipole interaction of the alpha carbon. To obtain the highest sensitivity for the psi angle determination, the following conditions are desired: (i) the recoupling pulse sequences for the CSA and the heteronuclear dipolar interactions are gamma encoded, in which the spatial parts of m=2 are selected; (ii) the homonuclear polarization transfer is based on the scalar spin-spin coupling. Experimental data were obtained for [U-13C, 15N]-alanine and N-acetyl-[U-13C, 15N]-d,l-valine under magic-angle spinning at 25kHz. Only three data points are required for the measurements and the dihedral angles determined are in excellent agreement with the diffraction data.     

Dual 13C, 15N labelling of terrestrial slugs (Deroceras reticulatum)

A simple, rapid and cost-effective laboratory method is described for labelling terrestrial slugs simultaneously with 13C and 15N. Slugs (Deroceras reticulatum) were provided with a mixture of [U-13C6]glucose, 15N-enriched lettuce powder, and wheat bran. Assimilation efficiencies for 13C (24.2%) and 15N (27.4%) were not affected by feeding regimes offering ad libitum or restricted access to unlabelled food during the labelling period. Body tissue was significantly more highly enriched in 13C but significantly less in 15N than cutaneous mucus after 15 days.     

NMR determination of the torsion angle psi in alpha-helical peptides and proteins: the HCCN dipolar correlation experiment

Several existing methods permit measurement of the torsion angles phi, psi and chi in peptides and proteins with solid-state MAS NMR experiments. Currently, however, there is not an approach that is applicable to measurement of psi in the angular range -20 degree to -70 degree, commonly found in alpha-helical structures. Accordingly, we have developed a HCCN dipolar correlation MAS experiment that is sensitive and accurate in this regime. An initial REDOR driven (13)C'--(15)N dipolar evolution period is followed by the C' to C(alpha) polarization transfer and by Lee--Goldburg cross polarization recoupling of the (13)C(alpha)(1)H dipolar interaction. The difference between the effective (13)C(1)H and (13)C(15)N dipolar interaction strengths is balanced out by incrementing the (13)C--(15)N dipolar evolution period in steps that are a factor of R(R approximately omega(CH)/omega(CN)) larger than the (13)C--(1)H steps. The resulting dephasing curves are sensitive to variations in psi in the angular region associated with alpha-helical secondary structure. To demonstrate the validity of the technique, we apply it to N-formyl-[U-(13)C,(15)N] Met-Leu-Phe-OH (MLF). The value of psi extracted is consistent with the previous NMR measurements and close to that reported in diffraction studies for the methyl ester of MLF, N-formyl-[U-(13)C,(15)N]Met-Leu-Phe-OMe.     

3D NMR spectroscopy for resonance assignment and structure elucidation of proteins under MAS: novel pulse schemes and sensitivity considerations

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.     

Use of the Carbonyl Chemical Shift to Relieve Degeneracies in Triple-Resonance Assignment Experiments

We illustrate an approach that uses the backbone carbonyl chemical shift to relieve resonance overlaps in triple-resonance assignment experiments conducted on protein samples. We apply this approach to two cases of simultaneous overlaps: those of ((1)H(N), (15)N) spin pairs and those of ((1)H(alpha), (13)C(alpha)) spin pairs in residues preceding prolines. For these cases we employed respectively CBCACO(N)H and H(CA)CON experiments, simple variants of the commonly used CBCA(CO)NH and HCA(CO)N experiments obtained by replacing one of the indirect dimensions with a carbonyl dimension. We present data collected on ribosomal protein S4 using these experiments, along with overlap statistics for four other polypeptides ranging in size from 76 to 263 residues. These data indicate that the CBCACO(N)H, in combination with the CBCA(CO)NH, can relieve >83% of the ((1)H(N), (15)N) and ((1)H(N), (13)C') overlaps for these proteins. The data also reveal how the H(CA)CON experiment successfully completed the assignment of triply and quadruply degenerate X-Pro spin systems in a mobile, proline-rich region of S4, even when X was a glycine. Finally, we discuss the relative sensitivities of these experiments compared to those of existing sequences, an analysis that reinforces the usefulness of these experiments in assigning extensively overlapped and/or proline-rich sequences in proteins.     

DNP enhanced frequency-selective TEDOR experiments in bacteriorhodopsin

We describe a new approach to multiple ¹³C–¹⁵N distance measurements in uniformly labeled solids, frequency-selective (FS) TEDOR. The method shares features with FS-REDOR and ZF- and BASE-TEDOR, which also provide quantitative ¹⁵N–¹³C spectral assignments and distance measurements in U-[¹³C,¹⁵N] samples. To demonstrate the validity of the FS-TEDOR sequence, we measured distances in [U-¹³C,¹⁵N]-asparagine which are in good agreement with other methods. In addition, we integrate high frequency dynamic nuclear polarization (DNP) into the experimental protocol and use FS-TEDOR to record a resolved correlation spectrum of the Arg-¹³C_γ–¹⁵N_ε region in [U-¹³C,¹⁵N]-bacteriorhodopsin. We resolve six of the seven cross-peaks expected based on the primary sequence of this membrane protein.     

Carbon-13 and fluorine-19 NMR spectroscopy of the supramolecular solid p-tert-butylcalix(4)arene.alpha,alpha,alpha-trifluorotoluene

The supramolecular 1:1 host-guest inclusion compound, p-tert-butylcalix[4]arene x alpha,alpha,alpha-trifluorotoluene, 1, is characterized by 19F and 13C solid-state NMR spectroscopy. Whereas the 13C NMR spectra are easily interpreted in the context of earlier work on similar host-guest compounds, the 15F NMR spectra of solid 1 are, initially, more difficult to understand. The 19F[1H] NMR spectrum obtained under cross-polarization and magic-angle spinning conditions shows a single isotropic resonance with a significant spinning sideband manifold. The static 19F[1H] CP NMR spectrum consists of a powder pattern dominated by the contributions of the anisotropic chemical shift and the homonuclear dipolar interactions. The 19F MREV-8 experiment, which minimizes the 19F-19F dipolar contribution, helps to identify the chemical shift contribution as an axial lineshape. The full static 19F[1H] CP NMR spectrum is analysed using subspectral analysis and subsequently simulated as a function of the 19F-19F internuclear distance (D(FF) = 2.25 +/- 0.01 A) of the rapidly rotating CF3 group without including contributions from additional libration motions and the anisotropy in the scalar tensor. The shielding span is found to be 56 ppm. The width of the centerband in the 19F[1H] sample-spinning CP NMR spectrum is very sensitive to the angle between the rotor and the magnetic field. Compound 1 is thus an attractive standard for setting the magic angle for NMR probes containing a fluorine channel with a proton-decoupling facility.     

Constant-time method for measuring inter-nuclear distances in static powders

We present a constant-time modification of a single-echo 2D technique for measuring the constants of spin-spin interaction between heteronuclei in static powder samples. Compared to the sequence with variable echo time, the new scheme provides higher resolution. Another important improvement is a possibility to eliminate the central peak from a natural-abundance matrix. The experimental results are presented for glycine-[13Calpha, 15N] and glycine-[13C', 15N].     

A 2D MAS solid-state NMR method to recover the amplified heteronuclear dipolar and chemical shift anisotropic interactions

A two-dimensional solid-state NMR method for the measurement of chemical shift anisotropy tensors of X nuclei (15N or 13C) from multiple sites of a polypeptide powder sample is presented. This method employs rotor-synchronized pi pulses to amplify the magnitude of the inhomogeneous X-CSA and 1H-X dipolar coupling interactions. A combination of on-resonance and magic angle rf irradiation of protons is used to vary the ratio of the magnitudes of the 1H-X dipolar and X-CSA interactions which are recovered under MAS, in addition to suppressing the 1H-1H dipolar interactions. The increased number of spinning sidebands in the recovered anisotropic interactions is useful to determine the CSA tensors accurately. The performance of this method is examined for powder samples of N-acetyl-(15)N-L-valine (NAV), N-acetyl-15N-L-valyl-15N-L-leucine (NAVL), and alpha-13C-L-leucine. The sources of experimental errors in the measurement of CSA tensors and the application of the pulse sequences under high-field fast MAS operations are discussed.     

Separating structure and dynamics in CSA/DD cross-correlated relaxation: a case study on trehalose and ubiquitin

We present two new sensitivity enhanced gradient NMR experiments for measuring interference effects between chemical shift anisotropy (CSA) and dipolar coupling interactions in a scalar coupled two-spin system in both the laboratory and rotating frames. We apply these methods for quantitative measurement of longitudinal and transverse cross-correlation rates involving interference of (13)C CSA and (13)C-(1)H dipolar coupling in a disaccharide, alpha,alpha-D-trehalose, at natural abundance of (13)C as well as interference of amide (15)N CSA and (15)N-(1)H dipolar coupling in uniformly (15)N-labeled ubiquitin. We demonstrate that the standard heteronuclear T(1), T(2), and steady-state NOE autocorrelation experiments augmented by cross-correlation measurements provide sufficient experimental data to quantitatively separate the structural and dynamic contributions to these relaxation rates when the simplifying assumptions of isotropic overall tumbling and an axially symmetric chemical shift tensor are valid.     

The first in vivo observation of (13)C-(15)N coupling in mammalian brain.

[5-(13)C,(15)N]Glutamine, with (1)J((13)C-(15)N) of 16 Hz, was observed in vivo in the brain of spontaneously breathing rats by (13)C MRS at 4.7 T. The brain [5-(13)C]glutamine peak consisted of the doublet from [5-(13)C,(15)N]glutamine and the center [5-(13)C,(14)N]glutamine peak, resulting in an apparent triplet with a separation of 8 Hz. The time course of formation of brain [5-(13)C,(15)N]glutamine was monitored in vivo with a time resolution of 20-35 min. This [5-(13)C,(15)N]glutamine was formed by glial uptake of released neurotransmitter [5-(13)C]glutamate and its reaction with (15)NH(3) catalyzed by the glia-specific glutamine synthetase. The neurotransmitter glutamate C5 was selectively (13)C-enriched by intravenous [2,5-(13)C]glucose infusion to (13)C-label whole-brain glutamate C5, followed by [(12)C]glucose infusion to chase (13)C from the small and rapidly turning-over glial glutamate pool, leaving (13)C mainly in the neurotransmitter [5-(13)C]glutamate pool, which is sequestered in vesicles until release. Hence, the observed [5-(13)C,(15)N]glutamine arises from a coupling between (13)C of neuronal origin and (15)N of glial origin. Measurement of the rate of brain [5-(13)C,(15)N]glutamine formation provides a novel noninvasive method of studying the kinetics of neurotransmitter uptake into glia in vivo, a process that is crucial for protecting the brain from glutamate excitotoxicity.     

Application of REDOR subtraction for filtered MAS observation of labeled backbone carbons of membrane-bound fusion peptides

Clean MAS observation of 13C-labeled carbons in membrane-bound HIV-1 and influenza fusion peptides was made by using a rotational-echo double-resonance spectroscopy (REDOR) filter of directly bonded 13C-15N pairs. The clean filtering achieved with the REDOR approach is superior to filtering done with sample difference spectroscopy. In one labeling approach, the peptide had labels at a single 13C carbonyl and its directly bonded 15N. The resulting chemical shift distribution of the filtered signal is used to assess the distribution of local secondary structures at the labeled carbonyl. For the influenza peptide, the Leu-2 carbonyl chemical shift distribution is shown to vary markedly with lipid and detergent composition, as well as peptide:lipid ratio, suggesting that the local peptide structure also has a strong dependence on these factors. Because most carboxylic- and amino-labeled amino acids are commercially available, this REDOR approach should have broad applicability to chemically synthesized peptides as well as bacterially synthesized proteins. In a second labeling approach, the HIV-1 fusion peptide had U-13C, 15N labeling over three sequential residues. When a 1.6 ms REDOR dephasing time is used, only backbone 13C signals are observed. The resulting spectra are used to determine spectral linewidths and to assess feasibility of assignment of uniformly labeled peptide.     

Determination of backbone angle psi in proteins using a TROSY-based alpha/beta-HN(CO)CA-J experiment

Transverse relaxation-optimized NMR experiment (TROSY) for the measurement of three-bond scalar coupling constant between (1)H(alpha)(i-1) and (15)N(i) defining the dihedral angle psi is described. The triple-spin-state-selective experiment allows measurement of (3)J(H(alpha)N) from (13)C(alpha), (15)N, and (1)H(N) correlation spectra H(2)O with minimum resonance overlap. Transverse relaxation of (13)C(alpha) spin is minimized by using spin-state-selective filtering and by acquiring a signal longer in (15)N-dimension in a manner of semi-constant-time TROSY evolution. The (3)J(H(alpha))(N) values obtained with the proposed alpha/beta-HN(CO)CA-J TROSY scheme are in good agreement with the values measured earlier from ubiquitin in D(2)O using the HCACO[N] experiment.     

Cross-correlated relaxation for the measurement of angles between tensorial interactions

Theory,experimental aspects, and use in structure calculation of cross-correlated relaxation rates measured on zero- and double-quantum coherences in liquid state NMR are presented. The relative size of the interaction depends on the projection angle between the two tensorial interactions. The tensorial interaction can be either a dipolar interaction or a chemical shift anisotropy relaxation mechanism (CSA). Effects of additional sources of relaxation on the cross-correlated relaxation rates are analyzed. Also, an easy-to-use formalism is given to manipulate different cross-correlated relaxation interactions. The application addresses measurement of the backbone angle psi in a protein by measuring dipole((15)N-(1)H)-dipole((13)C(alpha)-(1)H(alpha)) and CSA((15)N)-dipole((13)C(alpha)-(1)H(alpha)) cross-correlated relaxation rates. It is shown that ambiguities due to the 3 cos(2)θ-1 dependence of one cross-correlated relaxation rate can be overcome by measuring additional cross-correlated relaxation rates. The use of cross-correlated relaxation rates is demonstrated in structure calculations.     

Sample optimization and identification of signal patterns of amino acid side chains in 2D RFDR spectra of the alpha-spectrin SH3 domain

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.     

Insight into the CSA tensors of nucleobase carbons in RNA polynucleotides from solution measurements of residual CSA: towards new long-range orientational constraints

Using residual chemical shift anisotropies (RCSAs) measured in a weakly aligned stem-loop RNA, we examined the carbon chemical shift anisotropy (CSA) tensors of nucleobase adenine C2, pyrimidine C5 and C6, and purine C8. The differences between the measured RCSAs and the values back-calculated using three nucleobase carbon CSA sets [D. Stueber, D.M. Grant, 13C and 15N chemical shift tensors in adenosine, guanosine dihydrate, 2'-deoxythymidine, and cytidine, J. Am. Chem. Soc. 124 (2002) 10539-10551; D. Sitkoff, D.A. Case, Theories of chemical shift anisotropies in proteins and nucleic acids, Prog. NMR Spectrosc. 32 (1998) 165-190; R. Fiala, J. Czernek, V. Sklenar, Transverse relaxation optimized triple-resonance NMR experiments for nucleic acids, J. Biomol. NMR 16 (2000) 291-302] reported previously for mononucleotides (1.4 Hz) is significantly smaller than the predicted RCSA range (-10-10 Hz) but remains larger than the RCSA measurement uncertainty (0.8 Hz). Fitting of the traceless principal CSA values to the measured RCSAs using a grid search procedure yields a cytosine C5 CSA magnitude (CSAa=(3/2.(delta11(2)+delta22(2)+delta33(2)))1/2=173+/-21 ppm), which is significantly higher than the reported mononucleotide values (131-138 ppm) and a guanine C8 CSAa (148+/-13 ppm) that is in very good agreement with the mononucleotide value reported by solid-state NMR [134 ppm, D. Stueber, D.M. Grant, 13C and (15)N chemical shift tensors in adenosine, guanosine dihydrate, 2'-deoxythymidine, and cytidine, J. Am. Chem. Soc. 124 (2002) 10539-10551]. Owing to a unique sensitivity to directions normal to the base plane, the RCSAs can be translated into useful long-range orientational constraints for RNA structure determination even after allowing for substantial uncertainty in the nucleobase carbon CSA tensors.     

Determination of distance of intra-molecular hydrogen bonding in (Ala-Gly)15 with silk I form after removal of the effect of MAS frequency in REDOR experiment

It is important to know the structure of silk I (Bombyx mori silk structure before spinning in the solid state) in order to understand the mechanism of fiber formation at the atomic level. In this study, 15N-dephased, 13C-observe REDOR has been carried out to determine the atomic distance of intra-molecular hydrogen bond between the 13C=O carbon of the 14th Gly residue and the 15N nitrogen of the 17th Ala residue of (AG)(6)A[1-13C]GAG[15N]AG(AG)(6) with silk I form after removal of the effect of MAS frequency on the re-coupling. The distance was determined to be 4.3A, which confirmed the intra-molecular hydrogen bonding formation between these two atomic sites.     

Triple resonance experiments for aligned sample solid-state NMR of (13)C and (15)N labeled proteins

Initial steps in the development of a suite of triple-resonance (1)H/(13)C/(15)N solid-state NMR experiments applicable to aligned samples of (13)C and (15)N labeled proteins are described. The experiments take advantage of the opportunities for (13)C detection without the need for homonuclear (13)C/(13)C decoupling presented by samples with two different patterns of isotopic labeling. In one type of sample, the proteins are approximately 20% randomly labeled with (13)C in all backbone and side chain carbon sites and approximately 100% uniformly (15)N labeled in all nitrogen sites; in the second type of sample, the peptides and proteins are (13)C labeled at only the alpha-carbon and (15)N labeled at the amide nitrogen of a few residues. The requirement for homonuclear (13)C/(13)C decoupling while detecting (13)C signals is avoided in the first case because of the low probability of any two (13)C nuclei being bonded to each other; in the second case, the labeled (13)C(alpha) sites are separated by at least three bonds in the polypeptide chain. The experiments enable the measurement of the (13)C chemical shift and (1)H-(13)C and (15)N-(13)C heteronuclear dipolar coupling frequencies associated with the (13)C(alpha) and (13)C' backbone sites, which provide orientation constraints complementary to those derived from the (15)N labeled amide backbone sites. (13)C/(13)C spin-exchange experiments identify proximate carbon sites. The ability to measure (13)C-(15)N dipolar coupling frequencies and correlate (13)C and (15)N resonances provides a mechanism for making backbone resonance assignments. Three-dimensional combinations of these experiments ensure that the resolution, assignment, and measurement of orientationally dependent frequencies can be extended to larger proteins. Moreover, measurements of the (13)C chemical shift and (1)H-(13)C heteronuclear dipolar coupling frequencies for nearly all side chain sites enable the complete three-dimensional structures of proteins to be determined with this approach.     

Metabolic effects of HAY's diet

The aim of the study was, to evaluate the metabolic effect of HAY's diet on protein turnover, fat oxidation, respiratory quotient, body fat and weight loss. Twelve healthy adults received an individually regular diet and thereafter a corresponding isocaloric and isonitrogenous 10-day HAY-diet. Protein turnover and 13C-fat oxidation were investigated after administration of [15N]glycine and an [U-13C]algae lipid mixture. The 15N and 13C enrichment in urine and breath were measured by isotope ratio mass spectrometry. The respiratory quotient was measured by indirect calorimetry. Body fat, total body water and lean body mass were estimated by bio-electric impedance analysis. HAY's diet led to a significantly higher 13C-fat oxidation (15.4 vs. 22.0% P < 0.01), corresponding to a lower respiratory quotient (0.88 vs. 0.81; P < 0.01), whereas the protein turnover remained constant in both diets (3.06 vs. 3.05 g/kg/day). HAY's diet did not reduce total body water, lean body mass, body fat and body weight (72.2 vs. 71.4 kg).     

NMR assignment of protein side chains using residue-correlated labeling and NOE spectra

A new approach for the isotopic labeling of proteins is proposed that aims to facilitate side chain resonance assignments. Residue-correlated (RC) labeling is achieved by the expression of a protein on a medium containing a mixture of labeled, e.g., [U-13C,15N]amino acids, and NMR silent, [U-2H]amino acids. De novo synthesis of amino acids was suppressed by feedback inhibition by the amino acids in the growth medium and by the addition of beta-chloro-L-alanine, a transaminase inhibitor. Incorporation of these amino acids into synthesized proteins results in a relative diminution of inter-residue NOE interactions and a relative enhancement of intra-residue NOEs. Comparison of the resulting NOE spectra with those obtained from a uniformly labeled sample allows identification of intra-residue NOE peaks. Thus, this approach provides direct information for sidechain assignments in the NOE spectra, which are subsequently used for structural analysis. We have demonstrated the feasibility of this strategy for the 143 amino acid nuclease inhibitor NuiA, both at 35 degrees C, corresponding to a rotational correlation time of 9.5 ns, and at 5 degrees C, corresponding to a rotational correlation time of 22 ns.