Carbon-13 NMR studies of 13CO binding to human hemoglobin

In the ¹³C NMR spectrum of hemoglobin A carbonylated with ¹³CO, separate resonances can be distinguished at 207.04 ppm and 206.60 ppm (with respect to the ¹³C resonance of external tetramethyl-silane) for ¹³Co bound to the α and β chains of the hemoglobin tetramer. A study of the ¹³Co derivatives of the isolated α and β chains, and of the abnormal hemoglobin M_IWATE which contains α chains which are in the met [Fe(III)] form and do not bind CO, has permitted an assignment of the high field (206.60 ppm) resonance to the β chain ¹³CO and the low field one to the α chain ¹³CO. The identification of these ¹³Co resonances permits a study of the differences in the chemistry of the α and β heme units in intact hemoglobin. Some results on the differences in the redox behavior of these chains are included.     

Identifying inter-residue resonances in crowded 2D 13C–13C chemical shift correlation spectra of membrane proteins by solid-state MAS NMR difference spectroscopy

The feasibility of using difference spectroscopy, i.e. subtraction of two correlation spectra at different mixing times, for substantially enhanced resolution in crowded two-dimensional ¹³C–¹³C chemical shift correlation spectra is presented. With the analyses of ¹³C–¹³C spin diffusion in simple spin systems, difference spectroscopy is proposed to partially separate the spin diffusion resonances of relatively short intra-residue distances from the longer inter-residue distances, leading to a better identification of the inter-residue resonances. Here solid-state magic-angle-spinning NMR spectra of the full length M2 protein embedded in synthetic lipid bilayers have been used to illustrate the resolution enhancement in the difference spectra. The integral membrane M2 protein of Influenza A virus assembles as a tetrameric bundle to form a proton-conducting channel that is activated by low pH and is essential for the viral lifecycle. Based on known amino acid resonance assignments from amino acid specific labeled samples of truncated M2 sequences or from time-consuming 3D experiments of uniformly labeled samples, some inter-residue resonances of the full length M2 protein can be identified in the difference spectra of uniformly ¹³C labeled protein that are consistent with the high resolution structure of the M2 (22–62) protein (Sharma et al., Science 330(6003):509–512, 2010).     

Preparation and comparison of model bilayer systems from chloroplasts thylakoid membrane lipids for 13C-NMR studies

Model bilayer systems from individual purified chloroplast thylakoid membrane lipids, from reconstituted mixtures of these purified lipids, and from leaf total polar lipid extracts have been prepared in water, and the longitudinal relaxation times (T's₁) of the individual carbon atoms of the fatty acyl chains measured by ¹³C-NMR spectroscopy. The T's₁ increasing distance of the carbon atoms from the polar headgroups in all cases, and as the results from each of the preparations are similar, all can be used as models of chloroplast membrane bilayers. Relaxation time measurements on intact chloroplast thylakoid membranes indicate the presence of chlorophyll resonances in the ¹³C-NMR spectrum of the membrane.     

Assignment strategies for aliphatic protons in the solid-state in randomly protonated proteins

Biological solid-state nuclear magnetic resonance spectroscopy developed rapidly in the past two decades and emerged as an important tool for structural biology. Resonance assignment is an essential prerequisite for structure determination and the characterization of motional properties of a molecule. Experiments, which rely on carbon or nitrogen detection, suffer, however, from low sensitivity. Recently, we introduced the RAP (Reduced Adjoining Protonation) labeling scheme, which allows to detect backbone and sidechain protons with high sensitivity and resolution. We present here a ¹H-detected 3D (H)CCH experiment for assignment of backbone and sidechain proton resonances. Resolution is significantly improved by employing simultaneous ¹³CO and ¹³Cβ J-decoupling during evolution of the ¹³Cα chemical shift. In total, ~90% of the ¹Hα-¹³Cα backbone resonances of chicken α-spectrin SH3 could be assigned.     

19 F-NMR studies of oxygen binding to hemoglobin

The binding of oxygen to hemoglobin has been investigated by ¹⁹F-nuclear magnetic resonance spectroscopy. The ¹⁹F-nmr spectrum of hemoglobin trifluoroacetonylated at cysteine β 93 exhibits chemical shift changes on binding of ligands, which differ depending on which chains are undergoing complexation. Comparison of these changes to the fractional ligation of all chains, determined concurrently from the fractional change in the visible spectrum, shows that initial oxygen molecules bind preferentially to α-chains. The ¹⁹F-nmr spectrum of partially oxygenated hemoglobin contains resonances at the normal chemical shift positions of the oxygenated and deoxy species, in addition to two small resonances at intermediate positions. Analysis of the relativ magnitudes of these four peaks as functions of oxygen pressure permits identification of the intermediate species     

In Vivo Natural-Abundance C Nuclear Magnetic Resonance Studies of Living Ectomycorrhizal Fungi : Observation of Fatty Acids in Cenococcum graniforme and Hebeloma crustuliniforme

Natural-abundance ¹³C nuclear magnetic resonance spectroscopy has been used to study intact mycelia of the ectomycorrhizal fungi Cenococcum graniforme (Ascomycetes) and Hebeloma crustuliniforme (Basidiomycetes). A number of sharp resonances are observed in living fungi. These signals primarily arise from fatty acyl chains and carbohydrate nuclei. The spectra are interpreted in terms of relative concentrations of the major fatty acids present in the fungal triglycerides. The small line width of fatty acids (mainly oleic, linoleic, and palmitic acids) resonances and spin-lattice relaxation time are indicative of fast rotational reorientations and are consequently thought to arise from fatty acyl chains in fat droplets. We were able to locate the site of lipids accumulation within mycelia using light microscopy and histological staining. Many lipid droplets were observed in mycelia of both species.

These results suggest that fatty acids droplets could be involved in carbon storage and metabolism from ectomycorrhizal fungi.

     

13C NMR evidence for three slowly interconverting conformations of the dihydrofolate reductase-NADP+-folate complex

The 3-carboxamido-¹³C resonance of NADP⁺ in its complex with $\text{Lactobacillus}\text{casei}$ dihydrofolate reductase and folate has been studied as a function of pH. At low pH a single resonance is observed, while at high pH two resonances are observed, neither of which has the same chemical shift as that seen at low pH. The rates of interconversion between the three states of the complex represented by these resonances are < 19 s^?1 at 11°C.     

Analysis of the carbon-13 and proton NMR spectra of bovine chromaffin granules

Natural abundance carbon-13 and proton NMR spectra of bovine chromaffin granules have been obtained and analyzed using computer simulation techniques. High resolution spectra show the presence of a fluid aqueous phase containing epinephrine, ATP and a random coil protein. The protein spectrum contains unusually intense resonances due to glutamic acid and proline and has been simulated satisfactorily using the known amino acid composition of chromogranin A.The lipid phase of chromaffin granules gives rise to intense, but very broad, resonances in the carbon-13 spectrum. Protons in the liquid phase are also observable as a very rapid component of the proton-free induction decay ($\text{T}{}_2\text{? 15 μ}\text{s}$).Linewidths of the carbon-13 spectra have been used to set upper limits on rotational correlation times and on the motional anisotropy in the aqueous phase. These limits show that the aqueous phase is a simple solution (not a gel) that is isotropic over regions much larger than solute dimensions. No gel transition is observed between ?3 and 25°C. The carbon-13 spectra are definitely inconsistent with a lipoprotein matrix model and chromaffin granules previously proposed by Helle and Serck-Hanssen ((1975) Mol. Cell. Biochem. 6, 127–146). Relative carbon-13 intensities of ATP and epinephrine are not consistent with the known 1:4 mol ration of these components. This fact suggests that epinephrine and ATP are not directly complexed in intact chromaffin granules.     

Optical properties of artificial chlorophyll membranes

Summary The composition and structure of lipid bilayer membranes containing chlorophylla have been studied with photometric and fluorometric methods. A sensitive double-beam spectrophotometer is described by which the pigment concentration in the bilayer can be determined. Up to 3×10¹³ chlorophyll molecules per cm² can be incorporated into the membrane, corresponding to a mean distance of 20 ? between the porphyrin rings. At high chlorophyll concentrations, the absorption peaks are shifted toward longer wavelengths, indicating an interaction between porphyrin rings in the film. Parallel to the spectral shifts, a large decrease in the fluorescence quantum yield and a depolarization of the fluorescence are observed. These findings suggest that transfer of excitation energy takes place between neighboring chlorophyll molecules in the membrane. When an oxidating agent (K₂S₂O₈) is added toone external phase, exactly half of the chlorophyll in the film is destroyed. This observation suggests that the chlorophyll molecules are localized in the membrane surfaces with the phytyl chains inserted into the hydrocarbon core of the membrane and the porphyrin rings facing the aqueous solution.     

The interaction of cyanocobalamin and some of its analogs with manganese(II) and gadolinium(III)

The influence of the paramagnetic ions Mn²⁺ and Gd³⁺ on the proton-decoupled ¹³C nuclear magnetic resonance spectra of three cyanocobalamin-monocarboxylic acids has been observed. The paramagnetic ions bind preferentially to the free carboxylate groups and cause the broadening of specific carbon resonances adjacent to these groups. These specific line-broadening effects have been used to assign the carbonyl carbons of the a-, f-, and g-acetamide side chains and have allowed us to confirm and/or correct the assignments of several carbon resonances that were assigned tentatively before.     

Resolution enhanced homonuclear carbon decoupled triple resonance experiments for unambiguous RNA structural characterization

Large RNAs (>30 nucleotides) suffer from extensive resonance overlap that can seriously hamper unambiguous structural characterization. Here we present a set of 3D multinuclear NMR experiments with improved and optimized resolution and sensitivity for aiding with the assignment of RNA molecules. In all these experiments strong base and ribose carbon–carbon couplings are eliminated by homonuclear band-selective decoupling, leading to improved signal to noise and resolution of the C5, C6, and C1′ carbon resonances. This decoupling scheme is applied to base-type selective ¹³C-edited NOESY, ¹³C-edited TOCSY (HCCH, CCH), HCCNH, and ribose H1C1C2 experiments. The 3D implementation of the HCCNH experiment with both carbon and nitrogen evolution enables direct correlation of ¹³C and ¹⁵N resonances at different proton resonant frequencies. The advantages of the new experiments are demonstrated on a 36 nucleotides hairpin RNA from domain 5 (D5) of the group II intron Pylaiella littoralis using an abbreviated assignment strategy. These four experiments provided additional separation for regions of the RNA that have overlapped chemical shift resonances, and enabled the assignment of critical D5 bulge nucleotides that could not be assigned using current experimental schemes.Supplementary material to this paper is available in electronic form at http://dx.doi.org/10.1007/s10858-005-5093-6     

Cross-polarization NMR of N-15 labeled soybeans

Cross-polarization ¹⁵N nmr spectra of ¹⁵N-labeled soybean seeds, pods, and leaves have been obtained at 9.12 MHz both with and without high-speed sample rotation at the magic angle. Spectral resolution is sufficient to permit a determination of the relative concentrations of amide and amine nitrogens, as well as of a few specific amino acid residues of proteins in the solid, intact samples. Utilization by soybean of nitrogen from labeled fertilizer in the presence of dinitrogen fixation can be determined from these spectra. A double-cross polarization ¹³C nmr spectrum of a spinning, ¹⁵N-labeled seed has been obtained in which resonances are observed only from these carbons directly bonded to nitrogens. This technique leads to a qualitative estimate of amino-acid composition of the protein which is complementary to that obtained directly from the ¹⁵N nmr spectrum.     

Three-dimensional solid-state NMR spectroscopy of a peptide oriented in membrane bilayers

Summary A three-dimensional ¹H chemical shift/¹H-¹⁵N dipolar coupling/¹⁵N chemical shift correlation spectrum was obtained on a sample of specifically ¹⁵N-labeled magainin peptides oriented in lipid bilayers between glass plates in a flat-coil probe. The spectrum showed complete resolution of the resonances from two labeled amide sites in all three dimensions. The three orientationally dependent frequencies associated with each resonance enabled the orientation of the peptide planes to be determined relative to the direction of the applied magnetic field. These results demonstrate the feasibility of multiple-pulse spectroscopy in a flat-coil probe, the ability to measure three spectral parameters from each site in a single experiment, and the potential for resolving among many labeled sites in oriented membrane proteins.     

Carbon-13 Nuclear Magnetic Resonance Analysis of Metabolism in Soybean Labeled by CO(2)

Fourier transform ¹³C nuclear magnetic resonance spectra have been obtained of intact, fresh soybean ovules (Glycine max L. cv. Dare) harvested from pods subtended by a trifoliolate exposed to ¹³CO₂ 1 to 3 days earlier. The high resolution spectra are interpreted in terms of the labeled sugars and lipids in the ovule. Comparison of the spectra taken over the 3-day period permits qualitative estimates of sugar metabolism and rates of lipid synthesis. The spectra also contain information about the distribution of labels within the lipid chains. This information leads to a method of estimating the extent to which glucose degradation in the synthesizing soybean ovule is involved in the reactions of the phosphogluconate pathway.     

Novel NMR tools to study structure and dynamics of biomembranes

Nuclear magnetic resonance (NMR) studies on biomembranes have benefited greatly from introduction of magic angle spinning (MAS) NMR techniques. Improvements in MAS probe technology, combined with the higher magnetic field strength of modern instruments, enables almost liquid-like resolution of lipid resonances. The cross-relaxation rates measured by nuclear Overhauser enhancement spectroscopy (NOESY) provide new insights into conformation and dynamics of lipids with atomic-scale resolution. The data reflect the tremendous motional disorder in the lipid matrix. Transfer of magnetization by spin diffusion along the proton network of lipids is of secondary relevance, even at a long NOESY mixing time of 300 ms. MAS experiments with re-coupling of anisotropic interactions, like the 13C-(1)H dipolar couplings, benefit from the excellent resolution of 13C shifts that enables assignment of the couplings to specific carbon atoms. The traditional 2H NMR experiments on deuterated lipids have higher sensitivity when conducted on oriented samples at higher magnetic field strength. A very large number of NMR parameters from lipid bilayers is now accessible, providing information about conformation and dynamics for every lipid segment. The NMR methods have the sensitivity and resolution to study lipid-protein interaction, lateral lipid organization, and the location of solvents and drugs in the lipid matrix.     

13C, 15N Resonance Assignment of Parts of the HET-s Prion Protein in its Amyloid Form

The partial ¹⁵N and ¹³C solid-state NMR resonance assignment of the HET-s prion protein fragment 218–289 in its amyloid form is presented. It is based on experiments measured at MAS frequencies in the range of 20–40 kHz using exclusively adiabatic polarization-transfer schemes. The resonance assignment within each residue is based on two-dimensional ¹³C––¹³C correlation spectra utilizing the DREAM mixing scheme. The sequential linking of the assigned residues used a set of two- and three-dimensional ¹⁵N––¹³C correlation experiments. Almost all cross peaks visible in the spectra are assigned, but only resonances from 43 of the 78 amino-acid residues could be detected. The missing residues are thought to be highly disordered and/or highly dynamic giving rise to broad resonance lines that escaped detection in the experiments applied. The line widths of the observed resonances are narrow and comparable to line widths observed in micro-crystalline samples. The 43 assigned residues are located in two fragments of about 20 residues. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

13C-NMR Investigation of the insertion of the bee venom melittin into lecithin vesicles

The orientation of melittin in lecithin membranes was investigated by means of ¹³C-NMR spectroscopy. Phospholipase-free melittin was labeled with ¹³C-methyl groups at the -amino side chains of lysine 7, 21, and 23. From the pH dependence of the corresponding ¹³C resonances, pK values of the lysine residues were derived that were different for free and membrane-bound melittin. The shift reagent Pr(NO₃)₃ induced shifts in the ¹³C resonance position of all three lysines when melittin and the shift reagent were added to a lecithin vesicle suspension, whereas Pr³⁺ ions included in the inner volume of the vesicles did not affect the ¹³C resonances of melittin bound to the outer vesicle membrane. A wedge-like structure was derived for the membrane-bound melittin, the lysine side chains of which are freely accessible to the aqueous solvent.Abbreviation NOE Nuclear Overhauser Enhancement     

Hysteretic kinetic behavior of beef liver pyruvate carboxylase.

Natural abundance ¹³C nuclear magnetic resonance (nmr) spectra have been obtained for samples of a variety of native collagens by use of cross-polarization (CP) techniques which permit high resolution natural abundance ¹³C nmr spectra of solids to be obtained with high sensitivity. The CP ¹³C nmr spectra of lyophilized skin and tendon collagens consisted of two broad resonance envelopes spanning a five kHz range. Hydrated tendon collagen gave rise to a CP spectrum very similar to that obtained for the lyophilized sample, indicating that it retains its solid-like properties. In contrast, hydrated skin collagen became denatured under the conditions of the CP experiment and subsequently gave rise to a conventional high-resolution Fourier transform (FT) nmr spectrum. The CP ¹³C nmr spectrum of ivory was similar to those of lyophilized skin and tendon collagens, demonstrating the solid-like character of the collagen in dentine, whereas the CP spectrum of bovine nasal cartilage reflected the presence of highly mobile proteoglycan components in addition to relatively rigid collagen molecules. In the case of ivory, the resolution of the CP spectrum was enhanced by “magic angle” spinning to a degree approaching that of conventional FT ¹³C nmr spectra of denatured collagen in solution. Because of its ability to probe the dynamic properties of solid-like biological molecules, CP ¹³C nmr spectroscopy should be a valuable investigative tool for future studies.     

Resonance assignment strategies for the analysis of nmr spectra of proteins

Determination of the high resolution solution structure of a protein using nuclear magnetic resonance (NMR) spectroscopy requires that resonances observed in the NMR spectra be unequivocally assigned to individual nuclei of the protein. With the advent of modern, two-dimensional NMR techniques arose methodologies for assigning the¹H resonances based on 2D, homonuclear¹H NMR experiments. These include the sequential assignment strategy and the main chain directed strategy. These basic strategies have been extended to include newer 3D homonuclear experiments and 2D and 3D heteronuclear resolved and edited methods. Most recently a novel, conceptually new approach to the problem has been introduced that relies on heteronuclear, multidimensional so-called triple resonance experiments for both backbone and sidechain resonance assignments in proteins. This article reviews the evolution of strategies for the assignment of resonances of proteins.     

In vivo assessment of hepatic triglycerides in murine non-alcoholic fatty liver disease using magnetic resonance spectroscopy

In vivo¹H magnetic resonance spectroscopy (MRS) was used to examine the progression of fatty liver in two murine models of progressive hepatic steatosis: leptin-deficient obese (ob/ob) mice and mice maintained on a diet deficient in methionine and choline (MCDD). Ob/ob mice displayed high levels of intracellular hepatic triglycerides as early as 9 weeks after birth, as observed with MRS and histopathology. Single voxel spectra of ob/ob liver displayed strong resonances arising from saturated (1.3 ppm) and unsaturated (2.8 and 5.3 ppm) fatty acyl chains that could be resolved in the absence of water suppression. Hepatic inflammation, induced by lipopolysaccharide administration, led to a significant increase in unsaturated and polyunsaturated fatty acyl chain resonances (P < 0.05), indicating a change in the composition of hepatic triglycerides in lipid droplets. Mice maintained on the MCDD displayed histological evidence of hepatic steatosis as early as two weeks, progressing to macrovesicular steatohepatitis at 10 weeks. The histological changes were accompanied by significant increases in saturated and unsaturated fatty acyl chain resonances and a significant decrease in the lipid/(water + lipid) ratio (P < 0.05). These results indicate that in vivo¹H MRS may be a suitable method to monitor the progression of steatohepatitis.