NMR in the SPINE Structural Proteomics project.

This paper describes the developments, role and contributions of the NMR spectroscopy groups in the Structural Proteomics In Europe (SPINE) consortium. Focusing on the development of high-throughput (HTP) pipelines for NMR structure determinations of proteins, all aspects from sample preparation, data acquisition, data processing, data analysis to structure determination have been improved with respect to sensitivity, automation, speed, robustness and validation. Specific highlights are protonless (13)C-direct detection methods and inferential structure determinations (ISD). In addition to technological improvements, these methods have been applied to deliver over 60 NMR structures of proteins, among which are five that failed to crystallize. The inclusion of NMR spectroscopy in structural proteomics pipelines improves the success rate for protein structure determinations.

Conformational analysis of the Sd(a) determinant-containing tetrasaccharide and two mimics in aqueous solution by using 1H NMR ROESY spectroscopy in combination with MD simulations.

The conformational behaviour of the spacer-linked synthetic Sd(a) tetrasaccharide beta-D-GalpNAc-(1-->4)-[alpha-Neu5Ac-(2-->3)]-beta-D-Galp-(1-->4)- beta-D-GlcpNAc-(1-->O)(CH2)5NH2 (1) and the two mimics beta-D-Galp-(1-->4)-[alpha-Neu5Ac-(2-->3)]-beta-D-Galp-(1-->4)-bet a-D-GlcpNAc-(1-->O)(CH2)5NH2 (2) and beta-D-GlcpNAc-(1-->4)-[alpha-Neu5Ac-(2-->3)]-beta-D-Galp-(1-->4)- beta-D-GlcpNAc-(1-->O)(CH2)5NH2 (3) were investigated by 1H NMR spectroscopy in combination with molecular dynamics (MD) simulations in water. Experimental 2D 1H ROESY cross-peak intensities (ROEs) of the tetrasaccharides were compared with calculated ROEs derived from MD trajectories using the CROSREL program. Analysis of these data indicated that the oligosaccharidic skeletons of the compounds 1-3 are rather rigid, especially the beta-D-Hex(NAc)-(1-->4)-[alpha-Neu5Ac-(2-->3)]-beta-D-Galp fragments. The alpha-Neu5-Ac-(2-->3)-beta-D-Galp linkage occurred in two different energy minima in the three-dimensional structure of the compounds 1-3 in aqueous solution. Experimental data and dynamics simulations supported the finding that the higher energy rotamer (CHEAT forcefield) was abundant in compounds 1 and 3 due to the existence of a hydrogen bond between the carboxyl group of the sialic acid and the acetamido group of the terminal monosaccharide (GalNAc or GlcNAc) unit. The conformational similarity between 1 and 3 leads to the suggestion that also their activities will be alike.

Structure elucidation of glycoprotein glycans and of polysaccharides by NMR spectroscopy.

The applicability of 1H-NMR spectroscopy for the determination of the primary and tertiary structure of carbohydrate-containing molecules is demonstrated. For classes of known compounds the characterization can be based on chemical shifts observed in 1D NMR spectra with or without the aid of a computer database. For more complex structure determinations 2D NMR techniques are required. Here the application of 2D NMR is demonstrated for the primary structure determination of two bacterial exopolysaccharides, for the spatial structure determination of a disaccharide and a glycoprotein hormone.

Mobilities of the inner three core residues and the Man(alpha 1--6) branch of the glycan at Asn78 of the alpha-subunit of human chorionic gonadotropin are restricted by the protein.

Human chorionic gonadotropin (hCG) is a heterodimeric glycoprotein hormone involved in the maintenance of the corpus luteum in early pregnancy. The free alpha-subunit of hCG has a biological activity of its own, namely, stimulation of prolactin secretion from term pregnancy decidual cells [Blithe, D. L., et al. (1991) Endocrinology 129, 2257-2259]. Glycosylation at Asn78 of the alpha-subunit is required for the stability of the protein, but the exact nature of the stabilizing effect is not known. In our previous study, it was indicated that GlcNAc-1 at Asn78 has a reduced mobility, whereas the glycan at Asn52 is highly mobile [De Beer, T., et al. (1996) Eur. J. Biochem. 241, 229-242]. In the present investigation, it is shown that the PNGase F susceptibility of the Asn52-linked glycan in the free alpha-subunit is absent in the heterodimer. Thus, the high mobility of the glycan at Asn52 may be characteristic for the free alpha-subunit. For accurate modeling of alpha hCG, knowledge of the behavior of each of the glycans is essential. In this context, the mobility of the glycans and their interactions with the protein are explored by NMR spectroscopy using desialylated, partially deglycosylated free alpha-subunit (as-pd alpha) carrying glycans at Asn78 only. NOEs between GlcNAc-2 and several amino acid residues indicate that GlcNAc-2 is involved in stabilizing alpha hCG. From the values of 13C relaxation parameters T2 and T1 rho of the constituting monosaccharide residues, it was concluded that the inner three residues have a severely restricted mobility. The Man-4 and Man-4' residues of the diantennary oligosaccharide exhibit a similar relaxation behavior, suggesting that the Man-4' branch occurs in a single conformation of the C5-C6 linkage of Man-3 instead of in rapidly interconverting conformations that are known to exist for this linkage for the free oligosaccharide.

NMR studies of the free alpha subunit of human chorionic gonadotropin. Structural influences of N-glycosylation and the beta subunit on the conformation of the alpha subunit.

Human chorionic gonadotropin (hCG) is a heterodimeric glycoprotein hormone that is involved in the maintenance of the corpus luteum in early pregnancy. Glycosylation at Asn52 of its alpha subunit (alpha hCG) is essential for signal transduction, whereas the N-glycan at Asn78 stabilizes the structure of the protein. In this study, an almost complete 1H-NMR and a partial 13C-NMR spectral assignment for the amino acids and the N-glycans of alpha hCG and of an enzymatically deglycosylated form, which had a single GlcNAc residue at each of its two glycosylation sites, has been achieved. The secondary structure of alpha hCG is solution, which was determined based on NOE data, is partially similar to that of the alpha subunit in the crystal structure of hCG, but large structural differences are found for amino acid residues 33-58. In the crystal structure of hCG, residues 33-37 and 54-58 of the alpha subunit are part of an intersubunit seven-stranded beta-barrel and residues 41-47 constitute a 3(10)-helix. In contrast, in free alpha hCG in solution, amino acids 33-58 are part of a large disordered loop, indicating that in intact hCG interactions with the beta subunit of hCG stabilize the conformation of the alpha subunit. The NMR data of alpha hCG and its deglycosylated counterpart are very similar, indicating that removal of carbohydrate residues other than GlcNAc-1 does not notably affect the conformation of the protein part. However, numerous 1H-NOEs between the GlcNAc-1 residue at Asn78 and several amino acid residues show that this GlcNAc residue is tightly packed against the protein, being an integral part of the structure of the alpha subunit. 1H-NOEs across the glycosidic linkages of the glycan, resonance-line widths, and 1H and 13C chemical shifts of the other monosaccharides suggest that the remainder of the glycans at Asn78, and the glycans at Asn52 are largely extended in solution.

Podacycline A and B, two cyclic peptides in the latex of Jatropha podagrica.

Two novel cyclic peptides were isolated from the latex of Jatropha podagrica, which we named podacycline A and B. Podacycline A is a cyclic nonapeptide with the sequence Gly1-Leu2-Leu3-Gly4-Ala5-Val6-Trp7-Ala8-Gly9+ ++-Gly1. The sequence of podacycline B, a cyclic heptapeptide, was determined to be Phe1-Ala2-Gly3-Thr4-Ile5-Phe6-Gly7-Phe1. The amino acid residues of both compounds were found to have the L-configuration.

Cyclogossine A: a novel cyclic heptapeptide isolated from the latex of Jatropha gossypifolia.

From the latex of Jatropha gossypifolia L. (Euphorbiaceae) a novel cyclic heptapeptide was isolated, which we named cyclogossine A. A combination of amino acid analysis, FAB mass spectrometry, and two dimensional 1H-NMR spectroscopy (TOCSY and ROESY) was used to determine the primary structure. The compound was found to contain one glycine, one alanine, one valine, two leucine, one threonine, and one tryptophan residue; its amino acid sequence is: Leu 1 - Ala 2 - Thr 3 - Trp 4 - Leu 5 - Gly 6 - Val 7. The absolute configurations of the amino acids were determined by chiral gas chromatography; all have the L-configuration.

Curcacycline A--a novel cyclic octapeptide isolated from the latex of Jatropha curcas L.

From the latex of Jatropha curcas L. (Euphorbiaceae) a novel cyclic octapeptide was isolated, which we named curcacycline A. The compound was found to contain one threonine, one valine, two glycine, and four leucine residues. By two-dimensional 1H-NMR spectroscopy (HOHAHA and ROESY), its sequence was determined to be Gly1-Leu2-Leu3-Gly4-Thr5-Val6-Leu7-Leu8-Gly1+ ++. Curcacycline A displays a moderate inhibition of (i) classical pathway activity of human complement and (ii) proliferation of human T-cells.

Conformational analysis of methyl beta-cellobioside by ROESY NMR spectroscopy and MD simulations in combination with the CROSREL method.

Methyl beta-cellobioside has been studied extensively by molecular dynamics (MD) simulations in water and by ROESY NMR spectroscopy in order to establish its solution structure. The MD simulations were started with four significantly different minimal energy conformations. The MD trajectories were analysed with respect to interproton distances and mobility, in order to find models for application in the analysis of NMR data. The ROESY spectra were analysed by using the CROSREL method, which allows quantitative analysis of ROESY spectra through correction for the offset dependence and incorporation of HOHAHA transfer estimates. These results were compared with data obtained from an initial rate analysis of the ROESY data and with the MD data. It is concluded that methyl beta-cellobioside in aqueous solution is in the same extended conformation that is also found in the solid state.

Structural characterisation of the exopolysaccharide produced by Lactobacillus delbrückii subspecies bulgaricus rr grown in skimmed milk.

The exopolysaccharide of Lactobacillus delbrückii subsp. bulgaricus rr, isolated from skimmed milk, is a heteropolymer of D-galactopyranosyl, D-glucopyranosyl, and L-rhamnopyranosyl residues in the molar ratio 5:1:1. The structure was established by linkage analysis and 1D and 2D NMR spectroscopy of the native polysaccharide, in combination with characterisation of oligosaccharide fragments, obtained by Smith degradation and partial acid hydrolysis, using methylation analysis, EIMS, and 1D and 2D 1H NMR spectroscopy. The polysaccharide has a branched heptasaccharide repeating unit with the following structure: -->2)-[beta-D-Galp-(1-->3)]-alpha-D-Galp-(1-->3)- beta-D-Glcp-(1-->3)-[beta-D-Galp-(1-->4)]-beta-D-Galp-(1-->4)-[alpha-L- Rhap-(1-->3)]-alpha-D-Galp-(1-->.

Structure of the exopolysaccharide produced by Lactococcus lactis subspecies cremoris H414 grown in a defined medium or skimmed milk.

The structure of the exopolysaccharide of Lactococcus lactis subsp. cremoris H414, isolated from a defined medium or skimmed milk, was established by linkage analysis on the native polysaccharide, and by characterisation of oligosaccharide fragments, obtained by Smith degradation and partial acid hydrolysis, using methylation analysis, FABMS, EIMS, and 1H-NMR spectroscopy. The polysaccharide has the branched-pentasaccharide repeating unit: [formula: see text]

A 1H-NMR and MD study of intramolecular hydrogen bonds in methyl beta-cellobioside.

The existence of an HO-3...O-5' intramolecular hydrogen bond in methyl beta-cellobioside in solution in Me2SO-d6 and H2O-CD3OD (4:1 w/w) was studied by 500-MHz 1H-NMR spectroscopy and MD simulations. Temperature coefficients for the chemical shift of the hydroxyl resonances in these solvents were determined and the rates of proton exchange in the latter solvent were obtained from NOE data. With H2O-CD3OD as the solvent, the HO-3...O-5' hydrogen bond was insignificant, but its presence in Me2SO-d6 was confirmed.

Application of 2D and 3D NMR experiments to the conformational study of a diantennary oligosaccharide.

By the application of homonuclear 3D NOE-HOHAHA and heteronuclear 3D HMQC-NOE experiments in studies of complex oligosaccharides, NOEs can be investigated which are hidden in conventional 2D NOE spectra. In the 3D NOE-HOHAHA spectrum omega 3 cross sections were considered to be the most suitable for assignment of NOEs. Alternatively, these cross sections could be measured separately in selective 2D HOHAHA-NOE spectroscopy. The advantages and limitations of the 2D alternative are compared with those of the 3D NOE-HOHAHA approach. In 3D HMQC-NOE spectroscopy the larger chemical shift displacement of the carbon spectrum with respect to the proton spectrum can be used to unmask NOEs hidden in the bulk region. If the extra proton dimension is not needed, 2D HMQC-NOE is a good alternative. The suitability of 2D and 3D NOE-HOHAHA and HMQC-NOE experiments for the estimation of proton-proton distances is demonstrated by comparing the results of these experiments on a diantennary asparagine-linked oligosaccharide with those of a conventional 2D NOE experiment. NOEs identified in the 2D and 3D NOE-HOHAHA as well as HMQC-NOE experiments, so far not identified or not quantified in 2D NOE experiments, are discussed in relation to each glycosidic linkage. The flexibility of the Man alpha (1-3)Man linkage is demonstrated, confirming the existence of an ensemble of conformations for this linkage.

Characterisation by 1H-n.m.r. spectroscopy of oligosaccharides, derived from arabinoxylans of white endosperm of wheat, that contain the elements ----4)[alpha-L-Araf-(1----3)]-beta-D-Xylp-(1---- or ----4)[alpha- L-Araf-(1----2)][alpha-L-Araf-(1----3)]-beta-D-Xylp-(1----.

The structure of penta- to hepta-saccharides, generated by digestion of purified wheat-endosperm arabinoxylan with endo-(1----4)-beta-D-xylanase and isolated by gel-permeation chromatography on Bio-Gel P-6 followed by high-performance anion-exchange chromatography with pulsed amperometric detection, was established using monosaccharide and methylation analysis, f.a.b.-m.s., and 1H-n.m.r. spectroscopy. The oligosaccharides had a core of (1----4)-linked beta-D-xylopyranosyl residues 3- or 2,3-substituted with single alpha-L-arabinofuranosyl groups, and gave 1H-n.m.r. spectra typical for each type.

ROESY studies and HSEA calculations on xylose-containing oligosaccharides related to N-glycoproteins.

Conformational studies on beta-D-Xyl-(1----2)-[alpha-D-Man-(1----6)]-beta-D-OMe, beta-D-Xyl-(1----2)-[alpha-D-Man-(1----3)]-beta-D-Man-OMe, and beta-D-Xyl-(1----2)-[alpha-D-Man-(1----3)]-[alpha-D-Man-(1----6)]-beta-D -Man-Ome have been carried out using rotating-frame n.O.e. experiments in combination with HSEA calculations. The estimated time-averaged torsional angles phi and psi about the various glycosidic linkages and the estimated time-averaged rotamer population around the C-5-C-6-linkage of beta-Man in the tetrasaccharide are similar to the corresponding parameters for both trisaccharides.

Conformational studies on the N-linked carbohydrate chain of bromelain.

1H- and 13C-NMR assignments for the carbohydrate part of the glycopeptide alpha-D-Man-(1----6)-[beta-D-Xyl-(1----2)]-beta-D-Man-(1----4)-beta-D- GlcNAc-(1----4)-[alpha-L-Fuc-(1----3)]-beta-D-GlcNAc-(1----N)-Asn approximately, derived from the proteolytic enzyme bromelain (EC 3.4.22.4), have been obtained using homo- and heteronuclear correlation spectroscopy, two-dimensional homonuclear Hartmann-Hahn and nuclear Overhauser enhancement experiments. A conformational model for the carbohydrate chain, deduced from the NMR data and consistent with hard-sphere exo-anomeric calculations shows that the rotamer population about the C-5--C-6 bond of beta-Man is restricted to the P omega = 180 rotamer, mainly.