"Perfecting" pure shift HSQC: full homodecoupling for accurate and precise determination of heteronuclear couplings.

Fully homodecoupled HSQC spectra can be obtained through the use of a new pulse sequence element, "perfectBIRD". By way of illustration, we show that perfectBIRD decoupling allows one-bond residual dipolar couplings (RDCs), which provide important NMR restraints for structure elucidation, to be measured with outstanding precision, even in methylene groups.

Molecular mechanism of the interaction between activated factor XIII and its glutamine donor peptide substrate.

BACKGROUND: Activated factor XIII (FXIII), a dimer of truncated A-subunits (FXIII-A2*), is a transglutaminase that crosslinks primary amines to peptide-bound glutamine residues. Because in the few natural substrates of FXIII-A2* no consensus sequence could be identified around the reactive glutamine, studying the interaction between individual substrates and FXIII-A2* is of primary importance. Most of the alpha2-plasmin inhibitor (alpha2PI) molecules become truncated by a plasma protease, and the truncated isoform (N1-alpha2PI) is an important substrate of FXIII-A2*. The crosslinking of N1-alpha2PI to fibrin plays a major role in protecting fibrin from fibrinolysis. METHODS: We studied the interaction of FXIII-A2* with its dodecapeptide glutamine donor substrate, N1-alpha2PI(1-12), the sequence of which corresponds to the N-terminal sequence of N1-alpha2PI. Kinetic parameters for N1-alpha2PI(1-12) and for its truncated or synthetic mutants were determined by a spectrophotometric assay. The interaction of N1-alpha2PI(1-12) with FXIII-A2* was investigated by proton nuclear magnetic resonance (NMR) and saturating transfer difference (STD) NMR. RESULTS AND CONCLUSIONS: Kinetic experiments with peptides in which the Asn1 residue was either truncated or replaced by alanine and proton NMR analysis of the FXIII-A2*-N1-alpha2PI(1-12) complex demonstrated that Asn1 is essential for effective enzyme-substrate interaction. Experiments with C-terminally truncated peptides proved that amino acids 7-12 are essential for the interaction of N1-alpha2PI(1-12) with the enzyme, and suggested the existence of a secondary binding site on FXIII-A2*. Hydrophobic residues, particularly Leu10 and the C-terminal Lys12, seemed to be especially important in this respect, and direct interaction between hydrophobic C-terminal residues and FXIII-A2* was demonstrated by STD NMR.

The solution structure and dynamics of human pancreatic ribonuclease determined by NMR spectroscopy provide insight into its remarkable biological activities and inhibition.

Human pancreatic ribonuclease (RNase 1) is expressed in many tissues; has several important enzymatic and biological activities, including efficient cleavage of single-stranded RNA, double-stranded RNA and double-stranded RNA-DNA hybrids, digestion of dietary RNA, regulation of vascular homeostasis, inactivation of the HIV, activation of immature dendritic cells and induction of cytokine production; and furthermore shows potential as an anti-tumor agent. The solution structure and dynamics of uncomplexed, wild-type RNase 1 have been determined by NMR spectroscopy methods to better understand these activities. The family of 20 structures determined on the basis of 6115 unambiguous nuclear Overhauser enhancements is well resolved (pairwise backbone RMSD=1.07 A) and has the classic RNase A type of tertiary structure. Important structural differences compared with previously determined crystal structures of RNase 1 variants or inhibitor-bound complexes are observed in the conformation of loop regions and side chains implicated in the enzymatic as well as biological activities and binding to the cytoplasmic RNase inhibitor. Multiple side chain conformations observed for key surface residues are proposed to be crucial for membrane binding as well as translocation and efficient RNA hydrolysis. (15)N-(1)H relaxation measurements interpreted with the standard and our extended Lipari-Szabo formalism reveal rigid regions and identify more dynamic loop regions. Some of the most dynamic areas are key for binding to the cytoplasmic RNase inhibitor. This finding and the important differences observed between the structure in solution and that bound to the inhibitor are indications that RNase 1 to inhibitor binding can be better described by the "induced fit" model rather than the rigid "lock-into-key" mechanism. Translational diffusion measurements reveal that RNase 1 is predominantly dimeric above 1 mM concentration; the possible implications of this dimeric state for the remarkable biological properties of RNase 1 are discussed.

Structural investigation of syringomycin-E using molecular dynamics simulation and NMR.

Syringomycin-E (SR-E) is a cyclic lipodepsinonapeptide produced by certain strains of the bacterium Pseudomonas syringae pv. syringae. It shows inhibitory effects against many fungal species, including human pathogens. Its primary biological target is the plasma membrane, where it forms channels comprised of at least six SR-E molecules. The high-resolution structure of SR-E and the structure of the channels are currently not known. In this paper, we investigate in atomic detail the molecular features of SR-E in water by NMR and in water and octane by molecular dynamics simulation (MD). We built a model of the peptide and examined its structure in water and octane in 200 ns MD simulations both with and without distance restraints derived from NMR NOE data. The resulting trajectories show good agreement with the measured NOEs and circular dichroism data from the literature and provide atomistic models of SR-E that are an important step toward a better understanding of the antifungal and antibacterial activity of this peptide.

Structural and biochemical characterization of neuronal calretinin domain I-II (residues 1-100). Comparison to homologous calbindin D28k domain I-II (residues 1-93).

This study characterizes the calcium-bound CR I-II domain (residues 1-100) of rat calretinin (CR). CR, with six EF-hand motifs, is believed to function as a neuronal intracellular calcium-buffer and/or calcium-sensor. The secondary structure of CR I-II, defined by standard NMR methods on 13C,15N-labeled protein, contains four helices and two short interacting segments of extended structure between the calcium-binding loops. The linker between the two helix-loop-helix, EF-hand motifs is 12 residues long. Limited trypsinolysis at K60 (there are 10 other K/R residues in CR I-II) confirms that the linker of CR I-II is solvent-exposed and that other potential sites are protected by regular secondary structure. 45Ca-overlay of glutathione S-transferase (GST)-CR(1-60) and GST-CR(61-100) fusion proteins confirm that both EF-hands of CR I-II have intrinsic calcium-binding properties. The primary sequence and NMR chemical shifts, including calcium-sensitive glycine residues, also suggest that both EF-hand loops of CR I-II bind calcium. NMR relaxation, analytical ultracentrifugation, chemical cross-linking and NMR translation diffusion measurements indicate that CR I-II exists as a monomer. Calb I-II (the homologous domain of calbindin D28k) has the same EF-hand secondary structures as CR I-II, except that helix B is three residues longer and the linker has only four residues [Klaus, W., Grzesiek, S., Labhardt, A. M., Buckwald, P., Hunziker, W., Gross, M. D. & Kallick, D. A. (1999) Eur. J. Biochem. 262, 933-938]. In contrast, Calb I-II binds one calcium cation per monomeric unit and exists as a dimer. Despite close homology and similar secondary structures, CR I-II and Calb I-II probably have distinct tertiary structure features that suggest different cellular functions for the full-length proteins.

Synthesis of the alpha-D-GlcpA-(1-->3)-alpha-L-Rhap-(1-->2)-L-Rha trisaccharide isolated from the cell wall hydrolyzate of the green alga, Chlorella vulgaris.

The title trisaccharide was synthesized from 6-O-acetyl-2,3,4-tri-O-benzyl-alpha-D-glucopyranosyl chloride (10), ethyl 2,4-di-O-benzyl-1-thio- (5) and benzyl 3,4-di-O-benzyl-alpha-L-rhamnopyranoside (9). The disaccharide 11 obtained from compounds 5 and 10 was used as the glycosyl donor to glycosylate the rhamnopyranoside derivative 9 having free OH-2 using the NIS-AgOTf-mediated glycosylation methodology. Zemplén deacetylation of the trisaccharide 12 resulted in the 6"-OH derivative (13), which was selectively oxidized with CrO3 to the uronic acid derivative 14. The benzyl groups were removed by catalytic hydrogenolysis to furnish the target trisaccharide (1).

J-modulated TROSY experiment extends the limits of homonuclear coupling measurements for larger proteins.

This paper describes the use of a TROSY experimental scheme and its variant extended with a scaled J-modulation spin-echo sequence for accurate and sensitive measurement of homonuclear 3J(H(N)H(alpha)) coupling constants in larger proteins with uniform 15N labeling. Exclusive selection of the most slowly relaxing component of a 15N-1H multiplet by the TROSY approach leads to substantial improvement in resolution; this is a prerequisite for accurate measurement of couplings from the 1H multiplets directly along the 1H frequency dimension or from the J-scaled doublets along the 15N frequency dimension.

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.

Synthesis, biology, NMR and conformation studies of the topographically constrained delta-opioid selective peptide analogs of [beta-iPrPhe(3)]deltorphin I.

Replacement of Phe3 in the endogenous delta-opioid selective peptide deltorphin I with four optically pure stereoisomers of the topographically constrained, highly hydrophobic novel amino acid beta-isopropylphenylalanine (beta-iPrPhe) produced four pharmacologically different deltorphin I peptidomimetics. Radiolabeled ligand-binding assays and in vitro biological evaluation indicate that the stereoconfiguration of the iPrPhe residue plays a crucial role in determining the binding affinity, bioactivity and selectivity of [beta-iPrPhe3]deltorphin I analogs: a (2S,3R) configuration of the iPrPhe3 residue in [beta-iPrPhe3]deltorphin I provided the most desirable biological properties with binding affinity (IC50 = 2 nM), bioassay potency (IC50 = 1.23 nM in MVD assay) and exceptional selectivity for the delta-opioid receptor over the mu-opioid receptor (30 000). Further conformational studies based on two-dimensional NMR and computer-assisted molecular modeling suggested a model for the possible bioactive conformation in which the Tyr1 and (2S,3R)-beta-iPrPhe3 residues adopt trans side-chain conformations, and the linear peptide backbone favors a distorted beta-turn conformation.

High-field NMR studies of 3beta-tetrahydropyranyloxy steroids.

Comprehensive NMR studies were carried out on 3beta-hydroxy-pregnene and cholestene analogs, each containing a tetrahydropyranyl ether group at the 3-position. Two-dimensional NMR experiments (COSY, TOCSY, HSQC, and HSQC-TOCSY) permitted the complete assignments of both the (1)H and (13)C resonances of these derivatives in deuterated benzene or chloroform. The aromatic solvent-induced NMR signal shifts (ASIS) were also investigated.

Deltorphin II analogues with 6-hydroxy-2-aminotetralin-2-carboxylic acid in position 1.

Two approaches to the design of very active and highly selective delta opioid peptides were used to obtain new deltorphin analogues with altered hydrophobic and stereoelectronic properties. Deltorphin II analogues were synthesized with the substitution of Ile instead of Val at positions 5 and 6 in the address domain and 6-hydroxy-2-aminotetralin-2-carboxylic acid (Hat) instead of Tyr(1) in the message domain. In the radioreceptor-binding studies, in which type-specific tritiated opioid ligands were used, (R)- and (S)-Hat-deltorphins exhibited similar K(i) values, revealing high delta selectivity. The peptides displayed agonist properties in the in vitro bioassay, with IC(50) values in the subnanomolar range in the mouse vas deferens assay and in the micromolar or higher range in the guinea pig ileum assay, again demonstrating a high selectivity toward delta receptors. The agonist property of the new ligands was confirmed by means of [(35)S]GTPgammaS-binding experiments in membranes of the rat frontal cortex.

A general scheme for suppression of ABX strong coupling signals in heteronuclear scalar and dipolar correlation experiments.

Enhanced versions of heteronuclear chemical shift correlation experiments which yield high-quality spectra with efficient suppression of extra peaks arising from strong coupling effects are proposed. The enhanced pulse sequences feature properly designed filtering schemes inserted during preparation, or prior to acquisition, or at both places depending on the particular experiment. These modifications extend the applicability of existing methods, since they exclude misinterpretation of spurious peaks and allow unambiguous assignment of the desired correlations. The general applicability of the filtering method is noteworthy; both scalar- and dipolar-correlated experiments with both X and 1H detection using phase cycling or gradient pulses for coherence selection can be freed of strong coupling artifacts.

A comparison of 1D and 2D (unbiased) experimental methods for measuring CSA/DD cross-correlated relaxation.

Conventional and enhanced 1D experiments and different NOESY experiments (the 2D unbiased method) were performed for measuring CSA/DD cross-correlated relaxation on trehalose, a compound which could be approximated as a spherical top, and on simple model compounds comprising C3v symmetry (CHCl3, triphenylsilane (TPSi)). The comparison gives experimental evidence for the equivalence of the methods within the limits of the two-spin approach. 1D data are evaluated with both the simple initial rate and the Redfield relaxation matrix approach. The 2D data are obtained from the so-called transfer matrix using the Perrin-Gipe eigenvalue/eigenvector method. For the improved performance of the 2D method, an X-filtered (HHH) NOESY is suggested at the natural abundance of 13C (or other dilute, low gamma species). Also, experimental parameters crucial for reliable CSA data are tested (e. g., the impact of insufficient relaxation delay). Error estimation is carried out for fair comparison of methods. Revised liquid state 1H and 13C (29Si) CSA data are presented for chloroform and TPSi.

Synthesis of phosphoramide mustard analogues of daunomycin and carminomycin.

New phosphoramide mustards (6-8) have been prepared from the antibiotics 2 and 3, and from 5. The mixture of cyclophosphamides could be separated by preparative layer and column chromatography. The assignments of configuration to the isomeric phosphoramidates was based on the magnetic anisotropy of the P = O bond. The synthesized compounds 6a,b-8a,b (mixture of isomers) were tested for inhibitory activity on the [3H]-thymidine incorporation into the DNA of tumor cells, using ovarian carcinoma cell line.

Synthesis of p-trifluoroacetamidophenyl (4,6-dideoxy-4-formamido-3-C-methyl-2-O-methyl-alpha-L-mannopyranosyl)- (1-->3)-(2-O-methyl-alpha-D-rhamnopyranosyl)-(1-->3)- (2-O-methyl-alpha-L-fucopyranosyl)-(1-->3)-(alpha-L-rhamnopyranosyl)- (1-->2)-6-deoxy-alpha-L-talopyranoside: a spacer-armed pentasaccharide glycopeptidolipid antigen of Mycobacterium avium serovar 14.

Syntheses of p-trifluoroacetamidophenyl glycosides of the haptenic pentasaccharide and the non-reducing disaccharide unit of the title pentasaccharide are reported. The synthesis of the terminal N-formylkansosamine unit started from methyl 6-deoxy-2,3-O-isopropylidene-alpha-L-lyxo- hexopyran-4-uloside which, after C-3 methylation, was transformed into a glycosyl donor [3-O-benzyl-4-N-benzylformamido-4,6-dideoxy-3-C-methyl-2-O-methyl- alpha,beta-L-mannopyranosyl trichloroacetimidate (20), and used for the synthesis of p-trifluoroacetamidophenyl (4-formamido-4,6-dideoxy-3-C-methyl-2-O-methyl-alpha-L-mannopyranosyl)- (1-->3)-6-deoxy-2-O-methyl-alpha-D-mannopyranoside (29). Ethyl (3-O-benzyl-4-N-benzylformamido-4,6-dideoxy-3-C-methyl-2-O-methyl- alpha-L-mannopyranosyl)-(1-->3)-4-O-benzyl-6-deoxy-2-O-methyl-1-thio- alpha-D-mannopyranoside (31), prepared by glycosylation of ethyl 4-O-benzyl-6-deoxy-2-O-methyl-1-thio-alpha-D-mannopyranoside with 20, served as glycosyl donor in a 2 + 3 block synthesis of the title pentasaccharide.

Gradient- and sensitivity-enhanced TOCSY experiments.

A pulsed field gradient version of the sensitivity-enhanced 2D TOCSY experiment is proposed which yields high-quality spectra with improved sensitivity and a minimum of two scans per t1 increment. For rapid acquisition of 1D TOCSY spectra, the 1D DPFGSE-TOCSY experiment was modified to include phase-encoded multiple-selective excitation followed by a simple spectral editing. Combination of these two building blocks is used in a sensitivity-enhanced 2D analog of the 3D TOCSY-TOCSY experiment which provides an efficient tool for resolving severely overlapped signals of oligomers in short experimental time.

Sensitivity- and gradient-enhanced hetero (omega1) half-filtered TOCSY experiment for measuring long-range heteronuclear coupling constants.

An enhanced version of the X (omega1) half-filtered TOCSY experiment for measurement of long-range heteronuclear coupling constants is proposed which yields high-quality spectra with substantially increased sensitivity and resolution. The modified method features gradient-enhanced X filtering sequences, broadband homonuclear decoupling during t1, optional 1JXH scaling in the F1 domain, and gradient coherence selection in combination with the sensitivity-enhanced protocol for the TOCSY transfer. These modifications extend the applicability of the method--coupling constants can be measured accurately for natural abundance samples at low concentrations and for compounds yielding complex spectra. Computer-aided analysis of E.COSY-type multiplets is applied for the determination of heteronuclear long-range coupling constants.

Sensitivity- and gradient-enhanced heteronuclear coupled/decoupled HSQC-TOCSY experiments for measuring long-range heteronuclear coupling constants.

A pulsed field gradient version of the sensitivity-enhanced 2D HSQC-TOCSY experiment is proposed for measurement of long-range heteronuclear coupling constants. The coupling constants are obtained by computer-aided analysis of mixed-phase multiplets with and without the heteronuclear splitting. Generation of pure phase data is not required. Since large 1JXH and JHH couplings are used for coherence transfer, small nJXH can be measured accurately, which could be difficult to obtain from purely heteronuclear polarization transfer experiments.

Conformational analysis of beta-methyl-para-nitrophenylalanine stereoisomers of cyclo[D-Pen2, D-Pen5]enkephalin by NMR spectroscopy and conformational energy calculations.

Solution conformations of beta-methyl-para-nitrophenylalanine4 analogues of the potent delta-opioid peptide cyclo[D-Pen2, D-Pen5]enkephalin (DPDPE) were studied by combined use of nmr and conformational energy calculations. Nuclear Overhauser effect connectivities and 3JHNC alpha H coupling constants measured for the (2S, 3S)-, (2S, 3R)-, and (2R, 3R)-stereoisomers of [beta-Me-p-NO2Phe4]DPDPE in DMSO were compared with low energy conformers obtained by energy minimization in the Empirical Conformational Energy Program for Peptides (ECEPP/2) force field. The conformers that satisfied all available nmr data were selected as probable solution conformations of these peptides. Side-chain rotamer populations, established using homonuclear (3JH alpha H beta) and heteronuclear (3JH alpha C gamma) coupling constants and 13C chemical shifts, show that the beta-methyl substituent eliminates one of the three staggered rotamers of the torsion angle chi 1 for each stereoisomer of the beta-Me-p-NO2Phe4. Similar solution conformations were suggested for the L-Phe4-containing (2S, 3S)- and (2S, 3R)-stereoisomers. Despite some local differences, solution conformations of L- and D-Phe4-containing analogues have a common shape of the peptide backbone and allow similar orientations of the main delta-opioid pharmacophores. This type of structure differs from several models of the solution conformations of DPDPE, and from the model of biologically active conformations of DPDPE suggested earlier. The latter model is allowed for the potent (2S, 3S)- and (2S, 3R)-stereoisomers of [beta-Me-p-NO2Phe4]DPDPE, but it is forbidden for the less active (2R, 3R)- and (2R, 3S)-stereoisomers. It was concluded that the biologically active stereoisomers of [beta-Me-p-NO2Phe4]DPDPE in the delta-receptor-bound state may assume a conformation different from their favorable conformations in DMSO.