Cross-peptide bond 13C--15N coupling constants by 13C and J cross-polarization 15N NMR

Comparative 13C--15N coupling constants are reported for the linear dipeptide tBoc-L-[U-13C]Ala-[15N]GlyOMe and the corresponding cyclic diketopiperazine, both in dimethylsulfoxide (DMSO) and, upon removal of the tBoc group, in water solutions. Spectra were obtained by 13C NMR and by the first application of J cross-polarization (JCP) 15N NMR, which greatly reduces the time required to accumulate 15N NMR spectra. In DMSO there was evidence for the formation of complexed species which were not present in water. The values obtained for the cross-peptide bond coupling constant 2J13C alpha--15N were consistently less (by 2.2 Hz in DMSO, 4.3 Hz in water) for the cyclic than for the linear peptide, which may be related to the cross-peptide bond conformation. The 15N resonance for the cyclic peptide was shifted only 2 ppm downfield from the linear peptide chemical shift value in both solvents.     

Solid-state 13C and 15N NMR study of the low pH forms of bacteriorhodopsin

The visible absorption of bacteriorhodopsin (bR) is highly sensitive to pH, the maximum shifting from 568 nm (pH 7) to approximately 600 nm (pH 2) and back to 565 nm (pH 0) as the pH is decreased further with HCl. Blue membrane (lambda max greater than 600 nm) is also formed by deionization of neutral purple membrane suspensions. Low-temperature, magic angle spinning 13C and 15N NMR was used to investigate the transitions to the blue and acid purple states. The 15N NMR studies involved [epsilon-15N]lysine bR, allowing a detailed investigation of effects at the Schiff base nitrogen. The 15N resonance shifts approximately 16 ppm upfield in the neutral purple to blue transition and returns to its original value in the blue to acid purple transition. Thus, the 15N shift correlates directly with the color changes, suggesting an important contribution of the Schiff base counterion to the "opsin shift". The results indicate weaker hydrogen bonding in the blue form than in the two purple forms and permit a determination of the contribution of the weak hydrogen bonding to the opsin shift at a neutral pH of approximately 2000 cm-1. An explanation of the mechanism of the purple to blue to purple transition is given in terms of the complex counterion model. The 13C NMR experiments were performed on samples specifically 13C labeled at the C-5, C-12, C-13, C-14, or C-15 positions in the retinylidene chromophore. The effects of the purple to blue to purple transitions on the isotropic chemical shifts for the various 13C resonances are relatively small. It appears that bR600 consists of at least four different species. The data confirm the presence of 13-cis- and all-trans-retinal in the blue form, as in neutral purple dark-adapted bR. All spectra of the blue and acid purple bR show substantial inhomogeneous broadening which indicates additional irregular distortions of the protein lattice. The amount of distortion correlates with the variation of the pH, and not with the color change.     

Biosynthetic uniform 13C,15N-labelling of zervamicin IIB. Complete 13C and 15N NMR assignment.

Zervamicin IIB is a member of the alpha-aminoisobutyric acid containing peptaibol antibiotics. A new procedure for the biosynthetic preparation of the uniformly 13C- and 15N-enriched peptaibol is described This compound was isolated from the biomass of the fungus-producer Emericellopsis salmosynnemata strain 336 IMI 58330 obtained upon cultivation in the totally 13C, 15N-labelled complete medium. To prepare such a medium the autolysed biomass and the exopolysaccharides of the obligate methylotrophic bacterium Methylobacillus flagellatus KT were used. This microorganism was grown in totally 13C, 15N-labelled minimal medium containing 13C-methanol and 15N-ammonium chloride as the only carbon and nitrogen sources. Preliminary NMR spectroscopic analysis indicated a high extent of isotope incorporation (> 90%) and led to the complete 13C- and 15N-NMR assignment including the stereospecific assignment of Aib residues methyl groups. The observed pattern of the structurally important secondary chemical shifts of 1H(alpha), 13C=O and 13C(alpha) agrees well with the previously determined structure of zervamicin IIB in methanol solution.     

Characterization of peptidoglycan stem lengths by solid-state 13C and 15N NMR

Lyophilized whole cells of Aerococcus viridans (Gaffkya homari) grown on a synthetic medium containing D-[2-13C, 15N]Ala, or containing both L-[1-13C]Lys and D-[15N]Ala, have been examined by double cross-polarization magic-angle spinning 13C and 15N nuclear magnetic resonance. Results from the double-labeled alanine experiment confirm the absence of metabolic scrambling of alanine by A. viridans. Results from the combined single-label experiment can be used to count directly the number of adjacent L-Lys and D-Ala units in peptide chains of cell-wall peptidoglycan. This count leads to the conclusion that there are no terminal D-Ala or D-Ala-D-Ala units in uncross-linked chains of the peptidoglycan of A. viridans.     

Sequential assignment of 1H, 13C and 15N resonances of human carbonic anhydrase I by triple-resonance NMR techniques and extensive amino acid-specific 15N-labeling

Summary The backbone NMR resonances of human carbonic anhydase I (HCA I) have been assigned. This protein is one of the largest monomeric proteins assigned so far. The assignment was enabled by a combination of 3D triple-resonance experiments and extensive use of amino acid-specific ¹⁵N-labeling. The obtained resonance assignment has been used to evaluate the secondary structure elements present in solution. The solution structure appears to be very similar to the crystal structure, although some differences can be observed. Proton-deuteron exchange experiments have shown that the assignments provide probes that can be used in future folding studies of HCA I.The chemical shift data have been deposited in the BioMagResBank in Madison, WI, U.S.A.     

1H, 13C and 15N chemical shift referencing in biomolecular NMR

Summary A considerable degree of variability exists in the way that ¹H, ¹³C and ¹⁵N chemical shifts are reported and referenced for biomolecules. In this article we explore some of the reasons for this situation and propose guidelines for future chemical shift referencing and for conversion from many common ¹H, ¹³C and ¹⁵N chemical shift standards, now used in biomolecular NMR, to those proposed here.Abbreviations TMS tetramethylsilane - TSP 3-(trimethylsilyl)-propionate, sodium salt - DSS 2,2-dimethyl-2-silapentane-5-sulfonate, sodium salt - TFE 2,2,2-trifluoroethanol - DMSO dimethyl sulfoxide     

Rapid corepressor exchange from the trp-repressor/operator complex: An NMR study of [ul-13C/15N]-l-tryptophan

Summary [ul-¹³C/¹⁵N]-l-tryptophan was prepared biosynthetically and its dynamic properties and intermolecular interaction with a complex of Escherichia coli trp-repressor and a 20 base-pair operator DNA were studied by heteronuclear isotope-edited NMR experiments. The resonances of the free and bound corepressor (l-Trp) were unambiguously identified from gradient-enhanced ¹⁵N–¹H HSQC, ¹³C–¹H HSQC, ¹³C-and ¹⁵N-edited 2D NOESY spectra. The exchange off-rate of the corepressor between the bound and free states was determined to be 3.4±0.52 s^–1 at 45°C, almost three orders of magnitude faster than the dissociation of the protein-DNA complex. Examination of the experimental NOE buildup curves indicates that it may be desirable to use longer mixing times than would normally be used for a large molecule, in order to detect weak intermolecular NOEs in the presence of exchange. Intermolecular NOEs from bound corepressor to trp-repressor and DNA were analyzed with respect to the mechanism of ligand exchange. This analysis suggests that, in order for the ligand to diffuse out of the complex, there must be significant movement or breathing of the protein and/or DNA.Abbreviations NOESY nuclear Overhauser enhancement spectroscopy - HSQC heteronuclear single-quantum coherence - PFG pulsed field gradient - l-Trp l-tryptophan     

Conformationally restricted 2-substituted wyosine derivatives. 1H, 13C, and 15N NMR study

It was found by 1H, 13C and 15N NMR study that substitution of 4,9-dihydro-4,6-dimethyl-9-oxo-3-(2',3',5'-tri-O-acetyl-beta-D-ribofuranosyl) imidazo [1,2-a]purine (wyosine triacetate, 1) at C2 position with electronegative groups CH30 and C6H5CH2O results in a noticeable electron distribution disturbance in the "left-hand" imidazole ring and a significant increase in the North conformer population of the sugar moiety.     

15N and 13C labeling of Escherichia coli tRNAs toward the NMR analysis.

Escherichia coli tRNAs were labeled with stable isotope 15N in vivo. Three species of tRNA, tRNA(Glu), tRNA(Lys) and tRNA(Ile), were purified by an HPLC system and their NMR spectra were observed. In heteronuclear 1H-15N multiple or single quantum coherence (HMQC or HSQC) spectra, the crosspeaks corresponding to NH3 of U and NH1 of G can be distinguished clearly since their 15N chemical shifts are significantly different from each other. Thus, this combination of 15N-labeling and the proton detected heteronuclear experiments are useful for the signal assignment and the conformational analysis of tRNAs. Furthermore, C1'- selective 13C-labeling of nucleotides was examined in vivo in order to resolve the H1' signals of tRNAs. By using a newly constructed E. coli mutant strain, the isotopic enrichments of more than 90% at C1' and of less than 10% for other ribose carbons were achieved.     

Improved 4D NMR experiments for the assignment of backbone nuclei in13C/15N labelled proteins

Summary We recently proposed a novel 4D NMR strategy for the assignment of backbone nuclei in¹³C/¹⁵N-labelled proteins (Boucher et al., 1992). Intra-residue (and many sequential) assignments are obtained from a HCANNH experiment, whereas sequential assignments are based on a complementary HCA(CO)NNH experiment. We present here new constant time 4D HCANNH, HCA(CO)NNH and HNCAHA experiments that are more sensitive. Some of the data were presented at the 33rd ENC held at Asilomar, California, U.S.A., in April 1992.     

1H, 15N and 13C assignments of an intramolecular LMO4-LIM1/CtIP complex

LMO4 is a broadly expressed LIM-only protein that is involved in neural tube development and implicated in breast cancer. Here we report backbone and side chain NMR assignments for an engineered intramolecular complex of the N-terminal LIM domain from LMO4 tethered to residues 641–685 of C-terminal binding protein interacting protein (CtIP/RBBP8).     

Detection of membrane packing defects by time-resolved fluorescence depolarization.

Packing defects in lipid bilayer play a significant role in the biological activities of cell membranes. Time-resolved fluorescence depolarization has been used to detect and characterize the onset of packing defects in binary mixtures of dilinoleoylphosphatidylethanolamine/1-palmitoyl-2- oleoylphosphatidylcholine (PE/PC). These PE/PC mixtures exhibit mesoscopic packing defect state (D), as well as one-dimensional lambellar liquid crystalline (L alpha) and two-dimensional inverted hexagonal (HII) ordered phases. Based on previous electron microscopic investigations, this D state is characterized by the presence of interlamellar attachments and precursors of HII phase between the lipid layers. Using a rotational diffusion model for rod-shaped fluorophore in a curved matrix, rotational dynamics parameters, second rank order parameter, localized wobbling diffusion, and curvature-dependent rotational diffusion constants of dipyenylhexatriene (DPH)-labeled PC (DPH-PC) in the host PE/PC matrix were recovered from the measured fluorescence depolarization decays of DPH fluorescence. At approximately 60% PE, abrupt increases in these rotational dynamics parameters were observed, reflecting the onset of packing defects in the host PE/PC matrix. We have demonstrated that rotational dynamics parameters are very sensitive in detecting the onset of curvature-associating packing defects in lipid membranes. In addition, the presence of the D state can be characterized by the enhanced wobbling diffusional motion and order packing of lipid molecules, and by the presence of localized curvatures in the lipid layers.     

1H, 13C, and 15N NMR assignments of the actinoporin Sticholysin I

Sticholysin I is an actinoporin, a pore forming toxin, of 176 aminoacids produced by the sea anemone Stichodactyla heliantus. Isotopically labelled ¹³C/¹⁵N recombinant protein was produced in E. coli. Here we report the complete NMR ¹⁵N, ¹³C and ¹H chemical shifts assignments of Stn I at pH 4.0 and 25°C (BMRB No. 15927).     

In vivo 13C and 15N NMR studies of methylamine metabolism in Pseudomonas species MA

Pseudomonas species MA was grown with methylamine as a sole source of carbon and nitrogen enabling the total flow of carbon and nitrogen into this organism to be simultaneously monitored in vivo using 13C and 15N NMR. [13C]Methylamine was rapidly and extensively incorporated into the methyl group of N-methylglutamate during high oxygenation of the cell suspension, but when the oxygenation rate was lower, a significant portion was also found in the methyl group of gamma-glutamylmethylamide. At later times the carbon label was found in intermediates of the serine assimilation pathway, with glutamate derived from the tricarboxylic acid cycle being the most abundant product. Incorporation of [15N]methylamine was only detected as N-methyl[15N]glutamate, but when protein synthesis was inhibited, the label was also detected in the amino nitrogen of glutamate. When oxygenation rates were lower, the 15N-labeled methylamine was found in the methylamide group of gamma-glutamylmethylamide in addition to being incorporated into N-methylglutamate. gamma-Glutamylmethylamide formation was linked to the overall energy state of the cell and was not affected by inhibition of the carbon assimilation pathway. Neither 5-hydroxy-N-methylpyroglutamate nor N-methyl-alpha-ketoglutaramate were detected to any significant extent. A mechanism was proposed for the role of gamma-glutamylmethylamide in the regulation of endogenous nitrogen supplies in this organism.     

High-level 2H/13C/15N labeling of proteins for NMR studies

Summary The protein human carbonic anhydrase II (HCA II) has been isotopically labeled with ²H, ¹³C and ¹⁵N for high-resolution NMR assignment studies and pulse sequence development. To increase the sensitivity of several key ¹H/¹³C/¹⁵N triple-resonance correlation experiments, ²H has been incorporated into HCA II in order to decrease the rates of ¹³C and ¹H_N T₂ relaxation. NMR quantities of protein with essentially complete aliphatic ²H incorporation have been obtained by growth of E. coli in defined media containing D₂O, [1,2-¹³C₂, 99%] sodium acetate, and [¹⁵N, 99%] ammonium chloride. Complete aliphatic deuterium enrichment is optimal for ¹³C and ¹⁵N backbone NMR assignment studies, since the ¹³C and ¹H_N T₂ relaxation times and, therefore, sensitivity are maximized. In addition, complete aliphatic deuteration increases both resolution and sensitivity by eliminating the differential ²H isotopic shift observed for partially deuterated CH_nD_m moieties.     

Identification of platination sites on human serum transferrin using 13C and 15N NMR spectroscopy

 Reactions between various apo and metal-bound forms of human serum transferrin (80 kDa) and the recombinant N-lobe (40 kDa) with [Pt(en)Cl₂] or cis-[PtCl₂(NH₃)₂] have been investigated in solution via observation of [¹H,¹⁵N] NMR resonances of the Pt complexes, [¹H,¹³C] resonances of the eCH₃ groups of the protein methionine residues, and by chromatographic analysis of single-site methionine mutants. For the whole protein, the preferred Pt binding site appears to be Met256. Additional binding occurs at the other surface-exposed methionine (Met499), which is platinated at a slower rate than Met256. In contrast, binding of similar Pt compounds to the N-lobe of the protein occurs at Met313, rather than Met256. Met313 is buried in the interlobe contact region of intact transferrin. After loss of one chloride ligand from Pt and binding to methionine sulfur of the N-lobe, chelate-ring closure appears to occur with binding to a deprotonated backbone amide nitrogen, and the loss of the other chloride ligand. Such chelate-ring closure was not observed during reactions of the whole protein, even after several days. Received: 5 May 1999 / Accepted: 26 July 1999