NMR studies of Azotobacter vinelandii and Pseudomonas putida seven-iron ferredoxins. Direct assignment of beta-cysteinyl carbon NMR resonances and further proton NMR assignments of cysteinyl and aromatic resonances.

Ferredoxins are proteins which contain iron and inorganic sulfide and are capable of electron transport. They are found in a wide range of organisms, from anaerobic bacteria, to plants and mammals. Although NMR spectroscopy has been used to study ferredoxins since the 1970s, little important structural or biochemical information has resulted from these investigations. The major difficulty has been the effect of the paramagnetic iron-sulfur clusters on the peptide resonances, hindering nuclear Overhauser effect (NOE) studies and causing broad line widths. These effects are most pronounced on resonances arising from the nuclei closest to the iron-sulfur center. Unfortunately, these are likely to be the most interesting nuclei, as they report the events and geometry in the vicinity of the active sites. In this paper, the first direct assignment of beta-cysteinyl 13C resonances for any iron-sulfur protein is reported for the spectrum of Pseudomonas putida ferredoxin. These resonances are of special significance, as they arise from the atoms on the protein closest to the iron centers, with the exception of the directly bound cysteinyl sulfur atoms. In addition, cysteinyl and ring system 1H NMR resonance assignments are made for the spectra of P. putida ferredoxin and Azotobacter vinelandii ferredoxin I.     

Complete assignment of aromatic 1H nuclear magnetic resonances of the tyrosine residues of hen lysozyme

The complete assignment of the aromatic proton nuclear magnetic resonances of the three tyrosine residues in hen lysozyme is reported. These assignments were made using double resonance techniques, specific chemical modifications of one residue (Tyr-23), and by interpretation of the effects of paramagnetic lanthanide ions. Some aspects of the behaviour of the tyrosine residues are reported, including pK values, reactivity towards modifying agents and conformational mobility.     

Specific assignment of resonances in the 1H nuclear magnetic resonance spectrum of the polypeptide cardiac stimulant anthopleurin-A

The specific assignment of resonances in the 300-MHz 1H nuclear magnetic resonance (NMR) spectrum of anthopleurin-A, a polypeptide cardiac stimulant from the sea anemone Anthopleura xanthogrammica, is described. Assignments have been made using two-dimensional NMR techniques, in particular the method of sequential assignments, where through-bond and through-space connectivities to the peptide backbone NH resonances are used to identify the spin systems of residues adjacent in the amino acid sequence. Complete assignments have been made of the resonances from 33 residues out of a total of 49, and partial assignments of a further 3. The resonances from several of the remaining residues have been identified but not yet specifically assigned. A complicating factor in making these assignments is the conformational heterogeneity exhibited by anthopleurin-A in solution. The resonances from a number of amino acid residues in the minor conformer have also been assigned. These assignments contribute towards identification of the origin of this heterogeneity, and permit some preliminary conclusions to be drawn regarding the secondary structure of the polypeptide.     

Assignment of aromatic resonances in the 1H nuclear magnetic resonance spectra of cardioactive polypeptides from sea anemones

High-resolution 1H NMR spectroscopy at 300 MHz has been used to investigate the aromatic residues of a series of homologous polypeptides from sea anemones: anthopleurin-A from Anthopleura xanthogrammica and toxins I and II from Anemonia sulcata. Using two-dimensional NMR techniques, specific assignments to individual protons have been made for all aromatic resonances in the spectra of these molecules. In all three polypeptides the resonances from the two conserved Trp residues, 23 and 33, are shifted significantly from their random coil values, and the indole NH resonance of Trp-23 is not observed. These shift perturbations are due in part to a mutual interaction of the two indole rings, which is also indicated by the observation of nuclear Overhauser enhancements between protons of the two rings. Several other nonpolar side chains also interact with these two Trp residues, forming a hydrophobic region, the overall structure of which is conserved throughout the series. The other aromatic residues in these polypeptides appear not to participate in this structural region.     

Classification of iron-sulfur cores in ferredoxins by 1H nuclear magnetic resonance spectroscopy

A 1H nuclear magnetic resonance (NMR) study was carried out on various ferredoxins which possess one of three types of iron-sulfur clusters, (2Fe-2S), (3Fe-3S), or (4Fe-4S). In the isolated form, (2Fe-2S) ferredoxins from spinach (Spinacea oleracia), pokeweed (Phytolacca americana), a blue-green alga (Spirulina platensis), and a halobacterium (Halobacterium halobium) exhibited two broad resonances common in chemical shift at the region downfield of 10 ppm. In their reduced forms, seven contact-shifted resonances appeared spread over 30 ppm. Although the positions of the contact-shifted resonances in the reduced state differed among the four, a common trend in the temperature dependence of their resonance positions was recognized. Two (4Fe-4S) ferredoxins from Bacillus stearothermophilus and Bacillus thermoproteolyticus exhibited almost indistinguishable spectral patterns in both the oxidized and reduced forms. The ferricyanide-treated ferredoxins of B. stearothermophilus and B. thermoproteolyticus showed characteristic contact-shifted resonances distinct from the spectra of the original (4Fe-4S) ferredoxins. This corresponds to the recent finding of the interconversion of (4Fe-4S) and (3Fe-3S) clusters with ferricyanide in the ferredoxin. Based on our data together with reported NMR data on other ferredoxins, contact-shift resonances of three types of clusters were tabulated. The reliability of NMR classification increases when we compare the NMR spectra of a ferredoxin with the classification standards at the two redox states. Moreover, not only the absolute values of the chemical shifts of contact-shifted resonances but also their temperature dependence give distinctive information applicable to iron core identification.     

A 15n-filtered 2D 1H TOCSY experiment for assignment of aromatic ring resonances and selective identification of tyrosine ring resonances in proteins: Description and application to Photoactive Yellow Protein

A new method to selectively detect the ring resonances of the aromatic residues in 15N-labelled proteins is presented. The experiment consists of a 2D 1H TOCSY sequence withremoval of the amide signals via 15N-filtering. Experiments are acquired in the absence andpresence of water inversion; combining the two spectra allows selective observation of thetyrosine ring resonances and enables the identification of their δ andε ring protons. The experiment is demonstrated on a 15N-labelled sample of Photoactive Yellow Protein and isshown to give good selectivity for tyrosine ring resonances under a wide range oftemperatures and pH values.     

Direct assignment of the dihydrouridine-helix imino proton resonances in transfer ribonucleic acid nuclear magnetic resonance spectra by means of the nuclear Overhauser effect

The NMR resonances from the hydrogen-bonded ring NH protons in the dihydrouridine stem of Escherichia colt tRNA1Val have been assigned by experiments involving the nuclear Overhauser effect (NOE) between adjacent base pairs. Irradiation of the 8-14 tertiary resonance produced a NOE to base pair 13. Irradiation of the CG13 ring NH produced NOEs to base pairs 12 and 14. Similarly, base pair 12 was shown to be dipolar coupled to 11 and 13, and base pair 11 was found to be coupled to 10 and 12. These sequential connectivities led to the assignment of CG13 at -13.05 ppm, UA12 at -13.84 ppm, CG11 at -12.23 ppm, and GC10 at -12.60 ppm. The results are compared with previous, less direct assignments for these four base pairs and with the expected proton positions from the crystal structure coordinates for this helix.     

1H and 15N nuclear magnetic resonance assignment and secondary structure of the cytotoxic ribonuclease alpha-Sarcin.

The ribosome-inactivating protein alpha-Sarcin (alpha S) is a 150-residue fungal ribonuclease that, after entering sensitive cells, selectively cleaves a single phosphodiester bond in an universally conserved sequence of the major rRNA to inactivate the ribosome and thus exert its cytotoxic action. As a first step toward establishing the structure-dynamics-function relationships in this system, we have carried out the assignment of the 1H and 15N NMR spectrum of alpha S on the basis of homonuclear (1H-1H) and heteronuclear (1H-15N) two-dimensional correlation spectra of a uniformly 15N-labeled sample, and two selectively 15N-labeled (Tyr and Phe) samples, as well as a single three-dimensional experiment. The secondary structure of alpha S, as derived from the characteristic patterns of dipolar connectivities between backbone protons, conformational chemical shifts, and the protection of backbone amide protons against exchange, consists of a long N-terminal beta-hairpin, a short alpha-helical segment, and a C-terminal beta-sheet of five short strands arranged in a + 1, + 1, + 1, + 1 topology, connected by long loops in which the 13 Pro residues are located.     

The downfield resonances in the 1H NMR spectra of Azotobacter vinelandii and Pseudomonas putida seven-iron ferredoxins

Pseudomonas putida and Azotobacter vinelandii ferredoxins each contain one [4Fe-4S] cluster and one [3Fe-4S] cluster. Their polypeptide chains are nearly identical, differing by only 15 residues out of a total of 106. T1 measurements and temperature dependence studies of the 1H NMR spectrum of each ferredoxin demonstrate that all six resolved downfield resonances are near an iron-sulfur center. The five most downfield resonances are shown to arise from protons on cysteinyl beta-carbons by incorporation of cysteine deuterated at the beta-carbon into cell protein. The sixth peak (10.5 ppm) is shown to be a non-cysteinyl proton. This peak resolves into two resonances of approximately equal intensity at temperatures below 15 degrees or above 25 degrees C. A nuclear Overhauser effect observed between the two downfield-most resonances of A. vinelandii ferredoxin indicates that they originate from a geminal pair of beta-cysteinyl protons. An Overhauser effect observed between the resonances at 22.3 and 15.7 ppm, in conjunction with other results, implies that the resonance at 22.3 ppm arises from a beta-proton on the 3Fe-center-bound Cys16, while the resonance at 15.7 ppm arises from Cys45 beta-proton, which is bound to the 4Fe center. The five most downfield resonances are pH-dependent. The sixth peak (10.5 ppm in P. putida ferredoxin) is pH-independent. Possible origins for the observed pH dependencies are discussed.     

The aromatic residues of bovine pancreatic ribonuclease studied by 1H nuclear magnetic resonance.

1. The aromatic proton resonances in the 360-MHz 1H nuclear magnetic resonance (NMR) spectrum of bovine pancreatic ribonuclease were divided into histidine, tyrosine and phenylalanine resonances by means of pH titrations and double resonance experiments. 2. Photochemically induced dynamic nuclear polarization spectra showed that one histidine (His-119) and two tyrosines are accessibly to photo-excited flavin. This permitted the identification of the C-4 proton resonance of His-119. 3. The resonances of the ring protons of Tyr-25, Tyr-76 and Tyr-115 and the C-4 proton of His-12 were identified by comparison with subtilisin-modified and nitrated ribonucleases. Other resonances were assigned tentatively to Tyr-73, Tyr-92 and Phe-46. 4. On addition of active-site inhibitors, all phenylalanine resonances broadened or disappeared. The resonance that was most affected was assigned tentatively to Phe-120. 5. Four of the six tyrosines of bovine RNase, identified as Tyr-76, Tyr-115 and, tentatively, Tyr-73 and Tyr-92, are titratable above pH 9. The rings of Tyr-73 and Tyr-115 are rapidly rotating or flipping by 180 degrees about their C beta--C gamma bond and are accessible to flavin in photochemically induced dynamic nuclear polarization experiments. Tyr-25 is involved in a pH-dependent conformational transition, together with Asp-14 and His-48. A scheme for this transition is proposed. 6. Binding of active-site inhibitors to bovine RNase only influences the active site and its immediate surroundings. These conformational changes are probably not connected with the pH-dependent transition in the region of Asp-14, Tyr-25 and His-48. 7. In NMR spectra of RNase A at elevated temperatures, no local unfolding below the temperature of the thermal denaturation was observed. NMR spectra of thermally unfolded RNase A indicated that the deviations from a random coil are small and might be caused by interactions between neighbouring residues.     

1H NMR spectra of vertebrate [2Fe-2S] ferredoxins. Hyperfine resonances suggest different electron delocalization patterns from plant ferredoxins

We report the observation of paramagnetically shifted (hyperfine) proton resonances from vertebrate mitochondrial [2Fe-2S] ferredoxins. The hyperfine signals of human, bovine, and chick [2Fe-2S] ferredoxins are described and compared with those of Anabaena 7120 vegetative ferredoxin, a plant-type [2Fe-2S] ferredoxin studied previously [Skjeldal, L., Westler, W. M., & Markley, J. L. (1990) Arch. Biochem. Biophys. 278, 482-485]. The hyperfine resonances of the three vertebrate ferredoxins were very similar to one another both in the oxidized state and in the reduced state, and slow (on the NMR scale) electron self-exchange was observed in partially reduced samples. For the oxidized vertebrate ferredoxins, hyperfine signals were observed downfield of the diamagnetic envelope from +13 to +50 ppm, and the general pattern of peaks and their anti-Curie temperature dependence are similar to those observed for the oxidized plant-type ferredoxins. For the reduced vertebrate ferredoxins, hyperfine signals were observed both upfield (-2 to -18 ppm) and downfield (+15 to +45 ppm), and all were found to exhibit Curie-type temperature dependence. This pattern and temperature dependence are distinctly different from those found with reduced plant-type ferredoxins which have signal centered around +120 ppm with Curie-type temperature dependence, assigned to cysteines which interact with Fe(III), and signals centered around +20 ppm with anti-Curie temperature dependence, assigned to cysteines which interact with Fe(II) [Dugad, L. B., La Mar, G. N., Banci, L., & Bertini, I. (1990) Biochemistry 29, 2263-2271].(ABSTRACT TRUNCATED AT 250 WORDS)     

Individual assignments of the methyl resonances in the 1H nuclear magnetic resonance spectrum of the basic pancreatic trypsin inhibitor.

In earlier work the resonances of the 20 methyl groups in the basic pancreatic trypsin inhibitor (BPTI) had been identified in the 360-MHz 1H nuclear magnetic resonance (NMR) spectra and most of the methyl lines had from spin-decoupling experiments been assigned to the different types of amino acid residues. The assignments to the different amino acid types were now completed by studies of the saturation transfer between the denatured and the globular forms of the inhibitor and by spin-decoupling experiments in nuclear Overhauser enhancement (NOE) difference spectra. These distinguished between the methyl resonances of Ala and Thr. Furthermore, for most of the methyl resonances, individual assignments to specific residues in the amino acid sequence were obtained from measurements of intramolecular proton-proton NOE's, use of lanthanide NMR shift and relaxation probes, and comparative studies of various chemically modified forms of BPTI. These data provide the basis for individual assignments of the methyl 13C NMR lines in BPTI and for detailed investigations of the relations between the spatial structure of the protein and the chemical shifts of the methyl groups. The methyl groups in BPTI are of particular interest since they are located almost exclusively on the surface of the protein and thus represent potential natural NMR probes for studies of the protein-protein interactions in the complexes formed between BPTI and a variety of proteases.     

Assignment of aromatic spin systems in the 1H nuclear magnetic resonance spectrum of adenylate kinase

A combination of selective spin decoupling, two-dimensional double quantum spectroscopy, correlated spectroscopy (COSY), and pH titration experiments brought about the assignment of all tyrosyl spin systems and completed the assignment of the histidyl spin systems in porcine adenylate kinase. In the detection of the tyrosyl spin systems it proved to be advantageous to resort to the COSY method rather than to two-dimensional double quantum spectroscopy. In the titration experiments, His189 revealed a second apparent pK value at pH 8.3, which is explained by deprotonation of the adjacent residue Cys187. None of the seven tyrosyl side-chains shows any evidence for deprotonation up to the point of denaturation of the protein, which took place around pH 10.     

Proton nuclear magnetic resonances study of bleomycin in aqueous solution. Assignment of resonances.

The 1H NMR spectrum of the glycopeptide antineoplastic antibiotic bleomycin has been examined in D2O solution (Fourier transform nuclear magnetic resonance, 270 MHZ) and in H2O solution (correlation nuclear magnetic resonance, 250 MHZ). Resonances have been assigned to specific hydrogens of the two most abundant congeners, bleomycin-A2 (BLM-A2) and bleomycin-B2 (BLM-B2), on the basis of (1) homonuclear spin decoupling, (2) comparison of the spectra of BLM-A2, BLM-B2, fragments of these antibiotics, and the related antibiotic phleomycin, and (3) the pH dependence of chemical shifts. Resonance assignments are presented for all the CH protons of BLM-A2 and BLM-B2 except for the saccharide groups, for which only the anomeric proton assignments are given. All of the NH protons have been identified with specific resonances except for the two primary amide groups, which yield four well-resolved peaks, whose specific assignment was not attempted. This study serves as a basis for future investigations of the conformation of bleomycin and its interaction with metals and nucleic acids.     

Assignment of resonances in the 1H nuclear magnetic resonance spectrum of the carbon monoxide complex of human hemoglobin alpha-chains

Assignments are reported for a substantial number of heme and amino acid proton resonances in the 1H nuclear magnetic resonance spectrum of the carbon monoxide complex of isolated hemoglobin alpha-chains. These resonances provide information on the solution conformation of the protein, particularly in the vicinity of the heme. The heme pocket structure is generally similar to that of carbonmonoxymyoglobin; several conserved residues adopt virtually identical positions relative to the heme in the two proteins. The largest conformational differences involve residues surrounding the ligand-binding site, notably Val62 (E11) and His58 (E7). The chemical shifts of the proximal His87 (F8) resonances are very similar in spectra of the two proteins, indicating a highly conserved coordination geometry and similar hydrogen bonding to the backbone carbonyl of Leu83 (F4).     

A new assignment strategy for the hyperfine-shifted 13C and 15N resonances in Fe2S2 ferredoxins

Assignment of hyperfine-shifted resonances in paramagnetic metalloproteins such as Fe2S2 ferredoxins poses a major experimental challenge due to hyperfine shifts and/or severe line broadening. We have explored the possibility of using structural data from homologous proteins as part of an assignment strategy for the sequence-specific assignment of hyperfine-shifted backbone carbonyl (13C') and nitrogen resonances (15N) in Fe2S2 ferredoxins. This strategy is based on the assignment of resonances in the paramagnetic region to particular types of amino acid residues using selective isotope labeling. Reduced metal-nuclear distances are then calculated from experimentally determined T1 relaxation times for those resonances and the calculated distances aligned with the distances of nuclei at corresponding amino acid sequence positions in the crystal structure of a structurally homologous protein. The comparative assignment approach has met with success in correctly predicting the 13C' and 15N assignments in Pdx degrees from the crystal structure data of two similar and related ferredoxins, namely bovine adrenodoxin and Anabaena ferredoxin. Sequence-specific assignments made in this fashion were verified by selective 13C'{15N} decoupling experiments.     

1H-NMR study of the lambda operator site OL1: assignment of the imino and adenine H2 resonances.

One- and two-dimensional proton NMR methods are being used to study the synthetic lambda operator site O-L1, a 17 base-pair DNA duplex recognized by lambda repressor and Cro protein. The complete assignment of the 17 imino protons, which participate in Watson-Crick hydrogen bonding, and of the eight adenine H2 protons, which lie in the minor groove of the double helix, is presented.