Solution conformation of conotoxin GI determined by 1H nuclear magnetic resonance spectroscopy and distance geometry calculations

Conformational analysis of conotoxin GI, one of the neurotoxic peptides produced by a marine snail, genus Conus, was performed by a combination of nuclear magnetic resonance spectroscopy (NMR) and distance geometry calculations. The resulting conformers on minimization of the target function were classified into two groups. The difference in the structures of the conformers is mainly due to the difference in the orientation of the side chain of the tyrosyl residue. The results show that the solution structure of conotoxin GI satisfies the conformational requirements for the biological activity of an antagonist toward nicotinic cholinergic receptors elucidated in a series of studies on alkaloids. The structure is discussed on the basis of the results of comparison of the atomic arrangements of the active sites of snake venom peptides and molecular models based on the results of secondary structure prediction.

Photo-CIDNP studies of Bence Jones proteins, immunoglobulins, and their proteolytic fragments

The results of photo-CIDNP measurements of Bence Jones proteins, immunoglobulins, and their proteolytic fragments are reported. The CIDNP spectra of constant region CL fragments, which were derived from lambda-type Bence Jones proteins with three different isotypes, gave polarizations originating from two Tyr and one Trp residues. From comparisons of the results obtained by using lambda-type Bence Jones proteins that possess the known amino acid sequences with those for the CL fragments, it was concluded that the CIDNP signals observed in the case of Bence Jones proteins are all due to the hypervariable region. On the basis of the results obtained by using IgG1, IgG2, IgG3, and IgG4 myeloma proteins along with their Fab, Fc, and pFc' fragments, it was concluded that CIDNP signals for the Fab region all originate from the variable region. The Fc region gives two Tyr polarizations, one of which has been assigned to Tyr-296. We have also shown that the second Tyr signal is due to Tyr-373. Interaction of Fc and staphylococcal protein A has also been examined by the CIDNP technique.

A 2H-NMR study on the glycerol backbone of phospholipids extracted from Escherichia coli grown under high osmotic pressure: evidence for multiconformations of phosphatidylethanolamine

A glycerol-requiring auxotroph was isolated from mutagenized Escherichia coli K-12 UFAts cells. This auxotroph was used for the specific deuteration of E. coli phospholipids. The cells were grown under high osmotic pressure (in the presence of 2.0% KCl). The membrane had a highly saturated fatty acid composition (76% phosphatidylethanolamine, 20% cardiolipin and 4% phosphatidylglycerol). The deuterium magnetic resonance spectra of coarse liposomes of the extracted phospholipids with perdeuterated glycerol incorporated into them were measured. To obtain well characterized information, phospholipid mixtures reconstituted from the deuterated and nondeuterated components at the same ratios as in the case of the total extract were used. On the analysis of the spectra, the following conclusions were drawn. (1) The whole polar region of cardiolipin is dynamically symmetric and quite rigid in the presence of phosphatidylethanolamine. (2) Although the quadrupole splittings of the deuterons at the C-2 and C-3 positions of the glycerol backbone were similar to each other, those at the C-1 position for phosphatidylethanolamine and cardiolipin are different, even in the same bilayer. (3) Furthermore, each C-1 deuteron of phosphatidylethanolamine gave rise to a doublet, suggesting the presence of two backbone conformations, between which there is slow exchange. (4) The polar head group of phosphatidylethanolamine interacts with cardiolipin and phosphatidylglycerol in different ways, which could be responsible for the different osmotic properties of the vesicles composed of them.

One- and two-dimensional NMR studies on the conformation of DNA containing the oligo(dA)oligo(dT) tract

The resonances of the imino protons and all of the non-exchangeable protons (except for H5'/H5'') of d(CGCAAAAAAGCG)d(CGCTTTTTTGCG) have been assigned by means of one- and two-dimensional NMR spectroscopies. Qualitative analyses showed that the overall structure is of the B-form, but local conformational deviations exist. The NOEs between the imino protons of thymines and H2 of adenines suggest that the A-T base pairs are propeller-twisted to almost the same degree as in crystals. A remarkable chemical shift of H1' was observed for the residue located just before the oligo(dA)oligo(dT) tract, suggesting the presence of conformational discontinuity at the junctions between the oligo(dA)oligo(dT) tract and the other portions. Analyses of cross peaks in NOESY spectra between H2 of adenines and H1' of the 3'-neighbouring residues on the complementary strand revealed that the minor groove of the oligo(dA)oligo(dT) tract is narrow and compressed gradually, from 5' to 3', along the tract.

The conformation of alpha-human atrial natriuretic polypeptide in solution

The three-dimensional structure of alpha-human ANP in solution was determined through the combined use of nuclear magnetic resonance spectroscopy and distance geometry. The results are based on distance constraints determined by nuclear Overhauser effect measurements and one disulfide bond. The structure is as follows. Three separate regions, which are Ser1-Cys7, Arg11-Ile15, and Gln18-Tyr28 each have some ordered structure. The remaining parts in the sequences of Gly9-Gly10 and Gly16-Ala17 act as hinges. And the C-terminal part is folded back toward the cyclic moiety. The conformation of alpha-hANP reported here is expected to give a better understanding of the relationships between its biological activities and three-dimensional structure.

A photo-chemically induced dynamic nuclear polarization NMR study on rabbit and bovine cytochrome b5

Although it has been indicated that proteins with chromophoric groups are not suitable for photo-chemically induced dynamic nuclear polarization (photo-CIDNP) measurements, we have successfully obtained these spectra for a heme protein, cytochrome b5. The characteristics of the spectra differed in some points from those so far reported. The intensities of the signals in the aromatic region were very weak, while those of the beta-methylene protons of one histidine and one tryptophan were extremely strong in comparison with the aromatic protons. It was demonstrated, on the basis of the photo-CIDNP spectrum, that one of seven histidines, all three tyrosines and a single tryptophan of the rabbit soluble cytochrome b5 are exposed on the surface of the protein. The results of comparison of the photo-CIDNP spectra for the rabbit soluble and intact, and bovine intact, cytochrome b5 led us to the conclusion that the conformation of the hydrophilic, catalytic part of cytochrome b5 is quite similar among these three proteins. In the presence of Chaps micelles, bovine intact cytochrome b5 was in monomeric form and the histidine signals disappeared from its photo-CIDNP spectrum. When bovine intact cytochrome b5 was reconstituted into egg yolk phosphatidylcholine liposomes, although separate signals due to the protein part were observed in the normal 1H-NMR spectrum, no photo-CIDNP signal could be detected. The normal spectrum suggests that the conformation of the protein embedded in liposomes is similar to that of the oligomeric form without lipids or a detergent.

Structures of sugar chains of ricin D

The toxic lectin, ricin D, contains mannose, fucose, xylose, and N-acetylglucosamine as sugar components. Sugar chains are linked to Asn-10 of the A-chain, and to Asn-95 and Asn-135 of the B-chain (Funatsu, G. et al. (1978) Agric. Biol. Chem. 42, 501-503; Araki, T. & Funatsu, G. (1985) FEBS Lett. 191, 121-124). Asparagine-linked sugar chains of each glycopeptide from ricin D were liberated by hydrazinolysis followed by N-acetylation. The reducing end residues of the sugar chains were coupled with 2-aminopyridine and the pyridylamino (PA-) derivatives obtained were purified by gel-filtration and reversed-phase HPLC. Eight main PA-sugar chains were obtained from three glycopeptides and the structures of these sugar chains were determined by component analysis, stepwise exoglycosidase digestions, partial acetolysis, and 500 MHz 1H-NMR spectroscopy. The results show that oligomannose type sugar chains (Man6-7GlcNAc2) are linked to Asn-95; Man5-7 GlcNAc2 and M4X (structure, see below) to Asn-135 of the B-chain, and M3FX and M3X to Asn-10 of the A-chain. (Formula: see text).

Hydrogen-exchange kinetics of the indole NH proton of the buried tryptophan in the constant fragment of the immunoglobulin light chain

The constant fragment of the immunoglobulin light chain (type lambda) has two tryptophyl residues at positions 150 and 187. Trp-150 is buried in the interior, and Trp-187 lies on the surface of the molecule. The hydrogen-deuterium exchange kinetics of the indole NH proton of Trp-150 were studied at various pH values at 25 degrees C by 1H nuclear magnetic resonance. Exchange rates were approximately first order in hydroxyl ion dependence above pH 8, were relatively independent of pH between pH 7 and 8, and decreased below pH 7. On the assumption that the exchange above pH 8 proceeds through local fluctuations of the protein molecule, the exchange rates between pH 7 and 8 through global unfolding were estimated. The exchange rate constant within this pH range at 25 degrees C thus estimated was consistent with that of the global unfolding of the constant fragment under the same conditions as those reported previously [Kikuchi, H., Goto, Y., & Hamaguchi, K. (1986) Biochemistry 25, 2009-2013]. The activation energy for the exchange process at pH 7.8 was the same as that for the unfolding process by 2 M guanidine hydrochloride. The exchange rates of backbone NH protons were almost the same as that of the indole NH proton of Trp-150 at pH 7.1. These observations also indicated that the exchange between pH 7 and 8 occurs through global unfolding of the protein molecule and is rate-limited by the unfolding.(ABSTRACT TRUNCATED AT 250 WORDS)

Proton nuclear magnetic resonance studies on the wild-type and single amino acid substituted tryptophan synthase alpha-subunits

In order to elucidate the effect of single amino acid substitutions on the conformation of the tryptophan synthase alpha-subunit from Escherichia coli in solution, 1H NMR spectra of the wild-type and mutant proteins were measured at various pHs. Two of the four His C2-proton resonances of the alpha-subunit were assigned to two His residues at positions 92 and 146 by using a mutant protein with Thr substituted for the His at position 92. The replacement did not affect the conformation of the protein significantly. The proton resonances of all the Tyr residues in the aromatic region could be picked up from other resonance peaks, employing the wild-type alpha-subunit deuterated at all of the Phe residues. On comparison of the spectra of the wild-type protein with those of the mutant protein with Met substituted for the Glu at position 49, it was concluded that the substitution affects only the residues close to the substituted residue at acidic pH but that a larger part of the protein is affected at alkaline pH. NOE experiments showed that the five Tyr residues, four of which are located in the proximity of position 49, are close to one another. The present results are discussed in the light of the conformational stability of the protein.

Base sequence-specific interactions of operator DNA fragments with the lambda-cro repressor coupled with changes in their conformations

The mechanism of interaction of the operator DNA with the lambda-cro repressor protein was investigated using proton n.m.r. and photo CIDNP. Three kinds of DNA duplexes, the lambda-OR3 17-mer, phi80-OR2 19-mer and CRP binding site 22-mer, were prepared, and all of their imino proton resonances of the complexes with lambda-cro were assigned to individual base pairs. By monitoring the assigned signals of the DNA fragments and lambda-cro, it was found that in the complex of lambda-cro with lambda-OR3, two subunits of the cro dimer bind to the right and left halves of the OR3, respectively, and the bidentate binding induces a structural distortion in the middle of the 17-mer. lambda-cro itself also undergoes a conformational change including loosening of the dimeric form. In the complex of lambda-cro with phi 80-OR2, which has a 6-bp sequence common to that of lambda-OR3, one subunit of the cro dimer seems to bind specifically to the common part. However, there is only a slight conformational change in the cro dimer. In the mixture of the CRP binding site 22-mer and lambda-cro, soft contact without any conformational change was observed between them.

Possible pathway for the processing of sugar chains containing xylose in plant glycoproteins deduced on structural analyses of sugar chains from Ricinus communis lectins

The structures of sugar chains from two lectins in seeds of the castor bean (Ricinus communis) were identified. The sugar chains were liberated from the lectins by hydrazinolysis. After N-acetylation, the reducing-end residues of the sugar chains were coupled with 2-aminopyridine. The pyridylamino derivatives thus obtained were purified by gel filtration and HPLC. The structures of the purified derivatives were identified by component sugar analysis, stepwise exoglycosidase digestion, partial acetolysis, and 500 MHz 1H-NMR spectroscopy. A new processing pathway for sugar chains in plant glycoproteins was proposed on the basis of the structures of the sugar chains.

The presence of the 30 nm filament structure of chromatins in intact chicken erythrocytes observed by 31P NMR

A 31P NMR spectrum of chicken erythrocyte chromatins in vivo was obtained. The spectrum was characterized by examining the spectra of isolated nuclei and nondigested chromatins under various conditions. The results have shown that most chromatins in chicken erythrocyte nuclei assume the 30 nm filament structure as a second step of condensation of DNA in vivo.

Dense deposit disease: its possible pathogenesis suggested by an observation of a patient

A girl, aged 8, was admitted to a hospital in a state of nephrotic syndrome of one year's duration. The renal biopsy showed mesangial and endocapillary proliferations with lobulation. Dense deposit was not demonstrated by electron microscopy, but lamellation of the lamina densa was found in most of the capillary loops. Her condition was improved by steroid treatment in a few months, but moderate proteinuria persisted. Five and half years later, follow-up biopsy showed typical pathological features of dense deposit disease. It is suggested that the lamellation of the lamina densa in the first biopsy could be related to the dense alteration of glomerular basement membrane in the second biopsy.

Association of polyene antibiotics with sterols

Molecular interaction between amphotericin B and sterols in non-aqueous solutions was examined quantitatively by spectroscopic methods in order to support the view point that selectivity of amphotericin B is more pronounced in the presence of ergosterol than of cholesterol. The most likely association complexes between ergosterol and amphotericin B are 4:1, 6:1 stoichiometric complex when the concentrations of amphotericin B are 3.93 x 10(-4) M, 1.94 x 10(-4) M respectively. The presence of 3 beta-OH group is necessary but not enough for the association with amphotericin B. It appears that the extent of spectral change of amphotericin B induced by complexing sterol is greater for ergosterol than cholesterol.

1H-NMR analysis of the sugar structures of glycoproteins as their pyridylamino derivatives

The 1H-NMR spectra of a series of pyridylamino (PA-) derivatives of oligosaccharides were obtained and compared with those of the corresponding asparagine-linked sugar chains in order to elucidate the effect of the PA-group on the chemical shifts of structural-reporter signals. The effects were found to be localized within the two residues from the end group. Thus, the data for asparagine-linked chains in the literature are applicable to PA-derivatives, so the combination of pyridylamination and NMR measurements greatly reduces the time required for structure analysis of sugar chains of glycoproteins, because the isolation and purification of the chains as PA-derivatives are easy and efficient.

Conformational studies by 1H nuclear magnetic resonance of the trypsin-chymotrypsin inhibitor B-III from peanuts and its enzymatically modified derivative

The conformation of the peanut inhibitor B-III was investigated by 1H NMR at 500 MHz. Resonances for about 30% of the residues were assigned and/or identified by conventional and two-dimensional 1H NMR measurements. The conformation of the modified inhibitor B-IIIRS, obtained by the cleavage of the peptide bonds of B-III at the first reactive site, Arg(10)-Arg(11), and second reactive site, Arg-(37)-Ser(38), was also investigated. Edman degradation was used to identify resonances of the residues adjoining the scissile sites. A comparison of the behavior of the resonances corresponding to Ala(12), Tyr(15), Phe(16), and Thr(37) in B-III and B-IIIRS indicated that the only conformational differences between the two proteins were those from the S-S loops containing the two reactive sites. From the similar behavior of Leu(7), Phe(24), His(26), Ala(29), five valine, and four threonine resonances in both proteins, it is suggested that the S-S loops that do not contain a scissile bond (the core region of the inhibitor) were rigid. Thus, no conformational change of the core region was observed upon cleavage of the reactive sites.

Structure of a sugar chain of a protease inhibitor isolated from barbados pride (Caesalpinia pulcherrima Sw.) seeds

An asparagine-linked sugar chain of a protease inhibitor from barbados pride (Caesalpinia pulcherrima Sw.) was liberated by hydrazinolysis. After N-acetylation, the reducing end residue of this carbohydrate unit was coupled with 2-aminopyridine and the pyridylamino (PA-) derivative was purified by gel-filtration and reversed-phase HPLC. The structure of the resulting PA-sugar chain was determined mainly by stepwise exoglycosidase digestions and 500 MHz 1H-NMR spectroscopy and proved to be as follows: (formula; see text).

Influence of metal ions and a local anesthetic on the conformation of the choline group of phosphatidylcholine bilayers studied by Raman spectroscopy

A Raman band assigned to the 'totally' symmetric stretching vibration of the choline C-N bonds is relatively strong and sensitive to the conformation of the choline backbone (Akutsu, H. (1981) Biochemistry 20, 7359-7366). By monitoring this Raman band, the influence of Eu3+, La3+, Ca2+ and a local anesthetic, dibucaine, on the conformation of the choline group was examined for the bilayers of dipalmitoylphosphatidylcholine and those of deuterated one at the choline methyl group (-N(C2H3)3). NMR lanthanide-shift studies proposed that the interaction with metal ions induces a conformational change from the gauche to the trans form in the O-C-C-N+ backbone of the choline group. However, present Raman work clearly showed that neither metal ions nor anesthetics induce such a conformational change. Therefore, a structural change in the polar group detected by 2H-NMR on addition of metal ions should not include a significant conformational change in the choline group as well. Deuterated phosphatidylcholine used here was proved to be more suitable for the direct detection of the amount of the trans conformation by Raman spectroscopy than the nondeuterated one. The spectra of the deuterated compound in the gel and liquid-crystalline states confirmed that the trans conformation of the choline group does not appear at all in both states.

Raman spectra of single crystals of r(GCG)d(CGC) and d(CCCCGGGG) as models for A DNA, their structure transitions in aqueous solution, and comparison with double-helical poly(dG).poly(dC)

The self-complementary oligonucleotides [r(CGC)d(CGC)]2 and [d(CCCCGGGG)]2 in single-crystal and solution forms have been investigated by Raman spectroscopy. Comparison of the Raman spectra with results of single-crystal X-ray diffraction and with data from polynucleotides permits the identification of a number of Raman frequencies diagnostic of the A-helix structure for GC sequences. The guanine ring frequency characteristic of C3'-endo pucker and anti base orientation is assigned at 668 +/- 2 cm-1 for both dG and rG residues of the DNA/RNA hybrid [r(GCG)d(CGC)]2. The A-helix backbone of crystalline [r(GCG)d(CGC)]2 is altered slightly in the aqueous structure, consistent with the conversion of at least two residues to the C2'-endo/anti conformation. For crystalline [d(CCCCGGGG)]2, the Raman and X-ray data indicate nucleosides of alternating 2'-endo-3'-endo pucker sandwiched between terminal and penultimate pairs of C3'-endo pucker. The A-A-B-A-B-A-A-A backbone of the crystalline octamer is converted completely to a B-DNA fragment in aqueous solution with Raman markers characteristic of C2'-endo/anti-G (682 +/- 2) and the B backbone (826 +/- 2 cm-1). In the case of poly(dG).poly(dC), considerable structural variability is detected. A 4% solution of the duplex is largely A DNA, but a 2% solution is predominantly B DNA. On the other hand, an oriented fiber drawn at 75% relative humidity reveals Raman markers characteristic of both A DNA and a modified B DNA, not unlike the [d-(CCCCGGGG)]2 crystal. A comparison of Raman and CD spectra of the aqueous [d(CCCCGGGG)]2 and poly(dG).poly(dC) structures suggests the need for caution in the interpretation of CD data from G clusters in DNA.

Conformational study of 13C-enriched fibroin in the solid state, using the cross polarization nuclear magnetic resonance method

Silk fibroin with the alanyl carboxyl carbon enriched with 13C was obtained by giving a diet containing 13C-enriched alanine to the larvae of Bombyx mori and Antheraea pernyi at the fifth instar. Sericin-free fibroin fibers were prepared from cocoons, and gut was made from the liquid silk in the gland. The final 13C content was about 13%. Cross polarization/magic angle sample spinning spectra at 25 MHz and 75 MHz were measured for each sample at different orientations. Spectra were simulated using the principal values and orientations of the shielding tensor in the alanine crystal. The results indicate that the beta-structure of the fibroin may be a little more flattened than the typical pleated sheet beta-structure.

Effects of purified ginseng saponins on multilamellar liposomes

To elucidate the mode of interaction between purified ginseng saponins and liposomes, the effects of ginseng saponins at concentrations below and above their critical micelle concentration on the osmotic behavior of liposomes were observed. Liposomes composed of egg phosphatidylcholine (PC), phosphatidic acid (PA) and/or cholesterol (Ch) behave as an ideal osmometer and this activity was described by the linear relationship between (1/A450)3/2 and Cin/Cout. Total saponin prepared from the lateral roots of ginseng cultivated in Korea interacted with multilamellar liposomes and prevented them from behaving as an ideal osmometer. 20-S-Protopanaxadiol saponin showed similar activity but 20-s-protopanaxatriol saponin had weak activity. Ginsenoside Rb1 whose genin is 20-S-protopanaxadiol, disturbed osmotic behavior of Ch-free liposomes but not Ch-containing liposomes as monomers and lyzed both liposomes as micelles. Rg1 whose genin is 20-S-protopanaxatriol, showed no activity on liposomes with or without Ch. It can be suggested that ginseng saponins may interact with and destroy liposomal membranes and that structure of sugar moiety is an important factor to their activities. Ch is not a target in this interaction but suppresses the activity of ginseng saponins.

An essential role of phosphatidylglycerol in the formation of the osmotically stable liposomes of Escherichia coli phospholipids

A temperature sensitive auxotroph of Escherichia coli K-12 requiring unsaturated fatty acids can grow normally at 28 degrees C, but requires an osmotic stabilizer such as a high amount of salt or sugar in the medium for the growth at 42 degrees C. Namely, the apparent osmotic stability of the cells at 28 degrees C and 42 degrees C is quite different. The osmotic properties of liposomes of the phospholipids extracted from these cells were investigated. The osmotically induced volume change of the multilamellar liposomes was examined by the turbidimetric method. The liposomes prepared from cells grown at 28 degrees C can swell and shrink under a wide range of hypo-and hypertonic conditions. However, those from cells grown at 42 degrees C could not swell under hypotonic conditions. These results exhibit a good correlation between the apparent osmotic stability of E. coli cells and the osmotic properties of the liposomes prepared from the extracted total phospholipids. To clarify the role of each phospholipid component, the osmotic properties of the liposomes reconstituted from the purified phospholipid species were further investigated. The results clearly showed that phosphatidylglycerol is the key factor that stabilizes the membranes of E. coli phospholipids against osmotic pressure.

Dynamic behavior of the imino protons of the gamma OR3 17mer in H2O solution studied by high-resolution NMR

The imino proton resonances of gamma OR3 17mer in water were observed at 500 MHz with the time-shared Redfield pulse train. All of the 17 imino proton resonances could be assigned specifically to individual base pairs by utilizing the trace of NOE connectivities between the imino and adenine C2H protons and between imino protons themselves. AT1 and 17 showed abnormally high chemical shifts in comparison with the other AT pairs. On raising the temperature, broadening of the signal occurred in a sequential manner from the terminals except for AT10 and AT11, which were broadened at a lower temperature than GC12. The relaxation rates of the imino protons were measured by the inversion recovery method. The rates at higher temperatures represent the exchange rates of the imino protons. From the temperature dependences, activation energies of about 15 kcal/mol for the AT imino protons and 23-26 kcal/mol for the GC imino protons were obtained.

Hybrid oligomer of cyclonucleotides and deoxynucleotides. A high anti left-handed double helical DNA structure

It has been shown by us that oligonucleotides containing cyclonucleosides with a high anti glycosidic conformation take left-handed, single and double helical structures (S. Uesugi, J. Yano, E. Yano and M. Ikehara, J. Am. Chem. Soc. 99,2313 (1977) and references therein). In order to see whether DNA can adopt the high anti left-handed double helical structure or not, a self-complementary hexanucleotide containing 6,2'-O-cyclocytidine (C 0). 8,2'-O-cycloguanosine (G 0), deoxycytidine and deoxyguanosine, C 0 G 0 dCdGC 0 G 0, was synthesized. Corresponding hexanucleotide containing only cyclonucleosides, C 0 G 0 C 0 G 0 C 0 G 0, was also synthesized. Their conformation was examined by UV, CD and 1H NMR spectroscopy. C 0 G 0 C 0 G 0 C 0 G 0 forms an unusually stable, left-handed duplex. Imino proton NMR spectra and the results of nuclear Overhauser effect experiments strongly suggest that C 0 G 0 dCdGC0 G 0 take a left-handed double helical structure where the deoxynucleoside residues are involved in hydrogen bonding and take a high anti glycosidic conformation. Thus it is revealed that DNA could form a high anti, left-handed double helix which is different from that of Z-DNA under some constrained conditions.

Alcohol induced B-A transition of DNAs with different base compositions studied by circular dichroism

The circular dichroic (CD) spectra of natural DNAs (from Cl. perfringens, T2 phage, calf thymus, E. coli, and M. lysodeikticus) as well as duplexes of synthetic DNAs (poly(dA) X poly(dT), poly(dA-dT), and poly(dG-dC] were measured in water-ethanol mixtures with 0.3 mM NaCl. A conformational change from the B to the A form was observed for the natural DNAs on adding ethanol. The ethanol concentration that induces the transition and the extent of the change in the CD spectrum are different for the five natural DNAs depending on their GC contents. The higher the GC content is, the more easily the transition to the A form takes place. The results indicate that the GC content of a DNA is an important factor for induction of the B-A transition. The results for the synthetic DNAs show that their properties cannot be inferred by simple extrapolation of those of natural DNAs. Coexisting ions and the molecular weight of a DNA were also found to affect the induction of the B-A transition.

Exposed tyrosine residues of lambda cro repressor protein evidenced by nitration and photo CIDNP experiments

The tyrosine residues of lambda cro repressor were partially nitrated with tetranitromethane under mild conditions. After digestion by Achromobacter protease I, the extent of nitration was determined by HPLC and amino acid analysis. Tyr 26 was most easily nitrated and Tyr 51 followed it. Tyr 10 was resistant to nitration. By comparison of the proton magnetic resonance spectrum of the partially nitrated cro protein with the above result, the aromatic proton resonances of the tyrosine side chains could be assigned to individual tyrosine residues. The extent of nitration is parallel to the accessibility to a flavin dye as measured by photo CIDNP (chemically induced dynamic nuclear polarization).

Photo CIDNP study on the complex formation of lambda cro protein with OR3

A photo CIDNP spectrum of lambda cro repressor protein showed that one of the three tyrosines and His 35 are quite accessible to the photosensitive dye. For the remaining two tyrosine residues one is slightly accessible, but the other is inaccessible. In comparison with the result of differential nitration at tyrosine side chains followed by the peptide analysis, it can be concluded that Tyr 26 is mostly exposed and Tyr 51 is slightly exposed on the surface of the cro dimer. On the addition of OR3 17mer, His 35 and Tyr 26 are no longer accessible to the dye, which indicates that they are involved in interaction. However, a similar phenomenon was observed by adding CAP binding site 22mer. The interaction mechanism will be discussed.

Phosphorus-31 nuclear magnetic resonance of highly oriented DNA fibers. 1. Static geometry of DNA double helices

The static geometry of the phosphodiesters in oriented fibers of DNA and a variety of polynucleotides was investigated by solid-state 31P nuclear magnetic resonance (NMR) spectroscopy. The structural parameters of the phosphodiester backbone expressed by two Euler angles beta and gamma were estimated on the basis of the NMR spectra of natural DNA, poly(dA).poly(dT), poly(rA).poly(dT), and poly-(rA).poly(rU). The Euler angles were calculated by using the known single crystal structures of a decamer, r(GCG)d(TATACGC), and a dodecamer, d(CGCGAATTCGCG). The distribution pattern of the Euler angles was quite different between these two oligonucleotides due to the different types of conformation, and it was fully consistent with the 31P NMR results, showing that the conformation of the B form DNA is very heterogeneous while that of the A or A' form is much more invariable with regard to the base composition. The structural parameters were also calculated by using various structures determined by the X-ray fiber diffraction studies, and they were evaluated on the basis of the 31P NMR data. Notably, poly(dA).poly(dT) fibers exhibited abnormal 31P NMR spectra which were very broad in line width and were not appreciably perturbed by hydration; a coiled double-helical structure is proposed as the most plausible model for this polymer.

Synthesis and conformational studies of ribooligonucleotides which contain an alternating C-G sequence and show unusual circular dichroism spectra

The poly [r(C-G)] duplex shows an unusually large negative CD band in the long wavelength region. In order to elucidate this phenomenon, r(C-G-C-G) and r(C-G-C-G-C-G) were synthesized by a phosphotriester method and their properties were examined by UV, CD, 1H and 31P NMR spectroscopy. These ribooligomers form self-duplexes at low temperature, the CD spectra of which show negative bands at around 290 nm and positive bands at around 265 nm. The results of 1H nuclear Overhauser effect experiments, 1H chemical shift-temperature profiles of base protons, and the sharp singlet observed for all H1' protons are consistent with a normal A-RNA structure but not with a Z-DNA like structure. The CD-temperature profiles and 31P NMR spectra support this conclusion. These results indicate that RNA duplexes with an alternating C-G sequence can give an unusually large negative CD band in the long wavelength region despite their right-handed helical structure.

The effect of protamine on serum complement activity in aminonucleoside nephropathy

Combined administration of protamine sulfate (Ps) and aminonucleoside (AN) to rats causes severe nephrotic syndrome and, histologically, focal glomerular sclerosis. These changes are more distinct than those produced by AN alone. While the exact mechanism of Ps acting on AN nephropathy is not known, marked hypocomplementemia was observed regularly after the Ps + AN injection, suggesting that complement is activated and consumed in the kidney. It is suggested that complement may play an important role in AN + Ps nephropathy.

Photochemically induced dynamic nuclear polarization study on microsomal NADPH-cytochrome P-450 reductase

Sedimentation equilibrium experiments with NADPH-cytochrome P-450 reductase showed that increasing 1-O-n-octyl-beta-D-glucopyranoside levels promoted disaggregation of the flavoprotein. The reductase was monomeric at a molar ratio of detergent to protein above 10(3). Addition of N3-carboxymethyllumiflavin to the flavoprotein in the presence of 1-O-n-octyl-beta-D-glucopyranoside results in photochemically induced dynamic nuclear polarization (CIDNP) signals in the aromatic region. The CIDNP spectrum of the holoprotein shows sharp resonances due to histidine residues. On removal of FMN from the protein, CIDNP signals originating from a tyrosine residue appeared, suggesting that the tyrosine residue is exposed to solvent after the depletion of FMN. However, this tyrosine residue appears to become inaccessible to the external dye after full incubation of FMN-depleted reductase with FMN. This suggests that the tyrosine residue could be located in the vicinity of the FMN-binding domain which constitutes the active center of the reductase.

Identification of oligonucleotide fragments produced in a strand scission reaction of the d(C-G-C-G-C-G) duplex by bleomycin

To elucidate the mechanism of DNA strand scission by bleomycin, a d(C-G-C-G-C-G) duplex was treated with the bleomycin-iron ion complex in the presence of H2O2 and degradation products (1, 2, cytosine and deoxyguanosine 5'-phosphate) were identified. 1 and 2 contain a carboxymethyl group attached to the 3'-terminal phosphoryl group of d(C-Gp) and d(C-G-C-Gp), respectively. These compounds were identified by UV, 1H and 31P NMR spectroscopy and paper electrophoresis. 1 was synthesized from the protected dinucleotide and glycolic acid and the proton NMR spectrum was identical to that of 1 obtained as a degradation product. Thus the oligonucleotide fragments produced by the action of bleomycin on DNA were directly identified and cleavage of the C3'-C4' bond of the sugar residues was proved.

Conformation of ribooligonucleotide duplexes containing an alternating C-G sequence which show an unusual circular dichroism spectrum

The poly[r(G-C)] duplex shows an unusually large negative band in the long wavelength region of the CD spectrum. In order to elucidate this phenomenon, r(C-G-C-G) and r(C-G-C-G-C-G) were synthesized chemically and their properties were examined by UV and CD, and 1H and 31P NMR spectroscopy. These ribooligomers form a self-complementary duplex at low temperature, the CD spectrum of which shows a negative band at around 290 nm and a positive band at around 265 nm with almost equal magnitudes. The proton resonances in the 1H NMR spectra of the oligo[r(C-G)] duplexes were assigned by nuclear Overhauser effect experiments. The chemical shift-temperature profiles of the base proton signals and the sharp singlets observed for all H1' protons are consistent with a normal A-RNA structure but not with a Z-DNA like structure. Moreover, a 500-MHz two-dimensional nuclear Overhauser effect experiment recorded for r(C-G-C-G-C-G) shows that all guanine bases adopt the normal anti-conformation. CD-temperature profiles and 31P NMR spectra of oligo[r(C-G)]s support this conclusion. These results indicate that duplexes of oligo- and polyribonucleotides containing alternating C-G sequences can give an unusually large negative CD band in the long wavelength region despite their right-handed helical structure.

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.

Origin of slow conformer conversion of triostin A and interaction ability with nucleic acid bases

The n.m.r. pattern of triostin A in weakly polar solvents was explained by the presence of two symmetrical conformers. Its S-benzyl derivative still shows the n.m.r. pattern of two conformers, while des-N-tetramethyltriostin A, which lacks the N-methyl groups, gives one conformer. Therefore the slow interconversion of two conformers arises from the cis-trans isomerization of the N-methyl peptide bonds, but not from the reversal of the chirality around the S-S bond. Only one of the two conformers of triostin A interacts with adenosine and guanosine derivatives. Des-N-tetramethyltriostin A can also interact with the purine nucleosides, but more preferentially with the adenosine derivative.

Determination of protonation sites in thermospermine and in some other polyamines by 15N and 13C nuclear magnetic resonance spectroscopy

The pK values of thermospermine, a novel asymmetric tetraamine (4,8-diazadodecane-1,12-diamine), have been determined for the first time by the conventional titration method with subsequent data analyses. It was found to be the most basic polyamine among naturally occurring tetraamines. The 15N NMR titration method was applied to determine its protonation site. Natural-abundance 15N magnetic resonance spectra of the polyamine have been recorded as a function of pH from its free to the protonated form. Its apparent pK values, as well as the intrinsic chemical shifts for each stage of protonation, have been calculated from the NMR titration curve by using a nonlinear least-squares method. The four protonation sites of thermospermine have been successfully determined to be N12, N1, N-8, and N-4 in that order from the free to the completely protonated form. In a similar manner the protonation sites of spermidine and two symmetric tetraamines, thermine and spermine, have been established. 13C NMR experiments for the four polyamines were almost consistent with those of 15N NMR. Owing to the much higher concentration of the polyamines furnished for NMR titration experiments, the pK values obtained by NMR were larger than those derived by the conventional titration methods.

N-Trimethylalanine, a novel blocked N-terminal residue of Tetrahymena histone H2B

Our previous study showed that the amino acid sequence of Tetrahymena histone H2B has a blocked N-terminal residue followed by 119 amino acid residues, X-Pro-Lys.... [J. Biochem. (1982) 91, 897-904]. Now, X has been found to be N-trimethylalanine by 1H nuclear magnetic resonance spectroscopy of the isolated X-Pro-Lys and X. This identification was supported by mass spectrometry of X-Pro-Lys and by column and paper chromatography of X. This is the first time that N-terminal blocking by methylation has ever been found in histones.

The effect of protamine on proteinuria and glomerular sclerosis in aminonucleoside nephropathy

An administration of protamine sulfate combined with aminonucleoside of puromycin (AN) could produce in rats severe nephrotic syndrome and histological changes similar to focal glomerular sclerosis more distinctly than AN alone. This may be attributed to the action of protamine which seemed to enhance the effect of AN, causing polyanion loss at the glomerular basement membrane.

Structure of the lambda tof repressor protein in solution. Heat stability and its relation to binding ability to DNA

The lambda tof repressor protein was purified from E. coli cells retaining lambda dv plasmids by applying DNA-cellulose chromatography. 3H-labeled lambda dv and lambda imm21dv DNA, carrying and lacking lambda operators, respectively, were prepared and the binding activity of the lambda tof protein to the DNA was examined. Non-specific binding to lambda imm21dv DNA is completely lost at 30 degrees C, whereas specific binding to the DNA carrying the operators is retained even above 40 degrees C. The conformation of the lambda tof protein was analysed by means of circular dichroism and 1H-NMR spectra. The change in the molar ellipticity at 222 nm vs. temperature in CD spectra indicated a transition between two states with Tm at 42 degrees C. The 360 MHz 1H-NMR spectra revealed the presence at 20 degrees C of another change in local conformation of interaction which was not detected by the CD spectra. 1H-NMR also indicated the coexistence of thermal transitions with exchange rates faster and slower than the NMR time scale at about 50 degrees C, which is explained by the presence of domain structures. The NMR titration curve of the His residue gave a normal pK value showing its location on the surface of the protein. These conformational behaviors are well correlated to the specific and non-specific DNA binding activity of the lambda tof protein. The assignments of 1H resonance signals to some specific residues, including His 35 and Tyr 26, were established. It will be useful to determine the tof-DNA interaction.