Detection of separated amino proton resonance signals of adenine derivatives of low temperature and its application to estimation of population of the adenine-uracil dimers in solution

Splitting of the amino proton signals of 9-ethyladenine derivatives was found in proton nuclear magnetic resonance spectra at low temperature (ca. -30 degrees C). One of the separated signals corresponds to the syn amino proton relative to the N(1) nitrogen in the adenine ring and the other to the anti one. The phenomenon is ascribable to slowing down of the hindered rotation around the N(6)-C(6) bond, which has partial double bond character. On the addition of 1-cyclohexyluracil derivatives, one of the separated signals shifts downfield. From the analysis of the concentration dependence of the signals we could estimate the population of two kinds of adenine-uracil (AU) dimers that employ the syn and anti protons, respectively. i.e. the Watson-Crick-type and the Hoogsteen-type dimers. Independent of the substitution on the uracil ring, the Hoogsteen type is predominant at 70% and the Watson-Crick type at 30% (at -56 degrees C). On the other hand, with mixtures of general kinds of 9-ethyladenine derivatives with 1-cyclohexyluracil. the substituents on the adenine ring cause the population to deviate to extreme values; i.e., either the Watson-Crick-type or the Hoogsteen-type dimer predominates. 2-Chloro-9-ethyladenine and N2-(dimethylamino)-9-ethyladenine take almost completely the Hoogsteen-type dimers, while 8-bromo-9-ethyladenine, N2-(methylamino)-9-ethyladenine, and 2-amino-9-ethylpurine predominant in the Watson-Crick-type dimers.

A 15N-NMR study on ribonuclease T1-guanylic acid complex

Ribonuclease T1 is highly specific for the guanylic acid residue in polyribonucleotides. To clarify the origin of the substrate specificity, the interaction sites of guanylic acid with ribonuclease T1 were investigated by the use of 15N-NMR. 95% 15N-enriched guanosine-3'-phosphate was prepared and mixed with purified ribonuclease T1. 15N-NMR spectra of the mixtures at different concentrations were obtained and compared with that of the 15N-enriched substrate alone. Upon complex formation, a 15N signal assigned to the amino group nitrogen at position 2 of guanine shifted and was significantly broadened, suggesting a strong interaction with the enzyme through the amino group. This observation is consistent with the results of studies on the substrate specificity of chemical modification. Nuclear Overhauser effects of signals assigned to N-7 and N-3 were also changed, but not shift was observed. The observations do not support the occurrence of protonation at N-7 upon complex formation, which was previously proposed.

NMR studies of base-pairing in 15N-labeled ribotetranucleotide GGCUp

95% N-15 enriched ribotetranucleotide GGCUp was prepared. Its aqueous solution gives three imino-proton resonances at 10.6, 12.0 and 13.6 ppm. The peak at 10.6 ppm split by N-15 into a doublet with coupling constant 90 Hz. On the preirradiation at this peak, the intensity of the 12.0 ppm peak decreased and the peak at 13.6 ppm remained unchanged. Therefore the 10.6 ppm peak was unambiguously assigned to the G imino proton and the 12.0 ppm peak to the U imino proton in the G:U base pair. By raising temperature the former two peaks coalesced at around 25 degrees C, while the signal of the G imino proton in the G:C pair was observed up to 35 degrees C. The G:U base pair seems to be disrupted first, then the break of the G:C pair is followed. Temperature dependences of the CH proton, N-15 and P-31 nuclei resonances were also measured.

Detection of proton-acceptor sites of hydrogen bonding in adenine X uracil base pairs by the use of 15N magnetic resonance

2',3',5'-Tri-O-acetyl[1,3,7,9,amino-15N]adenosine(ac3Ado) and its 8-2H and 8-bromo derivatives (ac3[8-2H]Ado and ac3br8Ado) were synthesized from 95% 15N-enriched adenosine which was obtained by microbial fermentation. The chemical shifts and nuclear Overhauser effects of 15N NMR of the adenosine derivatives were measured by changing the concentration of the mixed 1-cyclohexyluracil (cHxUra) in chloroform. The limiting shift of each 15N resonance was calculated by using the association constants obtained from proton magnetic resonances of the ac3Ado/cHxUra and ac3br8Ado/cHxUra systems. From the quantitative analysis of the 15N chemical shifts of the N-1 and N-7 atoms it could be concluded that ac3Ado X cHxUra dimers prefer the Hoogsteen-type pair while the Watson-Crick-type pairs are predominant in the ac3br8Ado X cHxUra dimers. The N-3 atom, which does not locate at the interaction site, showed a fairly large induced shift. Thus the induced shift of 15N resonance by association does not always mean the involvement of the corresponding nucleus to the interaction site. The effect of intermolecular hydrogen bonding on the nuclear Overhauser enhancement of the 15N-7 resonance was observed in the ac3[8-2H]Ado/cHxUra mixture. The presence of the Hoogsteen-type hydrogen bonding was proposed by the use of 15N NMR spectra. The present information will be useful for the elucidation of non-Watson-Crick-type base-pair interaction in transfer TNA and oligonucleotides.

Morphological changes in an early phase of norepinephrine-induced acute renal failure in unilaterally nephrectomized dogs

The morphological factors contributing to the reduction GFR in an early phase of NE-induced ARF (0.75 microgram/kg/min) were evaluated by comparing renal morphology at the end of NE infusion with that 2 hr later in unilaterally nephrectomized dogs. GFR 2 hr after NE infusion was reduced to 50% of the preinfusion level in a 30 min infusion group (N = 6), to 13% in a 60 min infusion group (N = 7), and to 2% in a 120 min infusin group (N = 5). On the other hand, simultaneous RBF was not significantly reduced in any group. Dilated PT lumina filled with eosinophilic granular materials in paraffin sections fixed in Zenker-Formol or with impacted swollen blebs in Epon sections fixed in diluted Karnovsky's solution and osmium were found diffusely immediately following 60 and 120 min NE infusion, but patchily after 30 min infusion. Similar changes were found 2 hr after the infusion, except that some PTs came to have dilated but transparent lumina in the 60 and 120 min NE infusion groups. Electron microscopic studies revealed that a part of the membrane-bounded cytoplasm of PT cells extruded into the tubular lumen and became impacted swollen blebs during NE-induced ischemia. There was no prominent foot process fusion in any group. It is concluded that the tubular obstruction by impacted swollen blebs generated in PT during ischemia is a major factor responsible for the reduction in GFR in the early phase of NE-induced ARF.

Evidence for phase separation in the membrane of an osmotically stabilized fatty acid auxotroph of E. coli and its biological significance

1. An unsaturated fatty acid auxotroph of Escherichia coli accumulated a high content of saturated fatty acids in its membrane when it was cultured under osmotically stabilized conditions. The physicochemical properties of the phospholipid extracts and of the membrane fraction from the cells were investigated by means of proton magnetic resonance, infrared spectroscopy and differential scanning calorimetry. 2. Physicochemical studies indicate that the phospholipid bilayers in the membranes exhibit at least two phase transitions, a minor one at approx. 19 degrees C and a major one at approx. 43 degrees C. Between the two temperatures, gel and liquid crystalline domains co-exist. Moreover, even in the gel state, phospholipids seem to segregated into domains containing different proportions of unsaturated fatty acids. 3. The Arrhenius plot of beta-galactoside transport rates is biphasic. The inflection point is at 22 degrees C. This means that the appearance of the fluid region in the bilayer at approx. 19 degrees C is important in the activation of membrane transport.

Conformational studies of oxytocin analogues with different ring sizes. I. Circular dichroism

Circular dichroic spectra were measured for three analogues of deamino-oxytocin of different ring sizes where the disulfide group of oxytocin is replaced by the (CH2)n group. Their backbone rings are composed of different numbers of atoms, i.e., they are nineteen, twenty and twenty-one for [1,6-aminopimelic acid]oxytocin (n = 1), [1,6-aminosuberic acid]oxytocin (n = 2) and [1,6-aminoazelaic acid]oxytocin (n = 3), respectively. The pH dependence of the circular dichroism spectra indicates that the conformation of [1,6-aminoazelaic acid]oxytocin is different from those of others and the temperature dependency reveals that the conformation of [1,6-aminopimelic acid]oxytocin is most rigid. [1,6-Aminosuberic acid]oxytocin is biologically most active among three derivatives and their biological activities are related to the conformation and internal motions of the peptide hormone analogues.

Resonance Raman spectra of carbon-13- and nitrogen-15-labeled riboflavin bound to egg-white flavoprotein

The resonance Raman spectra of [2-13C]-, [4a-13C]-, [4-13C]-8 [10a-13C]-, [2,4,4a, 10a-13C]-, [5-15N]-, [1,3-15N]-, and [1,3,5-15N]riboflavin bound to egg-white proteins were observed for N(3)-H and N(3)-D forms with spontaneous Raman technique by using the 488.0-nm excitation line of an argon ion laser. The fluorescence of riboflavin was quenched by forming a complex with egg-white riboflavin binding protein. The in-plane displacements of the C(2), C(4a), N(1), N(3), and N(5) atoms during each Raman active vibration were calculated from the observed isotopic frequency shifts. The 1252-cm-1 mode of the N(3)-H form was found to involve large vibrational displacements of the C(2) and N(3) atoms and to be strongly coupled with the N(3)-H bending mode. This line can be used as an indicator for state of N(3)-H...protein interaction. The 1584-cm-1 mode, which is known to be resonance-enhanced upon excitation near the 370-nm absorption band, was accompanied by the displacement of the N(5) atom in particular. The 1355-cm-1 mode was most strongly resonance-enhanced by the 450-nm absorption band and involved the displacements of all carbon atoms of ring III. Both lines can be used as structure probes for elucidating the structure of electronically excited states of isoalloxazine.

Resonance Raman studies of hepatic microsomal cytochromes P-450: evidence for strong pi basicity of the fifth ligand in the reduced and carbonyl complex forms

Resonance Raman spectra have been measured for cytochromes P-450 purified from liver microsomes of phenobarbital-treated rabbits (PB P-450 and PB P-448) and of 3-methylcholanthrene-treated rabbits (MC P-448). In the reduced state, all three cytochromes P-450 exhibit Raman spectra of ferrous high-spin type but show the so-called "oxidation state marker" (band IV) at unusually low frequencies, indicating extensive delocalization of electrons from the iron dpi orbital to the porphyrin II (eg) orbital and, consequently, the strong pi basicity of the fifth ligand of the heme iron. The reduced CO complexes of the cytochromes P-450 also exhibit band IV at markedly lower frequencies than CO complexes of hemoglobin and myoglobin. These anomalies observed for the reduced form and CO complex disappear upon conversion of the cytochromes to the catalytically inactive form called cytochrome P-420. Oxidized PB P-450 shows a Raman spectrum which is characteristic of typical ferric low-spin heme compounds, whereas those of PB P-448 and MC P-448 are of the ferric high-spin type. PB P-450 is also clearly distinguishable from the two P-448 preparations in the reduced state. The reduced form of cytochrome P-420, produced by laser illumination, exhibits two sets of Raman lines and, therefore, seems to be a mixture of both high- and low-spin species.

Nitrogen-15 and carbon-13 nuclear magnetic resonance of reduced flavins. Comparative study with oxidized flavins

Nitrogen-15 and carbon-13 nuclear magnetic resonance spectra of the fully reduced form of flavin were studied with riboflavin tetrabutyrate (RBUT), an organic solvent-soluble derivative of riboflavin. For the measurement of 15N resonances, 99% enriched [1,3-15N]RBUT and [1,3,5-15N]RBUT wwere synthesized. In order to assign the 13C resonances, 90% enriched [2-13C]RBUT, [4a-13C]RBUT, [4,10a-13C]RBUT, and [8-2H3]RBUT were employed. The upfield shift of N(5) resonance upon reduction was remarkable (286 ppm), while the N(1) signal moved only by 79 ppm. The one-bond 15N-H spin-spin coupling constant 1J[15N(5)-H] of the reduced RBUT was smaller than its 1J[15N(1)-H] and 1J[15N(3)-H]. These observations indicate that N(5) changed into sp3 hybridization upon reduction and lost the character of planar nitrogen. Most of the 13C nuclei of the reduced form resonated at higher field than did those of the oxidized form, which is well explained by the increase in pi-electron densities. Among the 13C resonances, the upfield shift of C(4a) was remarkable (32 ppm), which explains the reactivity of C(4a) in oxygen flavoprotein complexation. 13C--15N spin-spin coupling constants were obtained from the measurements of 13C magnetic resonance of 15N-enriched RBUT. The values of the one-bond 13C--15N coupling constants increased markedly with protonation at N(1) and N(5) upon reduction.

Resonance Raman study of the pH-dependent and detergent-induced structural alterations in the heme moiety of Rhodospirillum rubrum cytochrome c'

The resonance Raman spectra and the structures of the heme moiety of Rhodospirillum rubrum cytochrome c' were investigated for its five states characterized by absorption spectra; Types-a and -n of the reduced form and Types-I, -II, and -III of the oxidized form. The frequency of the ligand-sensitive Raman line suggested the coordination of lysine (Nepsilon) at the sixth position of the heme iron of Type-n. The sixth ligand of Type-III was deduced to be either lysine or histidine but would not be methionine. Type-a and Type-II gave the Raman spectra of rather normal high spin type but Type-I was unusual in the sense that the frequencies of the Raman lines associated primarily with methine-bridge CC-stretching vibrations were relatively high in comparison with those of other high spin hemoproteins. Type-I was converted directly to Type-III upon the addition of SDS or 2-propanol but the conversion occurred via Type-II when pH was increased. Structural difference between the high spin hemes of Type-I and Type-II was discussed in detail.

The pH dependence of the resonance raman spectra and structural alterations at heme moieties of various c-type cytochromes

The pH dependence of resonance Raman spectra were studied for ferrous and ferric cytochromes c, c2, c3, c-551, and c-555. The frequencies of the 1565 cm-1 (ferric) and 1539 cm-1 lines (ferrous) were sensitive to the replacement of the sixth ligand. The titration curve for the 1565 cm-1 line of cytochrome c was parallel with that for the 695 nm band. The pH dependence of the 1539 cm-1 line of ferrous cytochrome c3 suggested the stepwise replacement of the sixth ligand of its four hemes, although such pH dependence was not recognized for the Raman spectra of other ferrous cytochromes investigated. The relative intensities of three Raman lines at 1639, 1587, and 1561 cm-1 of ferric protoporphyrin bis-imidazole complex were changed clearly by the presence of detergents. The relative intensities of the corresponding three Raman lines of cytochromes b5 and c were close to those of the ferric porphyrin complex in the presence and absence of detergents, respectively, suggesting an appreciable difference in their heme environments. Reduced hemin in detergent solution, unexpectedly, gave the Raman spectrum of ferric low spin type.

Phase transitions of phospholipid bilayers from an unsaturated fatty acid auxotroph of Escherichia coli

Total phospholipids were extracted from cells of temperature sensitive unsaturated fatty acid auxotrophs of Escherichia coli (K-12 UFAts) grown at 28degrees C (PL28), and at 42degrees C in the presence of 2% KCl as an osmotic stabilizer (PL42 (KCl)). From the analysis of fatty acids, it was shown that the content of unsaturated fatty acids of PL42 (KCl) is only 9% of the total fatty acids, while that of PL28 is 54%. The thermal phase transitions of the bilayers prepared from the phospholipid fractions were studied by proton magnetic resonance. The line widths of the methylene signals and the sums of the methylene and methyl signal intensities were plotted against reciprocal values of absolute temperature 1/T or temperature itself. From the plots phase transitions were detected at about 19degrees C for PL28 and at 43degrees C for PL42 (KCl). In spite of its complex composition of fatty acids a highly cooperative transition was observed in the case of PL42 (KCl). It was also suggested that the phospholipids bilayers in the biomembranes of this strain at the growth temperature (42 degrees C) are in the state where the gel and liquid crystalline phases coexist.

Conformational difference in the polar groups of phosphatidylcholine and phosphatidylethanolamine in aqueous phase

Proton and phosphorus nuclear magnetic resonance was used to investigate conformations of o-phosphorylcholine(OPC), o-phosphorylethanolamine(OPE) and L-alpha-glycerophosphorylethanolamine in aqueous solution, and the conformations of dipalmitoyl-3-sn-phosphatidylcholine and phosphatidylethanolamine from E. coli in methanol and chloroform solutions. It has been shown that in every case the O-C-C-N system prefers a gauche conformations, but in the choline moiety the dihedral angle around the C-C bond is distorted from the usual gauche angle, 60 degrees, to a larger one. The dihedral angle of OPC is shown to be more variable than that of OPE. This may be due to the curvature of its potential curve, i.e. asymmetrical curvature around the gauche minima. This property of the phosphatidylcholine molecule may be partly responsible for the flexibility of the phosphatidylcholine bilayer. The coupling is dominant in the P-O-C-C systems of the 5 compounds examined. The results also indicated that the two hydrocarbon chains in phosphatidylcholine or phosphatidylethanolamine are apt to take nearly parallel orientation in methanol solution. This characteristic is favourable for the formation of the bilayer structure.

Proton magnetic resonance spectra of tRNA-Met-f from Thermus thermophilus

220 MHz proton magnetic resonance spectra of tRNAs in bulk and tRNA-Met-f from Thermus thermophilus have been measured and compared with those of tRNAs from E. coli. Temperature dependences and chemical shift positions of the bulk tRNAs are well explained by the difference in their GC contents. It is known that the base sequence of the double helical regions in the cloverleaf structure of T. thermophilus tRNA-Met-f is different from that of E. coli tRNA-Met-f only at two positions in TpsiCarm; one more C:G pair is contained instead of a U:G pair of E. coli tRNA-Met-f and a C:G pair of E. coli is replaced by a G:C pair. In spite of the resembrance in the base sequences, nmr patterns around 13 ppm are fairly different from each other. The difference is discussed in relation with their tertiary structures and with the origin of chemical shift displacements.

An anomaly in the resonance Raman spectra of cytochrome P-450cam in the ferrous high-spin state

Resonance Raman spectra of cytochrome P-450cam (P-450cam) and its enzymatically inactive form (P-420) in various oxidation and spin states were measured for the first time. The Raman spectrum of reduced P-450cam was unusual in the sense that the "oxidation-state marker" appeared at an unexpectedly lower frequency (1346 cm-1) in comparison with those of other reduced hemoproteins (approximately 1355-approximately 1365 cm-1), whereas that of oxidized P-450cam was located at a normal frequency. This anomaly in the Raman spectrum of reduced P-450cam can be explained by assuming electron delocalization from the fifth ligand, presumably a thiolate anion, to the antibonding pi orbital of the porphyrin ring. The corresponding Raman line of reduced P-420 appeared at a normal frequency (1360 cm-1), suggesting a status change or replacement of the fifth ligand upon conversion from P-450cam to P-420. The Raman spectrum of reduced P-450cam-metyrapone complex was very similar to that of ferrous cytochrome b5.

15N nuclear magnetic resonance of flavins

Ninety-nine percent 15N-enriched flavins were synthesized and their proton decoupled 15N resonances were observed. The enriched compounds were [1,3-15N]riboflavin, [1,3,5-15N]riboflavin, [1,3-15N]riboflavin 5'-phosphate, [1,3,5-15N]riboflavin 5'-phosphate, and [1,3,5-15N] flavin adenine dinucleotide, [1,3,5-15N] lumiflavin, and [1,3,5-15N] lumichrome. By comparison of their spectra and from th- nuclear Overhauser effect data each 15N resonance peak could be assigned to each 15N nucleus. The order of the chemical shifts well corresponds to that of the calculated pi-electron densities. The N-3 nucleus gives the most intense inverted peak and the N-5 nucleus a small noninverted peak. By changing pH from neutral to alkaline, the chemical shift and the intensity of signal were mostly affected in the N-3 resonance of riboflavin 5'-phosphate. The N-5 signal of flavin adenine dinucleotide showed a fairly large downfield shift with the increase of temperature. These observations can be well interpreted by the chemical structure and the proposed conformation of riboflavin 5'-phosphate and flavin adenine dinucleotide.

Conformational analysis of phosphatidylethanol-amine in multilayers by infrared dichroism

Built-up films of L-alpha-dipalmitoyl phosphatidylethanolamine were prepared. Infrared dichroism was measured for the sample and analysed by a new method. This method has been developed for the determination of the directions of transition moments in a film sample, in which there is an axis of symmetry of perpendicular to the film plane. The directions of transition moments were determined for the six vibrations assigned to the CH2 antisymmetric stretching, CH2 symmetric stretching, CH2 scissoring, C=O stretching, PO2- antisymmetric stretching, and C-C-N+ antisymmetric stretching modes. The results indicate that hydrocarbon chains are inclined at about 75 degrees to the film plane and the polar groups orient parallel to the plane in the builtup film. A structural model of the phosphatidylethanolamine in the built-up film is proposed.

Resonance Raman scattering from hemoproteins. Effects of ligands upon the Raman spectra of various C-type cytochromes

Resonance Raman spectra were measured for various C-type cytochromes (mammalian cytochrome c, bacterial cytochrome c3, algal photosynthetic cytochrome f, and alkylated cytochrome c) and a B-type cytochrome (cytochrome b5) in their reduced and oxidized states. (1) For ferrous alkylated cytochrome c, a Raman line sensitive to the replacement of an axial ligand of the heme iron uas found around 1540 cm=1. This ligand-sensitive Raman line indicated the transition from acidic (1545 cm-1) to alkaline (1533 cm-1) forms with pK 7.9. The pH dependence of the Raman spectrum corresponded well to that of the optical absorption spectra. (2) For ferrous cytochrome f, the ligand-sensitive Raman line was found at the same frequency as cytochrome c (1545 cm-1). Accordingly two axial ligands are likely to be histidine and methionine as in cytochrome c. (3) For ferrous cytochrome c3, the frequency of the ligand-sensitive Raman line was between those of cytochrome c and cytochrome b5. Since two axial ligands of the heme iron in cytochrome c3 might be histidines. However, a combination of histidine and methionine as a possible set of two axial ligands was not completely excluded for one or two of the four hemes. (4) In ferrous cytochrome b5, two weak Raman lines appeared at 1302 and 1338 cm-1 instead of the strongest band at 1313 cm-1 of C-type ferrous cytochromes. This suggests the practical use of these bands for the identification of types of cytochromes. The difference in frequency and intensity between B- and C-types of hemes implies that the low effective symmetry of the heme in ferrous cytochrome c is due to vibrational coupling of ring modes with peripheral substituents rather than geometrical disortion of heme.

Infrared and Raman spectra of phosphatidyl-ethanolamine and related compounds

Infrared and Raman spectra of phosphatidylethanolamine from Escherichia coli, L-alpha-glycero-phosphorylethanolamine and 0-phosphorylethanolamine were obtained. Most of the bands were assigned to each vibrational mode based on the N deuteration effect, comparison of the intensity in the infrared and Raman spectra and the depolarization degree measurement in the Raman spectra. The spectra of phosphatidylethanolamine can be interpreted by assuming that the molecule takes the dipolar ionic structure both in non-polar solvent and in solid.