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Biomedical subjects

Y Kyogoku

Publications and source records attributed to Y Kyogoku.

At least 127 records · Page 7Linked to original sources
PubMed1987

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.

Amino Acids↗
PubMed1987

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.

Base Sequence↗
PubMed1987

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.

Amphotericin B↗
PubMed1987

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.

Carbohydrate Sequence↗
PubMed1987

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.

Basement Membrane↗
PubMed1986

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.

Asparagine↗
PubMed1986

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.

Amino Acid Sequence↗
PubMed1986

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.

Anesthetics, Local↗
PubMed1986

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.

Crystallization↗
PubMed1986

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.

Animals↗
PubMed1986

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).

Carbohydrate Conformation↗
PubMed1986

An NMR study on the structure of OR3 in the lambda cro-OR3 complex.

1H-NMR spectra of lambda-OR3 17mer in the complex with lambda-cro has been analysed and the change in its conformation on the complexation has been deduced. The changed conformation is retained until the duplex melts above 55 degrees C. Increase in heat stability of the cro dimer was observed. The result was compared with those of other DNA fragments phi 80-OR2 19 mer and the CRP binding site 22mer mixed with lambda-cro.

Amino Acid Sequence↗
PubMed1985

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.

Brassica↗
PubMed1985

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.

Escherichia coli↗