Biomedical subjects

I Shimada

Publications and source records attributed to I Shimada.

At least 109 records · Page 6Linked to original sources

PubMed1992

Detailed structural analysis of asparagine-linked oligosaccharides of the nicotinic acetylcholine receptor from Torpedo californica.

The structures of the major oligosaccharide moieties of the nicotinic acetylcholine receptor (AcChoR) protein from Torpedo californica have been reported [Nomoto, H., Takahashi, N., Nagaki, Y., Endo, S., Arata, Y. and Hayashi, K. (1986) Eur. J. Biochem. 157, 233-242] to be high-mannose types. Here we report detailed analyses of the structures of the remaining oligosaccharides in this receptor. The sialylated oligosaccharides released by glycopeptidase (almond) digestion were separated according to the number of sialic acid residues using high-performance anion-exchange chromatography with pulsed amperometric detection. After removal of sialic acid from each fraction, the resulting neutral oligosaccharides were separately pyridylaminated and were analyzed by a combination of sequential exoglycosidase digestion and HPLC, then identified on a two-dimensional sugar map. The structures of two desialylated pyridylamino-oligosaccharides were further analyzed by high-resolution proton NMR. Each oligosaccharide was composed of species containing varying numbers of sialic acids. The desialylated complex-type oligosaccharides of AcChoR consisted of ten, eight and one different biantennary, triantennary and tetraantennary oligosaccharide, respectively. The biantennary oligosaccharides were divided into two groups; oligosaccharides with fucose at the proximal N-acetylglucosamine (six varieties) and oligosaccharides without fucose (four varieties). Each group consisted of species differing in the number of terminal galactose residues. The major component of the biantennary oligosaccharides had two galactose residues at the non-reducing termini. The terminal alpha-galactose residue(s) linked to C3 of beta-galactose were found in the fucose-containing biantennary oligosaccharides (two varieties). The triantennary oligosaccharides were also divided into two groups; oligosaccharides with (four varieties) and without (four varieties) besecting N-acetylglucosamine. These groups were composed of species differing in the number of terminal galactose residues. The major component of the triantennary oligosaccharides was fully galactosylated with three galactose residues. An unusual group, Gal beta 1-3GlcNAc, was present in low levels in the triantennary oligosaccharides. In contrast, the tetraantennary oligosaccharide was composed of only one species, which is fully galactosylated with four galactose residues.

Animals↗

PubMed1992

Dynamical structure of the antibody combining site as studied by 1H-15N shift correlation NMR spectroscopy.

The Fv fragment, which is a smallest antigen-binding unit of immunoglobulin, has been used for a 1H-15N shift correlation NMR study of the dynamical structure of the antibody combining site. Fv has been prepared by clostripain digestion of a mouse anti-dansyl IgG2a monoclonal antibody that lacks the entire CH1 domain. We have previously reported that of the six hypervariable regions, three each from the heavy chain (H1, H2, and H3) and the light chain (L1, L2, and L3), H3 is primarily responsible for the antigen binding in the anti-dansyl Fv fragment. The backbone amide nitrogens of all non-proline amino acid residues in H3 have been multiply labeled with 15N. [15N]T2 relaxation times and hydrogen-deuterium exchange rates of the amide groups of the main chain were measured in the absence and presence of epsilon-dansyl-L-lysine (DNS-Lys). It has been shown that (1) in the absence of DNS-Lys H3 displays a significant degree of internal motion and (2) antigen binding induces a significant change in the dynamical structure of H3.

Amino Acid Sequence↗

PubMed1992

A 1H-NMR study of the solution conformation of cyclo(GRGDSPA): conformational effects on the physiological activity.

Solution conformations of cyclo(GRGDSPA) have been analyzed by the use of two-dimensional proton nuclear magnetic resonance spectroscopy and the dynamical simulated annealing calculation. It has been shown that the RGDS segment in cyclo(GRGDSPA) takes a beta-turn conformation. We have concluded that this beta-turn conformation is essential for the physiological activity of cyclo(GRGDSPA).

Amino Acid Sequence↗

PubMed1992

[Studies on acute surgical therapy for DeBakey III aortic dissection: especially on the CT images and the operative indication].

Nine patients with DeBakey type III aortic dissection (type III a; 6, type III b; 3) that underwent acute surgical therapy were studied with particular emphasis on the preoperative CT images and operative indication. It took 6 approximately 192 hours (mean 40.6 +/- 56.0) from onset of the disease to the operation. The reasons why operations were required in acute phase were prolonged pain; 2, fluid retensionin in thoracic cavity; 3, increasing fluid retension; 3, shock state; 1, anuria; 1.6 (75%) of 8 thoracic aortic dissection cases showed intra-thoracic fluid retension in chest roentogenogram or CT image. We performed prosthetic interposition of descending thoracic aorta in 8 patients and Y-graft interposition of abdominal aorta in a patient. During the operations, we found fluid retension in the thoracic and pericardial cavity in 83% (5 cases) of 6 non-ruptured cases. To diagnose ruptured aneurysm, CT image played very important role. But we could not discriminate between ruptured aneurysm and intrapleural serous fluid retension on the CT image. Puncture of intra-thoracic fluid is effective procedure to diagnose rupture of the aneurysms but it is impossible in some cases and traumatic tap may lead misdiagnosis. Therefore we think moderate or increasing fluid retension in the thoracic cavity should be added to the operative indication of acute DeBakey type III aortic dissection and that the early operation will make mortality rate lower.

Acute Disease↗

PubMed1992

[Surgical therapy of aortic regurgitation due to aortitis syndrome--effectiveness and extended indication of Bentall's operation].

Fourteen patients with aortic regurgitation due to aortitis syndrome that underwent surgical therapy were studied with particular emphasis on the long term merits of Bentall's operations over the conventional valve replacement. They were divided into two groups; Group A: 6 aortic valve replacements (AVRs) and Group B: 8 Bentall's operations. Post operative complications related to aortitis syndrome developed in 3 cases; a case of paravalvular leakage (Group A) and two cases of aneurysm formation at the coronary artery anastomotic sites (Group B). We speculated that these complications were due to abnormal healing and recurrent inflammatory process of the disease. Therefore we think that conventional valve replacement is not suited to cope with these problems. Since 1984, we have adopted the policy to perform Bentall's operations for all patients with aortitis requiring valve replacement. Bentall's operation required longer aortic cross-clamp time (212.1 +/- 53.9 min) than AVRs (73.0 +/- 25.0) and was more aggressive. However no patients with our current technique to reimplant the coronary artery button and distal graft to aorta anastomosis, which has been used since 1984, has developed pseudoaneurysm or valvular leakage. We conclude that our modified Bentall's operation is effective even for patients who have active aortitis syndrome or need redo operations.

Adult↗

PubMed1991

Carbon-13 NMR study of switch variant anti-dansyl antibodies: antigen binding and domain-domain interactions.

A 13C NMR study is reported of switch variant anti-dansyl antibodies, which possess the identical VH, VL, and CL domains in conjunction with highly homologous but not identical heavy-chain constant regions. Each of these antibodies has been selectively labeled with 13C at the carbonyl carbon of Trp, Tyr, His, or Cys residue by growing hybridoma cells in serum-free medium. Spectral assignments have been made by following the procedure described previously for the switch variant antibodies labeled with [1-13C]Met [Kato, K., Matsunaga, C., Igarashi, T., Kim, H., Odaka, A., Shimada, I., & Arata, Y. (1991) Biochemistry 30, 270-278]. On the basis of the spectral data collected for the antibodies and their proteolytic fragments, we discuss how 13C NMR spectroscopy can be used for the structural analyses of antigen binding and also of domain-domain interactions in the antibody molecule.

Amino Acid Sequence↗

PubMed1991

Multinuclear NMR study of the structure of the Fv fragment of anti-dansyl mouse IgG2a antibody.

A multinuclear NMR study is reported of Fv, which is a minimum antigen-binding unit of immunoglobulin. Fv has been prepared by clostripain digestion of a mouse anti-dansyl IgG2a monoclonal antibody that lacks the entire CH1 domain [Takahashi, H., Igarashi, T., Shimada, I., & Arata, Y. (1991) Biochemistry 30, 2840-2847]. A variety of Fv analogues labeled with 2H in the aromatic rings and with 13C and/or 15N in the peptide bonds have been prepared and used for multinuclear NMR analyses of Fv in the absence and presence of epsilon-dansyl-L-lysine (DNS-Lys). It has been shown that 1H-15N shift correlation spectra of Fv sensitively reflect the antigen binding and can be used along with 1H and 13C spectral data for the structural analyses of antigen-antibody interactions. Hydrogen-deuterium exchange of the amide protons has been followed in the absence and presence of DNS-Lys by using the 1H-15N shift correlation spectra. Use of the beta-shift observed for the carbonyl carbon resonances has also been helpful in following the hydrogen-deuterium exchange. On the basis of the NMR data obtained, the static and dynamic structure of the Fv fragment in the absence and presence of DNS-Lys has been discussed.

Amino Acid Sequence↗

PubMed1991

Preparation of the Fv fragment from a short-chain mouse IgG2a anti-dansyl monoclonal antibody and use of selectively deuterated Fv analogues for two-dimensional 1H NMR analyses of the antigen-antibody interactions.

The Fv fragment, a univalent antigen-binding unit with a molecular weight of 25,000, has successfully been prepared in high yield by limited proteolysis with clostripain of a short-chain mouse IgG2a anti-dansyl monoclonal antibody in which the entire CH1 domain is deleted [Igarashi, T., Sato, M., Takio, K., Tanaka, T., Nakanishi, M., & Arata, Y. (1990) Biochemistry 29, 5727-5733]. The Fv fragment obtained is stable at room temperature and retains its full antigen-binding capability. It has been shown that selective deuterium labeling of the Fv fragment, which is half the size of the Fab fragment, provides 1H NMR spectral data at a sufficient resolution for a detailed structural analysis of the antigen-combining site. NOESY spectra of an Fv analogue, in which all aromatic protons except for His C2'-H and Tyr C3',5'-H had been deuterated, were measured in the presence of varying amounts of dansyl-L-lysine. On the basis of the NOESY data obtained, it was possible to assign all the ring proton resonances for the dansyl group that is bound to the Fv fragment. It was also possible to obtain information about His and Tyr residues of the Fv fragment in the absence and presence of the antigen. On the basis of the NMR data obtained, we have shown that at least two Tyr residues along with one of the amide groups are directly involved in antigen binding. The mode of interaction of the dansyl ring with these residues in the Fv fragment has briefly been discussed.

Animals↗

PubMed1991

Complete assignment of the methionyl carbonyl carbon resonances in switch variant anti-dansyl antibodies labeled with [1-13C]methionine.

A 13C NMR study is reported of switch variant anti-dansyl antibodies developed by Dangl et al. [(1982) Cytometry 2, 395-401], who had used the fluorescence-activated cell sorter to select and clone these variants. These switch variant antibodies possess the identical VH, VL, and CL domains in conjunction with different heavy chain constant regions. In the present study, switch variant antibodies of IgG1, IgG2a, and IgG2b subclasses were used along with a short-chain IgG2a antibody, in which the entire CH1 domain is deleted. The switch variant antibodies were specifically labeled with [1-13C]methionine by growing hybridoma cells in serum-free medium. Assignments of all the methionyl carbonyl carbon resonances have been completed by using the intact antibodies along with their fragments and recombined proteins in which either heavy or light chain is labeled. A double labeling method [Kainosho, M., & Tsuji, T. (1982) Biochemistry 21, 6273-6279] has played a crucial role in the process of the spectral assignments. The strategy used for the assignments has been described in detail. In incorporating 15N-labeled amino acids into the antibodies for the double labeling, isotope dilution caused a serious problem except in the cases of [alpha-15N]lysine and [15N]threonine, both of which cannot become the substrate of transaminases. It was found that beta-chloro-L-alanine is most effective in suppressing the isotope scrambling. So far, spectral assignments by the double labeling method have been possible with 15N-labeled Ala, His, Ile, Lys, Met, Ser, Thr, Tyr, and Val.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

PubMed1991

[Treatment of mediastinal infection after coronary artery bypass surgery by transposition of the greater omentum].

From January, 1986 to May, 1990 twenty one adult patients (men 16, women 5, age 64 +/- 7 years old) underwent transposition of the greater omentum to control mediastinal infection after coronary artery bypass surgery. Upon diagnosing mediastinitis, the mediastinum was drained open and irrigated with 0.5% povidone iodine-saline solution until the omental transposition. The interval between the diagnosis of mediastinitis and the omental transposition ranged from 0 to 171 (mean 19) days. Three quarters of the patients had the omentum transposed within 14 days. In nineteen of 21 patients (90%) the mediastinitis was effectively controlled. In the remaining two patients the infection could not be controlled and proceeded to succumb from multiple organ failure. There was no complication related to the omental transposition in itself. We conclude that transposition of the greater omentum is a safe and effective method for treating mediastinal infection after coronary artery bypass surgery.

Aged↗

PubMed1991

[Bilateral diaphragmatic plication for an adult patient].

Bilateral phrenic nerve paralysis is a very rare complication in open-heart surgery. An 65-year-old woman sustained respiratory distress after coronary artery bypass grafting because of bilateral phrenic nerve paralysis. Bilateral diaphragmatic plication was performed on the 43rd postoperative day. She successfully weaned from ventilator support without difficulty a few days after plication. We believe that surgical plication of the diaphragm is a safe and effective technique for a distressed adult patient with paralyzed diaphragm.

Aged↗

PubMed1991

[Coronary artery bypass surgery for chronic total occlusion of the left main coronary artery by means of intermittent antegrade cold blood cardioplegia].

From January, 1984 to May, 1990 eleven patients (men 9, women 2) underwent coronary artery bypass surgery for chronic total occlusion of the left main coronary artery by means of intermittent antegrade cold blood cardioplegia. The ages ranged from 33 to 74 (mean 56) years. The causes of the total occlusion of the left main coronary artery were atherosclerosis in 10 patients and aortitis syndrome in one. Four patients had history of a previous myocardial infarction. Preoperative selective coronary arteriography revealed well developed collateral vessels from the RCA to the LCA in all patients. One to five coronary arteries were bypassed. Myocardial protection was obtained in the usual fashion: antegrade intermittent cold blood cardioplegia with topical cardiac cooling. All patients were successfully weaned off from cardiopulmonary bypass without the need of IABP assist. No patient developed perioperative myocardial infarction. All grafts were patent postoperatively. Treadmill testing was negative in all patients. We believe that coronary artery bypass surgery for chronic total occlusion of the left main coronary artery can be performed safely with intermittent antegrade cold blood cardioplegia.

Adult↗

PubMed1990

Proton nuclear magnetic resonance study of human interleukin 6: chemical modifications and partial spectral assignments for the aromatic residues.

Partial assignments for the 1H-NMR resonances of the aromatic residues in human interleukin 6 (IL-6) are reported. The homonuclear Hartmann-Hahn spectrum clearly shows all connectivities for the histidine, tyrosine and tryptophan residues that exist in IL-6. Using a deuterium exchange method, the imidazole proton resonances of His-16 and His-165 have been assigned. Iodination of the tyrosine residues led to the assignment of Tyr-32. Photo-chemically induced dynamic nuclear polarization data have shown that His-16, Tyr-32 and Trp-158 are exposed to solvent, whereas His-165, Tyr-98 and Tyr-101 are buried. Iodination of Tyr-32 gave no significant effect on IL-6 activity, suggesting that Tyr-32 is not responsible for IL-6 activity.

Binding, Competitive↗

PubMed1990

Sequential 1H NMR assignments and secondary structure of the B domain of staphylococcal protein A: structural changes between the free B domain in solution and the Fc-bound B domain in crystal.

The recombinant B domain (FB) of staphylococcal protein A, which specifically binds to the Fc portion of immunoglobulin G (IgG), has been investigated with the use of two-dimensional proton nuclear magnetic resonance spectroscopy. All backbone and side-chain proton resonances of FB (60 amino acid residues), except the amide proton resonance of Ala2, were assigned by the sequential assignment procedures by using double-quantum-filtered correlated spectroscopy (DQF-COSY), homonuclear Hartmann-Hahn spectroscopy (HOHAHA), and nuclear Overhauser enhancement spectroscopy (NOESY). On the basis of the NOESY data, three helical regions, Glu9-His19, Glu25-Asp37, and Ser42-Ala55, were identified in the free FB in solution. Existence of two of the three helical regions, Glu9-His19 and Glu25-Asp37, in consistent with the X-ray crystallographic structure of the Fc-bound FB [Deisenhofer, J. (1981) Biochemistry 20, 2361-2370]. By contrast, in the Fc-bound FB as revealed by the X-ray analysis, the Ser42-Glu48 segment is extended and no structural information has been available in the Ala49-Ala55 segment. We suggest that a significant conformation change is induced in the C-terminal region of FB when it is bound to the Fc portion of IgG.

Amino Acid Sequence↗

PubMed1990

1H nuclear magnetic resonance study of the solution conformation of an antibacterial protein, sapecin.

The solution conformation of an antibacterial protein sapecin has been determined by 1H nuclear magnetic resonance (NMR) and dynamical simulated annealing calculations. It has been shown that the polypeptide fold consists of one flexible loop (residues 4-12), one helix (residues 15-23), and two extended strands (residues 24-31 and 34-40). It was found that the tertiary structure of sapecin is completely different from that of rabbit neutrophil defensin NP-5, which is homologous to sapecin in the amino acid sequences and also has the antibacterial activity. The three-dimensional structure determination has revealed that a basic-residue rich region and the hydrophobic surface face each other on the surface of sapecin.

Amino Acid Sequence↗

PubMed1990

15N nuclear magnetic resonance studies of the B domain of staphylococcal protein A: sequence specific assignments of the imide 15N resonances of the proline residues and the interaction with human immunoglobulin G.

15N nuclear magnetic resonance (NMR) studies of the B domain (FB) of Staphylococcus protein A, which is uniformly labeled with 15N, are reported. The alpha CH(i)-15N(i) connectivity in the 1H-15N HMBC spectrum and the 13C(i-1)-15N(i) spin coupling in the 15N spectrum of a 13C-, 15N-doubly labeled FB were used to establish the assignments of the imide 15N resonances for all three Pro residues that exist in FB. Addition of human IgG caused a significant downfield shift of the Pro-39 resonance. This result is quite consistent with our previous suggestion that a significant conformation change is induced in the Ser-42-Ala-55 helical region of FB when it is bound to human IgG.

Binding Sites↗

PubMed1990

A 1H-NMR study of the solution conformation of Icaria chemotactic peptide and its [Lys7] analog: effects on the physiological activity of a substitution of proline to lysine at position 7.

Solution conformations of Icaria chemotactic peptide isolated from the Ropalidian wasp venom and its [Lys7] analog have been analyzed by the use of two-dimensional proton nuclear resonance spectroscopy. It has been shown that Icaria chemotactic peptide takes alpha helical conformation in the C-terminal 8-13 segment with the N-terminal 1-7 segment disordered. By contrast, the [Lys7] analog takes alpha helical conformation over a wider range from residues 3 to 13. The present results indicate that the substitution of proline to lysine at position 7 results in a drastic change in solution conformation, providing the Icaria chemotactic peptide with new physiological functions.

Amino Acid Sequence↗

PubMed1990

Occurrence of tetra- and pentasaccharides with the sialyl-Le(a) structure in human milk.

The occurrence of two novel oligosaccharides in human milk was investigated. These oligosaccharides were purified by affinity chromatography on a column of an immobilized monoclonal antibody, MSW 113. Structural studies, involving 500-MHz 1H NMR spectroscopy and fast atom bombardment-mass spectrometry, indicated the structures of these compounds to be NeuAc alpha 2----3Gal beta 1----3(Fuc alpha 1----4) GlcNAc and NeuAc alpha 2----3Gal beta 1----3(Fuc alpha 1----4) GlcNac beta 1----3Gal. This constitutes the first evidence for the occurrence of N-acetylglucosamine or galactose as the reducing-end residue of human milk oligosaccharides. These two oligosaccharides bound MSW 113 to nearly the same extent as sialyl-Lea hexasaccharide but to another sialyl-Le(a) structure-directed monoclonal antibody, NS-19-9, only weakly.

Antigens, Tumor-Associated, Carbohydrate↗