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Biomedical subjects

K Toma

Publications and source records attributed to K Toma.

33 records · Page 2Linked to original sources
PubMed1999

Underglycosylation of IgA1 hinge plays a certain role for its glomerular deposition in IgA nephropathy.

This study was performed to isolate and investigate the IgA1 that could accumulate in glomeruli (glomerulophilic IgA1). IgA1 was fractionated by the electric charge and the reactivity to Jacalin. Serum IgA1 of IgA nephropathy patients was separated and fractionated using a Jacalin column and subsequent ion-exchange chromatography. The fractions were divided into three groups of relatively cationic (C), neutral (N), and anionic (A). IgA1 was also divided into Jacalin low (L), intermediate (I), and high (H) affinity fractions by serial elution using 25, 100, and 800 mM galactose. The left kidneys of Wistar rats were perfused with 2, 5, or 10 mg of each group of IgA1. The rats were sacrificed 15 min, 30 min, 3 h, or 24 h after the perfusion. The accumulation of each IgA1 in the glomeruli was then observed by immunofluorescence. The IgA1 of the fractions N and H separated by the two methods was definitely accumulated in the rat glomeruli with a similar pattern. The electrophoresis revealed that the macromolecular IgA1 was increased in fraction H compared with other fractions. Therefore, Jacalin high-affinity IgA1(fraction H) was applied on a diethylaminoethyl column and divided into electrically cationic (HC), neutral (HN), and anionic (HA). Only the asialo-Galbeta1,3GalNAc chain was identified in the fraction HN IgA1 by gas-phase hydrazinolysis. Furthermore, the IgA1 fraction was strongly recognized by peanut agglutinin, Vicia Villosa lectins, and antisynthetic hinge peptide antibody. These results indicated that the IgA1 molecules having the underglycosylated hinge glycopeptide played a certain role in the glomerular accumulation of IgA1 in IgA nephropathy.

Animals↗
PubMed1998

Evidence for a site-specific fucosylation of N-linked oligosaccharide of immunoglobulin A1 from normal human serum.

Glycopeptides containing the N-linked oligosaccharide from human serum IgA1 were analyzed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOFMS). Two glycopeptides, GP1 and GP2, prepared from the endoproteinase Asp-N digest of the IgA1 heavy chain, were derived from the CH2 domain (N-glycan site at Asn263) and the tailpiece portion (N-glycan site at Asn459), respectively. The structure of the attached sugar chain was deduced from the mass number of the glycopeptide and confirmed by a two-dimensional mapping technique for a pyridylaminated oligosaccharide. GP1 was composed of two major components having a fully galactosylated bianntena sugar chain with or without a bisecting N-acetylglucosamine (GlcNAc) residue. On the other hand, the GP2 fraction corresponded to the glycopeptides having a fully galactosylated and fucosylated bianntena sugar chain partly bearing a bisecting GlcNAc residue. Thus, the site-specific fucosylation of the N-linked oligosaccharide on the tailpiece of the alpha1 chain became evident for normal human serum IgA1.

Amino Acid Sequence↗
PubMed1998

Protective role of IgA1 glycans against IgA1 self-aggregation and adhesion to extracellular matrix proteins.

The aim of this study was to investigate the role of carbohydrate moieties attached to IgA1 hinge region in IgA1 self-aggregation and adhesion to extracellular matrix (ECM) proteins previously reported in IgA nephropathy. Serum IgA1 samples isolated from healthy individuals were digested with neuraminidase (NA), NA + beta-galactosidase, and NA + beta-galactosidase + alpha-N-acetylgalactosaminidase to remove the carbohydrates from the hinge region and were named asialo, agalacto, and naked IgA1, respectively. First, polyacrylamide gel electrophoresis was performed under the native condition, and consequently, a broad band indicating IgA1 self-aggregation was clearly observed in asialo, agalacto, and naked IgA1, but not in native IgA1. However, the broad band disappeared in sodium dodecyl sulfate-polyacrylamide gel electrophoresis under the nonreducing condition. Second, it was shown that IgA1 adhesion activities to type IV collagen, fibronectin, and laminin were significantly higher in asialo, agalacto, and naked IgA1 than in native IgA1, using enzyme-linked immunosorbent assay (asialo, agalacto, and naked versus native: P < 0.01). In addition, agalacto IgA1 had the highest affinity for all of the ECM proteins among the deglycosylated IgA1 (agalacto versus asialo and naked, P < 0.05). These results indicated that the removal of carbohydrates from the IgA1 molecule resulted in noncovalent self-aggregation and a significant increase in adhesion to the ECM proteins. It was therefore suggested that the IgA1 glycans played a protective role against aggregation and adhesion and that the underglycosylation of the IgA1 molecule found in IgA nephropathy could be involved in the nonimmunologic glomerular accumulation of IgA1.

Electrophoresis, Polyacrylamide Gel↗
PubMed1993

Protein three-dimensional structure generation with an empirical hydrophobic penalty function.

Given current computational environments, it is worthwhile to establish amino acid residue-level functions which approximate protein folds quite well. Such functions must be the interim steps toward protein three-dimensional structure prediction. I have shown that an empirical hydrophobic penalty function of protein, derived from the number of residues in a sphere around each residue, could be utilized to distinguish the correctly folded structure from the incorrect ones. In order to assess the predictive power of the penalty function, I have generated conformations by randomly changing main chain dihedral angles, and applied the penalty function to them. If only a local region was allowed to change its conformation, native-like structures could be generated within a reasonable computational time. In global simulations, however, a considerable number of nonnative conformations, which gave as small a penalty value as that of the native protein, were found. Although some of the conformations were compact and globular, they were quite different from the native structure in that they lacked most of the secondary structures. This result shows that the penalty function alone cannot define the native structure, and that substructure information may help the penalty function to reach the correctly folded structure.

Algorithms↗
PubMed1991

Number of residues in a sphere around a certain residue can be used as a hydrophobic penalty function of proteins.

A novel hydrophobic penalty function of proteins is proposed and assessed with several test cases. The number of residues in a defined sphere around a certain residue is averaged over the data set proteins. Differences between the standard values thus obtained and calculated values are summed up, residue by residue, with the weight of standard deviations to give the penalty value. This penalty function is applied to the structures of randomly shuffled sequences, incorrectly folded structures and partially denatured structures displayed on a graphics terminal, and is shown to discriminate the native structure from others fairly well, although the present parameter set is tuned for proteins of about 100-150 residues. From the results of present study and the known correlation with other hydrophobic parameters of amino acids, the penalty function can be considered as a practical amino acid residue-level hydrophobic penalty function.

Amino Acid Sequence↗
PubMed1989

Structure prediction of protease inhibitor region in amyloid precursor protein of Alzheimer's disease.

Recent findings of the protease inhibitor domain in amyloid precursor protein of Alzheimer's disease (APPI) raised a novel hypothesis on the mechanism of amyloid deposition in the brain. APPI has significant amino acid sequence homology with Kunitz-type basic trypsin inhibitor super-family proteins, and the gene expression product showed real inhibitory activity. Since the three-dimensional model of APPI would help in understanding biological phenomena in molecular detail, we constructed an atomic model of APPI based on the structure of bovine pancreatic trypsin inhibitor (BPTI). The substitution of BPTI side chains by best-fitting corresponding amino acid structures was followed by the removal of van der Waals overlappings by molecular mechanics energy minimization with the AMBER force field, to give the feasible model of APPI. We also built serine protease models based on the structure of trypsin and investigated the target enzyme specificity of the inhibitory activity by the active-site mapping method. The models can explain the relative enzyme spectra of APPI and BPTI.

Amino Acid Sequence↗
PubMed1989

Mapping active sites of blood coagulation serine proteases--activated protein C and thrombin--on simple graphics models.

Employing the known three-dimensional (3D) structure of trypsin, we constructed simple graphics models of human-activated protein C and thrombin catalytic domains. Considering the structural analysis of bovine trypsin and pancreatic trypsin inhibitor complex, the difference of active-site amino acid sequences of human protein C inhibitor and antithrombin III and their inhibitory selectivity toward activated protein C and thrombin, we estimated the enzymatic subsites of activated protein C and thrombin and mapped them on the graphics models. Predicted favorable contacts can explain substrate selectivity of the enzymes. In this study, we used two types of modified ALPHA representations extensively. Since almost no report on the 3D structure of a blood coagulation factor has appeared and even an extensive molecular mechanics or dynamics calculation cannot produce satisfying results, simple graphics representation has several advantages.

Amino Acid Sequence↗
PubMed1987

Three-dimensional structure of protein C inhibitor predicted from structure of alpha 1-antitrypsin with computer graphics.

The three-dimensional structure of a proteolytically modified protein C inhibitor, a member of the serine protease inhibitor superfamily, was constructed with computer graphics based on its amino acid sequence homology with that of the modified alpha 1-antitrypsin whose structure had been elucidated by X-ray crystallography. The intact form of protein C inhibitor was predicted with an alpha-carbon model based on its hydrophilicity and hydrogen bond pattern. Furthermore, a model of its interaction with activated protein C was constructed based on the structure of the complex between trypsin and its inhibitor, which had been determined by X-ray crystallography.

Amino Acid Sequence↗
PubMed1987

Nucleotide sequences of the genes for two distinct cephalosporin acylases from a Pseudomonas strain.

Two genes, acyI and acyII, for distinct cephalosporin acylases from Pseudomonas sp. strain SE83 (A. Matsuda, K. Matsuyama, K. Yamamoto, S. Ichikawa, and K.I. Komatsu, J. Bacteriol. 169:5815-5820, 1987) were sequenced. Each sequence contained a single open reading frame for two nonidentical subunits, predicting a common precursor. Some homologies at the amino acid level were found between the acyII-encoded enzyme, but not the acyI-encoded one, and other related acylases.

Amidohydrolases↗