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T Ooi

Publications and source records attributed to T Ooi.

At least 73 records · Page 4Linked to original sources
PubMed1985

Comparison of amino acid sequences between phosphoenolpyruvate carboxylases from Escherichia coli (allosteric) and Anacystis nidulans (non-allosteric): identification of conserved and variable regions.

Amino acid sequences of phosphoenolpyruvate carboxylases of Escherichia coli (allosteric) and a cyanobacterium Anacystis nidulans (non-allosteric) were aligned. The pattern of homology suggests that the enzyme molecule is comprised of two distinct regions, namely, a conserved region (C-terminal half) and a variable region (N-terminal half). Among the amino acid residues which have previously been presumed essential for the catalytic activity, three histidine residues were found to be conserved, but cysteine residues were not. Furthermore, the conserved sequence unique to the enzyme was identified by comparison of the enzyme sequence with amino acid sequences in our data bank.

Allosteric Regulation↗
PubMed1985

Energy difference associated with proline isomerization in ribonuclease A.

We examined energy differences caused by the cis-trans transformation of every proline residues in the native structure of RNAase A. The results show that the cis form of Pro-93 and Pro-114 gave the lowest conformational energy, i.e., conformations after conversion of one of the proline residues to the trans form had a little higher energy; the transformation of Pro-42 and Pro-117 to the cis form, on the other hand, caused a much higher energy increase.

Isomerism↗
PubMed1984

The complete nucleotide sequence of the adenylate cyclase gene of Escherichia coli.

The complete nucleotide sequence of the cya gene from E. coli was determined. The gene encodes a polypeptide consisting of 848 amino acid residues with a calculated molecular weight of 97,542. The deduced protein structure reveals that cyclase is comprised of two domains, an amino-terminal region exhibiting catalytic activity and a carboxy-terminal region possibly carrying regulatory function. The frequent appearance of rare codons in the beginning of the gene as well as the sequence duplication in the promoter-initiator region suggest possible regulation(s) at the translational level. An unknown gene (cyaX) which seems to code for a very hydrophobic protein was found following the cya gene. Sequence analysis suggests that the cyax is a part of the cya operon.

Adenylyl Cyclases↗
PubMed1984

Multiple pathways for regenerating ribonuclease A.

This paper is concerned with the pathways for the regeneration of RNase A from the reduced protein by a mixture of GSSG and GSH. Experimental work on the regeneration has led to the identification of several different pathways, depending on the concentrations of GSH and GSSG, and an energetic analysis has provided information about the stabilities of the various intermediates. The equilibrium and kinetic data for the regeneration process have led to two models of protein-folding pathways. The intermediates in the regeneration process were trapped without chemical modification, and were fractionated on a carboxymethyl-cellulose column. The regeneration pathway(s) could be represented in terms of two simple reactions (Eqs. (1) and (2)). The system rapidly reaches a pre-equilibrium among the intermediates prior to the rate-limiting steps, and the concentrations of the intermediates (and hence the equilibrium constants among them) were determined. The regeneration process was also re-started from several of the isolated intermediates, and led to the predicted distribution of intermediates in the pre-equilibrium. Kinetic data, obtained by following the time dependence of the regain of enzymatic activity, together with the distributions of the intermediates at pre-equilibrium, led to the identification of the rate limiting steps, which differed according to the concentrations of GSH and GSSG. The relative apparent standard state conformational chemical potentials of the intermediates were estimated by using data for the apparent equilibrium constants (among the species in pre-equilibrium) and for the redox potentials of cysteine/cystine and GSH/GSSG. The two models deduced from the equilibrium and kinetic data are designated as growth-type and rearrangement-type models. In the growth-type model, nucleation of the native-like structure occurs in the folding process, in the rate-limiting step(s), and subsequent folding around the nucleation sites proceeds smoothly to form the native disulfide bonds and conformation. In the rearrangement-type model, proper nucleation does not occur in the folding process; instead, non-native interactions play a significant role in the folding pathways and lead to metastable intermediate species. Such non-native interactions must be disrupted or rearranged to nucleate the native interactions (in the rate limiting step(s)) for the protein to fold. Other protein foldings, reported in the literature, can be shown to conform to this model.

Glutathione↗
PubMed1983

Structural homology of lens crystallins. II. Homology expressed by correlation coefficients and hydropathy profiles.

Bovine lens alpha A- and alpha B-crystallin polypeptides show extensive sequence homology with each other, but apparently none with beta Bp- and gamma 2-crystallin. Despite only 30% sequence homology, the latter two proteins are assumed to have a strong correspondence in tertiary structure, consisting of four structurally similar folding units of antiparallel beta-sheet. We have tested for internal structural repeats in all crystallins, and structural homology between crystallins, by comparing various physical properties of the amino acid residues, such as bulkiness and propensity to form beta-sheet and beta-turn structure. Two procedures used a combination of five physical parameters to calculate correlation coefficients. The 4-fold structural repeat in gamma 2-crystallin and the internal duplication in beta Bp-crystallin were readily detectable, as was also the strong structural homology between corresponding folding units in beta Bp- and gamma 2-crystallin. However, for alpha-crystallin polypeptides, no conclusive support was obtained for either a four-unit or a six-unit folding, the two models previously considered by us. The third procedure compared smoothened hydropathy plots, representing hydrophilic and hydrophobic regions along the polypeptide sequences. Hydropathy profiles were found to show strong correspondence, particularly between alpha B-crystallin and beta Bp-crystallin. These observations support a similar 4-fold folding pattern for all bovine crystallins. A possible role in subunit interactions of the N-terminal folding unit, which has hydrophobic surface characteristics in both alpha- and beta-crystallin polypeptides, is proposed.

Amino Acid Sequence↗
PubMed1983

The erbB gene of avian erythroblastosis virus is a member of the src gene family.

The erbB gene of an avian erythroblastosis virus, AEV-H, was determined to be 1812 nucleotides long and was predicted to code for a protein of 67,638 daltons. Unexpectedly, a sequence of 285 amino acids in the middle of the protein showed a significant homology (38%) with the sequence in the carboxy terminus of p60src. The nucleotide sequence of a mutant of AEV-H, td-130, which induces sarcomas but not erythroblastosis in chicken, was also analyzed. A deletion of 169 nucleotides was identified in the 3' half of the erbB gene, indicating that the gene codes for a truncated protein with the predicted molecular weight of 46,667. These findings suggest that the homologous domain of erbB protein with its N-terminal portion is sufficient for the transformation of fibroblasts and that one-third of the carboxy-terminal domain has a key role for the transformation of erythroid cells.

Alpharetrovirus↗
PubMed1983

Cross-linking study on skeletal muscle actin: interaction of suberimidate-treated actin with deoxyribonuclease I.

We have recently reported that actin modified with dimethyl suberimidate takes a filamentous form even under depolymerizing conditions, and this phenomenon is accounted for by the conformational fixation caused by the introduction of an intramolecular cross-link (Ohara, O., Takahashi, S., Ooi, T., & Fujiyoshi, Y. (1982) J. Biochem. 91, 1999-2012). The suberimidate-treated actin (SA) is not immediately depolymerized by deoxyribonuclease I (DNase I) but is depolymerized after incubation for one day, i.e., depolymerization is much slower than that for intact F-actin. The results on circular dichroic spectra of a mixture of SA and DNase I suggest that DNase I flips the conformation of SA into a G-actin-like state from the F-actin-like one when a tight SA-DNase I complex is formed. The suberimidate cross-link introduced in an SA molecule does not completely prevent the conformational change from the F-state to the G-state but stabilizes the actin conformation very greatly in the F-state.

Actins↗
PubMed1983

Classification of proteins into groups based on amino acid composition and other characters. I. Angular distribution.

Data on amino acid composition were collected in order to classify proteins into groups. The composition of a protein is expressed as a point in an orthogonal coordinate system, taking fractions of amino acids along 18 axes, which represent 18 amino acids (we use Asx and Glx for the sum of Asp and Asn and that of Glu and Gln, respectively). Thus, proteins of known amino acid compositions (356 single polypeptides chains) are distributed as points in this composition space. Since the radial distribution of the points from the origin (the average composition) did not show any distinct separation into groups, we checked the angular distribution of points in the space. Thirteen groups were found by a computer method based on the density. Analysis of the groups in terms of various characters of proteins, such as source (eukaryote or prokaryote), location in an organism, biological function, etc. revealed that the groups have strong correlations to the location (inside or outside the cell) and functional character (enzyme or nonenzyme). Also, the presence of disulfide bond(s) seems to be characteristic of extracellular proteins. Protein source, molecular size and ability to form an oligomer had little correlation to the grouping. Therefore, proteins may be classified into four types as follows: BI, intracellular enzymes; BII, intracellular nonenzymes; BIII, extracellular enzymes; and BIV, extracellular nonenzymes.

Amino Acids↗
PubMed1983

Classification of proteins into groups based on amino acid composition and other characters. II. Grouping into four types.

Correlations of the amino acid composition of a protein to its location in an organism, biological function, folding type, and disulfide bond(s) were examined for 356 proteins. In the present data set, 325 proteins of known location and biological characters were divided into 122 intracellular enzymes (BI), 73 intracellular non-enzymes (BII), 45 extracellular enzymes (BIII), and 85 extracellular nonenzymes (BIV). The composition of these proteins were expressed as points in the composition space of 18 orthogonal axes, each representing the content of an amino acid. The distributions of points of BI and BIII were narrow and approximately spherical but those of BII and BIV were distributed rather widely. The groups are separated from each other in the space. We divided the space into four regions (A1 to A4) corresponding to the groups BI to BIV. A protein could be assigned to one of the four groups (A1 to A4) from its amino acid composition: The proteins correctly assigned amounted to 177 out of 195 intracellular proteins, and 94 out of 130 extracellular proteins. The correspondence was about 80% for classification into intracellular and extracellular proteins and 66% for that into the four groups. The folding type also had a significant correlation to the above groups, i.e., intracellular enzymes are rich in alpha/beta, nonenzymes alpha, extracellular enzymes beta and alpha + beta, and nonenzymes beta. The differences in average composition between intra- and extracellular proteins, and between enzymes and nonenzymes were related to the structural characters, i.e., intracellular proteins contain more amino acids favoring alpha-helix than extracellular ones, and enzymes contain more hydrophobic amino acids than nonenzymes. The statistics on 213 Cys-containing proteins showed that disulfide bond(s) are found mostly (90%) in the extracellular proteins. The results indicate that amino acid composition is well correlated to location in an organism, biological function, folding type, and disulfide bonding. The implications of the new findings are discussed from the protein-taxonomical point of view, and the validity of the present method is assessed.

Amino Acids↗
PubMed1983

[Effects of extracorporeally induced systemic hyperthermia on cell-mediated immunity].

We have studied the effects of extracorporeally induced systemic hyperthermia on cell-mediated immunity in 12 patients. Also, the effect of heating and anti-cancer drugs on ADCC activity 3 Plaque forming method and 51Cr release method) and NK activity (51Cr release method. target: K-562 cells) of normal human lymphocytes was studied in vitro. The following results were obtained: Lymphocytes, T-cells and IgGFcR+ T-cells counts slightly decreased during the hyperthermotherapy in patients. During initiation of the hyperthermotherapy (Rectal temp. 41.6-41.8 degrees), ADCC activity, PHA, and Con-A induced lymphocyte blastogenesis were slightly depressed, while NK activity was slightly enhanced. At the end of the hyperthermia, ADCC activity, lymphocyte blastogenesis and NK activity were extremely depressed. In vitro, 1 hour of heating at more than 40 degrees C extremely depressed ADCC activity. By heating at 42 degrees C, ADCC activity was depressed depending on heating time, while NK activity was slightly enhanced for the first 10 minutes and then depressed depending on heating time. The administration of anti-cancer drugs (MMC, 5-FU, ADM) did not affect NK activity at all during the heating at 42 degrees C. From these results, it is highly suggested that immunopotentiators should be used during extracorporeally induced systemic hyperthermia in order to make up for the depressed cell-mediated immunity.

Adult↗
PubMed1982

Correspondence of homologies in amino acid sequence and tertiary structure of protein molecules.

According to the method developed previously (Kubota, Y., Takahashi, S., Nishikawa, K. and Ooi, T. (1981) J. Theor, Biol. 91, 347-361), homology among proteins may be estimated quantitatively. We extended the method to investigate the relationship of an amino acid sequence to its teritary structure and identify homologous segments which have homologous native conformations in proteins. First, we selected proper indices for the computation of correlation coefficients from 32 properties inherent to amino acids, such as hydrophobicity. The arithmetic average of correlation coefficients using six indices gave rise to a good correlation for the CD- and EF-hand regions (Ca2+ binding sites) in carp parvalbumin, but poor ones for other segments. We then applied the method to homologous proteins, the three-dimensional structures of which are known: horse hemoglobin alpha-chain and beta-chain; cytochrome c and c2; serine proteases, chymotrypsinogen and elastase; alpha-lytic protease and protease A from prokaryotic organisms. The results show that the sequence homology estimated by the present method has a good correspondence to the homology in three-dimensional structures and therefore the method is promising for the identification of important sites in sequences which have similar native conformations. For an example of the application of the method, two sequences of human interferon, one from fibroblast and the other from leukocyte, are compared, suggesting functional sites in the molecule.

Amino Acid Sequence↗
PubMed1982

Regeneration of RNase A from the reduced protein: models of regeneration pathways.

Two models of protein-folding pathways are proposed on the basis of equilibrium and kinetic data in the literature. One is a growth-type model--i.e., nucleation of the native-like structure occurs in the folding process, in the rate-limiting step(s), and subsequent folding around the nucleation sites proceeds smoothly to form the native disulfide bonds and conformation. The other is a rearrangement-type model--i.e., proper nucleation does not occur in the folding process; instead, non-native interactions play a significant role in the folding pathways and lead to metastable intermediate species. Such non-native interactions, including incorrect disulfide bonds and proline cis-trans isomerization, must be disrupted or rearranged to nucleate the native interactions [a process that is included in the rate-limiting step(s)] for the protein to fold. The rate-limiting steps in the pathways for regeneration of RNase A from the reduced protein are classified as growth- or rearrangement-type pathways. The growth-type pathway is the one accompanying the formation of an intramolecular disulfide bond in the rate-limiting step. The rearrangement-type pathway is the one accompanying the reshuffling or disruption of a disulfide bond in the rate-limiting step. The folding of other proteins, accompanying oxidation of the reduced form, and the folding of denatured proteins with intact disulfide bonds are discussed in terms of the growth- and rearrangement-type models.

Endoribonucleases↗