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S Kuhara

Publications and source records attributed to S Kuhara.

63 records · Page 4Linked to original sources
PubMed1984

GENAS: a database system for nucleic acid sequence analysis.

A database system, named GENAS (GENe Analyzing System), for computer analysis of sequence was constructed using Adbis which is a relational database management system (1). GENAS enables us to retrieve any sequence data from EMBL nucleotide sequence data library (2) and readily to analyze them (if necessary, together with private data) by various application programs in a interactive manner. Analysis of structure of replication origin of replicons was demonstrated using this system.

Base Sequence↗
PubMed1983

Complete nucleotide sequence of the 26S rRNA gene of Physarum polycephalum: its significance in gene evolution.

The complete nucleotide sequences of the 5.8S and 26S rRNA genes of Physarum polycephalum and the transcribed spacer between them were determined. Comparison of the sequences with those of the Escherichia coli 23S rRNA and yeast 26S rRNA genes showed that there are 16 highly homologous regions in the sequences of Physarum and E. coli and that eukaryotes have some eukaryote-specific extra sequences. The sequence immediately following the 5.8S-like region of E. coli 23S rRNA was found to be highly homologous to the 5' terminus of Physarum 26S rRNA, indicating that the eukaryote-specific 5.8S rRNA gene is derived from the 5'-terminal region of the prokaryote large rRNA gene.

Base Sequence↗
PubMed1982

Estimation of the free energy change of substrate binding lysozyme-catalyzed reactions.

The binding constant and binding free energy of each subsite of lysozyme upon substrate binding have been customarily estimated from the experimental data with assumptions regarding the binding mode of substrate and the additivity of binding free energy of each subsite. In the present study, the binding constants and binding free energy of subsites were estimated from experimentally obtained overall binding constants on native and Trp 62-modified lysozymes. The estimations of binding constants and binding free energy were carried out by an optimization method, the modified Powell method, without assuming the binding mode for substrate. First the binding free energies of subsites A, B, and C were estimated from the experimental binding constants of (GlcNAc)1 to (GlcNAc)3, and the binding free energies of subsites D, E, and F were determined from the estimated free energies of subsites A, B, and C, and the experimentally obtained reaction time-courses of substrate (GlcNAc)5. Finally, the values of three rate constants in the lysozyme-catalyzed reaction of chitooligosaccharide were estimated from the experimental time-course by using the binding free energies obtained by the modified Powell method.

Animals↗
PubMed1982

Human lysozyme-catalyzed reaction of chitooligosaccharides.

The time-courses of the human lysozyme-catalyzed reaction of chitopentaose were measured by high-performance gel-filtration in comparison with those of hen egg-white lysozyme. Human lysozyme has considerably larger rate constants for the cleavage of glycosidic linkages and transglycosylation than those of hen lysozyme, in agreement with the fact that human lysozyme exhibits a large lytic activity. It has been reported that binding subsite D in human lysozyme has negative free energy on substrate binding, whereas subsite D in hen lysozyme has unfavorable positive free energy due to the distortion of a sugar residue. The time-courses calculated under the assumption that subsite D in human lysozyme has negative free energy on substrate binding did not fit the experimentally obtained time-courses, even though the combination of values of rate constants in the enzymatic reaction widely varied in the calculation of the time-courses. Thus, it was concluded that subsite D in human lysozyme may not have negative binding free energy, but positive values similar to hen lysozyme.

Animals↗
PubMed1982

Enzymatic activity of Trp 62-modified lysozyme.

The time-courses of action of Trp 62-modified lysozymes on the initial substrate chitopentaose were measured by means of high-performance gel-filtration. The activities of the modified lysozymes, represented by the rate of disappearance of the initial substrate (overall rate) were lowered to various extents depending on the method of the modification. On the other hand, the time-courses were calculated by changing the values of rate constants, using the binding free energy of each subsite estimated by the optimization technique (Kuhara et al. (1982) J. Biochem.). For NBS- and NPS-lysozymes, the calculated time-courses were not in good agreement with the experimental ones, when the binding free energies estimated by the optimization technique were used for the calculation. Therefore, the binding free energies of the subsites were estimated from the experimental time-courses with the assumption that the values of the rate constants do not change upon modification of Trp 62 in subsite C. As a result, it was found that, though the modification was at subsite C, the binding free energy of subsite A was profoundly lowered, while that of subsite B remained almost unchanged.

Energy Metabolism↗
PubMed1981

Nucleotide sequence of the ribosomal RNA gene of Physarum polycephalum: intron 2 and its flanking regions of the 26S rRNA gene.

The 26S ribosomal RNA gene of Physarum polycephalum is interrupted by two introns, and we have previously determined the sequence of one of them (intron 1) (Nomiyama et al. Proc.Natl.Acad.Sci.USA 78, 1376-1380, 1981). In this study we sequenced the second intron (intron 2) of about 0.5 kb length and its flanking regions, and found that one nucleotide at each junction is identical in intron 1 and intron 2, though the junction regions share no other sequence homology. Comparison of the flanking exon sequences to E. coli 23S rRNA sequences shows that conserved sequences are interspersed with tracts having little homology. In particular, the region encompassing the intron 2 interruption site is highly conserved. The E. coli ribosomal protein L1 binding region is also conserved.

Animals↗
PubMedDate not supplied

L1 family of repetitive DNA sequences in primates may be derived from a sequence encoding a reverse transcriptase-related protein.

Primate and rodent genomes contain a family of highly repetitive, long interspersed sequences, designated the L1 family or LINE-1. Characteristic features of the L1 family sequences such as an A-rich stretch at the 3' end, a truncated 5' end, the existence of significantly long open reading frames (ORFs) and the presence of L1 family transcripts in various types of cells, including pluripotential embryonic cells, suggest that the L1 family is derived from a sequence encoding a protein(s) and dispersed in the genome through an RNA-mediated process. These features of the L1 family are believed to be due to reverse transcription beginning at the 3' end of the L1 transcript and terminating prematurely and to the site duplication caused by the insertion of the complementary DNA. It is likely that this type of transcript is converted to cDNA and inserted into the chromosome through a process similar to that of the formation of processed pseudogenes. The above model, however, does not necessarily explain why the L1 family should produce the extraordinarily large number of copies (more than 10(4) per haploid genome) seen during evolution. It seems likely that the progenitor of the L1 family itself carries (or carried) a function which promotes the active dispersion of the L1 family sequence. We reasoned that such a function, if present, must be conserved during evolution and may be shown by comparative analysis of L1 family sequences from evolutionarily distant species. We show here that the L1 family sequence contains an ORF possessing significant sequence homology to several RNA-dependent DNA polymerases of viral and transposable element origins.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗