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Journal Articles

Alternative splicing in human transcriptome; Functional and structural influence on proteins

Yura, Kei; Shionyu, Masafumi*; Hagino, Kei*; Hijikata, Atsushi*; Hirashima, Yoshinori*; Nakahara, Taku*; Eguchi, Tatsuya*; Shinoda, Kazuki*; Yamaguchi, Akihiro*; Takahashi, Kenichi*; et al.

Gene, 380(2), p.63 - 71, 2006/10

 Times Cited Count:49 Percentile:27.16(Genetics & Heredity)

Alternative splicing is a molecular mechanism that produces multiple proteins from a single gene, and is thought to produce variety in proteins translated from a limited number of genes. Here we analyzed how alternative splicing produced variety in protein structure and function, by using human full-length cDNAs, on the assumption that all of the alternatively spliced mRNAs were translated to proteins. We found that the length of alternatively spliced amino acid sequences, in most cases, fell into a size shorter than that of average protein domain. We evaluated comprehensively the presumptive three-dimensional structures of the alternatively spliced products to assess the impact of alternative splicing on gene function. We found that more than half of the products encoded proteins which were involved in signal transduction, transcription and translation, and more than half of alternatively spliced regions comprised interaction sites between proteins and their binding partners, including substrates, DNA/RNA, and other proteins. Intriguingly, 67% of the alternatively spliced isoforms showed significant alterations to regions of the protein structural core, which likely resulted in large conformational change. Based on those findings, we speculate that there are a large number of cases that alternative splicing modulates protein networks through significant alteration in protein conformation.

Oral presentation

Relationship between genome and protein structures in eukaryotes

Yura, Kei; Shionyu, Masafumi*; Go, Michiko*

no journal, , 

Open reading frames in eukaryotic genome is composed of introns and exons, and selection of appropirate exons is the mechanism of alternative splicing. In this lecture, we will discuss the correlation of intron/exon structures with protein three-dimensional structures and effect of alternative splicing in protein structures.

Oral presentation

X-ray structure analysis of the single-chain derivatives of HIV-1 protease in complex with inhibitor

Adachi, Motoyasu; Hatanaka, Takaaki*; Ito, Yuji*; Hidaka, Koshi*; Tsuda, Yuko*; Kiso, Yoshiaki*; Kuroki, Ryota

no journal, , 

HIV protease is known as a drug target protein. It is important to clear relationship between structural data and kinetic and physicochemical parameters for drug design. We prepared single-chained enzyme linked by two amino acids and cross-liked enzyme bridged by disulfide bond. The two single-chained enzymes were expressed as inclusion body and refolded by dilution method. The purified enzyme complexed with inhibitor KNI-272 was crystallized, and solved the crystal structures. The designed sc- and cl-HIV-PR will be useful for evaluate the affinity of newly designed inhibitors from kinetic and thermodynamic point of view. Finally, we also report the results of analysis in affinity of inhibitors by surface plasmon resonance.

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