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Journal Articles

Key interactions in integrin ectodomain responsible for global conformational change detected by elastic network normal-mode analysis

Matsumoto, Atsushi; Kamata, Tetsuji*; Takagi, Junichi*; Iwasaki, Kenji*; Yura, Kei

Biophysical Journal, 95(6), p.2895 - 2908, 2008/09

 Times Cited Count:18 Percentile:42.73(Biophysics)

Protein is activated, but the activation mechanism and generality of the conformational change remain to be elucidated. We performed normal mode analysis of the elastic network model on integrin $$alpha$$$$_{V}$$$$beta$$$$_{3}$$ ectodomain in the bent form and identified key residues which were influential on molecular motions. Iterative normal mode calculations demonstrated that the specific non-bonded interactions involving the key residues work as a snap to keep integrin in the bent form. The importance of the key residues for the conformational change was further verified by mutation experiments. Conservation pattern of amino acid residues among integrin family showed that the characteristic pattern of residues seen around these key residues is found in the limited groups of integrin $$beta$$ chains.

Journal Articles

Discrimination of class I cyclobutane pyrimidine dimer photolyase from blue light photoreceptors by single methionine residue

Miyazawa, Yuji*; Nishioka, Hirotaka*; Yura, Kei; Yamato, Takahisa*

Biophysical Journal, 94(6), p.2194 - 2203, 2008/03

 Times Cited Count:22 Percentile:50.28(Biophysics)

DNA photolyase recognizes ultraviolet-damaged DNA and breaks improperly formed covalent bonds within the cyclobutane pyrimidine dimer. Theoretical analysis of the electron-tunneling pathways of the DNA photolyase derived from Anacystis nidulans can reveal the active role of the protein environment in the electron transfer reaction. Here, we report the unexpectedly important role of the single methionine residue, Met-353, where busy trafficking of electron-tunneling currents is observed. The amino acid conservation pattern of Met-353 in the homologous sequences perfectly correlates with experimentally verified annotation as photolyases. The bioinformatics sequence analysis also suggests that the residue plays a pivotal role in biological function. Consistent findings from different disciplines of computational biology strongly suggest the pivotal role of Met-353 in the biological function of DNA photolyase.

Journal Articles

coliSNP database server mapping nsSNPs on protein structures

Kono, Hidetoshi; Yuasa, Tomo*; Nishiue, Shinya*; Yura, Kei

Nucleic Acids Research, 36(Database), p.D409 - D413, 2008/01

 Times Cited Count:18 Percentile:34.94(Biochemistry & Molecular Biology)

We have developed coliSNP, a database server (http://yayoi.kansai.jaea.go.jp/colisnp) that maps non-synonymous single nucleotide polymorphisms (nsSNPs) on the three-dimensional (3D) structure of proteins. Once a week, the SNP data from the dbSNP database and the protein structure data from the Protein Data Bank (PDB) are downloaded, and the correspondence of the two data sets is automatically tabulated in the coliSNP database. Given an amino acid sequence, protein name or PDB ID, the server will immediately provide known nsSNP information, including the amino acid mutation caused by the nsSNP, the solvent accessibility, the secondary structure and the flanking residues of the mutated residue in a single page. The position of the nsSNP within the amino acid sequence and on the 3D structure of the protein can also be observed. The database provides key information with which to judge whether an observed nsSNP critically affects protein function and/or stability. As far as we know, this is the only web-based nsSNP database that automatically compiles SNP and protein information in a concise manner.

Journal Articles

The H-Invitational Database (H-InvDB); A Comprehensive annotation resource for human genes and transcripts

Yamasaki, Chisato*; Murakami, Katsuhiko*; Fujii, Yasuyuki*; Sato, Yoshiharu*; Harada, Erimi*; Takeda, Junichi*; Taniya, Takayuki*; Sakate, Ryuichi*; Kikugawa, Shingo*; Shimada, Makoto*; et al.

Nucleic Acids Research, 36(Database), p.D793 - D799, 2008/01

 Times Cited Count:51 Percentile:71.37(Biochemistry & Molecular Biology)

Here we report the new features and improvements in our latest release of the H-Invitational Database, a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of fulllength cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 protein-coding and 642 non-protein-coding loci; 858 transcribed loci overlapped with predicted pseudogenes.

Journal Articles

Analysis of the function of a large-scale supra-biomolecule system by molecular dynamics simulation system, SCUBA (Simulation Codes for hUge Biomolecular Assembly)

Ishida, Hisashi; Yura, Kei; Kano, Takuma; Matsumoto, Atsushi

Annual Report of the Earth Simulator Center April 2006 - March 2007, p.257 - 263, 2007/09

The Earth Simulator has the highest power ever achieved to perform molecular dynamics simulation of large-scale supra-molecular systems. We are developing a molecular dynamics simulation system, called SCUBA, which is designed to run a system composed of more than a million particles efficiently on parallel computers. This fisical year, the arrays used in the program of SCUBA were intensively optimized to reduce the amount of memory use. This optimization enabled SCUBA to perform molecular dynamics simulations of large-scale supra-molecular systems comprised of more than a million atoms on the Earth Simulator. Moreover, the Martyna-Klein-Tuckerman algorithm was extended to utilize the multiple time step method, which increases the time step length significantly. Then, in order to elucidate the dynamics of the 70S ribosome, molecular dynamics simulation of the 70S ribosome including its explicit solvent, a system which is composed of about two million atoms, has been performed using SCUBA. A model of a nascent polypeptide was included in the system to investigate how the nascent polypeptide passes through the exit tunnel within the large subunit of the 70S ribosome. The ratchet-like motion of the 70S ribosome, which is thought to be important for the genetic translation, was successfully observed.

Journal Articles

BAAQ; An Infrastructure for application integration and knowledge discovery in bioinformatics

Gong, X.*; Nakamura, Kensuke; Yura, Kei; Go, Nobuhiro

IEEE Transactions on Information Technology in Biomedicine, 11(4), p.428 - 434, 2007/07

 Times Cited Count:3 Percentile:27.87(Computer Science, Information Systems)

The emerging grid computing technologies enable bioinformatics scientists to conduct their researches in a virtual laboratory. However, the development of grid applications is still a nightmare for general bioinformatics scientists, due to the lack of grid programming environments. Here, we present a system, which we named Bioinformatics: Ask Any Questions (BAAQ), to automate this development procedure as much as possible. BAAQ allows scientists to store and manage remote biological data and programs, to build analysis workflows that integrate these resources seamlessly, and to discover knowledge from available resources. This paper addresses two issues in building grid applications in bioinformatics: how to smoothly compose an analysis workflow using heterogeneous resources and how to efficiently discover and re-use available resources in the grid community. Correspondingly an intelligent grid programming environment and an active solution recommendation service are proposed.

Journal Articles

Contribution of computational biology and structural genomics to understand genome and transcriptome

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

Frontiers of Computational Science, p.75 - 80, 2007/00

Genome sequencing and structural genomics projects are both proceeded to gain a new perspective of life, that is global views on mechanisms of life with comprehensive and unbiased fashion. We now have genome sequences of human and other species, and are going to have a three-dimensional structure of whole proteins. Those massive pieces of information can only be deciphered with collaboration of computational biology. In this paper, we will discuss the amount of data we have at the moment and one of the new views on mechanisms of cellular function regulation obtained based on the computational analyses of those data.

Journal Articles

Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction

Kim, O. T. P.*; Yura, Kei; Go, Nobuhiro

Nucleic Acids Research, 34(22), p.6450 - 6460, 2006/12

 Times Cited Count:96 Percentile:85.09(Biochemistry & Molecular Biology)

Protein-RNA interactions play essential roles in a number of regulatory mechanisms for gene expression such as RNA splicing, transport, translation and post-transcriptional control. As the number of available protein-RNA complex three-dimensional (3D) structures has increased, it is now possible to statistically examine protein-RNA interactions based on 3D structures. We performed computational analyses of 86 representative protein-RNA complexes retrieved from the Protein Data Bank. Interface residue propensity was calculated for each amino acid residue type (residue singlet interface propensity). In addition to the residue singlet propensity, we introduce a new residue doublet interface propensity. The residue doublet interface propensity contains much more information than the sum of two singlet propensities alone. The prediction of the RNA interface using the two types of propensities plus a position-specific multiple sequence profile can achieve a specificity of about 80 percent.

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:55 Percentile:72.39(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.

Journal Articles

Conformational analysis of the structure of ribosome fit into electron microscopy density maps with normal mode analyses and molecular dynamics simulations

Ishida, Hisashi; Matsumoto, Atsushi; Tsutsumi, Yu*; Yura, Kei

Proceedings of 16th International Microscopy Congress (IMC 2006), P. 242, 2006/09

Supra-biomolecules, which contain numerous proteins and nucleic acids, function when the constituent molecules are assembled. Therefore, it is important to determine not only the 3D structures of the constituent molecules but also the 3D structure of the supra-biomolecule. Although X-ray crystallography can determine the atomic coordinates of biomolecules, it has difficulty in handling supra-biomolecules, because crystals of huge molecules cannot be made with ease. Single particle analysis using an electron microscope (EM) has been used to observe the structure of supra-biomolecules, but the resolution of the EM image has only achieve to the atomic level in a limited situation. Therefore, several attempts have been carried out to determine the 3D structure of supra-biomolecules in atomic resolution by fitting the constituent molecules, determined by X-ray crystallography, into an EM density map. In those attempts, each constituent molecule is usually fit into the EM density map manually, and the constituent molecules may have atomic collisions at their interfaces.

Journal Articles

Biomolecule, Protein, Conformation change in protein structure, RNA, DNA, Contact map, DALI, Combinatorial extension

Yura, Kei

Baio Infomateikusu Jiten, p.251 - 257, 2006/07

no abstracts in English

Journal Articles

Coverage of whole proteome by structural genomics observed through protein homology modeling database

Yura, Kei; Yamaguchi, Akihiro*; Go, Michiko*

Journal of Structural and Functional Genomics, 7(2), p.65 - 76, 2006/06

We have been developing FAMSBASE, a protein homology-modeling database of whole ORFs predicted from genome sequences. The latest update of FAMSBASE (http://daisy.nagahama-i-bio.ac.jp/Famsbase/), which is based on the protein three-dimensional (3D) structures released by November 2003, contains modeled 3D structures for 368,724 open reading frames (ORFs) derived from genomes of 276 species. Those 276 genomes are predicted to have 734,193 ORFs in total and the current FAMSBASE contains protein 3D structure of approximately 50% of the ORF products. Assuming that this rate would be maintained, whole soluble protein model structures of prokaryotes without the putative disordered regions will be in hand within 15 years. For eukaryotic proteins, they will be in hand within 25 years.

Journal Articles

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs

Takeda, Junichi*; Suzuki, Yutaka*; Nakao, Mitsuteru*; Barrero, R. A.*; Koyanagi, Kanako*; Jin, L.*; Motono, Chie*; Hata, Hiroko*; Isogai, Takao*; Nagai, Keiichi*; et al.

Nucleic Acids Research, 34(14), p.3917 - 3928, 2006/00

 Times Cited Count:34 Percentile:54.48(Biochemistry & Molecular Biology)

We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and computational analyses for 56 419 completely sequenced and precisely annotated full-length cDNAs selected for the H-Invitational human transcriptome annotation meetings, we identified 6877 alternative splicing genes with 18 297 different alternative splicing variants. A total of 37 670 exons were involved in these alternative splicing events. The encoded protein sequences were affected in 6005 of the 6877 genes. Notably, alternative splicing affected protein motifs in 3015 genes, subcellular localizations in 2982 genes and transmembrane domains in 1348 genes. Genome-wide annotations of alternative splicing, relying on full-length cDNAs, should lay firm groundwork for exploring in detail the diversification of protein function which is mediated by the alternative splicing variants.

Journal Articles

Sequence analysis of the gliding protein Gli349 in ${it Mycoplasma mobile}$

Metsugi. Shoichi; Uenoyama, Atsuko*; Kubo, Jun*; Miyata, Makoto*; Yura, Kei; Kono, Hidetoshi; Go, Nobuhiro

Biophysics, 1, p.33 - 43, 2005/05

The motile mechanism of Mycoplasma mobile remains unknown but is believed to differ from any previously identified mechanism in bacteria. Gli349 of M. mobile is known to be responsible for both adhesion to glass surfaces and mobility. We therefore carried out sequence analyses of Gli349 and its homolog MYPU2110 from M. pulmonis to decipher their structures. We found that the motif "YxxxxxGF" appears 11 times in Gli349 and 16 times in MYPU2110. Further analysis of the sequences revealed that Gli349 contains 18 repeats of about 100 amino acid residues each, and MYPU2110 contains 22. No sequence homologous to any of the repeats was found in the NCBI RefSeq non-redundant sequence database, and no compatible fold structure was found among known protein structures, suggesting that the repeat found in Gli349 and MYPU2110 is novel and takes a new fold structure. Proteolysis of Gli349 using chymotrypsin revealed that cleavage positions were often located between the repeats, implying that regions connecting repeats are unstructured, flexible and exposed to the solvent.

Journal Articles

Sequence analysis of the gliding protein Gli349 in ${it Mycoplasma mobile}$

Metsugi, Shoichi*; Uenoyama, Atsuko*; Adan, J.*; Miyata, Makoto*; Yura, Kei; Kono, Hidetoshi; Go, Nobuhiro

Biophysics, 1, p.33 - 43, 2005/00

no abstracts in English

Journal Articles

Enlarged FAMSBAS; Protein 3D structure models of genome sequences for 41 species

Yamaguchi, Akihiro*; Iwadate, Mitsuo*; Suzuki, Eiichiro*; Yura, Kei; Kawakita, Shigetsune*; Umeyama, Hideaki*; Go, Michiko*

Nucleic Acids Research, 31(1), p.463 - 468, 2003/01

 Times Cited Count:15 Percentile:25.27(Biochemistry & Molecular Biology)

Enlarged FAMSBASE is a relational database of comparative protein structure models for the whole genome of 41 species, presented in the GTOP database. The models are calculated by FAMS, Full Automatic Modeling System. Enlarged FAMSBASE provides a wide range of query keys, such as name of ORF (open reading frame), ORF keywords, PDB ID, PDB heterogen atoms, and sequence similarity. Heterogen atoms in PDB include cofactors, ligands, and other factors that interact with proteins, and are a good starting point for analyzing interactions between proteins and other molecules. The data may also work as a template for drug design. The present number of ORFs with protein 3D models in FAMSBASE is 183,805, and the database includes an average of three models for each ORF. FAMSBASE is available at http://famsbase.bio.nagoya-u.ac.jp/famsbase/.

Journal Articles

Protein function prediction based on genome sequence

Yura, Kei

Puroteomikusu No Saishin Gijutsu, p.93 - 101, 2002/11

Determination of genome sequences has massive impacts on biology. Genome sequence is a blueprint of the species, and analyses of genome sequence may uncover every components of the species. However, when a whole genome of Haemophilus influenzae was sequenced, biologists realized that one was not able to deduce biological information out of the sequence. The genome sequence is full of information that knowledge based on conventional genetics and molecular biology can retrieve. Bioinformatics is the field that find niche in this area. In this chapter, we will overview the current status and the future of bioinformatics.

Journal Articles

3D-keynote; Genome function prediction based on protein module

Yura, Kei; Go, Michiko*

Tampakushitsu Kakusan Koso, 47(8), p.1090 - 1096, 2002/06

no abstracts in English

Oral presentation

Structure-based bioinformatics analyses of protein-RNA interface toward developing a computational method to predict protein-RNA interface

Kim, T. P. O.; Yura, Kei; Go, Nobuhiro

no journal, , 

Protein-RNA interactions play essential roles in a number of regulatory mechanisms of gene expression such as RNA splicing, transport and translation. Computational analyses of protein-DNA interface have been carried out a lot, while those of protein-RNA interface are rare. As the number of available protein-RNA complexes have increased, it is now possible to examine protein-RNA interactions based on 3D structures. We carried out computational analyses of protein-RNA complexes retrieved from PDB. The interface residue propensity was used as a parameter to predict protein-RNA interface. The accuracy of the prediction method was tested by jackknife method, which attained 60% on average. The prediction method was applied to RNA-binding proteins with known 3D structures (mRNA export factors TAP and Mex67).

Oral presentation

Supramolecular database for deducing high resolution structure

Yura, Kei

no journal, , 

no abstracts in English

50 (Records 1-20 displayed on this page)