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Yang, L.-W.*; Kitao, Akio*; Huang, B.-C.*; Go, Nobuhiro*
Biophysical Journal, 107(6), p.1415 - 1425, 2014/09
Times Cited Count：18 Percentile：53.93(Biophysics)Kai, Takeshi; Tokuhisa, Atsushi*; Moribayashi, Kengo; Fukuda, Yuji; Kono, Hidetoshi; Go, Nobuhiro*
Journal of the Physical Society of Japan, 83(9), p.094301_1 - 094301_5, 2014/09
Times Cited Count：1 Percentile：11.57(Physics, Multidisciplinary)no abstracts in English
Tokuhisa, Atsushi*; Arai, Junya*; Jochi, Yasumasa*; Ono, Yoshiyuki*; Kameyama, Toyohisa*; Yamamoto, Keiji*; Hatanaka, Masayuki*; Gerofi, B.*; Shimada, Akio*; Kurokawa, Motoyoshi*; et al.
Journal of Synchrotron Radiation, 20(6), p.899 - 904, 2013/11
Times Cited Count：5 Percentile：29.00(Instruments & Instrumentation)Tokuhisa, Atsushi*; Taka, Junichiro*; Kono, Hidetoshi; Go, Nobuhiro*
Acta Crystallographica Section A, 68(3), p.366 - 381, 2012/05
Times Cited Count：20 Percentile：81.63(Chemistry, Multidisciplinary)Higuchi, Mariko; Fujii, Jumpei*; Yonetani, Yoshiteru; Kitao, Akio*; Go, Nobuhiro*
Journal of Structural Biology, 173(1), p.20 - 28, 2011/01
Times Cited Count：2 Percentile：6.12(Biochemistry & Molecular Biology)MutT distinguishes substrate 8-oxo-dGTP from dGTP and also 8-oxo-dGMP from dGMP despite small differences of chemical structures between them. In this paper we show by the method of molecular dynamics simulation that the transition between conformational substates of MutT is a key mechanism for a high resolution molecular recognition of the differences between the very similar chemical compounds. The native state MutT has two conformational substates with similar free energies, each characterized by either open or close of two loops surrounding the substrate binding active site. Between the two substates, the open substate is more stable in free MutT and in dGMP-MutT complex, and the closed substate is more stable in 8-oxo-dGMP-MutT complex. A hydrogen bond between H7 atom of 8-oxo-dGMP and the sidechain of Asn119 plays a crucial role for maintaining the closed substate in 8-oxo-dGMP-MutT complex.
Go, Nobuhiro
Progress of Theoretical Physics Supplement, (170), p.198 - 213, 2008/01
Fujii, Satoshi*; Kono, Hidetoshi; Takenaka, Shigeori*; Go, Nobuhiro; Sarai, Akinori*
Nucleic Acids Research, 35(18), p.6063 - 6074, 2007/09
Times Cited Count：98 Percentile：86.42(Biochemistry & Molecular Biology)Proteins recognize specific DNA sequences not only through direct contact between amino acids and bases, but also indirectly based on the sequence-dependent conformation and deformability of the DNA (indirect readout). We used molecular dynamics simulations to analyze the sequence-dependent DNA conformations of all 136 possible tetrameric sequences sandwiched between CGCG sequences. The deformability of dimeric steps obtained by the simulations is consistent with that by the crystal structures. The simulation results further showed that the conformation and deformability of the tetramers can highly depend on the flanking base-pairs. The conformations of xATx tetramers show the most rigidity and are not affected by the flanking base-pairs and the xYRx show by contrast the greatest flexibility and change their conformations depending on the base-pairs at both ends, suggesting tetramers with the same central dimer can show different deformabilities. These results suggest that analysis of dimeric steps alone may overlook some conformational features of DNA and provide insight into the mechanism of indirect readout during protein-DNA recognition. Moreover, the sequence dependence of DNA conformation and deformability may be used to estimate the contribution of indirect readout to the specificity of protein-DNA recognition as well as nucleosome positioning and large-scale behavior of nucleic acids.
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：27.79(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.
Ishida, Hisashi; Higuchi, Mariko; Yonetani, Yoshiteru*; Kano, Takuma; Jochi, Yasumasa*; Kitao, Akio*; Go, Nobuhiro
Annual Report of the Earth Simulator Center April 2005 - March 2006, p.237 - 240, 2007/01
no abstracts in English
Yonetani, Yoshiteru*; Kono, Hidetoshi; Fujii, Satoshi*; Sarai, Akinori*; Go, Nobuhiro
Molecular Simulation, 33(1-2), p.103 - 107, 2007/01
Times Cited Count：5 Percentile：16.55(Chemistry, Physical)DNA tetramer sequences AATT and TTAA are known to be conformationally more rigid and flexible, respectively. In this study, we carry out molecular dynamics simulations of these two sequences, and investigate the characteristic hydration pattern. The rigid AATT is found to be more likely to construct the hydration spine in the minor groove than the flexible TTAA. The result suggests that the hydration water molecules play a critical role for determining the sequence dependent deformability of DNA conformation.
Kim, O. T. P.*; Yura, Kei; Go, Nobuhiro
Nucleic Acids Research, 34(22), p.6450 - 6460, 2006/12
Times Cited Count：97 Percentile：85.16(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.
Nakagawa, Hiroshi; Kataoka, Mikio*; Jochi, Yasumasa*; Kitao, Akio*; Shibata, Kaoru; Tokuhisa, Atsushi*; Tsukushi, Itaru*; Go, Nobuhiro
Physica B; Condensed Matter, 385-386(2), p.871 - 873, 2006/11
Times Cited Count：13 Percentile：51.94(Physics, Condensed Matter)The boson peak of a protein was examined in relation to hydration using staphylococcal nuclease. Although the boson peak is commonly observed in synthetic polymers, glassy materials and amorphous materials, the origin of the boson peak is not fully understood. The motions that contribute to the peak are harmonic vibrations. Upon hydration the peak frequency shifts to a higher frequency and the effective force constant of the vibration increases at low temperatures, suggesting that the protein energy surface is modified. Hydration of the protein leads to a more rugged surface and the vibrational motions are trapped within the local minimum at cryogenic temperatures. The origin of the protein boson peak may be related to this rugged energy surface.
Kitao, Akio*; Yonekura, Koji*; Yonekura, Saori*; Samatey, F.*; Imada, Katsumi*; Namba, Keiichi*; Go, Nobuhiro
Proceedings of the National Academy of Sciences of the United States of America, 103(13), p.4894 - 4899, 2006/03
Times Cited Count：45 Percentile：63.15(Multidisciplinary Sciences)no abstracts in English
Ishida, Hisashi; Higuchi, Mariko; Yonetani, Yoshiteru*; Kano, Takuma; Jochi, Yasumasa*; Kitao, Akio*; Go, Nobuhiro
Annual Report of the Earth Simulator Center April 2004 - March 2005, p.241 - 246, 2005/12
no abstracts in English
Go, Nobuhiro; Yonetani, Yoshiteru*
Seitai No Kagaku, 56(6), p.626 - 631, 2005/12
no abstracts in English
Nakamura, Kensuke; Go, Nobuhiro
Cellular and Molecular Life Sciences, 62(18), p.2050 - 2066, 2005/09
Times Cited Count：214 Percentile：86.69(Biochemistry & Molecular Biology)Multicopper blue proteins (MCBPs) are multi-domain proteins that utilize the distinctive redox ability of copper ions. There are variety of MCBPs that have been roughly classified into three different groups, (1)nitrite reductase-type with two domains, (2)laccase-type with three domains, and (3)ceruloplasmin-type with six domains. Together, the second and third group are often commonly called multicopper oxidases (MCOs). The rapid accumulation of genome sequence information in recent years has revealed several new types of proteins containing MCBP domains, mainly from bacteria. In this review, the recent research on the functions and structures of MCBPs is summarized, mainly focusing on the new types. The latter half of this review focusses on the two-domain MCBPs, which we propose as the evolutionary intermediate of the MCBP family.
Jochi, Yasumasa*; Kitao, Akio*; Go, Nobuhiro
Journal of the American Chemical Society, 127(24), p.8705 - 8709, 2005/06
Times Cited Count：27 Percentile：61.11(Chemistry, Multidisciplinary)no abstracts in English
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.
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
Basu, G.*; Sivanesan, D.*; Kawabata, Takeshi*; Go, Nobuhiro
Journal of Molecular Biology, 342(3), p.1053 - 1066, 2004/09
Times Cited Count：23 Percentile：35.43(Biochemistry & Molecular Biology)no abstracts in English
