Affiliation: RIKEN Brain Science Institute
- Topological analysis of MAPK cascade for kinetic ErbB signalingTakashi Nakakuki
Cellular Systems Biology Team, Computational and Experimental Systems Biology Group, RIKEN Genomic Sciences Center, Tsurumi ku, Yokohama, Kanagawa, Japan
PLoS ONE 3:e1782. 2008..Such characteristics of the signaling cause the preferential binding of the Grb2-SOS complex to heterodimer-mediated signaling molecules...
- Function approximation approach to the inference of reduced NGnet models of genetic networksShuhei Kimura
Faculty of Engineering, Tottori University, 4 101 Koyama Minami, Tottori, Japan
BMC Bioinformatics 9:23. 2008..On the basis of this problem definition, we propose in this study a new method to infer reduced NGnet models of genetic networks...
- System properties of ErbB receptor signaling for the understanding of cancer progressionMariko Hatakeyama
Cellular Systems Biology Team, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
Mol Biosyst 3:111-6. 2007..Spatio-temporal analyses of the cellular process can explain the biochemical role of the receptor tyrosine kinases in cancer development from a system point of view...
- Transformation potency of ErbB heterodimer signaling is determined by B-Raf kinaseM Hatakeyama
Bioinformatics Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
Oncogene 23:5023-31. 2004..The present study suggests that B-Raf kinase, which was specifically activated in the cells coexpressing ErbB1 and ErbB4 receptors, elevates total ERK activity within the cell and, therefore, can induce cellular transformation...
- Novel mechanism of interaction of p85 subunit of phosphatidylinositol 3-kinase and ErbB3 receptor-derived phosphotyrosyl peptidesAtsushi Suenaga
Bioinformatics Group and Protein Research Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
J Biol Chem 280:1321-6. 2005..91. The total electrostatic solvation energy between the N-SH2 domain and P-peptide was the dominant factor for its binding affinity...
- Mutation of epidermal growth factor receptor is associated with MIG6 expressionTakeshi Nagashima
Cellular Systems Modeling Team, Computational Systems Biology Research Group, Advanced Computational Sciences Department, RIKEN Advanced Science Institute, Yokohama, Kanagawa, Japan
FEBS J 276:5239-51. 2009..Taking all the above together, an EGFR mutation can cause transcriptional changes to accommodate the activation potency of the original signaling pathway at the cellular level...
- Molecular dynamics simulations reveal that Tyr-317 phosphorylation reduces Shc binding affinity for phosphotyrosyl residues of epidermal growth factor receptorAtsushi Suenaga
Computational and Experimental System Biology Group, RIKEN Genomic Sciences Center, Yokohama, Kanagawa 230 0046, Japan
Biophys J 96:2278-88. 2009..e., tyrosine phosphorylation of Shc within its linker region regulates the binding affinity of SH2 and PTB domains for phosphorylated Shc partners, with important implications for signaling dynamics...
- Quantitative transcriptional control of ErbB receptor signaling undergoes graded to biphasic response for cell differentiationTakeshi Nagashima
Cellular Systems Biology Team, Computational and Experimental Systems Biology Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Yokohama, Kanagawa 230 0045, Japan
J Biol Chem 282:4045-56. 2007....
- Expression of the ErbB4 receptor causes reversal regulation of PP2A in the Shc signal transduction pathway in human cancer cellsNoriko Yumoto
Cellular Systems Biology Team, Computational and Experimental Systems Biology Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa, 230 0045, Japan
Mol Cell Biochem 285:165-71. 2006..Thus, PP2A regulates the ERK activity in a cell-specific manner, and it is speculated that distinct regulation of PP2A in the ErbB4 receptor signalling pathway may cause a difference in progression of cancer phenotypes...
- Tyr-317 phosphorylation increases Shc structural rigidity and reduces coupling of domain motions remote from the phosphorylation site as revealed by molecular dynamics simulationsAtsushi Suenaga
Bioinformatics Group, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
J Biol Chem 279:4657-62. 2004....
- A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signallingMariko Hatakeyama
RIKEN Genomic Sciences Center, 1 7 22 Suehirocho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
Biochem J 373:451-63. 2003....
- Phosphoproteome and transcriptome analyses of ErbB ligand-stimulated MCF-7 cellsTakeshi Nagashima
Computational and Experimental Systems Biology Group, RIKEN Genomic Sciences Center, Yokohama, Kanagawa 230 0045, Japan
Cancer Genomics Proteomics 5:161-8. 2008..05). The proteome datasets of EGF and HRG contain molecules that are related to Axon guidance, ErbB signaling and VEGF signaling at a high rate...
- Integrative genome-wide expression analysis bears evidence of estrogen receptor-independent transcription in heregulin-stimulated MCF-7 cellsTakeshi Nagashima
Computational and Experimental Systems Biology Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan
PLoS ONE 3:e1803. 2008..6%) and 13 E2-regulated (30.8%) gene groups. These results indicated that while E2 and HRG may induce common TFs, the regulatory mechanisms that govern HRG- and E2-induced gene expression differ...
- Molecular dynamics, free energy, and SPR analyses of the interactions between the SH2 domain of Grb2 and ErbB phosphotyrosyl peptidesAtsushi Suenaga
Bioinformatics Group, RIKEN Genomic Sciences Center, Yokohama, Kanagawa, Japan
Biochemistry 42:5195-200. 2003....
- OBIYagns: a grid-based biochemical simulator with a parameter estimatorShuhei Kimura
Bioinformatics Group, RIKEN Genomic Sciences Center, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
Bioinformatics 20:1646-8. 2004..AVAILABILITY: OBIYagns example models, methods and user guide are available at https://access.obigrid.org/yagns/ SUPPLEMENTARY INFORMATION: Please refer to Bioinformatics online...
- Inference of S-system models of genetic networks using a cooperative coevolutionary algorithmShuhei Kimura
Bioinformatics Group, RIKEN Genomic Sciences Center 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
Bioinformatics 21:1154-63. 2005..To verify the effectiveness of the proposed method, we apply it to two artificial genetic network inference problems. Finally, the proposed method is used to analyze the actual DNA microarray data...
- Ligand-dependent responses of the ErbB signaling network: experimental and modeling analysesMarc R Birtwistle
Department of Chemical Engineering, University of Delaware, Newark, DE, USA
Mol Syst Biol 3:144. 2007..Sensitivity analysis leads to the hypothesis that ERK activation is robust to parameter perturbation at high ligand doses, while Akt activation is not...
- Comparison of the characteristic of estrogenic action patterns of beta-HCH and heregulin beta1 in MCF-7 human breast cancer cellsMariko Hatakeyama
Department of Environmental Toxicology and the Center for Environmental Health Sciences, University of California, Davis, CA 95616, USA
J Biochem Mol Toxicol 16:209-19. 2002..These differences may account for their differential sensitivities to 4-hydroxytamoxifen...
- Compensation effect of the MAPK cascade on formation of phospho-protein gradientsTakashi Naka
Faculty of Information Science, Kyushu Sangyo University, Matsukadai 2 3 1, Higashi ku, Fukuoka 813 8503, Japan
Biosystems 83:167-77. 2006....
- The International Consortium on Systems Biology of Receptor Tyrosine Kinase Regulatory NetworksYoshiyuki Sakaki
Syst Biol (Stevenage) 152:53-4. 2005