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Research paper : A systematic analysis of protein interaction networks leading to the drug discovery (S. Iemura et al.)−119 Synthesiology - English edition Vol.1 No.2 (2008) greatest bottleneck of protein experiment was, needless to say, the preparation of samples. Therefore, we decided to challenge the big projects that required 50~100 people in Europe and US with just a few people and limited time by improving throughput of analysis through “attainment of ultra high sensitivity.” In fact, we achieved high sensitivity “that surpassed our expectation” by creating new elemental technology called gradient method, but it was not useful in practice. That was because the S/N ratio worsened due to noise from the environment. We painfully realized that improvement of S/N ratio is necessary to implement ‘real’ high-sensitive analysis by MS, or battle against noise, and we also understood the reason why development of micro liquid chromatography was not undertaken elsewhere in the world.The developed prototype lacked durability, was damaged easily by dust particles, and required much time for maintenance. One success was the beginning of the next suffering. However, we have been using them, rather than improving ease of maintenance of the LC system. This was only possible since we designed the entire device all the way to its screw. Although our device and system was full of defects, we believed it was more important to “use it and get data,” and set that as priority. The subject of analysis was initially narrowed down to known molecules that were very well characterized, in spite of analyzing unknown molecules. We had two reasons to this. First, if the analysis system we developed had truly high sensitivity and high throughput, there must be a new discovery even in an area that was already thoroughly characterized. Second, if there was a new discovery, we could validate and publish the data, because there is plenty of information and knowledge for well known molecules. These were our aims.7 ConclusionTo claim a new system to be “high sensitive” or “high throughput,” the system has to generate large-scale and highly accurate data. And the only way to demonstrate this is by publishing such data in as many high quality journals as possible. We thought there was no other way of objectively demonstrating the superiority of our newly developed system. This was particularly true because our strategies were steady improvements and gradual accumulation of know-how. We were unable to demonstrate our results as intellectual property by publishing papers that claimed novelty or innovativeness of methodology. In fact, the only thing we can call innovation in our development was a single-pump gradient method, and all other technologies were adaptation of existing elemental technology of other fields (semiconductors and industrial robots). We simply utilized them and thoroughly optimized the classic biochemical experiment method. Fortunately, these strategies and tactics turned out successful, and we realized the “flow” of microquantity of 100 nanoliters or less per minute. We hope this flow initiate new mainstream of drug discovery.AcknowledgementsWe received support of the Japan Science and Technology Corporation for the development of new gradient method, and support of NEDO for protein network analysis. We express our deepest gratitude.Note(47)−Term 1.Famous episode in which massively parallel computer with 8,000 CPU beat a chess master.References[1][2] [3][4][5][6][7][8][9][10][11]T. Natsume, Y. Yamauchi, H. Nakayama, T. Shinkawa, M. Yanagida, N. Takahashi and T. Isobe: A direct nanoflow liquid chromatography-tandem mass spectrometry system for interaction proteomics, Anal Chem, 74(18), 4725-4733 (2002).M. Komatsu, T. Chiba, K. Tatsumi, S. Iemura, I. Tanida, N. Okazaki, T. Ueno, E. Kominami, T. Natsume and K. Tanaka: A novel protein-conjugating system for Ufm1, a ubiquitin-fold modifier, Embo J., 23(9), 1977-1986 (2004).T. Higo, M. Hattori, T. Nakamura, T. Natsume, T. Michikawa and K. Mikoshiba: Subtype-specific and ER lumenal environment-dependent regulation of inositol 1,4,5-trisphosphate receptor type 1 by ERp44, Cell, 120(1), 85-98 (2005).Y. Hirano, K.B. Hendil, H. Yashiroda, S. Iemura, R. Nagane, Y. Hioki, T. Natsume, K. Tanaka and S. Murata: A heterodimeric complex that promotes the assembly of mammalian 20S proteasomes, Nature, 437(7063), 1381-1385 (2005).N. Matsuda, K. Azuma, M. Saijo, S. Iemura, Y. Hioki, T. Natsume, T. Chiba, K. Tanaka and K. Tanaka: DDB2, the xeroderma pigmentosum group E gene product, is directly ubiquitylated by Cullin 4A-based ubiquitin ligase complex, DNA Repair (Amst), 4(5), 537-545 (2005).T. Moriguchi, S. Urushiyama, N. Hisamoto, S. Iemura, S. Uchida, T. Natsume, K. Matsumoto and H. Shibuya: WNK1 regulates phosphorylation of cation-chloride- coupled cotransporters via the STE20-related kinases, SPAK and OSR1, J. Biol. Chem., 280(52), 42685-42693 (2005). K. Yoshida, T. Yamaguchi, T. Natsume, D. Kufe and Y. Miki: JNK phosphorylation of 14-3-3 proteins regulates nuclear targeting of c-Abl in the apoptotic response to DNA damage, Nat. Cell Biol., 7(3), 278-285 (2005).A. Hishiya, S. Iemura, T. Natsume, S. Takayama, K. Ikeda and K. Watanabe: A novel ubiquitin-binding protein ZNF216 functioning in muscle atrophy, Embo J., 25(3), 554-564 (2006). T.S. Kitajima, T. Sakuno, K. Ishiguro, S. Iemura, T. Natsume, S.A. Kawashima and Y. Watanabe: Shugoshin collaborates with protein phosphatase 2A to protect cohesin, Nature, 441(7089), 46-52 (2006). J. Hamazaki, S. Iemura, T. Natsume, H. Yashiroda, K. Tanaka and S. Murata: A novel proteasome interacting protein recruits the deubiquitinating enzyme UCH37 to 26S proteasomes, Embo J., 25(19), 4524-4536 (2006). Y. Hirano, H. Hayashi, S. Iemura, K.B. Hendil, S. Niwa, T. Kishimoto, M. Kasahara, T. Natsume, K. Tanaka and S. TerminologyParticipation of Takatsugu Hirokawa, Research Team Leader, Drug Discovery Molecular Design Team, Computational Biology Research Center.

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