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Research paper : A systematic analysis of protein interaction networks leading to the drug discovery (S. Iemura et al.)−117 Synthesiology - English edition Vol.1 No.2 (2008) superiority of the result, and was able to install a simple clean booth in the analysis lab. However, as a practical problem, heat produced by the mass spectrometer was too large, temperature inside the booth quickly rose to over 35 °C, and it could not be used for a long time, as the device would get damaged. We strongly felt the necessity for a fully equipped clean room to conduct stable and continuous analysis.In the spring of 2001, the AIST Tokyo Waterfront was newly opened and we obtained the opportunity to install a clean room. We visited several semiconductor plants to learn about clean rooms from basics. However, not until the opening of Tokyo Waterfront annex in 2005 and the construction of second-generation super clean room did we solve the dust issue.4 Execution of Type 2 Basic Research (issue of sample preparation)After successfully developing the elemental technology for liquid chromatography, we thought it was important to move on to product realization research in order to make the hardware available commercially. However, as mentioned in the previous section, we discovered that the developed technology was useless unless the analytical environment was constructed properly. My real objective was to construct a mass spectrometry system with the highest sensitivity in the world, to conduct large-scale and high-precision protein network analysis, and to efficiently find disease mechanisms and discovery of new drug targets.In fact, the effectiveness of developed LC system and mass spec facility was extremely significant. There was no necessity for steps of separating the sample by electrophoresis, and in about one hour, interaction complex composed of over 200 different types of proteins could be completely identified at sub-femto level. Before, sample had to be prepared from several tens to hundreds of liter volume and the analysis took several months, while now it can be done in 2~3 days. Also, since multiple analyses can be conducted, 10~20 analyses can be done simultaneously. Conducting large-scale analysis at high throughput became a reality.By increasing throughput, it became possible to consider in details the conditions of sample preparation for high-precision analysis. There are various parameters such as affinity refinement of proteins, incubation time, and lysis of cells. To combine multiple parameters, several thousand analyses were necessary, and such analyses could not be accomplished by one researcher in his/her lifetime. Therefore, optimization of conditions for sample preparation was never done at comprehensive and thorough manner, and normally sample preparation designed on trial-and-error based on a researcher’s experience and intuition. In fact, we sought sample preparation optimization through several thousand analyses, and developed an extremely precise method eliminating foul positive data maximally.We investigated diverse parameters, and the conclusion obtained was simple: “work fast.” Since sensitivity of conventional analysis methods was low, it was common knowledge to maximize yield of a sample as high as possible. However, more time was required to recover higher yield, and unstable protein denatured and aggregated to produce “dirty” data. As high-sensitivity analysis became possible, it was no longer necessary to concern ourselves with “yield” of a sample. Rather, the most important concern was to increase “quality” or to prepare the samples as fast as possible before the proteins denatured and aggregated. However, it was not easy to do this in practice, and the technician in charge developed thorough protocol for sample preparation. This involved everything from ways to hold the test tube to arrangement of reagents on the bench, and emphasis was placed on the efficiency of the operator. Also, movement of the operator was filmed on video and studied to remove any unnecessary movements. Finally, we created and executed protocol where work, which previously took several hours or overnight, could be completed within one hour.5 Research results and commercializationThrough these technological developments, we conducted large-scale protein network analyses using 2,200 human cDNA in about 5 years. There were over 16,000 analysis sessions. We were able to discover new cellular mechanisms functioned by proteins. The results were published in nearly 30 papers including twice in Nature and 6 times in Nature affiliated journals. We succeeded in analyzing protein networks of several disease-related genes, more than initially expected. We obtained findings that may lead to discovery and understanding of molecular disease mechanism as well Fig. 3 Discovery of assembly factor of proteasome.We discovered 4 assembly factors that composed the proteasome. Rather than inhibiting the proteasome itself, there is less side effect and higher possibility of being effective against wide range of cancer cells by inhibiting these assembly factors. They are better drug discovery targets.(45)−DSCR2 and HCCA3 form heterodimer and interacts to α5 and α7 subunits.Ump1 induces β subunit (orange) to form a ring formation. MGC10911 masks the upper part of the ring of intermediate body to prevent the α rings (pink) from bonding with each other.Completion of proteasome complex bodyDSCR2HCCA3α5Ump1α7Ump1MGC10911

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