Team:ASIJ Tokyo/Human Practices
Human Practice
Reaching Out to the Community
Integrated Human Practices
Presentation at International Christian University (June 21)
We had the opportunity to meet with Dr. Kose and Dr. Mizoguchi from the International Christian University, as well as Harvard Student Edward. After presenting our project in its initial stages, we received valuable feedback on how we could improve our methodology. In addition to suggestions on smaller details that could impact our whole project in the long run, such as being aware of how adding GFP or Histidine tags could affect our results, we also received advice on our proposed modification to the 0.19 protein. By lowering the efficiency of the pepsin- 0.19 binding site, we could increase the resistance of 0.19 to pepsin. Though this was not our final project direction, the meeting nonetheless proved invaluable in providing us with an initial, critical review of our project in its developing stages.
Meeting with Professor Yamamoto(July 21)
Dr. Yamamoto introduced us to Dr. Hirokawa at Sansoken Laboratory and Mr. Nakamura from Biomodeling Research Company. From this exchange, we were able to receive advice regarding protein modeling on PyMol and some future steps for our project. Dr. Yamamoto also provided us with 3D models of our designs in October.
Diabetes Clinic Visit (July 24)
During the summer, our team met with the Mitaka Diabetes Clinic to learn more about the various treatment strategies for Type II Diabetes. Emphasizing the importance of diet and activity, as well as self-discipline and personal habits in conjunction with insulin medications, the clinic introduced valuable perspectives on diabetes treatments. From this meeting, we deduced that creating a yeast-based food additive could provide a potential support to the existing, preferred treatment methods of daily habit control. Decreasing dietary restrictions without invasive procedures would be conducive to diabetes treatment through lifestyle changes.
Meeting with Dr. Ikebukuro (July 29 & August 21)
Image of Dr. Ikebukuro taken from http://web.tuat.ac.jp/~kakusan/members.html
Our team was also able to contact Dr. Ikebukuro, a researcher at Tokyo University of Agriculture and Technology. Dr. Ikebukuro provided valuable insight on protein modeling and modification, suggesting we consider electrostatic attractions as well as how we could interchange amino acids to strengthen bonds. We were also provided with potential contacts for professionals who could assist us with computer docking simulations. Through this interview, we were able to receive specific, targeted advice on concrete ways to alter our genetic sequences.
On August 21st, two members of our team scheduled an appointment with Hiraka Kentaro and Miyazaki Masahiro, graduate students from Tokyo University of Agriculture and Technology. In the previous meeting, Dr. Ikebukuro recommended that we talk to them for more specific questions about the dry lab aspects of our project. They explained how to fully utilize PyMOL, a protein modeling software, and introduced us to an online resource for PyMOL created by Osaka University. With their help, we were able to insert a mutagenesis in out alpha amylase inhibitor protein.
Sansoken Laboratory Visit (August 1)
Dr. Hirokawa suggested us to do “Homology Modeling” using the Swiss-Model software in order to create our own PDB file of the 0.19-amylase complex. In this method, an already existing PDB file of similar protein (Ragi amylase inhibitor and mealworm a-amylase) complex will act as a template for creating a docking simulation for 0.19 inhibitor and human a-amylase. Swiss-Model software allows us to substitute the protein in an already-existing PDB file, so 0.19 inhibitor will replace Ragi inhibitor and human a-amylase will replace mealworm a-amylase.
Here, we are assuming that the orientation of 0.19 & human amylase complex will be the same as Ragi & mealworm a-amylase complex, since the sequence similarity mealworm and human a-amylase is 30%, which is high enough to be substituted in homology modelling, according to Dr. Hirokawa.
For the modification, we will be targeting regions within 4 angstrom (distance between 2 amino acids) of a certain amino acid in the a-amylase. Since disrupting alpha-helix and beta-sheet may change the protein structure, so modification should be done on amino acid in the loop structure.
Quantifying protein stability will require knowledge and molecular dynamics and supercomputer calculations, so our modification will only consider charged residues and hydrophobicity.
Tokyo East Japan Meetup (August 16)
Over the summer, iGEM teams from across Japan attended an annual meetup held by Tokyo Tech University. Teams presented the progress they had made on their projects, and held Q&A sessions to discuss their ideas. Our team received helpful advice on improving the human practices aspect of our project by interviewing a diabetes patient on their lifestyle habits, and were also inspired to rethink our proposed modifications- to consider our rationale and narrow down our options for how we could alter the structure of 0.19.
Diabetes Awareness Posters
