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Structure Investigation of Fam20C, A Golgi Casein Kinase

Structure Investigation of Fam20C, A Golgi Casein Kinase. Sharon Grubner National Taiwan University Fourth Weekly report – July 17 th , 2013. Progress. Calculated and plotted RMSF for P-loop and 300-306 loop

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Structure Investigation of Fam20C, A Golgi Casein Kinase

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  1. Structure Investigation of Fam20C, A Golgi Casein Kinase Sharon Grubner National Taiwan University Fourth Weekly report – July 17th, 2013

  2. Progress • Calculated and plotted RMSF for P-loop and 300-306 loop • Measured the distances between alpha carbons of P-loop and C-terminal lobe to measure opening and closing of the binding pocket • Completed calculations and plots for interactions between specific residues in the ATP binding pocket of FAM20C • Calculated the percentage of simulation time there are salt bridges between these residues • Learned how to use VolMap Tool in VMD • Looking at the percentage of water molecules present inside the ATP binding pocket • Clustering • Learned how to prepare pdb files of trajectory and active site for submission • Sent the active side residues for verification before sending my clustering job • My progress is being updated on a daily basis and shared with my mentors on Evernote.

  3. Goals for Next Week • Qualitative analysis • Read relevant papers and learn about the process of structure and data analysis for drug discovery purposes • Watch the motion of various loops within Fam20C structure • Analysis of RMSF results • Watch trajectory and draw conclusions for drug discovery purposes • Clustering • Send my first clustering job

  4. Culture We survived a typhoon… S.Y.S Memorial Hall National Palace Museum

  5. Acknowledgments • UCSD (University of California San Diego) • Dr. RommieAmaro • Dr. Gabriele Wienhausen • Dr. Peter Arzberger • Teri Simas • NTU (National Taiwan University) • Dr. Jung-HsinLin • Julia Brown Research Scholarship

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