Structure Investigation of Fam20C, A Golgi Casein Kinase Sharon Grubner National Taiwan University Second weekly report – July 3 rd, 2013.

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Presentation transcript:

Structure Investigation of Fam20C, A Golgi Casein Kinase Sharon Grubner National Taiwan University Second weekly report – July 3 rd, 2013

Progress Attended the first Taiwan-Korea Bilateral Biophysics Conference—my first conference in Taiwan! 130ns of the first free dynamics simulation, ~8ns of the second third simulations Practiced using AutoDock Vina Learned how to use various useful tools in VMD, such as: MultiSuq- aligning two pdb structures RMSD Visualizer Tool Use Tk Console to show bond lengths between specific residues Read more papers about Fam20C and its structure Prepared presentations about Israel and my research project for the lab meeting on Thursday My progress is being updated on a daily basis and shared with my mentors on Evernote.

RMSD Visualizer Tool RMSD for 118ns of simulation of the entire protein

Bond lengths between Lys192-Glu213 Analysis of salt bridge interactions between the nitrogen of K and the oxygens of E Measurement of the bond lengths throughout the simulation What percentage of the time there is a salt bridge interaction (below 4A) – this value is not in this presentation

Bond lengths between Lys192-Glu218

Goals for the Next Week Once the first simulation is done: Watch the motion of various loops within the structures (K171-K178, p-loop, A300-R306): Quantitative analysis – RMSD Visualizer Tool Qualitative analysis- watch trajectory and draw conclusions for drug discovery purposes Measure and plot distances between alpha carbons of certain residues (G173-H308, G174- H369, K192-E213 vs. E218) Install and start learning how to use electrostatics plugin DeIEE in VMD

Our friends took us to a beautiful restaurant on Yangming mountain overlooking Taipei Culture

One dinner – 4 different languages Our friends took us to their favorite place to get shaved ice at Shiling night market

Acknowledgments UCSD (University of California San Diego) Dr. Rommie Amaro Dr. Gabriele Wienhausen Dr. Peter Arzberger Teri Simas NTU (National Taiwan University) Dr. Jung-Hsin Lin Julia Brown Undergraduate Research Scholarship