Progress Report for: H5N1 Receptor Specificity

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Progress Report for H5N1 Receptor Specificity

• July 23, 2007
• By Hsing Pao

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1st Step Done

• Finished determining strains desired.
• Did multiple sequence alignment.
• Have a database with key mutations in 26 strains
  of H5N1 that I am going to analyze.

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Modeller

• Learned how to use Modeller.
• Folded both chains of all 26 proteins.

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Example of Protein Fold from Modeller
MEKIVLLFAIVSLVKSDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILE
KKHNGKLCDLDGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKAN
PVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSA
CPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDA
AEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILK
PNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGA
INSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSPQRERRRKKRGLFG
AIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNS
IIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMEN
ERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRN
GTYDYPQYSEEARLKREEISGVKLESIGIYQILSIYSTVASSLALAIMVA
GLSLWMCSNGSLQCRICI
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Protein Fold Verification

• Checked protein folds to make sure they are
  accurate.
• Ran scripts to check low DOPE scores (way to
  evaluate low energy state)
• Ran Procheck to make sure valid protein identity.

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Protein Fold Verification (Contd)

• Used gnuplot to graph energies of residues.
• Compared all strains to multiple templates 2FK0,
  2IBX, 1JSM

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An example of verification of protein fold
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Parts of 2nd Step Done

• Got access to another server to run my NAMD
  simulations.
• Learned how to use most of the NAMD program and
  plug-ins.
• Made mutant strains.
• Adjusted pH of protein files to bloods pH at
  7.40.
• Got optimal body temperature for simulation for
  310 K.

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Whats next?

• Prepare a little more for running NAMD.
• Run NAMD simulations
• Run simulations on those mutants.

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So whats happening culturally?

• Ive been learning a lot about who I am.
• Ex Went to an English Corner and learned what
  many people think about Shanghainese people.
• Got to see how much China has changed since I was
  last here.
• Beijing 7 years ago.

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Got to eat some good food.
Saffron shark fin soup
Guess how much this cost.
218 RMB 28.51
Peking duck oven
Duck brain.
bbq eel
What kind of soup is this?
Guess what this is
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Some PicturesMe and My Olympic Buddies
More to come!
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More pictures
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Until next time Thats all folks!