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Team:Washington/Flu
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Revision as of 01:22, 29 September 2012
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Methods
Method of computational design
Gathering information about specific hemagglutinin
Since we would like to improve the binding of our flu binder to a specific hemagglutinin, we have to understand the structure of that specific hemagglutinin. We searched the specific hemagglutinin structure on Protein Data Bank (http://www.rcsb.org/pdb/home/home.do). If we succeed to find the desired hemagglutinin, we would download the PDB file of that hemagglutinin for making the model in Foldit. If we could not find the exact structure of that hemaglutinin, we would search for the protein sequence of that hemaglutinin.
Making model of Foldit
With the PDB file, we would use a protein analyzing program, PYMOL for making a model in Foldit. First, we would align that specific hemagglutinin to hemagglutinin one in PYMOL. Then, we would record the difference in side chains between that specific hemagglutinin and hemagglutinin one because we have a Foldit model in which the flu binder is binding to hemagglutinin one. On that Foldit model, we would transform hemagglutinin one to that specific hemagglutinin by changing the side chains of the hemagglutinin one. Then, a Foldit model that showcases the binding action of the flu binder to that specific hemagglutinin would be made.
Without the PDB file, we would align the protein sequence of a specific hemagglutinin we obtained to that of hemagluttinin one by using Clustalw2 (http://www.ebi.ac.uk/Tools/msa/clustalw2/). Next, we would make homologous models of the desired hemaggluttinin by changing the side chains of the hemaggluttinin in Foldit according to the protein sequence differences we found.
Proposing mutation on the model
After preparing the Foldit model, we would be able to propose mutations on the flu binder in order to improve its binding to the desired hemagglutinin. There is a score total in Foldit which indicates the energy of the whole protein structure. It is our understanding that the protein structure is more stable when its energy is lower. Thus, our primary goal was to decrease the score total in Foldit. We did that in three different ways, filling the holes, making space, and balancing the electrostatic. Holes that did not exist in hemagglutinin one would be created with the replacement of different side chains. We would mutate the corresponding side chain on the flu binder so that it extends out and fill the hole on the hemagglutinin. Making space is the exact opposite of filling the holes. Some side chains of certain hemaggluttinin would be more projected out in space than that of hemagluttinin one. Therefore, we would mutate the corresponding side chains of the flu binder in order to provide room for the more extended side chains. Some variations of side chain on hemaggluttinin causes some electrostatic changes. We would mutate the corresponding side chains of the flu binder so as to counter balance the electrostatic changes. For example, if a certain area on the helix is changed to be more electronegative, we would introduce an electropositive side chain on the flu binder for improving the binding and vice versa.
