types of amino acids that appear conserved (apolar/polar/charged)?
- d) Based on “c” what prediction would you make about the structural similarity of these two proteins (similar or not and why)?
- Choose the ykkC or the ykkD pump to perform a series of predictions using the link below http://www.expasy.ch/tools/protparam.html; pI (isoelectric point), MW and amino acid composition. You may use the ykkC or the ykkD pump sequence for this excersize!
- a) List pI (isoelectric point) and molecular weight (MW) of this protein.
- b) What are the three most common amino acids in this protein?
- c) What can you tell about the general physical properties (polar/apolar; acidic/basic) of this protein? Would you expect this protein to be water soluble?
- Predict the secondary structure of the ykkC or the ykkD pump by using: http://www.compbio.dundee.ac.uk/www-jpred/
- a) Paste the result of the secondary structure prediction into your report!
- b) What is the major secondary structural motif in this protein?
- c) Based on your secondary structure prediction which amino acids are prone to form a-helix?
- Using the link below predict membrane topology of the pump used in “3”. http://phobius.sbc.su.se/. Answer the questions below
- a) Paste the prediction here.
- b) Based on the secondary structure prediction in “3” and the previous topology prediction sketch how the pump is inserted into the membrane.
- Tertiary structure prediction: Below is the sequence of the MexA multidrug resistance efflux pump from the pathogenic organism Pseudomonas aeruginosa. This organism mostly affects patients with compromised immune system. It is the main culprit behind infections caused by medical implants (like catheter).
Perform tertiary structure prediction on this protein using the link and the sequence below!
Warning! Performing this modeling will take a while (10-20min). Do not use the back button on your browser; just wait patiently until it is done.
MQRTPAMRVLVPALLVAISALSGCGKSEAPPPAQTPEVGIVTLEAQTVTLNTEL PGRTNAFRIAEVRPQVNGIILKRLFKEGSDVKAGQQLYQIDPATYEADYQS AQANLASTQEQAQRYKLLVADQAVSKQQYADANAAYLQSKAAVEQARINLRY TKVLSPISGRIGRSAVTEGALVTNGQANAMATVQQLDPIYVDVTQPSTAL LRLRRELASGQLERAGDNAAKVSLKLEDGSQYPLEGRLEFSEVSVDEGTGSVTIRAV FPNPNNELLPGMFVHAQLQEGVKQKAILAPQQGVTRDLKGQATALVVNAQNKVEL RVIKADRVIGDKWLVTEGLNAGDKIITEGLQFVQPGVEVKTVPAKNVASAQKADAA PAKTDSKG
a.Paste the picture of the resulting structural model into your report!
b.What can you tell about the distribution of polar and apolar amino acids in a membrane protein as compared to a water soluble protein?