Download Protein bioinformatics 260.655 Lab3 Homology Modeling and

Protein bioinformatics 260.655
Lab3 Homology Modeling and Quality Assessment
1. Model the acyl carrier protein from P. falciparum
a. Look in the class folder for a file called ‘PfACP.txt’. This file contains the
sequence of PfACP. Find structures in the PDB with the closest amino acid sequence
identity to PfACP. What is the closest match? What quality of model is likely to result
from using this structure as a template?
b. Go to the Swiss-Model website
http://swissmodel.expasy.org//SWISS-MODEL.html
Use the ‘First Approach mode’ to model PfACP. You will have to list an
email address for the result.
c. The model will take 2-7 minutes. While you are waiting, check out other links
on the Swiss-Model website. In particular, look at How SWISS-MODEL works.
d. When the model arrives by email, look at this file. What is recorded here?
Open the file using the ‘SPDV’ viewer. Does this look like a real protein structure? The
modeled structure should be the same (or similar) to file ‘ACP1.pdb’ in the class
directory. Submit this file to the Verify3D structure assessment program at
http://nihserver.mbi.ucla.edu/Verify_3D/
e. Open the file ‘PfACP.pdb’ and ‘ACP1.pdb’ from the class folder. Compare
the model (ACP1.pdb) with the mostly-refined crystal structure (PfACP.pdb). What is
the RMSD of the alpha carbon atoms? To calculate this, go to DALI
http://www.ebi.ac.uk/dali/dali_email.html
Scroll down to the ‘interactive submission form’. Do a pairwise comparison.
2. Model dopamine beta-monooxygenase from rat.
a. Go to the Swiss-Model website
http://swissmodel.expasy.org//SWISS-MODEL.html
Use the ‘First Approach mode’ to model DBM. The amino acid sequence
is in the folder DBM1 as ‘rDBM.txt’.
b. When the model arrives by email, look at this file. Alternatively, open the
already calculated model file ‘DBM1.pdb’ using the ‘SPDV’ viewer. Does this look like
a real protein structure? What happened here and why?
c. Try to identify the individual domains in the file rDBM.txt using any of the
domain parsing algorithms discussed during the previous lab. Think about the modeling
results in terms of domains.
d. Go to the DBM2 folder and look at the file ‘PHMDBM.txt’. Use the first two
sequences (1PHM and rDBM) to calculate a multiple sequence alignment in ClustalW.
Now use the second two sequences (PHM_A and DBM_A). Compare these sequence
alignments. The second alignment is saved as “clustalw-20060504-15084163_aln.txt”.
Use this file and the pdb ID code 1SDW to use the ‘alignment interface’ part of
SwissModel. This will yield a model based on your sequence alignment of this domain
alone.
e. Compare the model of DBM_A (also saved in the folder as DBM2.pdb) with
your old model (DBM1.pdb). Compare both with template structures such as 1SDW.pdb.