Clustal-Omega

Construct a multiple sequence alignment using Clustal-omega the BPTI-like superfamily proteins in the table to BPTI. Also using pymol construct a structural alignment  
a) How similar are the sequences? The structures? If you were to provide a definition for the BPTI superfamily, what would it be based on these results?  
b) Using the sequence alignment as a guide, color regions in the structural alignment that are identical using one color, amino acids that are similar with another, and amino acids that are different with a third color. What kinds of amino acids are highly conserved? Where on the structure are they located? Why do you think they are highly conserved?  
3. Review the catalytic mechanism of Trypsin. Using the structure of trypsin in complex with BPTI (PDB 2PTC) show the key feature of the catalytic triad, and show where the peptide would be cleaved if BPTI were not an inhibitor  
4. Compare the structures of Trypsin in complex with BPTI (PDB 2PTC) with that of Trypsin in complex with Leupeptin (PDB - 1AGI). Leupeptin forms a stable covalent acyl enzyme intermediate.  Compare these structures and come up with a hypothesis as to how BPTI inhibits proteolysis



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