Practical
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After this practical you will:
Understand the basic concepts behind (multiple) sequence alignment;
Be able to 'read' information from a multiple sequence alignment;
Understand the relation between sequence alignment and the other
parts of the course (especially homology modelling).
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Lets start with a simple question.
Question 77:
Which is the active site residue in this molecule:
MEKKRIYLFCSAGMSTSLLVSKMKAQAEKYDVPVLIDAYPETLAGEKGQDADLVLLGPQI
AYMLPEIQQQLPGKPVEVIDTLLYGKVD
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Some hints:
- Run BLAST on it (against SwissProt should be enough).
- Run Clustal on the hits.
- Check if any BLAST hits should be removed from the multiple sequence alignment,
and if you think that those three should be removed, remove them and run Clustal
again.
- Do you also see two major families in the multiple sequence alignment?
- So, if we are going to search for an active site residue where roughly should
we search?
- And if we search there, what do we search for?
- And, once we have found the conserved residues, who will be your favourite?
Answer
This active site residue doesn't work alone. No active site residue can ever work
alone. There always must be partner residues in the active site. These partners
will do tasks like (not all these tasks in one active site of course):
- Activate the active site residue
- Bind the active site water
- Bind the ligand
- Stabilize the intermediate complex
- Provide the required mobility
- Provide a charge
- Be part of a binding pocket
And now the more difficult question.
Question 78:
Knowing that both families execute their activity rather differently, can you
look at the sequences and find which are the partner residues of the active
site cysteine?
Answer