Exercise written by: Morten Nielsen
In yesterdays exercise you used the BLAST program to perform fast alignments of DNA and protein sequences. As
shown in todays lecture BLAST will often fail to recognize relationships between proteins with low sequence
similarity. In todays exercise, you shall use the iterative BLAST program (PSI-BLAST) to calculation sequence
profiles and see how such profiles can used to
- Identify relationships between proteins with low sequence similarity
- Identify conserved residues in protein sequences (residues important for the structural
stability or function of the protein)
First part. When BLAST fails
Say you have a sequence Query
and you what to make predictions about its function and structure. As seen in last weeks exercise, you will
most often use BLAST to do this. However what happens when BLAST fails?
You shall use the Protein blast search program. Go to the
Now select the protein blast option. Paste in the query sequence
Set the database to pdb, and press
Now go back to the BLAST web-site.
Select the PSI-BLAST option. Paste in the query sequence
Set the database to nr, and press Blast.
- Q1 How many significant hits does BLAST find (E-value < 0.005)?
- Q2 How many significant hits does BLAST find (E-value < 0.005)?
- Q3 How large a fraction of the query sequence does the significant
hits match (excluding the identical matches)?
- Q4 Do you find any PDB hits among the significant hits (search for pdb in the
hit list or look for the colored S to the right of the E-value))?
Now run a second BLAST iteration. Press Run PSI-Blast iteration 2.
- Q5 How many significant hits does BLAST find (E-value < 0.005)?
- Q6 How large a fraction of the query sequence does the significant
Make sure you understand what is going on.
- Q7 Why does BLAST come
up with more significant hits in the second iteration?
- Q8 Do you find any PDB hits among the significant hits (search for pdb in the
hit list or look for the red colored S to the right of the E-value)?
If you did not find a PDB match, do a third Blast iteration.
- Q9 What is the PDB identifier for the best PDB hit?
- Q10 What is the sequence simularity between the query and this PDB hit?
- Q11 What is the function of this protein?
Identifying conserved residues
You have now (hopefully) identified a structural relationship between the Query sequence and
a protein sequence in the PDB database of protein structures. Say you would like to validate this
relationship. This one could do by mutating (substituting) essential residues in the query sequence
and test if the protein function (or structure) is affected by these mutations.
The protein sequence of the query is large (more than 400 amino acids) and a complete mutation study
including all residues would be extremely costly. Instead one can use PSI-BLAST and sequence profiles
to identify conserved residues that are likely to be essential for the protein structure and/or
Below you find a set of 8 residues from the Query protein sequence. You shall use the PSI-BLAST and HHpred
programs to select four of the eight residues for a mutagenesis study (you shall select the four
residues based on sequence conservation only).
- (a): H271
- (b): R287
- (c): E290
- (d): Y334
- (e): F371
- (f): R379
- (g): R400
- (h): Y436
You shall use the HHpred program to identify
which residues are conserved in the Query protein sequence. Go to the HHpred web-site and upload
the Query sequence and
press submit (note it might take some minutes before your job is completed).
Find the PDB hit identified by PSI-BLAST.
- Q12 Does HHpred agree that this hit is significant?
Stroll down to the alignment of the Query and the hit identified by PSI-BLAST (hit number 2). Next click
on the Show histograms icon
Now, from the histogram bars you can identify which residues are conserved in the query/template alignment.
- Q13 Which of the eight residues listed above are most conserved and hence most likely
to be essential for the protein stability and/or function?
Go to the PDB database and download the structure of 1A0P (use Google to find the link to the PDB
database if you do not know it).
From the HHpred alignment identify the four essential residues
from Q13 in the 1A0P sequence. Use PyMol to visualize the 1A0P structure and show the
location of the four essential residues. Note, that the residue numbering is 1A0P is dfferent
from the numbering in the query sequence.
Now you have seen the power of sequence profiles in general and the PSI-BLAST program in
particular. Using sequence profiles you have been able to identify a relationship
between protein sequences fare below 30% sequence similarity. Further, you have made qualified
predictions on the protein function and selected a set of essential amino acids suitable for
experimental validation of the structural and functional predictions.