Prediction of protein disorder
DISPROT database and analyzing calcineurin A
- Find calcineurin A (PP2BA_HUMAN) in DISPROT www.disprot.org
You can start from UNIPROT, it has a link to DISPROT
or search DISPROT directly by keyword, or sequence.
- What kind of information can you find on this page?
- Which regions are marked as disordered in DISPROT?
- Which regions are marked as ordered DISPROT?
- By what experimental techniques?
- What is the role of the disordered segments?
Go to the search page in Disprot
and select source organism
Can you find proteins in Disprot from
– your favourite species?
Look at some of the examples
Disorder prediction methods
Collect prediction outputs for calcineurin A using
– IUPred http://iupred.enzim.hu
– Globplot http://globplot.embl.de/
– PONDR-FIT http://www.disprot.org/pondr-fit.php
– PredictProtein http://ppopen.informatik.tu-muenchen.de/
(MD, UCON, Norsp, Profbval)
- and any other method you like.
The input can be:
- the amino acid sequence in FASTA format
- amino acid sequence in raw format (without header)
- UNIPROT ID or accession number
Please note, some methods are sensitive to line breaks !
Minimum and maximum length of sequence !
NOTE: Cutoff values, False positive rates, different types of output
- Do the predictions agree with the experimental characterization of disorder?
- Do the predictions agree with each other?
DISPROT DP00039 : a highly disordered protein
- Predict protein disorder for DISPROT DP00039
- Count number of positively charged amino acids
- Count number of negatively charged amino acids
- Calculate net charge
(or use the protparam server)
- Check low complexity segments (you can take these from PFAM through uniprot)
- Check PFAM domains
Is there a contradiction between PFAM domain assignments and predicted disorder?
One of the main applications of disorder prediction methods is to find
suitable targets for structure determination.
- Which region of this protein you would try to crytallize?
- Check the Uniprot entry, which region could be be solved?
Check Pfam domains and disordered regions in these three proteins
What type of domains do they have in common?
Where are the disordered regions located, if there are any?
What is the likely relationship among these proteins?
Disordered binding regions in the N-terminal region of p53
The N-terminal region of p53 contains at least three binding regions:
- Use ANCHOR http://anchor.enzim.hu
- run ANCHOR on p53
- Are the experimentally determined disordered binding regions located in the N-terminal agree with the known disordered binding regions?
You can add motifs to ANCHOR prediction
For example search for the MDM2 motif and check if it coincides with disordered binding region
The nucleoprotein of measles virus
Which region is ordered, which region is disordered?
Does this protein have disordered binding region?
Find beta catenin in Uniprot (CTNB1_HUMAN)
- Go to the natural variants section. You will see multiple sites are associated with cancer. Where are most of them located?
- Characterize the site of mutations structurally and functionally.
- Use the ANCHOR,
Identification of binding sites based on patterns of conservation
- Collect the sequence for uniprot entry Q9UK97
- Predict disordered binding regions using ANCHOR
- Run the prediction for this entry using the SlimPrints server
- Which is the most significant hit?
- Look at the alignment. How conservative are the motif positions?
- Can you find this motif in other proteins?
Use the slimsearch server
- Compare the domain organization of the two proteins. How similar are they?