HI Jiyong,
If you still have protein left, you may try to sequence it. In some cases,
even N-terminal digestion is very helpful. In my previous, I always got a
90KDa protein, which was very close to my target kinase. Based on the
protein sequencing, we identified it was one of those chaperones.
Dear Pedro Matias,
Thanks for you advice.
After I manually changed the side chain of the residues, I got a "artificial"
primary structure. I did a blast by using this primary structure.
Finally, I found the amino acid sequence of this protein. The electron density
could perfectly match the
To keep this thread on topic - there is no Blue Stone on the Galveston island.
Lots of white sand beaches, lots of black birds, lots of new BMW cars in the
port (they unload the ship here), a few oil rigs, an occasional cruise ship,
but no Blue Stone…
Petr
I wonder why you assume know there are "about 20 point mutation sites” if "this
protein is an unknown protein”.
It looks like you are comparing the sequence of a protein you do not know what
it is to the sequence of a protein you dont really know what it is (1).
I would consider it more
Hi Jiyong,
Try running the FITMUNK server in the sequencing mode:
http://witold.med.virginia.edu/fitmunk/server/
More information on using FITMUNK to identify your protein:
https://www.ncbi.nlm.nih.gov/pubmed/26894674
And here:
https://www.ncbi.nlm.nih.gov/pubmed/26660914
Ivan
With
In this case you know the protein is closely relaed to whatefer contaminer
found, and you have good sequence data, so I agree the next step is blast.
Maybe it is an isozyme of the structure used.
In cases where you solve an unknown by heavy atom derivatives and have no idea
what it is; and
Wow, pretty cool—you must have solved it to very high resolution to know the
sequence from the structure. I cannot imagine, however, how you got this
contaminant—maybe phage infection of your bacterial culture? Anyway, I agree
with BLAST-ing the sequence, seeing what you get that is closest.
Hello,
Welcome to the club of unexpected results!
You don't provide a lot of background, but based on what you wrote you can:
1. Do a BLAST search using a known part of your sequence to find whether
this sequence has been deposited.
2. Assign the different residues based on the chemical
