Amino Acid Motifs - (Mar/31/2007 )
Dear all,
My PI is suspecting 2 proteins (one of which I am currently working on) are toxic to E. coli cells. Therefore, he would like me to search for the amino acid motifs present in the 2 proteins, which may be responsible for the toxicity in E. coli cells.
I have browsed through and tried the list of programmes available in Expasy as well as EBI, but I failed to find a right programme.
Can anyone please suggest to me which programme should I use and how should I go about with this analysis?
Thank you.
Have you done a growth (or in your case, a lack of growth) curve of the expression of your protein? That might be the easiest way to check for toxicity. You might need to try inducing at several ODs, just to get a more complete picture of what's happening.
I didn't think a 'toxicity' listing has been done. It would require a massive test of every possible motif for toxicity, so as far as I'm aware, toxicity is an empirical determination.
I didn't think a 'toxicity' listing has been done. It would require a massive test of every possible motif for toxicity, so as far as I'm aware, toxicity is an empirical determination.
We hardly get any colony after we spreaded the transformation culture on the plate (2 separate labs are currently working on the same protein).
Therefore, my PI hypothesized that there is leakage of protein expression and leads to the "killing" of our bacterial cells. He would like me to investigate if there is any common amino acid motif presents in both proteins.
I didn't think a 'toxicity' listing has been done. It would require a massive test of every possible motif for toxicity, so as far as I'm aware, toxicity is an empirical determination.
We hardly get any colony after we spreaded the transformation culture on the plate (2 separate labs are currently working on the same protein).
Therefore, my PI hypothesized that there is leakage of protein expression and leads to the "killing" of our bacterial cells. He would like me to investigate if there is any common amino acid motif presents in both proteins.
IS your PI interested ion using the proteins, or is he trying to find the 'toxic' motif? If the former, you might have to clone into a cell like BL21(DE#) pLys S or pLys E, because the control on expression is really tight. If it's the toxic motif, I think you're in for a few sessions with pBLAST! How related are the proteins generally?
So you want to do a database scan - looking for protein motifs. You then want to see if that motif is toxic to your cells?
If this is the case then a scan against something like pfam and or prints - even prodom may help in the identification of motifs - you could also try CDD.
As for the toxicity i think you will have toruble findhing that in the databases.
If this is the case then a scan against something like pfam and or prints - even prodom may help in the identification of motifs - you could also try CDD.
As for the toxicity i think you will have toruble findhing that in the databases.
Thank you, Swanny and Perlmunky. I agree that it is rather difficult to look up for a toxicity motif in the databases, as no one publishes negative result. Well, we are interested at the proteins and my PI is very curious to know what is the toxicity amino acid motif presents in the proteins.
I will try those databases suggested by you.
Thanks.