prediction of protein phosphorylation sites, how? - (Jun/06/2006 )
He,
I am working on a protein which might be phorsphorylated by PKA. My boss asked me to predict the phosphorylation sites of this protein by using an on-line data base (or something else with this function). But...... how? which site? which animo acid? To my limited knowledge, since I have known where is the serine, threonine and Tyrosines in amino acid sequence, these are the phosphorylation sites, aren't they... or is there any requirement to reach for them to be phorsphorylated?............could anyone enlighten me? Thanks in advance
I am working on a protein which might be phorsphorylated by PKA. My boss asked me to predict the phosphorylation sites of this protein by using an on-line data base (or something else with this function). But...... how? which site? which animo acid? To my limited knowledge, since I have known where is the serine, threonine and Tyrosines in amino acid sequence, these are the phosphorylation sites, aren't they... or is there any requirement to reach for them to be phorsphorylated?............could anyone enlighten me? Thanks in advance
you could perhaps use something like protein prospector (google it) which i think takes mass spec data and from that you can predict the phosphorylation sites. This is done by looking at the masses of each STY amino acid from which you should be able to tell if the amino acid is normal or phosphorylated
i can't remember exact figures as i've only had minimal training on this but i'm sure someone else can tell you more than me
I am working on a protein which might be phorsphorylated by PKA. My boss asked me to predict the phosphorylation sites of this protein by using an on-line data base (or something else with this function). But...... how? which site? which animo acid? To my limited knowledge, since I have known where is the serine, threonine and Tyrosines in amino acid sequence, these are the phosphorylation sites, aren't they... or is there any requirement to reach for them to be phorsphorylated?............could anyone enlighten me? Thanks in advance
I suggest that you go to EXPASY, this site can give a lot of information about your protein including its predicted phosphrylation sites and the phosphorylation potential as well!
Hi Yeping,
I agree with the others looking at a database of some kind is probably a good bet (Expasy would be a good start). From looking on Pubmed, Protein Kinase A seems to be a serine/threonine kinase so your protein's tyrosine residues aren't going to be affected.
Kinases tend to have a consensus amino acid motif surrounding the serine, threonine or tyrosine which they will phosphorylate. Try to find this consensus motif either through Pubmed or a database search of kinase motifs and you will hopefully be able to predict the phosphorylation sites. Some companies (I think Upstate or Cell signalling) are beginning to sell antibodies raised against these motifs as a specific kinase substrate antibody (e.g. antibody against phosphorylated Akt/PKB substrates).
Hope that helps,
Ceri
I almost understand now.....
Thank you all for the kind replys, I have found all these websites, pubmed, expasy and ProteinProspector... 