6 replies to this topic

[Charline]

Hi, does anybody know a free program that predicts the possible substrates for a kinase?
Also, does anybody have experience with protoarray (KSI) from Invitrogen, is it any good?

Thanks in advance
Charline

[laurequillo]

Charline, on 17 August 2010 - 10:50 PM, said:

Hi, does anybody know a free program that predicts the possible substrates for a kinase?
Also, does anybody have experience with protoarray (KSI) from Invitrogen, is it any good?

Thanks in advance
Charline

well, you can predict sites for known kinases within a given protein (I dont know by heart the sites, but if you check in google with prediction phosphorylation or something like that you will find some places). You can check as well phosphosite.org to find the sites in a given substrate

[Charline]

laurequillo, on 17 August 2010 - 11:28 PM, said:

Charline, on 17 August 2010 - 10:50 PM, said:

Hi, does anybody know a free program that predicts the possible substrates for a kinase?
Also, does anybody have experience with protoarray (KSI) from Invitrogen, is it any good?

Thanks in advance
Charline

well, you can predict sites for known kinases within a given protein (I dont know by heart the sites, but if you check in google with prediction phosphorylation or something like that you will find some places). You can check as well phosphosite.org to find the sites in a given substrate

Thanks, I have found several programs for predicting the phosphorylation sites on my kinase, but how do I find the potential substrates that can be phosphorylated by my kinase?

[laurequillo]

Charline, on 17 August 2010 - 11:59 PM, said:

laurequillo, on 17 August 2010 - 11:28 PM, said:

Charline, on 17 August 2010 - 10:50 PM, said:

Hi, does anybody know a free program that predicts the possible substrates for a kinase?
Also, does anybody have experience with protoarray (KSI) from Invitrogen, is it any good?

Thanks in advance
Charline

well, you can predict sites for known kinases within a given protein (I dont know by heart the sites, but if you check in google with prediction phosphorylation or something like that you will find some places). You can check as well phosphosite.org to find the sites in a given substrate

Thanks, I have found several programs for predicting the phosphorylation sites on my kinase, but how do I find the potential substrates that can be phosphorylated by my kinase?

Well, I never used such a program...is quite a wide search dont you think? maybe there are some programs for that, but it would be easier if you have some target protein which you want to know if it is phosphorylated by your kianse. Then the programs will give you some predicted sites. But fo some kinases those conserved motif are quite open, so in a protein you could have several "predicted" sites, but it doesnt mean that your kinase is gonna phosphorylate those sites for sure...
I dont know if it helps you

[Rsm]

Here's another alternative for kinase profiling: http://www.pepscanpr...index.php?id=27 (PepChip). I am going to try their trial slide, which has 200 known kinase targets, and is not really expensive...
Disadvantage: If you need a scaffold or linker protein for your kinase action (like for all the MAP kinases), it won't work. Then I'd recommend something like fishing phosphorylated proteins after kinase treatment of a crude dephosphorylated cellular extract. There you'll get the consensus kinase target sequence.


Cheers,
Rsm

Edited by Rsm, 18 August 2010 - 02:32 AM.

[Charline]

Rsm, on 18 August 2010 - 02:26 AM, said:

Here's another alternative for kinase profiling: http://www.pepscanpr...index.php?id=27 (PepChip). I am going to try their trial slide, which has 200 known kinase targets, and is not really expensive...
Disadvantage: If you need a scaffold or linker protein for your kinase action (like for all the MAP kinases), it won't work. Then I'd recommend something like fishing phosphorylated proteins after kinase treatment of a crude dephosphorylated cellular extract. There you'll get the consensus kinase target sequence.


Cheers,
Rsm

Thanks!!!

[Rupam]

For the kinase substrate you can use PlosOne as a program it may help you and i dont have any experience with protoarray but it seems ok for your work.

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Regards
Rupam Mittal

Edited by Rupam, 24 August 2010 - 10:09 PM.