Jump to content

  • Log in with Facebook Log in with Twitter Log in with Windows Live Log In with Google      Sign In   
  • Create Account

Submit your paper to J Biol Methods today!
Photo
- - - - -

substrate for kinase


  • Please log in to reply
6 replies to this topic

#1 Charline

Charline

    member

  • Members
  • Pip
  • 3 posts
0
Neutral

Posted 17 August 2010 - 10:50 PM

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

#2 laurequillo

laurequillo

    The Goddamn Batman!

  • Active Members
  • PipPipPipPipPipPipPipPipPipPip
  • 265 posts
1
Neutral

Posted 17 August 2010 - 11:28 PM

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
"He must be very ignorant for he answers every question he is asked" Voltaire

"This is SPARTA!"

"Im the goddamn batman"

#3 Charline

Charline

    member

  • Members
  • Pip
  • 3 posts
0
Neutral

Posted 17 August 2010 - 11:59 PM


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?

#4 laurequillo

laurequillo

    The Goddamn Batman!

  • Active Members
  • PipPipPipPipPipPipPipPipPipPip
  • 265 posts
1
Neutral

Posted 18 August 2010 - 12:25 AM



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
"He must be very ignorant for he answers every question he is asked" Voltaire

"This is SPARTA!"

"Im the goddamn batman"

#5 Rsm

Rsm

    Post Dog

  • Active Members
  • PipPipPipPipPipPipPipPipPipPip
  • 376 posts
8
Neutral

Posted 18 August 2010 - 02:26 AM

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.

I got soul, but I'm not a soldier

#6 Charline

Charline

    member

  • Members
  • Pip
  • 3 posts
0
Neutral

Posted 23 August 2010 - 09:28 PM

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!!!

#7 Rupam

Rupam

    member

  • Banned
  • Pip
  • 22 posts
0
Neutral

Posted 24 August 2010 - 03:02 PM

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.

for further queries:[url="[url]http://www.wiziq.com/tests/biology"]biology[/url] test papers[/url]

Regards
Rupam Mittal

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





Home - About - Terms of Service - Privacy - Contact Us

©1999-2013 Protocol Online, All rights reserved.