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How do you calculate or predict the charge of a protein at pH 7 given a fasta sequence?

Any papers or online servers to do this is well appreciated.

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Check this answer biology.stackexchange.com/questions/2459/… –  friveroll Jun 19 '12 at 5:46
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2 Answers

up vote 4 down vote accepted

ExPASy to the rescue! Although I didn't comb through all the tools, this nifty website provides quite the myriad of bioinformatics resources which most certainly contains the tool to calculate what you want.

Bear in mind though, most tools will tell you the isoelectric point of your protein. However, bearing in mind the relationship between pI and pH (i.e. if pI < pH, then protein is - charged, and vice versa), you can easily figure out the charge of a protein at pH 7.

http://expasy.org/tools/

*Update

Here's the exact tool to calculate isoelectric points: http://web.expasy.org/compute_pi/

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Thanks for the info. Saw that though, so how would you calculate the charge - any hint on that? –  VanJeer Jun 19 '12 at 5:54
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Here's a tool that will give you charge: scripps.edu/~cdputnam/protcalc.html –  jp89 Jun 19 '12 at 5:57
    
Thanks! But wish it could in batch... –  VanJeer Jun 19 '12 at 7:45
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To calculate the charge at different pH:

At pH 3 K, R, H are + and D,E have no charge so add up all of the K,R,H in the sequence and that is your net charge at pH 3 At pH 6 K, R, H are + but now D,E are (-) so subtract one total from the other to figure if your net charge is + or -. At pH 8 K and R are +, H has no charge and D,E are (-). At pH 10 R is +, K, H have no charge and D,E are (-).

That can give you a general idea. You can estimate the charge at pHs in between.

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