AMBER Archive (2009)

Subject: RE: [AMBER] Why does protein carry charges?

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat May 23 2009 - 13:06:57 CDT

Hi Lin,

> I got the protein crystal structures from the PDB file.
> There are only residues and water in the PDB files.
>
> Why does the protein carry charges?
> Why aren't they electrically neutral?

Many residues are protonatable or deprotonatable. You should take a look at
an introductory biochemistry text book for an overview of amino acids, their
pKa values and thus protonation states at different pH values.
 
> What are their intrinsic counter ions ?

The counter ions are a function of the solution in which the protein exists.
Typically one uses sodium or chlorine in analogy to a saline solution
although other ions, such as potassium can also be used.

All the best
Ross

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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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