I have generated electrostatic potential maps of a protein at different pH values using a software. I am an experimentalist and hence I am not quite sure how to interpret the blue-white-red colors on the surface of my protein model
Hello Colina,
I will need a little more information to help guide you. However, the blue/white/red colors on the surface of your protein model correspond to the electrostatic surface potential at a particular point on the surface of your protein model. Or put another way, it gives you the charge (+, -, or neutral) on the surface of your protein. Generally the red symbolizes negative charge, blue positive and white is neutral (depends on the settings of your software).
So now what does it mean and how is it biologically relevant? Well, it depends on your your protein. However, as an example, a DNA-binding protein will most likely have a pocket of positive charges, which helps it to bind DNA (remember that DNA is covered in negative charges from the phosphates). If you are looking at two proteins that might interact you can look for a pocket of negative charge on one protein and a bump of positive charge on the other (or vice versa) that might indicate a possible interaction site.
From what you have said you have made maps of your protein at different pH values. If you do not know the pI of your protein this might be a good way to help you find it as the surface of your protein will be neutral at the pH that corresponds to your protein's pI.
Hi James,
Thank you so much for your detailed answer. My protein is insulin, so its pI is known. It's 5.3. I am studying some of its properties at pH 2.0, 5.3, 7.0 and 8.8 and I have generated their electrostatic surface potentials using the APBS software. I have mostly red surface with some white and blue at pH 2.0 and a completely blue surface at pH 8.8. With a pI of 5.3, I know insulin will have a net negative charge at pH 8.8 and positive charge at pH 2.0. However, my electrostatic surface potential shows negative at pH 2.0 and positive at pH 8.8 and in between at pH 5.3 and 7.0. I am not sure how to connect the overall charge and the info obtained from surface maps.
Since you mentioned that the surface will be neutral at the pI, my map at pH 5.3 has all the colors (red/white/blue).
Hi Colina,
About your surface at the pI - that is probably ok. It is the overall charge that is neutral at the pI, which means you may have some positive and negative charges visible but when averaged they should be neutral.
About the other pH values, it sounds like what you are getting is the exact opposite of what you would expect, which makes me think that the settings are reversed from normal, maybe?
About connecting the overall charge and the surface map info, if you want to have a visualization/image of the protein you can do that using PyMOL (http://www.pymol.org/). There is a good "how-to" on this at the APBS website (http://www.poissonboltzmann.org/docs/visualizing-results/). This is of course assuming you don't want to get the image from the APBS website.
Once you have a visualization, connecting the info really depends on what it is that you are looking for. Are you looking for potential binding sites? or potential sites for alteration? or maybe something else?
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