Electrostatics

Most charged residues occur on, or near, the surface of proteins. Electrostatic interactions are relatively long-range forces. When charged residues are buried within the protein, they must make specific 'salt-bridge' charge-pairs (burying a charge without a partner would be very destabilizing).

Practical work

View this structure (lysozyme, 7lyz) again using PyMOL. We will now highlight the charged residues and observe their location.

Show your molecule as cartoons and Colour->chain
Now click in the bottom left corner of the screen and type
select resn arg+lys
after the PyMOL>
This selects all positively charged amino acids. You can modify the display of a selection by using the S, H, and C buttons next to (sele). For this selection
Show->sidechain->sticks Colour->blue

Now let's colour the negatively charged amino acids red. Click in the bottom left corner of the screen and type
select resn asp+glu
after the PyMOL>

For this selection
Show->sidechain->sticks Colour->red

Now rotate the structure and look at where the coloured residues occur - are they on the surface, or buried? Keep rotating the structure to get a sense of depth.

Now we will look at an example of a buried salt bridge in which an arginine interacts with a glutamate.

Download this structure (catalase, 8cat) and view using PyMOL.How would you describe the quaternary structure of this protein? What about the tertiary structure?

Select
Show->cartoons Hide->Lines Colour->chain

This protein consists of two chains and these commands colour the two chains in green and blue rendering them as cartoons.

Now we will look at the specific residues forming the salt bridge. These are Arginine 111 and Glutamic acid 329.

Select residue 111 by typing
select resi 111
at the bottom left corner of the screen.
Now Show this selection as sticks and Colour->orange
Repeat for residue 329.

Look at the location of the arginine and glutamate noting how the charged ends of the sidechains are close to one another.