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).

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Practical work

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

• In the RasMol command window, type:
  select *
• From the menus, select:
  Display->Wireframe
  Colours->Monochrome

This has the effect of rendering the whole structure in white wireframe (note that the first two steps are not necessary if you have just loaded the structure).

• In the RasMol command window, type:
  select arg or lys
  colour blue
  select asp or glu
  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.

• In the RasMol command window, type:
  select *
• From the menus, select:
  Display->Cartoons
• In the RasMol command window, type:
  select (arg or lys or asp or glu) and (sidechain or *.ca)
  wireframe 50

Here you have rendered the whole structure as cartoons then selected the sidechain and alpha-carbon atoms from the charged residues and rendered them in thick wireframe. The SELECT command is rather complex - ask a demonstrator to explain it!

Using this alternative rendering scheme, you may find it easier to see where the charged sidechains lie.

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

View this structure (catalase, 8cat) using RasMol.

• From the menus, select:
  Display->Cartoons
• In the RasMol command window, type:
  select *:a
  colour green
  select *:b
  colour cyan
  select 111:a
  colour blue
  spacefill
  select 329:a
  colour red
  spacefill

This protein consists of two chains and these commands colour the A chain in green and the B chain in cyan rendering them as cartoons. Arg-111 in chain A is then spacefilled and coloured blue while Glu-329 in chain A is spacefilled and coloured red.

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

The residues, particularly the glutamate, may not look particularly buried, but try the following:

• In the RasMol command window, type:
  select *
• From the menus, select:
  Display->Spacefill