My favourite… protein structure.

A bit of deadly but beautiful biology…

Crystal structures are intricate models of great complexity and beauty. Some of them may simply just resemble 3 dimensional squiggles that happen to bring the right combination of molecular groups together in space to allow some funky chemistry to happen, or some highly specific binding event. Some other them, however, look like pieces of art…

Bacteria are scavengers – tiny little single celled organisms whose raison d’etre is to proliferate, thrive and survive. (This is also your raison d’etre, but humans have developed all sorts of clever distractions to make us think that life is something more that just an advanced way of passing genetic information from generation to generation.) In order for bacteria to do this, they need lots of  chemicals – both to metabolise for energy and to serve as building blocks for components they need to fulfil their task.

It just so happens that nature has provided bountiful supplies of those chemicals almost everywhere you look – Us.

Human (and indeed all animal) cells are essentially bags of chemicals – exactly the chemicals that are so highly prized by bacteria. Which is why the bacteria have devised many cunning ways of extracting those chemicals from the bags in which they reside – one of the more formidable weapons in the bacterial arsenal is that of the “pore forming toxin” or PFT.

Pore forming toxins do exactly what they say on the tin – they form pores in cell membrane. In the short term, these pores will lead to nutrients flowing out of the cell – where the bacteria can get hold of them. In the long term, loss of membrane integrity often leads to the death of the cell – important cellular processes stop due to lack of important chemicals, and the concomitant influx of water into the cell makes it swell uncontrollably and burst – even more goodies for the bug to get hold of!

PFTs are interesting proteins to work with – partly because they are schizophrenic. They have a happy and often easy to handle soluble form, where then generally exist as single molecules (monomers) and act as normal soluble proteins. Then they have a hydrophobic (water “hating”) pore form, where they exist as large complexes (multiple proteins join together) to form the active pore. The pore mode is generally a pain in the backside to work with, as they aggregate and precipitate very easily. As a result of this, many crystal structures of PFT tend to capture them in the soluble state. However, there is one very notable exception to this rule.

In 1996, Song et al crystallised α-hemolysin (grr, US spelling) and managed to isolate it in the pore conformation. And it’s a beaut.

Sometimes crystal structures need months of evaluation and further experiments to determine the implications of the structure and develop a full picture of how the protein accomplishes it’s biological role.

Fig1: alpha-hemolysin's stalk is perfectly designed to span the plasma mebmrane of eukaryotes

In the case of α-hemolysin, one look is all you need – it is (hopefully) very obvious how structure relates to function.

To get a better sense of the 3D-nature of this beasty, I’ve knocked up a quick animated gif – view here (give it a while – it’s a bit jerky to start with)

7 monomers (each a different colour in the figures) come together in a ring – each monomer donates 2 -beta- hairpins – these form the ‘stalk’ that protrudes from the bottom of the structure. This stalk is hydrophobic/lipophilic, and is 2.8nm long. The cell membrane it’s designed to punch though? Made of lipids and ~2.5nm deep. So the stalk of the protein has just the right dimensions  and chemical composition to span the membrane of your cells.

Fig 2: Looking down alpha-hemolysin's pore...

In figure 1, what you can’t see is the pore – running from top to bottom of the stucture – figure 2 shows this better. It’s identical to figure 1 but rotated 90º top-towards you.

You can see that right though the middle of the structure is a hole – the pore through which the nutrients flow out, and water flows in.

The 7-fold rotational symmetry (a bit of a rarity) also adds to the curious attraction of this molecule.

Anyway – ever since I first stumbled across this structure in 2000, it’s been my favourite, even though my own attempts to replicate it failed. ( or did they? – work still in progress 😉 )

In my humble opinion, this structure is one of the best example of how the structure of a protein is related to its function, and also how well adapted bacteria are to explioting host biology.

EDIT – Since I did this, the wonderful guys at proteopedia have been in touch via the medium of twitter (@proteopedia) about using this as a basis for a page on α-hemolysin. If you’re interested, follow them on twitter and have a look around the proteopedia wiki. Good page to start with is ‘the ribosome

3 Responses to My favourite… protein structure.

  1. Fascinating! I wonder how this method of breaking cells open like piñatas evolved…!

    • xtaldave says:

      Weeellllll… it is hypothesised that these proteins evolved from proteins that cross membranes for more benign reasons, like transporter proteins…

      But PFTs are only one part of the bacterial arsenal:

      Binary (sometimes called AB) toxins consist of a pore forming toxin + an enzymatic payload that gets delivered into the target cell to disrupt function from inside the cell.

      Proteases that degrade target proteins.

      Phospholipases that degrade target cell membrane.

      Superantigens that cause a massive, misdirected immune response (particularly nasty).

      They are sneaky little buggers!

  2. Wayne says:

    Thanks for the plug you added in the ‘EDIT’.

    Plus, I recently upgraded into a full topic page the page I began using yours as a starting point. So it is no longer at the page associated with the pdb file 7ahl; however that directs people to the topic page at

    We’d still love you to come on over and contribute and we thank you for directing your readers to our site.

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