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Monday, March 10, 2008

β Strands and β Sheets

The &alpha helix is one form of secondary structure in proteins. When a polypeptide chain contains the right sequence of amino acids it can adopt a helical conformation.

There are other conformations commonly found in proteins. One of them is the β structure, which is characterized by long extended polpeptide chains in contrast to the compact helix of the α helix. Single β strands are rarely found in proteins because the structure is not that much more stable than a random coil. However, when two adjacent β strands line up they can from bridges of hydrogen bonds. This creates a very stable structure known as a β sheet. In the example shown (left) three parallel β strands line up edge to edge to form a highly stable sheet with multiple hydrogen bond (shown in yellow).

β sheets can also be formed when antiparallel β strands align edge to edge. As a matter of fact, the antiparallel conformation is more stable, and more common, than the parallel conformation.

β strands are usually drawn as wide arrows with the tip of the arrow head representing the C-terminal end of the polypeptide chain. As shown in the cartoon on the right, the strands are often twisted and the amino acid side chains project above and below the plane of the β strand.

The amino acid composition of β strands tends to favor hydrophobic (water fearing) amino acid residues. The side chains of these residues tend to be less soluble in water than those of more hydrophilic (water loving) residues. As you might imagine, β structures tend to be found inside the core structure of proteins where the hydrogen bonds between strands are protected from competition with water molecules.

One of the common motifs in proteins is the β sandwich, formed when two β sheets are stacked on top of one another. The example shown below is the coat protein of grass pollen grains [PDB 1BMW]. For those people who are allergic to grass pollen, this protein is the main culprit. This example is the simplest form of a β sandwich since each sheet consists of only two β strands.

In order to appreciate why this is such a stable (and common) motif we need to add in the amino acid side chains. (They are usually ignored in the kinds of structures shown above so we can trace the polypeptide backbone.) In the figure on the right I've drawn the hydrophobic side chains in blue so you can see how they cluster together to form the interior "filling" of the sandwhich. You can think of these hydrophobic regions as being like the oil in a mixture of oil and water. The oil droplets tend to come together to exclude the water molecules. Similarly, the hydrophobic residues tend to come together in the middle of the protein and exclude water molecules. This is called hydrophobic interaction and it's one of the dominent weak forces n biochemistry.

Most proteins are made up of combinations of α helices and β strands. The third kind of secondary structure is turns.

[Figures are from Horton et al. (2006) © Laurence A. Moran, Pearson/Prentice Hall]

Horton, H.R., Moran, L.A., Scrimgeour, K.G., perry, M.D. and Rawn, J.D. (2006) Principles of Biochemisty. Pearson/Prentice Hall, Upper Saddle River N.J. (USA)


Sparky said...

That's a good introduction to this structural element. I especially liked the discussion of amphipathicity in strands. Showing an integral membrane protein like porin might reinforce the point, while also displaying part of the great diversity of structures possible with β strands.

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heyitsezra said...

Great post, I'm taking biochem and this as very useful.