Two Layers
The ribbons representing the backbones show the two layers of α-helices. The are shown in ball and stick with one layer colored green and the other cyan. Notice that these side chains are mostly located between the layers and that few are on the exterior of the molecule. The are now ball & stick, and they tend to be on the surface of the molecule where they can associate with . More clearly see polar groups on the surface by so that axis of helix aligns with z-axis.
Three Layers
Load the and rotate it to observe the three layers. Hopefully you positioned it similar to these . Show the hydrophobic residues in . With the CyanDark layer being the middle layer most of its side chains are nonpolar. The hydrophobic side chains are again nearly all located between the layers. Toggling spin off and rotating the structure to align the helical axis with the z-axis gives an even better view of this effect. Display the polar residues in . The polar side chains are almost exclusively on the surface of the molecule, and therefore the middle CyanDark layer has very few polar side chains.
Circular Layers
Load the . The circular layers formed by the β-sheet barrel (yellow) and α-helix barrel are clearly seen in this view, giving what would appear to be two layers. shows that hydrophobic residues occupy the central circular cavity as well as the space between the two circular layers. With this being the case one could say that the isomerase had four layers of backbone. . As the structure rotates one can see that most of the polar residues are on the surface, but there are few within the central cavity and between the two circular layers.
Five Layers
Load . Rotate the structure and attempt to identify the five layers.
The five layers are in colors Brown through Red. Display; it is not as obvious as with the previous proteins, but as the structure rotates one can see that most of the spheres are in the interior between the layers. Looking at the , as it rotates one can observe more spheres on the edges of the structure than were seen in the previous scene.
Other Examples
Other examples in this category of attractions formed between layers will be presented according to their content of α-helix and β-sheets.
α-Helix Predominate
The peptides in this class have a high contain of α-helix and because of the loops and turns which are present the α-helical strands will be antiparallel with respect to their adjacent strands.
- - transports oxygen in some lower animals. Notice that the change in direction produced by the loops creates the antiparallel conformation.
- - forms the capsid of the virus. Again the α-helices, loops and turns are prominent features, and the α-helices are antiparallel.
- - stores molecular oxygen in muscle tissue. Structure of myoglobin is more complex, but again the striking feature is the antiparallel α-helices.
Did you notice that the backbones of all of these can be divided into two layers?
β-Sheets Predominate
- - As its name implies this protein inhibits the enzyme trypsin, and this inhibitory effect must be deactivated in the process of preparing soybeans for use in animal feed, so that the proteins in soybeans are hydrolyzed by trypsin. This protein is an example of the antiparallel β-barrel because the circular antiparallel sheet is barrel shaped. As you can see it is not as clearly defined as the parallel β-barrel (see below), but you can look through the barrel whenever one of the open ends rotates to face the screen. Since an outer layer of α-helices is not present like it is in the parallel β-barrel, the side chains projecting from the outer surface of the sheet are polar and make contact with water.
- - Example of a lectin, plasma membrane proteins that bind oligsaccharides and glycoproteins and are involved in cell-cell recognition. There are two antiparallel β-sheets, and the hydrophobic sides of the sheets are facing each other. They are interlocking β-Sheets or have Greek Key Topology. Observe that after laying down a strand in a sheet, often the peptide chain loops over to the other sheet and lays down a strand in that sheet.
- - A protein that is a component of the eye lense. Look closely and you will see that this protein is another example of interlocking β-sheet, two of the Greek key bilayers are connected by a looping peptide segment.
In addition to having pure parallel β-sheets, some of the proteins in this class contain a β-sheet that has one or two antiparallel strands giving a mixed β-sheet. A characteristic of parallel β-sheets is that both sides of the sheet have hydrophpbic side chains[1]. A consequence of this is that parallel or mixed β-sheets must be located in the interior of the molecule. This type of sheet can not be on the surface exposing the hydrophobic chains to water.
Mixture of α-helix and β-Sheet
In the peptides of this class side-by-side strands of a β-sheet run in opposite directions. One side of the sheet will have polar side chains projecting from it, and the other side will have hydrophobic chains. The polar side of the sheet can be on the surface of the molecule, but the hydrophobic side must be covered with another nonpolar layer of side chains. Peptides in this class can have as few as two layers of backbone. The examples given below show the hydrophobic layer being covered in different ways. One of these methods result in a barrel or cylindrical shape. The barrel formed by the parallel β-sheet, as seen above, is more symmetrical, but the antiparallel β-barrel is more common. A second way is to cover the hydrophobic sheet with a layer of backbone made up of α-helices and extended loops. The third way is to form two interlocking antiparallel β-sheets or Greek Key Topology. The sheets are interlocking in the sense that after laying down an antiparallel strand in one sheet the peptide chain loops over and lays down an antiparallel strand in the opposing sheet.
- - The β-sheet of the barrel is parallel because after forming a strand of the sheet the peptide chain loops out, forms an α-helix and then loops back to form another strand of the sheet running in the same direction as the previous strand and, thereby, making the sheet parallel. Find the four layers of backbone in this example.
- - This type of structure is also called doubly wound parallel β-sheet because of the loops of α-helices on both sides of the sheet. In some cases these doubly wound sheets contain a few antiparallel strands forming a mixed β-sheet. Can you find the three layers of backbone in these doubly wound sheets contain?
- - There is one antiparallel strand in the sheet making it a mixed β-sheet, and the double winding is more extensive.
- - Redoxins are sufhydryl containing proteins that participate in redox reactions. Another example of a β-Barrel, in this case α-helices and loops help form the shape of the barrel. The α-helices aid in covering the hydrophobic side of the sheet.
- - Subtilisin is a bacterial protease, and this protein is an inhibitor of this enzyme. β-Sheet covered with α-helices and loops: As the structure rotates you can see the two distinct layers, an antiparallel β-sheet and the hydrophobic side of this sheet covered with a layer made up of α-helices and loops.
