Globular Proteins

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.

Non-stabilizing Layers

Load . Even though backbone layers can be identified in these molecular structures, the layers are not extensive enough and/or positioned well enough for the hydrophobic side chains to have significant interaction so the hydrophobic attractions do not make a major contribution to their stability. Display . There are fewer hydrophobic side chains in the interior, and therefore weaker hydrophobic attraction, so the major force involved in maintaining the tertiary structure is the covalent Disulfide Bonds (yellow rods) which were not present in the examples covered above. As one would expect the are plentiful on the surface of the protein.

Antiparallel α-Helix

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. The examples which follow are colored N-C rainbow so that the N-terminus and C-terminus of the α-helices can be determined. The amino end of the protein starts with Blue, and moving to the carboxyl end of the peptide the coloration proceeds through the colors of the rainbow and ends with Red. Comparing the colors which are present at the ends of a helical strand one can determine which is the N-terminus and C-terminus, and thereby determine if adjacent helices are parallel or antiparallel.

• - transports oxygen in some lower animals. Notice that the change in direction produced by the loops creates the antiparallel conformation. Color as .
• - 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?

Parallel or Mixed β-Sheets

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.

• - 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.

Antiparallel 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.

• - 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, and as you can see it is not as clearly defined as the parallel β-barrel, but you can look through the barrel whenever one of the open ends rotates to face the screen. Notice that an outer layer of α-helices is not present like it is in the parallel β-barrel.
• - 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.
• - 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.

The metal-rich and disulfide-rich proteins have some characteristics in common. Some of the proteins in these two classes are small in size and therefore do not have large amounts of backbone that can be organized into layers. Others have significant layers of backbone, but the layers are not well organized, and therefore the side chain interactions are not strong. For the proteins in this class, the disulfide bonds or the bonds formed between metal ions and ligands are as important or more than the hydrophobic interactions of the side chains.

Disulfide-Rich Proteins

• - Among its functions is the regulation of glucose uptake by cells. Small peptide contains A and B chains that are connected by disulfide bonds, and the tertiary structure of the A chain is also held in place by a disulfide bond.
• - Plant seed peptide. Small single chain peptide with no significant backbone layers but has disulfide bonds to stabilize the tertiary structure. Disulfide bonds, also, have an important role of keeping the relatively high proportion of loops in place.
• - Part of a class of hydrolases that degrade glycerophospholipids. This one specifically hydrolyzes the second acyl group on the glycero group. This example is larger than the other two, but it still does not have well organized backbone layers in part due to the extensive loops.

Metal-Rich Proteins

• - An iron-sulfur protein that has an unusually high redox potential. The Fe's of the iron-sulfur (yellow) center are complexed with the side chains of Cys which are part of different loops of the peptide. Without a large number of hydrophobic groups to form attractions these sulfur-metal bonds are important in maintaining the tertiary structure.
• - Protein with two iron-sulfur centers; the major function of iron-sulfur proteins is involvement in redox reaction. Both iron-sulfur centers are complexed with the side chains of Cys and aid in maintaining the tertiary structure.