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 and not between the layers. 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. 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 an α-helix strand will be antiparallel with respect to its 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 confirmation.

• Tobacco mosaic virus protein - forms the capsid of the virus. Again the α-helices, loops and turns are prominent features, and the α-helices are antiparallel. Protein Explorer did not recognize the β-sheets that are present in Figure 6.29 of (1).

• Myoglobin - stores molecular oxygen in muscle tissue. Structure is more complex, but again the striking feature is the antiparallel α-helices. Also notice that the backbone can be divided into two layers.