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. 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.
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 of protein having the characteristic of layered backbones will be divided into three categories - predominately α-helix, predominately β-sheets and mixed α-helix and β-sheets.
Predominately 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.
- - transports oxygen in some lower animals. Notice that the change in direction produced by the loops creates the antiparallel conformation.
- - small peptide in humans that stimulates cell division and growth in select tissues.
- - stores molecular oxygen in muscle tissue. Structure of myoglobin is more complex, but again the striking feature is the antiparallel α-helices.
- - an α-helical barrel. Catalytic core of 1,4-beta glucan-glucanohydrolase from Clostridium thermocellum.
- - a novel structural motif. It is an iron-sulfur protein from Azotobacter vinelandii and involved in redox reactions of nitrogen fixation.
Predominately β-Sheets
- - 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. It is not as clearly defined as the parallel β-barrel, described above, but it is more common. You can look through the barrel whenever one of the open ends rotates to face the screen. An outer layer of α-helices is not present like it is in the parallel β-barrel, so the side chains projecting from the outer surface of the sheet are polar and make contact with water.
- - a mannose specific lectin from the bulb of snowdrop. A lectin is a protein that bind oligsaccharides and glycoproteins and is involved in cell-cell recognition. Notice the prism like shape that is formed by the β-sheets.
- - water soluble fragment (head) of the iron-sulfur protein from bovine heart. It is a component of Complex III of the mitochondrial respiratory chain.
- - from R. solanacearum. It is an example of a protein having a quaternary structure, in this case it is trimeric - . This type of structure is called a six-bladed propellor or β-propellor. Each subunit contributes two propellors.
Mixed α-helix and β-Sheet
- - forms the capsid of the virus. Again the α-helices, loops and turns are prominent features, and the α-helices are antiparallel.
- - integral protein from the outer membrane of E. coli. Since the barrel structure is inserted into the interior of the membrane, the outer surface that contacts the membrane must be largely , but the ends, which contact water, and much of the interior is . shown together.
- - Example of another lectin. Notice that the tertiary structures of the three lectins are different revealing that the structures can be different but yet have the same general function. There are two antiparallel β-sheets with the hydrophobic sides of the sheets facing each other. They are interlocking β-Sheets or have Greek Key Topology, i.e. 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. This protein is another example of interlocking β-sheet, two of the Greek key bilayers are connected by a looping peptide segment.
- - from B. stearothermophillus, a prokayote. The length of the long α-helix is invariant with other prokayotic L9 proteins.
- - 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, and the double winding is more extensive.
- - endoribonuclease from E. coli that cleaves the RNA strand of a RNA:DNA duplex and produces oligonucleotides. This activity is involved in bacterial replication and required for retrovirial infection. The E. coli enzyme is homologous with retrovirial proteins.
- - E. coli protein that binds DNA along with RuvB, a helicase, and both are involved in DNA repair, SOS response and DNA recombination. Residues 143-156 are misssing.
- - contains leucine-rich repeats.
