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, compare this scene with a similarly aligned display of the hydrophobic side chains.

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 Helices

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 turns and 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 binds 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.

Disulfide-Rich Proteins

• - Among its functions is the regulation of glucose uptake by cells. The 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.

Intrinsically Unstructured Proteins

• , lymphoid enhancer-binding factor 1. LEF-1 is missing residues 26-47, and these residues are most likely missing because they form an unordered segment. Fill in this gap in your mind's eye, and you will see the large with which LEF-1 (yellow) binds to β-catenin. Apparently the binding strength of the missing segment is such that it is not converted to an ordered segment. You may notice that residues 550-561 of β-catenin are also missing, again an unordered segment.
• - Domain N2 of synaptosomal-associated protein 25 (blue) from human bound to botulinum neurotoxin type A light chain (botox) from C. botulinum. shown unbound but having the same conformation as the bound peptide.
• - SMAD Anchor for Receptor Activation SMAD-Binding Domain bound to SMAD2 MH2 domain. SARA SBD is the domain of the receptor that binds SMAD, and thereby activates the transforming growth factor-beta signaling pathway. shown unbound and displayed as cartoon but having the same conformation as the bound peptide.
• - Hypoxia-inducing factor 1α (C-terminal activation domain) bound to transcription activation zinc finger domain of CREB-binding protein. shown unbound and displayed as cartoon but having the same conformation as the bound peptide. The data of this model was generated NMR analysis of an aqueous solution of the peptides, and the analysis is rapid enough to distinguish the vibrations of the peptides so that more than one model is produced. It is possible to animate these multiple model and simulate the vibrations of the peptides. Notice that the vibrations are the greatest in the molecules where the attractive forces are the weakest. Animate peptides: Unbound ; Bound
• - Cyclin-dependent kinase 2 bound to its activator cyclin A and both bound with a fragment (blue) of p27 which is a kinase inhibitor. Cyclin-dependent kinases have an important role in moving the cell from one phase of the cell cycle to another. shown unbound but having the same conformation as the bound peptide.
• - different data file than the one above containing a smaller fragment of p27 bound to complex. shown unbound but having the same conformation as the bound peptide. Compare the conformation of this small fragment to that of the yellow colored fragment shown unbound above. Since the binding site is the same in both models when the peptides bind, regardless of the length, the peptides generate the same conformation.