Tutorial developed by Ross Feldberg, Dept. of Biology, Tufts University
A second major regular secondary structure is the beta strand. Often, several beta strands lie alongside one another to form a structure known as the beta sheet. Beta strands are sequences generally 5-10 amino acids in length in which the bond angles along the peptide bond give rise to an extended conformation in which the amino acid side chains (R groups) point alternatively above and below the plane of the strand. Although in textbooks beta strands are generally drawn as linear and flat, in actual proteins they tend to have bends and adjacent strands tend to lie not in a single plane, but to take on a twist. H bonds between amino hydrogens and carboxylic oxygens takes place between chains rather then within a single chain (as seen with the alpha helix)
Back to beta tutorialThe beta strand shown here is made up of residues 37 to 46 in the ras protein. Note that the peptide backbone is not completely extended, but takes on a slight zig-zap (pleated) chain. Beta strands are generally protrayed in textbooks as long linear extended sheets. Is that the case for this strand? The peptide backbone (HN-Ca-CO) is emphasized by being represented by a thicker bond. When the animation is over, rotate this structure until you are looking down its long axis. How long is the linear part of this beta strand? What is the disposition of the R groups along the strand? Why do you suppose the amino acid sidechains are arranged in this way? By clicking on a carbon, you can identify the amino acid. Can you identify the carboxy end and the amino ends of this beta strand?
By convention, beta strands are represented as broad yellow arrows in which the arrowhead is the carboxyl end of the peptide. How do we decide which end is the carboxyl end? (hint, you will have to go back to button one to answer this).
In the context of the protein in which this strand is found, it lies next to another strand of beta sheet, the two strands lined up antiparallel (i.e. tracing the peptide amino to carboxyl end, one strand runs right to left, while the other runs left to right in going amino to carboxyl terminus). The blue loop is termed a beta bend and consists of asp47 and gly48. Glycine is a compact amino acid (R = H) and is required to design a sharp bend to allow to beta strands to run antiparallel. Again notice that the two beta sheets do not lie on a perfectly flat plane, but that each has a definite bend and the two sheets together have a distinct twist to them.
This view shows the two chains. Unlike the alpha helix where H bonds occur between groups in the same chain, in beta sheet H-bonds form between amino hydrogens and carboxylic oxygens on different strands. Two H-bonds are shown here in green. How many H-bonds total could form between these two strands?
In this protein a third beta sheet is associated with the first two. Note that the backbone is fully extended and that R groups do project alternately to opposite sides of the backbone. It is difficult to make out the beta sheets in wireframe representation, but in cartoon representation it is clear that strand 3 is parallel to strand 2 and antiparallel to strand 1 and the three strands define not a simple flat plane as implied by most books, but a sheet with both a bend in each strand and an overall twist to the sheet.
This view shows more of the structure which includes the first 59 amino acids of the ras protein. This region contains not only the three beta sheets reviewed above, but also a segment of alpha helix in residues 16-25. Random coil is shown in white while turns are shown as blue.
This view shows the region of secondary structure we have been examining (residues 1- 59) in the context of the whole ras protein and the GTP cofactor. Residues 1-59 are shown in cartoon form while the rest of the protein is displayed as a backbone chain with alpha helix in red and beta sheet is yellow. In addition, the GTP cofactor for this protein is displayed as spacefill and colored green. Note where the cofactor binds relative to the beta sheet and alpha helix. Do you see any other beta sheet structures in this protein? If so, what is their relationship to the sheet we have been examining? Do you suppose this beta sheet structure might have any amphipathic character? Use the Chime Menu (Display) to change the overall representation to Cartoons. What is the order of beta structure and helices in ras protein?