Secondary Structure
(Click and drag with the right mouse button to rotate the molecule for a better view of the repressor bound to the operon.)
The trp repressor is a biologically interesting molecule. It is involved in the regulation of transcription of the genes for the enzymes that E. coli need to make the amino acid tryptophan. The trp repressor regulates the level of tryptophan through negative control. When the concentration of tryptophan is high, the products of the genes are not needed and the repressor binds to the operon region of the genes, shutting off transcription.
The repressor is made as an aporepressor by a gene upstream of the trp operon. The aporepressor alone cannot bind to the operon of the trp genes. Tryptophan must be bound to the aporepressor. Tryptophan is a hydrophobic amino acid that occupies a hydophobic pocket in the aporepressor. When the tryptophan occupies the pocket, the shape of the protein is changed. This changes the conformation of the alpha helix that recognizes and binds to the DNA, allowing it to hydrogen bond with the operator.
The binding between the repressor and the ligand is not direct. The binding is facilitated by water through hydrogen bonds. This changes the conformation, allowing the repressor to bind to the DNA and block transcription of the trp genes. By rotating the molecule it will be evident that there are two protein molecules bound to the DNA. This is due to the fact that the trp repressor must bind to the DNA as a dimer in order to be effective. Each monomer of the repressor must have a tryptophan molecule bound to it.
Conformational Energy
The energy for the protein bound to the DNA was calculated. As expected, the calculated energy is negative, indicating that the protein is fairly stable in its bound conformation. However, the majority of the individual energy terms are positive and not as close to zero as expected. This indicates that the bond angles in this conformation are strained and that something else must be stabilizing the bound conformation. An energy minimization was attempted but failed.
Secondary Structure
It is clear from this display that the trp repressor is made of many alpha helices. The supersecondary structure is predominantly in the helix-turn-helix motif. This can also be visualized through the Ramachandran plot. It is apparent from the region around (-50, -45) that the majority of the protein is indeed right-handed alpha helix.
View Active Site
From the cartoon view it appears that the alpha helices of the protien contact the DNA at the DNA backbone. It is expected that the interaction between the protein and DNA backbone is facilitated by hydrogen bonds.
Use the left mouse button to pull up an option menu on the molecule screen to change the color scheme to Amino Acid.
In this view only the hydrogen bonds within the alpha helices of the protein are shown. The hydrogen bonds between the protein and the DNA and within the DNA double helix are not visible. This may be because many of the hydrogen bonds between the trp repressor and operator are facilitated by water. Since there are no water molecules in this rendition, the hydrogen bond interactions are not displayed.
Solvent-accessible Surfaces
View Active Site
The red dots on the above rendition of the molecule indicate the presence of oxygen, and therefore the presence of water. Clearly, solvent molecules are embedded between the two bound molecules, indicating that water may indeed facilitate the hydrogen bonding of the trp repressor to the trp operon.
The tryptophan contacts the pocket through Arginine 54 and Arginine 84, forcing the Arg residues apart. When it does so it points the alpha helix towards the major groove of the operator. Only one of the repressor-DNA interactions occurs between an amino acid and a nitrogenous base (through hydrogen bonds with water). For the most part, the repressor interacts with phosphates in the DNA backbone. Such interactions are not specific. However, the DNA in the operator is bent in such a way that allows an unusually large contact surface with the repressor. The contacts between the DNA and repressor protein are not direct, rather they are often facilitated by hydrogen bonds through water molecules.
Return to original view