By Timothy Providence, Leonard Arthur and Francis Insaidoo
The E. coli genome contains over 3000 genes. Not all of these genes are needed at any one. It would be energetically inefficient for the E. coli to use all of the genes at one time. Some method is needed to regulate gene activity within a cell. One of the main transcription regulators are repressor proteins.
There are several repressor proteins that bind tightly to specific sites on DNA. These include RNA polymerase, lac repressor, trp repressor, lamba repressor and the 434 repressor. The 434 repressor is a phage repressor that has characteristics similiar to the Lamda repressors and other known repressors.
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The 434 repressor binds as a dimer. This is shown by the green and yellow protein structures. 434 binds with a section of DNA known as 14-mer. The DNA strands(which are shown in varing shades of blue) are slighty distorted as the protein complesexs.There is a noticeable overall bend in the DNA and a narrowing of the minor groove at the center of the model.
The space filling computer model of the distorted DNA in the 434 repressor-DNA complex shows the repressor-DNA complex with a repressor in white, red and blue. Notice how the DNA conforms to the shape of the protein to promote intimate with the two. Careful looking shows an amino group projected into the minor groove of the DNA near the center of the 434-repressor complex.
The active site of 434 repressor
The structure above shows the 434 repressor fragments-DNA fragments show close interaction between several amino-acid groups, phosphates and/or phosphate groups in the DNA backbone. This, therefore, implies that there is possible hydrogen bonding interaction between the protein and DNA at these sites. Further studies also have revealed a potential van der waals interaction between the amino acid and the basis of the operator. There is also an ionic interaction between the positively charged protein and the negatively charged DNA molecule.
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*Space filling
* van der waals Radii
The tight binding of this fit is accurately portrayed in the view. The close proximty between the molecules means that van der waals forces are a part of the binding.
The Ramachandran plot below shows a large degree of right-handed alpha helices, a relatively small beta sheet, and significantly small left- handed alpha helix. This consistent with literature survey which shows 434 repressor to consist of four alpha helices and no beta sheets. However, the Ramachandran plot gives us some possibility of beta sheets principally or primarily due to the amino-acid sequence that makes up the 434 repressor. The small possibility of forming the left-handed alpha helix is valid given the fact that the amino acids are taken from nature and are structurally prone to forming right handed alpha-helices instead of left-handed Alpha-helices
The shot below shows a a structure of the minimize bonding energy of the 434 repressor-DNA complex. A summary of the different energy components are shown below. It should be noticed that electrostatic interactions comprise a large section of the of the bond. It is this electrostatic interaction between the positive charge on the protein and the negative charge on the ion.
Bond energy 152.6088
Angle energy 700.2420
Dihedral energy 448.5768
Improper energy 197.5887
Leonard-Jones energy 1052.3584
Electrostatic energy -4351.6763
Constraints, other 0.000
It is energetically favorable for cell to selectively express or suppress genes. This seems to be the primary action of the 434 repressor as well as the other repressors about. The mode of binding either hydrogen bonding, electrostatic or van der waals makes it less expensive to fund the binding. Addtionally, the other alpha-helices bind in a specific way to hold the active units that engage in the DNA-protein interaction in the groove. Ramachandran plot shows that the protein contains mostly right-handed alpha helices. This is acceptable because it would take alot of energy to change conformation to adopt a different shape. The energy values for the protien are also very important. They indicate that the binding interaction is mostly electrostatic interactions between the protein. The electrostatic interaction is aided by the abililty of the protien to fit within the minor groove of DNA. Hence, the reverse reaction is also feasible because the reverse reaction is also possible because once the operator molecule binds with the complex it's shape will change in a manner that will remove this fit.