Linker

What are E/K Coils?

E/K coils are synthetic coiled-coil domains designed specifically to bind to each other with high affinity and specificity (Litowski and Hodges, 2002) (Figure 1). They are composed of a heptad repeat that forms a coil structures that are able to interact with each other. These coils are able to interact with each other in an anti-parallel fashion that makes them useful for applications such as peptide capture, protein purification and in biosensors. For our project we decided to make use of the IAAL E3/K3 coils due to the balance they offer between affinity and specificity (Table 1).

How do these Coils Work?

These E3/K3 coils are able to form heterodimers due to the hydrophobic residues contained within the heptad repeat. In our case these are isoleucine and leucine residues. Designated by empty arrows in the helical wheel diagram below (Figure 2) these residues form the core of the binding domain of the coils. In order to prevent the homodimerization of these coils charged residues are included in the design. The electrostatic interactions between glutamic acid and lysine residues prevent an E-coil from binding with an E-coil for example. We selected the use of E3/K3 coiled-coils over other synthetic E/K coils as the isoleucine residue present shows a significant increase in the heterodimer over valine found in other coils. The alpha-helical propensity of the residues outside of the core interacting residues is also increased by utilizing an alanine residue instead of the serine residue found in ISAL and VSAL E/K coils. This selection maximizes the stability and specificity of the coils used in our system.

So do these Coils Actually Bind?

After putting in gratuitous effort to build parts containing these coils and successfully purifying these proteins it was necessary to determine if the coils could actually bind to each other. For this purpose we prepared a preliminary qualitative blot assay that we could use as a foundation to gather more quantitative data in other assays in the future. In the case of the coils were were interested to see if the K-coil on a TALE protein could bind to the E-coil found on one of our Prussian blue ferritin constructs. To complete this task we placed the TALE on the membrane, washed and blocked the membrane. The ferritin protein with the complimentary coil was then added to the membrane. If this coil successfully binds the other coil then the ferritin will not be washed off during the next wash step. We can then see if Prussian blue ferritin is bound by adding a TMB substrate solution that will cause a colour change. To this extent we saw a blue ring in this trial indicating a positive result. This suggests that our coils are actually binding in an in vitro system.

Another interesting element of this assay that is interesting is why we used two variants of the TALE K-coil negative control. We feared that during the second protein application and wash step that some of the ferritin with coil proteins would drift over and bind to the TALE K-coils on the nitrocellulose. The blue ring suggests that exactly this occurred. This is why we performed this control in a separate tray. In this instance we did not see any colour rings. Another element of our system that was tested in this assay was whether or not a TALE by itself and a TALE fused with ferritin could bind separate target sequences on a strand of DNA. No positive results were seen for this assay. This could be due to a failure to bind or due to the lower catalytic activity of the Prussian blue ferritin we synthesized with fused TALEs. We will re-investigate this binding again in the near future.

Ferritin Scaffold

One of the previously mentioned coils, the E coil, will be attached to ferritin a ubiquitous 24-subunit iron storage protein. By attaching a K coil to our protein of choice, TALE, we can fuse this protein to our ferritin scaffold. By using this method, we can bind multiple reporter proteins to the ferritin as well in order to amplify our output signal. In addition, the use of coils for fusions avoids the possibility of our large fusion protein causing problems in protein folding and nanoparticle assembly. The result of this system is our DNA-binding protein, TALE, will be bound to ferritin, as well as multiple reporter proteins that can create an output for our system.

Upon further thought into this system, we determined the ferritin-coiled-coil system could be used for more than the detection of our E.coli sequence. We can use this system to detect other sequences of DNA by exploiting the ability of the TALE system to be easily engineered and modified, along with the interchangeability of the coiled-coil system. Thus by attaching K coils to TALEs that target alternative sequences, we can use this system as a platform for any variety of DNA sequences. Furthermore, we can expand this system towards proteins and other molecules as well by replacing the TALEs with antibodies or other binding proteins. This system shows the potential to bind a large number of ligands, only being restricted by the number of binding proteins that are currently known.

Another aspect of the ferritin nanoparticle that can be exploited is its composition, being composed of 24 subunits, as well as its potential as a novel reporter. Ferritin is typically composed of two chains, heavy and light. In our system, each one of these subunits can be bound to a reporter, effectively amplifying our catalytic activity by 24 due to the increased number of bound reporter proteins. But this activity can be scaled down through previously reported heavy-light chain fusions (Huh and Kim 2003). Rather than 24 subunits the nanoparticle would be reduced to 12 subunits, as in our system, and thus the number of reporter proteins would decrease accordingly. We can scale this down even further due to our ability to transform the iron core of the protein into a catalytic active substance called Prussian Blue (Zhang 2012). Thus, instead of multiple bound reporter proteins we can further scale down the output of our system to a system with essentially one reporter. The ability of our system to scale up and down according to the need of detection means this system is applicable in areas ranging from low sensitivity to high sensitivity.