Difference between revisions of "Part:BBa K1189010:Experience"
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| − | 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 | + | 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 a 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 (BBa_K118901, BBa_K1189011) due to the balance they offer between affinity and specificity (Table 1). |
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Latest revision as of 15:56, 1 September 2015
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Team Wageningen UR 2012 worked with E/K coil pairs, however only submitted a single E coil fused to GFP. As these parts are only useful when the complementary coil is used, and order for these parts to be more capable of being used for a wide variety of dimerization and tagging purposes on any protein of interest, we have submitted the E and K coil parts on their own (with Frieburg cutsites to allow for protein fusions to be created), with His tags in order to allow for protein purification, and with GFP fusions to allow for tagging of proteins with a reporter.
Team Queens Canada 2015 also worked with the E/K coil BioBricks. We submitted an E coil fused with Type III Antifreeze Protein, an E coil-Antifreeze Protein with a His tag, and a K coil with a T3-10 Scaffold subunit protein plus His tag. However, we noticed a discrepancy in the main description of Calgary's E/K coils. The nature of Calgary’s project placed the E-coil on the N-terminus of the ferritin scaffold and the K-coil on the C-terminus of the TALE proteins. Thus while the interaction appears anti-parallel in their design, the orientation of the coils relative to one another are parallel. Therefore, The E/K coil system presented interacts in a parallel fashion, in a strong, highly specific coiled coil motif (Lindhout et al. 2004). The NMR-resolved structure of this heterodimer is shown in the PDB file for the motif, 1U0I, demonstrating the parallel nature of the interaction. This is an important note in considering the use of these BioBricks in the design of an attachment mechanism for proteins. We have corrected this in the parts' main pages.
Applications of BBa_K1189010
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 a 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 (BBa_K118901, BBa_K1189011) due to the balance they offer between affinity and specificity (Table 1).
Figure 1. Ribbon visualization of the E3/K3 IAAL coiled-coils.
| Coil Name | Peptide Sequence |
| IAAL E3 | NH2-EIAALEKEIAALEKEIAALEK-COOH |
| IAAL K3 | NH2-KIAALKEKIAALKEKIAALKE-COOH |
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. These parts were already in the registry, however the DNA was never received, so we built, sequenced and re-submitted them.
Figure 2. A helical wheel representation of the IAAL E3/K3 coiled-coil heterodimer viewed as a cross-section based off of a similar figure created by Litowski and Hodges (2002). The peptide chain propagates into the page from the N- to the C- terminus. Hydrophobic interactions between the coils are indicated by the clear wide arrows. The intermolecular electrostatic interactions between the coils are displayed by the thin curved arrow (eg. Between Glu15 and Lys20) Letters a, b, c,and d designate the positions of IAAL repeat in the heptapeptide. The e and g positions are occupied by the charged residues.
We evaluated the binding of our coils using other constructs that make use of the E and K coil parts submitted. In the case of the coils we were interested to see if the K-coil fused to TALE proteins (BBa_K1189029, BBa_K1189030) could bind to the E-coil found on one of our Prussian blue ferritin constructs (BBa_K1189018). 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 to 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 is why we used two variants of the TALE K-coil negative control. A blue ring on our TALE negative control confirmed our fear 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. This did not occur for our separate negative control (Figure 3).
Figure 3. This basic qualitative assay was used to inform us whether certain elements of our system are able to bind to each other. Our TALE proteins were mounted to the membrane along with positive controls of three Prussian blue variants; two recombinant ferritins and one commercial protein. The membranes were then washed and blocked. Prussian blue ferritin with a coil was added to our TALE protein containing a coil. Prussian blue ferritin with a TALE that could bind to the DNA held by another TALE on the membrane was also added. A TMB substrate solution was added to cause a colourimetric change over 5 minutes. Positive results are indicated by dark rings of colour. Negative controls include a TALE with a coil on the same membrane and the same TALE and bovine serum albumin on separate membranes that were treated separately. Image contrast was altered to make the results more clear on a digital monitor; the same changes were applied to each element of the figure.
We also performed an immunoprecipitation assay to demonstrate the binding of the E/K coils (Figure 4.)
Figure 4. Assay showing coiled-coil interaction in vitro. Crude lysates from a negative control (RFP), GFP-Ecoil and His-Kcoil were combined together to investigate interaction and immunoprecipitated with GFP or an isotype control and then further probed with α-His antibody. Only in the presence of both GFP and a His tag we see a band indicating interaction.
We also performed an assay using the kinetic activity of Prussian blue ferritin which revealed that using coiled-coils to connect the TALE proteins to ferritin was much more effective than using direct fusions of TALE proteins (Figure 4).
Figure 4. Samples of our parts that were converted to Prussian Blue ferritin were mole balanced in order to ensure that the same number of effective ferritin cores are present in every sample. Additionally the ferritin-coil fusion was incubated with the TALE-coil fusion part in order to allow their binding for a separate trial. Negative controls include unconverted recombinant ferritin, bovine serum albumin and a substrate only control. Samples were incubated with a TMB substrate solution for 10 minutes at a pH of 5.6. Absorbance readings were taken at the 10 minute time-point at a wavelength of 650 nm. An ANOVA (analysis of variants) was performed upon the values to determine that there was statistical difference in the data gathered (based off of three replicates). A t-test was then performed which determined that the * columns are significantly different from the ** column (p=0.0012). Neither * column is significantly different from each other (p=0.67).
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