Results

Correct folding study of target protein

Structure analysis of our targets and their interactions

Interactions of HER2 and its affibody

After definition of the interfaciual atoms, electrostatic interactions in the interface can be defined and visualized as shown in Figure 1.

Figure 1 - Electrostatic interactions between HER2 and its affibody.

Conservation study of HER2

The conservation study of HER2 was performed using 11 structures from different organisms. The multiple sequence alignment which is required for the calculation can be seen here. Looking at the binding interface of HER2 and its affibody, we can state that the regions where both get into contact are rather conserved.

Figure 2 - HER2 conservation - calculated using 11 HER2 structures from different organisms.

Visualization of the B-factor for the affibody ZHER2

In crystallography the B-factor, also called temperature factor or "Debye-Waller factor", describes the displacement of an atom from its mean position in a crystal structure. The displacement may be the result of temperature-dependent atomic vibrations or static disorder in a crystal lattice. Static disorder means that some regions of the molecule may adopt different conformations in different copies of the molecule, each molecule's conformation being relatively stable. In the case of our affibody static disorder is not so probable, since it is a very small protein, designed to adopt a stable conformation.

Reflecting the disorder of an atom, the B-factor is therefore an indicator for flexibility caused by thermal motion.

As depicted in the following pictures the affibody has low B-factor values, meaning that it stays in a stable position without any larger fluctuations (indicated by the blue color). Only at the ends of the molecule a slight increase of the B-factor can be stated. This is normal and due to thermal motion, since the atoms have less interaction partners there, which can hold them on place. This stable position of the affibody suggests a high binding affinity at this position.

Affibody ZHER2 surface coloured by b-factor	Affibody ZHER2 structure coloured by b-factor	Affibody ZHER2 structure coloured by b-factor

Video

The following video shows the structure of the extracellular regions of HER2 with the affinity matured 3-helix affibody ZHER2 (PDB-ID: 3MZW) and focuses on their interaction, whereas hydrogen bonds are represented as dashed yellow lines and then the complete interacting interface is represented as surface, colored by atom type (N-blue, O-red).

Investigation of P3 threshold for E. coli resistance

Conversion of BACTH into an iGEM standard and analysis of function

Set up of flow system

Here you can describe the results of your project and your future plans.

What should this page contain?

• Clearly and objectively describe the results of your work.
• Future plans for the project
• Considerations for replicating the experiments

Project Achievements

You can also include a list of bullet points (and links) of the successes and failures you have had over your summer. It is a quick reference page for the judges to see what you achieved during your summer.

• A list of linked bullet points of the successful results during your project
• A list of linked bullet points of the unsuccessful results during your project. This is about being scientifically honest. If you worked on an area for a long time with no success, tell us so we know where you put your effort.

Inspiration

See how other teams presented their results.

• 2014 TU Darmstadt
• 2014 Imperial
• 2014 Paris Bettencourt