Team:TU Dresden/Project/Results
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.
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.
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.
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| Affibody ZHER2 surface coloured by b-factor | Affibody ZHER2 structure coloured by b-factor | Affibody ZHER2 structure coloured by b-factor |
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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
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