As proof of concept of our lab project and to show the possibilities of interactions between aptamer and biomarker, we simulated the docking between aptamer and biomarker via online protein docking server HDOCK and visualized using Pymol. With guidance from the Tokyo University of Agriculture, we were able to show the possibility of our aptamer-biomarker complex.
We were able to find existing PDB files for all three of our biomarkers: Mammaglobin B, HER-2, and Mucin 1. However, we could only find a PDB file for one of our aptamers, MUCIN 1.3 (2E7V)—so we needed a solution to predict the 3d structure of our aptamers before simulating docking on HDOCK. To do this, we used the following servers:
As a quick summary of the servers, we predicted the secondary structure of our aptamer from the DNA sequence using the first server above. Next, the structure was converted to dot bracket format using CT2Dot. Finally, 3dRNA combined the dot bracket information with the aptamer DNA sequence to predict the top models for our 3D aptamer structure and produced a PDB file.
Next, we used HDOCK, a server by the School of Physics Huazhong University of Science and Technology. The server uses “docking based on a hybrid algorithm of template-based modeling and ab initio free docking” in order to predict protein-protein and protein-DNA interactions.
The server contains 4 different available inputs, including a PDB file option which we used for both our aptamer (ligand molecule) and biomarker (receptor molecule). The server will then return the top 100 scored predictions (with an example of interaction between HER-2 and aptamer #5) which can be downloaded in a zip file. The receptor-ligand interface value pairs are also provided with the output (shown below) , which can then be used to show the specific locations of interactions between the aptamer and biomarker on PyMol.
On PyMol, we took the top scored prediction from HDOCK and selected the sequences respective to the receptor-ligand interface residue value pairs to visualize the regions of interest. The image shows the selections of regions of the HER-2 and aptamer #5 ( as a continuation to the image above)
Below is the image of our final model of the interaction between HER-2 (blue) and aptamer HeA2_1(red), with the yellow region as the interaction sites.
We completed the sames steps for each of the other models, which are shown below: