Part D: Structure prediction and docking in Protean 3D

In this portion of the tutorial, you will use Protean 3D and the NovaApps to create a homology model of the sequence and simulate docking of the predicted antibody structures to the target epitope.

1. Launch Protean 3D and click the Structure Prediction tab on the left.

2. To create homology models of sequence you just exported from MegAlign Pro, choose New antibody structure with NovaFold Antibody. This launches the NovaFold Antibody wizard at the Sequences screen.

3. Click Add File and open Untitled1-ungapped-sequences.fasta. Click Submit to begin the antibody model prediction. Once you see the Close button, press it.

4. To see the status of the prediction, click on the Predictions tab. This prediction will take approximately 20 minutes. Once the prediction is complete, a blue link will appear under Status.

5. Click the blue link to open the structure in Protean 3D.

6. Save the structure using File > Export Data > Export Structure.

In the next steps, you’ll be using NovaDock to simulate docking of the predicted antibody structure to its target epitope. In real life, you could use the file you just exported. However, this tutorial utilized artificial reads, so that exported antibody does not correspond with a known antigen. Therefore, the rest of this tutorial will use separately provided antibody and antigen structures.

7. Choose Structure > Predict Structures > New Protein-Protein Complex with NovaDock.

8. In the Structures screen, click Enter.

9. In the Receptor section above, Browse to the file 4TSB-selA.pdb. In the Ligand section below, Browse to the file 4TSB-selHL.pdb. Press OK.

10. Press Submit to begin the prediction. When the Close button appears, click on it.

11. Use the Predictions tab to monitor the prediction status. This prediction will take approximately 7 hours. When the prediction is finished, you will see a blue link in the Status section with the word “Energy” in it.

12. Click on the link to open the docking model predictions in Protean 3D.

13. Open Model 1 by clicking the link Open model in new document.

14. (optional) Explore the antigen/antibody interface by doing one or more of the following:
    
    
    • Use View > Style > Rendering to apply a Surface to the sequence.
      
      
    • Use View > Style > Sequence, then choose Color by Track from the drop-down menu. By choosing different types of tracks, you could ascertain, for example, that the molecule is binding to the epitope in an area with a polar charge difference.
      
      
    • Find residues within a specified number of angstroms of any selected residue. To do this, select a residue in any view, then choose Structure > Select Neighbors. To change the angstrom value, choose Edit > Preferences, then choose Proteins from the left. Change the Cutoff distance value as desired. You could then use the Style panel to color the selected neighboring residues differently from other parts of the molecule.
      
      
    • Export the data in .csv format using File > Export Data > Export Report.