Herceptin ADCP MOA
Client:
Amami Antia-Obong
Programs used:
Uniprot, RCSB, PDB, VMD,
Swiss-Model, Alphafold, & Cinema4D
Role:
Research, 3D Modeling, Animation,
& Molecular Visualization
Target Audience:
HCP
The aim of this animation was to accurately and concisely visualize the disease state of HER2+ breast cancer and its molecular underpinnings in an interesting and engaging manner. A key challenge during its development was visualizing the HER2 protein receptor in its entirety. No entry in the RSCB Protein Data Bank currently exists (Figure 3).
The following research process was implemented to ensure both the accuracy of the binding complex between HER2/Trastuzumab (Figure 1) and HER2’s protein structure (Figure 10).
The aim of this animation was to accurately and concisely visualize the disease state of HER2+ breast cancer and its molecular underpinnings in an interesting and engaging manner. A key challenge during its development was visualizing the HER2 protein receptor in its entirety. No entry in the RSCB Protein Data Bank currently exists (Figure 3).
The following research process was implemented to ensure both the accuracy of the binding complex between HER2/Herceptin (Figure 1) and HER2’s protein structure (Figure 10).
Research
The complex shown above, was downloaded from the RCSB Protein Data Bank and exported into VMD to understand and later visualize the binding complex between the HER2 protein receptor and the Herceptin antibody (Hao, Y. et al., 2019).
Figure 1. 6OGE: HER2 Extracellular Domain & Herceptin Complex
Figure 2. Conformational changes of HER2
The following article showed conformational changes between the bound and unbound HER2 complex to be insignificant for the animation portrayal. (Diwanji et al., 2021)
Figure 2. Conformational changes of HER2
The following article showed conformational changes between the bound and unbound HER2 complex to be insignificant for the animation portrayal. (Diwanji et al., 2021)
Figure 3. RSCB PDB entries for HER2
Figure 3. RSCB PDB entries for HER2
No complete entry for HER2 exists in the RCSB Protein Data Bank (Figure 3). This is not uncommon for large transmembrane proteins and a variety of approaches was considered before proceeding forward. Puzzling together multiple entries was initially considered, but deemed not possible due to incomplete structures found for the cytoplasmic domain.
Figure 4. Alphafold Entry for HER2 Protein Receptor
During the initial literature review the Alphafold entry for HER2 was viewed (Figure 4), but the option to use it was quickly disgarded due to the entry’s poor predicted align error (PAE) score (Jumper et al., 2021).
Ideal PAE score
RCSB PDB
RCSB PDB
Figure 7. Swiss-Model Viewport
Figure 6. Uniprot Isoform Sequence for HER2
Swiss-Model
While viewing the existing literature, a paper with the epidermal growth factor (EGFR) receptor’s modelled monomer (in it’s entirety) was found (Arkhipov et al., 2013). EGFR is a homologous structure to HER2 and therefore can be used as a template protein for it in Swiss-Model, a protein structure homology-modeling server. Combining it with HER2’s isoform sequence, sourced from Uniprot (Figure 6), meant the sequential generated model from Swiss-Model (Figure 7 & 8) was as scientifically accurate as possible (The Uniprot Consortium, 2023).
Figure 8. Swiss-Model Generated Model for HER2
Figure 5. Arkhipov Paper
Figure 5. Arkhipov Paper
Figure 6. Uniprot Isoform Sequence for HER2
Figure 7. Swiss-Model Viewport
Figure 9. VMD Viewport of HER2 Protein Receptor
The Swiss-Model generated structure (Figure 8) was downloaded into VMD (Figure 9), and exported to Cinema4D to be refined and animated (Figure 10).
VMD to Cinema4D
Figure 10. Still From Final Animation
Works Cited:
Arkipov, A., Shan, Y., Das, R., Endres, N. F., Eastwood, M. P., Wemmer, D. E., Kuriyan, J., & Shaw. D. E. (2013). Architecture and membrane interactions of the EGF receptor. Cell. 152, 3: 557-569. DOI: 10.1016/j.cell.2012.12.030.
Diwanji, D., Trenker, R., Thaker, T. M., Wang, F., Agard, D. A., Verba, K. A., & Jura, N. (2021). Structures of the HER2-HER3-NRG1β complex reveal a dynamic dimer interface. Nature. 600: 339-343. DOI: 10.1038/s41586-021-04084-z
Hao, Y., Yu, X., Bai, Y., McBride, H. J., & Huang, X. (2019). Cyro-EM structure of HER2 extracellular domain-Trastuzumab Fab-Pertuzumab Fab complex. PLOS ONE. 14(5): e0216095 DOI: 10.1371/journal.pone.0217716
Jumper, J. et al. (2021). Highly accurate protein structure prediction with AlphFold. Nature. 596: 583-589. DOI: 10.1038/s41586-021-03819-2
The UniProt Consortium. (2023). Uniprot: The universal protein knowledgebase in 2023. Nucleic Acids Research. 51, 1: 523-531. DOI: 10.1093/nar/gkac1052
Works Cited:
Arkipov, A., Shan, Y., Das, R., Endres, N. F., Eastwood, M. P., Wemmer, D. E., Kuriyan, J., & Shaw. D. E. (2013). Architecture and membrane interactions of the EGF receptor. Cell. 152, 3: 557-569. DOI: 10.1016/j.cell.2012.12.030.
Diwanji, D., Trenker, R., Thaker, T. M., Wang, F., Agard, D. A., Verba, K. A., & Jura, N. (2021). Structures of the HER2-HER3-NRG1β complex reveal a dynamic dimer interface. Nature. 600: 339-343. DOI: 10.1038/s41586-021-04084-z
Hao, Y., Yu, X., Bai, Y., McBride, H. J., & Huang, X. (2019). Cyro-EM structure of HER2 extracellular domain-Trastuzumab Fab-Pertuzumab Fab complex. PLOS ONE. 14(5): e0216095 DOI: 10.1371/journal.pone.0217716
Jumper, J. et al. (2021). Highly accurate protein structure prediction with AlphFold. Nature. 596: 583-589. DOI: 10.1038/s41586-021-03819-2
The UniProt Consortium. (2023). Uniprot: The universal protein knowledgebase in 2023. Nucleic Acids Research. 51, 1: 523-531. DOI: 10.1093/nar/gkac1052
Figure 10. Still From Final Animation