Difference between revisions of "Part:BBa K5271000"
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<partinfo>BBa_K5271000 short</partinfo> | <partinfo>BBa_K5271000 short</partinfo> | ||
| − | The EGFR binding peptide is a 124 amino acid long nanobody with a molecular weight of 13.4 kDa. | + | The EGFR-binding peptide is a 124 amino acid long nanobody with a molecular weight of 13.4 kDa that specifically binds to EGFR. |
===Profile=== | ===Profile=== | ||
| − | *Name: EGFR binding peptide | + | *Name: EGFR-binding peptide |
*Base Pairs: 372 bp | *Base Pairs: 372 bp | ||
*Amino acid: 124 a.a | *Amino acid: 124 a.a | ||
| Line 15: | Line 15: | ||
===Usage and Biology=== | ===Usage and Biology=== | ||
| − | The epidermal growth factor receptor (EGFR) has been always found to be over-expressed in various type of drug-resistant human cancers, including pancreatic cancer and non-small cell lung cancer. It is a target of antibody-based chemotherapeutics for targeted immunotherapy. This EGFR binding peptide is a 124 amino acid long nanobody with an inhibitory effect on ligand-induced EGFR activation. It inhibits the EGFR activation by a steric blockade on the binding of ligands to EGFR. The EGFR binding peptide consists of the variable domains of heavy chain (VHH) only, which is the smallest antigen-binding modules occurs in the nature. The structure of the nanobody has been resolved using X-ray crystallography [Schmitz et al., 2013]. | + | The epidermal growth factor receptor (EGFR) has been always found to be over-expressed in various type of drug-resistant human cancers, including pancreatic cancer and non-small cell lung cancer. It is a target of antibody-based chemotherapeutics for targeted immunotherapy. This EGFR binding peptide is a 124 amino acid long nanobody with an inhibitory effect on ligand-induced EGFR activation. It inhibits the EGFR activation by a steric blockade on the binding of ligands to EGFR. The EGFR binding peptide consists of the variable domains of heavy chain (VHH) only, which is the smallest antigen-binding modules occurs in the nature. The structure of the nanobody has been resolved using X-ray crystallography [Schmitz ''et al.'', 2013]. |
| + | |||
:::https://ars.els-cdn.com/content/image/1-s2.0-S0969212613001664-gr2.jpg | :::https://ars.els-cdn.com/content/image/1-s2.0-S0969212613001664-gr2.jpg | ||
| − | Figure 1. The 7D12 Binding Site on Domain III of sEGFR | + | '''Figure 1. The 7D12 Binding Site on Domain III of sEGFR''' <br>'''(A)''' Cartoon is shown with 7D12 colored green and sEGFRd3 colored gray. CDRs are highlighted in light green and labeled. '''(B)''' In this view, the structure has been rotated ∼180° about a vertical axis relative to (A). The expected locations of domains I, II, and IV of sEGFR are in light blue, based on the structure of tethered sEGFR in PDB ID 1NQL (Ferguson et al., 2003). '''(C)''' View of the interface region between 7D12 and sEGFRd3 in a similar orientation to (A). Side chains that participate in key interactions are shown as sticks, as is the sugar group on sEGFRd3. Predicted salt-bridge (≤4.5 Å) or hydrogen-bond (≤3.5 Å) interactions are indicated with dashed lines. Kabat numbering is used. |
| − | (A) Cartoon is shown with 7D12 colored green and sEGFRd3 colored gray. CDRs are highlighted in light green and labeled. (B) In this view, the structure has been rotated ∼180° about a vertical axis relative to (A). The expected locations of domains I, II, and IV of sEGFR are in light blue, based on the structure of tethered sEGFR in PDB ID 1NQL (Ferguson et al., 2003). (C) View of the interface region between 7D12 and sEGFRd3 in a similar orientation to (A). Side chains that participate in key interactions are shown as sticks, as is the sugar group on sEGFRd3. Predicted salt-bridge (≤4.5 Å) or hydrogen-bond (≤3.5 Å) interactions are indicated with dashed lines. Kabat numbering is used. | + | [Excerpt from Schmitz ''et al.'', 2013] |
| − | [Excerpt from Schmitz et al., 2013] | + | |
===Design Note=== | ===Design Note=== | ||
| − | The DNA sequence was obtained from Schmitz et al., and | + | The DNA sequence was obtained from Schmitz ''et al.'', and performed codon optimization for prokaryotic expression system (''E.Coli'' -BL21DE3). |
===Source=== | ===Source=== | ||
| − | The VHH domain of the nanobody was isolated from a phage library generated from Llama glama lymphocytes that had been immunized with A431 epidermoid carcinoma cells [Roovers et al., 2007] | + | The VHH domain of the nanobody was isolated from a phage library generated from ''Llama glama'' lymphocytes that had been immunized with A431 epidermoid carcinoma cells [Roovers ''et al.'', 2007] |
===Reference=== | ===Reference=== | ||
| − | Roovers, R. C., Laeremans, T., Huang, L., De Taeye, S., Verkleij, A. J., Revets, H., ... & van Bergen en Henegouwen, P. M. P. (2007). Efficient inhibition of EGFR signalling and of tumour growth by antagonistic anti-EGFR Nanobodies. Cancer immunology, immunotherapy, 56, 303-317. | + | *Roovers, R. C., Laeremans, T., Huang, L., De Taeye, S., Verkleij, A. J., Revets, H., ... & van Bergen en Henegouwen, P. M. P. (2007). Efficient inhibition of EGFR signalling and of tumour growth by antagonistic anti-EGFR Nanobodies. Cancer immunology, immunotherapy, 56, 303-317. |
| − | Schmitz, K. R., Bagchi, A., Roovers, R. C., en Henegouwen, P. M. V. B., & Ferguson, K. M. (2013). Structural evaluation of EGFR inhibition mechanisms for nanobodies/VHH domains. Structure, 21(7), 1214-1224. | + | *Schmitz, K. R., Bagchi, A., Roovers, R. C., en Henegouwen, P. M. V. B., & Ferguson, K. M. (2013). Structural evaluation of EGFR inhibition mechanisms for nanobodies/VHH domains. Structure, 21(7), 1214-1224. |
Latest revision as of 09:52, 28 September 2024
EGFR-binding peptide
The EGFR-binding peptide is a 124 amino acid long nanobody with a molecular weight of 13.4 kDa that specifically binds to EGFR.
Profile
- Name: EGFR-binding peptide
- Base Pairs: 372 bp
- Amino acid: 124 a.a
- Origin: Llama glama
- Properties: EGFR specific nanobody that sterically inhibit the ligands for EGFR activation
Usage and Biology
The epidermal growth factor receptor (EGFR) has been always found to be over-expressed in various type of drug-resistant human cancers, including pancreatic cancer and non-small cell lung cancer. It is a target of antibody-based chemotherapeutics for targeted immunotherapy. This EGFR binding peptide is a 124 amino acid long nanobody with an inhibitory effect on ligand-induced EGFR activation. It inhibits the EGFR activation by a steric blockade on the binding of ligands to EGFR. The EGFR binding peptide consists of the variable domains of heavy chain (VHH) only, which is the smallest antigen-binding modules occurs in the nature. The structure of the nanobody has been resolved using X-ray crystallography [Schmitz et al., 2013].
Figure 1. The 7D12 Binding Site on Domain III of sEGFR
(A) Cartoon is shown with 7D12 colored green and sEGFRd3 colored gray. CDRs are highlighted in light green and labeled. (B) In this view, the structure has been rotated ∼180° about a vertical axis relative to (A). The expected locations of domains I, II, and IV of sEGFR are in light blue, based on the structure of tethered sEGFR in PDB ID 1NQL (Ferguson et al., 2003). (C) View of the interface region between 7D12 and sEGFRd3 in a similar orientation to (A). Side chains that participate in key interactions are shown as sticks, as is the sugar group on sEGFRd3. Predicted salt-bridge (≤4.5 Å) or hydrogen-bond (≤3.5 Å) interactions are indicated with dashed lines. Kabat numbering is used.
[Excerpt from Schmitz et al., 2013]
Design Note
The DNA sequence was obtained from Schmitz et al., and performed codon optimization for prokaryotic expression system (E.Coli -BL21DE3).
Source
The VHH domain of the nanobody was isolated from a phage library generated from Llama glama lymphocytes that had been immunized with A431 epidermoid carcinoma cells [Roovers et al., 2007]
Reference
- Roovers, R. C., Laeremans, T., Huang, L., De Taeye, S., Verkleij, A. J., Revets, H., ... & van Bergen en Henegouwen, P. M. P. (2007). Efficient inhibition of EGFR signalling and of tumour growth by antagonistic anti-EGFR Nanobodies. Cancer immunology, immunotherapy, 56, 303-317.
- Schmitz, K. R., Bagchi, A., Roovers, R. C., en Henegouwen, P. M. V. B., & Ferguson, K. M. (2013). Structural evaluation of EGFR inhibition mechanisms for nanobodies/VHH domains. Structure, 21(7), 1214-1224.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal AgeI site found at 43
Illegal AgeI site found at 175 - 1000COMPATIBLE WITH RFC[1000]