Part:BBa_K4768007

Split T7 RNA polymerase (Cterm) conjugated to Trastuzumab with a transmembrane linker

Part for expression of the split T7 RNA polymerase (Cterm) conjugated to Trastuzumab with a transmembrane linker

Sequence and Features

Assembly Compatibility:

• 10
  INCOMPATIBLE WITH RFC[10]

  Illegal XbaI site found at 40
  
• 12
  COMPATIBLE WITH RFC[12]
• 21
  COMPATIBLE WITH RFC[21]
• 23
  INCOMPATIBLE WITH RFC[23]

  Illegal XbaI site found at 40
  
• 25
  INCOMPATIBLE WITH RFC[25]

  Illegal XbaI site found at 40
  Illegal NgoMIV site found at 1080
  Illegal AgeI site found at 549
  
• 1000
  INCOMPATIBLE WITH RFC[1000]

  Illegal BsaI.rc site found at 21
  

Introduction

Figure 1: Trastuzumab-TM-T7Cterm structure.

The CALIPSO part BBa_K4768007 is composed of the anti-HER2 antibody Pertuzumab fused to the C-terminal of the T7 RNa polymerase (residues 181 to 704) through an optimized linker sequence containing a transmembrane domain. This gene is under transcriptional control of an SP6 promoter and T7 terminator.

This part, coupled to the part BBa_K4768008 containing the N-terminal subunit of the T7 RNA polymerase, has been designed to develop a split T7 RNAP-based biosensor capable of recognizing HER-2, an epidermal growth factor that is overexpressed in cancer cells [1]. This biosensor will be incorporated into the liposome membrane to detect cancer cells via HER2-targeting antibodies and activate the expression of a gene of interest inside the liposome.

The HER2-induced T7 RNAP complex was designed from two existing constructs: a split T7 RNAP-based biosensor for the detection of rapamycin [2] and a split luciferase conjugated with antibodies capable of recognizing HER2 [3]. We decided to merge the relevant functionalities of these two constructs and created a new biosensor that transduces HER2 binding to gene expression activation.

Figure 2: Recognition of HER2 extracellular domain induces functional assembly of the split T7 RNA polymerase, which enables gene expression of target gene under control of a T7 promoter.

The part BBa_K4768007 was only studied in silico by molecular modeling to optimize the transmembrane linker for adequate flexibility.

Molecular Modeling

As the biosensor encompasses both extracellular and intracellular domains, the challenge was to find a transmembrane linker that is flexible enough to enable complementation of the split T7 RNAP and simultaneous recognition of HER2.

We first studied the extracellular structure of our biosensor involving the simultaneous interaction of the two antibodies with the soluble extracellular domain of HER2. We retrieved the known structure from the Protein Data Bank (1S78 [4] and 1N8Z [5]) to verify that there were no steric hindrances when both antibodies were bound to HER2. Figure 3 shows the simultaneous binding of the antibodies to distinct epitopes of HER2. In addition, the two anchoring points of the linker sequences are located on the opposite side of the interface with HER2, and are thus accessible.

Figure 3: Simultaneous interaction of Pertuzumab (gray) and Trastuzumab (green) with HER2 extracellular domain (red). Zoom-in images of each antibody reveal that the sites for connecting the linker sequences (pink spheres) are not buried in the molecule.

As the structural conformation of the split T7 RNA polymerase is not known, we reconstructed the natural T7 RNAP structure from the two fragments of our split T7: N-term part from residue 1 to 180, and C-term part from residue 181 to 704. This was achieved using AlphaFold2 with MMseqs2 [6], a relaxation step, and the structure of the full-length T7 RNAP from PDB (1CEZ [7]) as a template, as shown in Figure 4 A and B.

Figure 4: (A) Structure of the complemented split T7 RNAP obtained with AlphaFold2 and PDB 1CEZ of the native protein as a template. N-term subunit is represented in grey, C-term subunit in green, and the linker-bound amino acid in red. (B) Comparison of the split T7 RNAP (in green) obtained with AlphaFold2 and the full-lengthT7 RNAP (in pink). (C) Predicted lDDT for position. The per-residue confidence score indicates the confidence of the position (high-confidence if higher than 90, low-confidence if lower than 50)

Once these structures were validated, we focused on the optimization of the transmembrane (TM) linker to allow adequate flexibility without being too long. The chosen TM part was ZipA (membranome ID: ZIPA_ECOLI [8]), a cell division protein localized in the inner membrane of Gram negative bacteria through a single TM segment. We selected this TM domain because it is from an E. coli protein from which PURE system derives, it consists of a single helix, and its length is compatible with the lipid composition of our liposomes. We included additional residues between the transmembrane segment and the adjacent structural domains to promote flexibility.

The disordered amino acid sequence we used as a basis was: GAAASEGGGSGGPGSGGEGSAGGGSAGGGS

We simulated different potential conformations of our biosensor (part BBa_K4768007 coupled to part BBa_K4768008) using a statistical algorithm called MoMA-FReSa [9] that was developed in the Laboratoire d’Analyse et d’Architecture des systèmes (LAAS, Toulouse). It samples protein conformations, including disordered regions, and gives a set of conformations that are statistically the most probable. We tested different lengths for the linker regions flanking the TM segment and chose the optimal one of residues by comparing it to a standard disordered linker as a reference : 52 amino acids between the antibodies and TM, and 32 amino acids between TM and the T7 RNAP. The results of the simulation comforted us in the disordered characteristic of the chosen sequence.

Optimal sequence of the transmembrane linker for T7Nterm-TM-Pertuzumab:

T7Nterm-SGGGASGGGASGEGGSGPGGSGGGESAAAGSGRLILIIVGAIAIIALLVHGFGASGEGGSGPGGSGGGESAAAGSGGGASGGGASGEGGSGPGGSGGGESAAAG-Pertuzumab

Optimal sequence of the transmembrane linker for Trastuzumab-TM-T7Cterm:

Trastuzumab-GAAASEGGGSGGPGSGGEGSAGGGSAGGGSGAFGHVLLAIIAIAGVIILILRGSGAAASEGGGSGGPGSGGEGSAGGGSAGGGS-T7Cterm

Figure 5 shows different conformations adopted by the chosen sequence.

Figure 5: Possible conformations of the Linker_V2. Red: HER2 extracellular domain. Grey from top to bottom: Pertuzumab linked to the N-term subunit of the T7 RNAP. Green from top to bottom: Trastuzumab linked to the C-term subunit of the T7 RNAP.

Conclusion and Perspectives

These results show that the part BBa_K4768007 coupled to the part BBa_K4768008 has the ability to create an anti-HER2 biosensor that promotes gene expression in the presence of the cancer biomarker HER2. In silico optimization of the linker sequences led to improved protein variants with greater flexibility on each side of the TM domain. We did not have time to study the engineered proteins experimentally. We encourage future iGEM teams to clone the selected HER2-induced RNAP variants and perform experimental assays of the biosensors, and to contact us for further details. This construction can be manipulated in a Biosafety level 1 laboratory.

References

1. Jois et al. 2021. Peptidomimetic Ligand-Functionalized HER2 Targeted Liposome as Nano-Carrier Designed for Doxorubicin Delivery in Cancer Therapy. Pharmaceuticals. 14(3). 221
2. Pu, J., Zinkus-Boltz, J., Dickinson, B. C. 2017. Evolution of a split RNA polymerase as a versatile biosensor platform. Nat Chem Biology 13(4). 432-438.
3. Stains, C. I., Furman, J. L., Porter, J. R., Rajagopal, S., Li, Y., Wyatt, R. T., Ghosh, I. 2010. A General Approach for Receptor and Antibody-Targeted Detection of Native Proteins utilizing Split-Luciferase Reassembly. ACS Chem Biol 5(10). 943-952
4. PDB. 1S78. Insights into ErbB signaling from the structure of the ErbB2-pertuzumab complex.
5. PDB. 1N8Z. Crystal structure of extracellular domain of human HER2 complexed with Herceptin Fab.
6. ColabFold v1.5.2-patch: AlphaFold2 using MMseqs2.
7. [11] PDB. 1CEZ. Crystal structure of a T7 RNA polymerase-T7 promoter complex.
8. Membrane. Cell division protein Zipa.
9. Cortés, J., Siméon, T., Remaud-Siméon, M., Tran, V. 2004. Geometric algorithms for the conformational analysis of long protein loops. Journal of computational chemistry. 25(7). 956-967.