Difference between revisions of "Part:BBa K404154"
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__NOTOC__ | __NOTOC__ | ||
<partinfo>BBa_K404154 short</partinfo> | <partinfo>BBa_K404154 short</partinfo> | ||
| + | <br> | ||
| + | {| style="color:black" cellpadding="6" cellspacing="1" border="2" align="left" | ||
| + | ! colspan="2" style="background:#66bbff;"|[https://parts.igem.org/Part:BBa_K404154 pCMV_Z-EGFR-1907_(AAV2)-VP23 (ViralBrick-587KO-Empty)] | ||
| + | |- | ||
| + | |'''BioBrick Nr.''' | ||
| + | |[https://parts.igem.org/Part:BBa_K404154 BBa_K404154] | ||
| + | |- | ||
| + | |'''RFC standard''' | ||
| + | |[https://parts.igem.org/Help:Assembly_standard_10 RFC 10] | ||
| + | |- | ||
| + | |'''Requirement''' | ||
| + | |pSB1C3<br> | ||
| + | |- | ||
| + | |'''Source''' | ||
| + | | | ||
| + | |- | ||
| + | |'''Submitted by''' | ||
| + | |[http://2010.igem.org/Team:Freiburg_Bioware FreiGEM 2010] | ||
| + | |} | ||
| + | <br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/> | ||
| + | <br>This part is used for cotranfection with parts containing VP1up (BBa_K404164-BBa_K404166)<br> | ||
| + | <h2>Affibody Z-EGFR-1907</h2> (BBa_K404302)<br> | ||
| + | Affibodies are small (6 kDa), soluble high-affinity proteins. They are derived from the IgG-binding B domain of the Staphylococcal protein A, which was engineered to specifically bind to certain peptides or proteins. This so-called Z domain consists of an antiparallel three-helix bundle and is advantageous due to its proteolytic and thermodynamic stability, its good folding properties and the ease of production via recombinant bacteria (Nord et al., 1997). Affibodies can be used for example for tumor targeting (Wikman et al., 2004) and diagnostic imaging applications (Orlova et al., 2006; Orlova et al., 2007). The ZEGFR:1907 Affibody was engineered to specifically bind the EGF receptor with an affinity determined to be KD = 2.8 nM (Friedman et al., 2008). | ||
| + | The EGF receptor is overexpressed in certain types of tumors, e.g. in breast (Walker & Dearing, 1999), lung (Hirsch et al., 2003) and bladder (Colquhoun & Mellon, 2002) carcinomas, and is therefore a suitable target for cancer imaging or therapeutic applications. Because of their good tumor uptake, and their property to become internalized into the target cells with an efficiency of 19 – 24% within one hour – compared to 45% of the natural ligand EGF - the ZEGFR:1907 Affibody was chosen for therapeutic applications by the Freiburg iGEM Team 2010 (Friedman et al., 2008; Göstring et al., 2010). | ||
| + | <br> | ||
| + | <h2>Capsid</h2><br>(BBa_K404006)<br> | ||
| + | The AAV capsid consists of 60 capsid protein subunits. The three cap proteins VP1, VP2, and VP3 are encoded in an overlapping reading frame. Arranged in a stoichiometric ratio of 1:1:10, they form an icosahedral symmetry. The mRNA encoding for the cap proteins is transcribed from p40 and alternative spliced to minor and major products. Alternative splicing and translation initiation of VP2 at a nonconventional ACG initiation codon promote the expression of VP1, VP2 and VP3. The VP proteins share a common C terminus and stop codon, but begin with a different start codon. The N-terminus of VP1 plays an important role in infection and contains a motif highly homologous to a phospholipase A2 (PLA2) domain and nuclear localization signals (BR)(+). VP2 contains basic regions, too. | ||
| + | <html><center><img src="https://static.igem.org/mediawiki/parts/a/a7/Freiburg10_Cap_proteins_VP1_2%263.png" width="600" height="auto"/></center></html> | ||
| + | <br> | ||
| + | <h2>Viral Brick 587-KO empty</h2> (BBa_K404210)<br> | ||
| − | + | The primary receptor of AAV-2 is the heparan sulfate proteoglycan (HSPG) receptor (Perabo et al. 2006). Its binding motif consists of five amino-acids located on the capsid surface: R484/R487, K532, R585/587. (Trepel et al. 2009). | |
| − | + | The positively charged arginine residues interact with the HSPGs' negatively charged acid residues. Opie et al. have shown that two point mutations (R585A and R588A) are sufficient to eliminate the heparin binding affinity in AAV2. | |
| − | + | (Opie et al. 2003). This ViralBrick has been created to introduce this knockout into other constructs. The biobricks with containing this knockout are annotated with „HSPG-ko“. <br> | |
| − | + | <h2>CMV</h2> | |
| − | + | CMV promoter is derived from human cytomegalovirus, which belongs to herpesvirus group. All family members share the ability to remain in latent stage in the human body. CMV is located upstream of immediate-early gene. However, CMV promoter is an example of widely used promoters and is present in mammalian expression vectors. The advantage of CMV is the high-level constitutive expression in mostly all human tissues [Fitzsimons et al., 2002]. <br> | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | <!-- Add more about the biology of this part here | |
| − | + | ===Usage and Biology=== | |
| − | + | ||
| − | + | <!-- --> | |
| − | + | <span class='h3bb'>Sequence and Features</span> | |
| − | + | <partinfo>BBa_K404154 SequenceAndFeatures</partinfo> | |
| − | + | ||
| − | + | ||
| − | + | <!-- Uncomment this to enable Functional Parameter display | |
| − | + | ===Functional Parameters=== | |
| − | + | <partinfo>BBa_K404154 parameters</partinfo> | |
| − | + | <!-- --> | |
| − | + | <br> | |
| − | + | <h2>References</h2> | |
| − | + | Mellon. 2002. Epidermal growth factor receptor and bladder cancer.Postgraduate | |
| − | + | medical journal78, no. 924 (October): 584-9. | |
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| − | + | ||
| − | + | ||
| − | Mellon. 2002. Epidermal growth factor receptor and bladder cancer. | + | |
| − | medical | + | |
doi:10.1136/pmj.78.924.584. | doi:10.1136/pmj.78.924.584. | ||
| − | http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1742539&tool=pmcentrez&rendertype=abstract.< | + | http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1742539&tool=pmcentrez&rendertype=abstract.<br> |
| − | + | Friedman, | |
Mikaela, Anna | Mikaela, Anna | ||
Orlova, Eva Johansson, Tove L J Eriksson, Ingmarie Höidén-Guthenberg, | Orlova, Eva Johansson, Tove L J Eriksson, Ingmarie Höidén-Guthenberg, | ||
| Line 362: | Line 66: | ||
evolution to low | evolution to low | ||
nanomolar affinity of a tumor-targeting epidermal growth factor | nanomolar affinity of a tumor-targeting epidermal growth factor | ||
| − | receptor-binding affibody molecule. | + | receptor-binding affibody molecule. Journal of molecular |
| − | + | biology376, | |
no. 5: 1388-402. doi:10.1016/j.jmb.2007.12.060. | no. 5: 1388-402. doi:10.1016/j.jmb.2007.12.060. | ||
| − | http://www.ncbi.nlm.nih.gov/pubmed/18207161.< | + | http://www.ncbi.nlm.nih.gov/pubmed/18207161.<br> |
| − | + | Göstring, | |
Lovisa, Ming Tsuey | Lovisa, Ming Tsuey | ||
Chew, Anna Orlova, Ingmarie Höidén-guthenberg, Anders Wennborg, Jörgen | Chew, Anna Orlova, Ingmarie Höidén-guthenberg, Anders Wennborg, Jörgen | ||
Carlsson, and Fredrik Y Frejd. 2010. Quantification of internalization | Carlsson, and Fredrik Y Frejd. 2010. Quantification of internalization | ||
of | of | ||
| − | EGFR-binding Affibody molecules: Methodological aspects. | + | EGFR-binding Affibody molecules: Methodological aspects. International |
| − | Journal of Oncology | + | Journal of Oncology 36, no. 4 (March): 757-763. |
doi:10.3892/ijo_00000551. | doi:10.3892/ijo_00000551. | ||
| − | http://www.spandidos-publications.com/ijo/36/4/757.< | + | http://www.spandidos-publications.com/ijo/36/4/757.<br> |
| − | + | Hirsch,Fred R, Marileila Varella-Garcia, Paul a Bunn, Michael V Di Maria, Robert Veve, Roy M Bremmes, | |
| − | Fred R, Marileila | + | Anna E Barón, Chan Zeng, and Wilbur a Franklin. 2003. Epidermal growth factor |
| − | Varella-Garcia, Paul a Bunn, Michael V Di Maria, Robert Veve, Roy M | + | receptor in non-small-cell lung carcinomas: correlation between gene copy number and protein expression and impact on prognosis. Journal of clinical oncology : official journal of the American Society of Clinical Oncology |
| − | Bremmes, | + | |
| − | Anna E Barón, Chan Zeng, and Wilbur a Franklin. 2003. Epidermal growth | + | |
| − | factor | + | |
| − | receptor in non-small-cell lung carcinomas: correlation between gene | + | |
| − | copy | + | |
| − | number and protein expression and impact on prognosis. | + | |
| − | of clinical | + | |
| − | oncology : official journal of the American Society of Clinical Oncology | + | |
21, no. 20 (October): 3798-807. doi:10.1200/JCO.2003.11.069. | 21, no. 20 (October): 3798-807. doi:10.1200/JCO.2003.11.069. | ||
| − | http://www.ncbi.nlm.nih.gov/pubmed/12953099.< | + | http://www.ncbi.nlm.nih.gov/pubmed/12953099.<br> |
| − | + | Nord, K, E Gunneriusson, J Ringdahl, S Ståhl, M Uhlén, and P A Nygren. 1997. Binding proteins selected from combinatorial libraries of an alpha-helical bacterial receptor domain. Nature biotechnology 15, no. 8 (August): 772-7. doi:10.1038/nbt0897-772. http://www.ncbi.nlm.nih.gov/pubmed/9255793.<br> | |
| − | E Gunneriusson, J | + | Orlova, |
| − | Ringdahl, S Ståhl, M Uhlén, and P A Nygren. 1997. Binding proteins | + | |
| − | selected | + | |
| − | from combinatorial libraries of an alpha-helical bacterial receptor | + | |
| − | domain. | + | |
| − | biotechnology | + | |
| − | doi:10.1038/nbt0897-772. | + | |
| − | http://www.ncbi.nlm.nih.gov/pubmed/9255793.< | + | |
| − | + | ||
Anna, Vladimir | Anna, Vladimir | ||
Tolmachev, Rikard Pehrson, Malin Lindborg, Thuy Tran, Mattias | Tolmachev, Rikard Pehrson, Malin Lindborg, Thuy Tran, Mattias | ||
| Line 405: | Line 93: | ||
2007. Synthetic affibody molecules: a novel class of affinity ligands | 2007. Synthetic affibody molecules: a novel class of affinity ligands | ||
for | for | ||
| − | molecular imaging of HER2-expressing malignant tumors. | + | molecular imaging of HER2-expressing malignant tumors. Cancer |
| − | research | + | research |
67, no. 5 (March): 2178-86. doi:10.1158/0008-5472.CAN-06-2887. | 67, no. 5 (March): 2178-86. doi:10.1158/0008-5472.CAN-06-2887. | ||
| − | http://www.ncbi.nlm.nih.gov/pubmed/17332348.< | + | http://www.ncbi.nlm.nih.gov/pubmed/17332348.<br> |
| − | + | Fitzsimons, H.L., Bland, R.J. & During, M.J., 2002. Promoters and regulatory elements that improve adeno-associated virus transgene expression in the brain. Methods San Diego Calif, 28(2), pp.227-236. Available at: http://www.ncbi.nlm.nih.gov/pubmed/12413421.<br> | |
| + | Walker, | ||
R a, and S J Dearing. | R a, and S J Dearing. | ||
1999. Expression of epidermal growth factor receptor mRNA and protein | 1999. Expression of epidermal growth factor receptor mRNA and protein | ||
in | in | ||
| − | primary breast carcinomas. | + | primary breast carcinomas. Breast cancer research and |
| − | + | treatment53, no. | |
| − | 2 (January): 167-76. http://www.ncbi.nlm.nih.gov/pubmed/10326794.< | + | 2 (January): 167-76. http://www.ncbi.nlm.nih.gov/pubmed/10326794.<br> |
| − | + | Wikman, | |
M, a-C Steffen, E | M, a-C Steffen, E | ||
Gunneriusson, V Tolmachev, G P Adams, J Carlsson, and S Ståhl. 2004. | Gunneriusson, V Tolmachev, G P Adams, J Carlsson, and S Ståhl. 2004. | ||
Selection | Selection | ||
| − | and characterization of HER2/neu-binding affibody ligands. | + | and characterization of HER2/neu-binding affibody ligands. Protein |
| − | engineering, design & selection : PEDS | + | engineering, design & selection : PEDS 17, no. 5 |
(May): 455-62. | (May): 455-62. | ||
| − | doi:10.1093/protein/gzh053. http://www.ncbi.nlm.nih.gov/pubmed/15208403.< | + | doi:10.1093/protein/gzh053. http://www.ncbi.nlm.nih.gov/pubmed/15208403.<br> |
| − | + | <br> | |
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Latest revision as of 15:31, 31 October 2010
pCMV_Z-EGFR-1907_[AAV2]-VP23 (ViralBrick-587KO-Empty)
| pCMV_Z-EGFR-1907_(AAV2)-VP23 (ViralBrick-587KO-Empty) | |
|---|---|
| BioBrick Nr. | BBa_K404154 |
| RFC standard | RFC 10 |
| Requirement | pSB1C3 |
| Source | |
| Submitted by | [http://2010.igem.org/Team:Freiburg_Bioware FreiGEM 2010] |
This part is used for cotranfection with parts containing VP1up (BBa_K404164-BBa_K404166)
Affibody Z-EGFR-1907
(BBa_K404302)Affibodies are small (6 kDa), soluble high-affinity proteins. They are derived from the IgG-binding B domain of the Staphylococcal protein A, which was engineered to specifically bind to certain peptides or proteins. This so-called Z domain consists of an antiparallel three-helix bundle and is advantageous due to its proteolytic and thermodynamic stability, its good folding properties and the ease of production via recombinant bacteria (Nord et al., 1997). Affibodies can be used for example for tumor targeting (Wikman et al., 2004) and diagnostic imaging applications (Orlova et al., 2006; Orlova et al., 2007). The ZEGFR:1907 Affibody was engineered to specifically bind the EGF receptor with an affinity determined to be KD = 2.8 nM (Friedman et al., 2008).
The EGF receptor is overexpressed in certain types of tumors, e.g. in breast (Walker & Dearing, 1999), lung (Hirsch et al., 2003) and bladder (Colquhoun & Mellon, 2002) carcinomas, and is therefore a suitable target for cancer imaging or therapeutic applications. Because of their good tumor uptake, and their property to become internalized into the target cells with an efficiency of 19 – 24% within one hour – compared to 45% of the natural ligand EGF - the ZEGFR:1907 Affibody was chosen for therapeutic applications by the Freiburg iGEM Team 2010 (Friedman et al., 2008; Göstring et al., 2010).
Capsid
(BBa_K404006)
The AAV capsid consists of 60 capsid protein subunits. The three cap proteins VP1, VP2, and VP3 are encoded in an overlapping reading frame. Arranged in a stoichiometric ratio of 1:1:10, they form an icosahedral symmetry. The mRNA encoding for the cap proteins is transcribed from p40 and alternative spliced to minor and major products. Alternative splicing and translation initiation of VP2 at a nonconventional ACG initiation codon promote the expression of VP1, VP2 and VP3. The VP proteins share a common C terminus and stop codon, but begin with a different start codon. The N-terminus of VP1 plays an important role in infection and contains a motif highly homologous to a phospholipase A2 (PLA2) domain and nuclear localization signals (BR)(+). VP2 contains basic regions, too.
Viral Brick 587-KO empty
(BBa_K404210)The primary receptor of AAV-2 is the heparan sulfate proteoglycan (HSPG) receptor (Perabo et al. 2006). Its binding motif consists of five amino-acids located on the capsid surface: R484/R487, K532, R585/587. (Trepel et al. 2009).
The positively charged arginine residues interact with the HSPGs' negatively charged acid residues. Opie et al. have shown that two point mutations (R585A and R588A) are sufficient to eliminate the heparin binding affinity in AAV2.
(Opie et al. 2003). This ViralBrick has been created to introduce this knockout into other constructs. The biobricks with containing this knockout are annotated with „HSPG-ko“.
CMV
CMV promoter is derived from human cytomegalovirus, which belongs to herpesvirus group. All family members share the ability to remain in latent stage in the human body. CMV is located upstream of immediate-early gene. However, CMV promoter is an example of widely used promoters and is present in mammalian expression vectors. The advantage of CMV is the high-level constitutive expression in mostly all human tissues [Fitzsimons et al., 2002].
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal NgoMIV site found at 665
- 1000INCOMPATIBLE WITH RFC[1000]Illegal BsaI site found at 2691
Illegal SapI site found at 1602
References
Mellon. 2002. Epidermal growth factor receptor and bladder cancer.Postgraduate
medical journal78, no. 924 (October): 584-9.
doi:10.1136/pmj.78.924.584.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1742539&tool=pmcentrez&rendertype=abstract.
Friedman,
Mikaela, Anna
Orlova, Eva Johansson, Tove L J Eriksson, Ingmarie Höidén-Guthenberg,
Vladimir
Tolmachev, Fredrik Y Nilsson, and Stefan Ståhl. 2008. Directed
evolution to low
nanomolar affinity of a tumor-targeting epidermal growth factor
receptor-binding affibody molecule. Journal of molecular
biology376,
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