Difference between revisions of "Part:BBa K404154"
 
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<partinfo>BBa_K404154 short</partinfo>
 
<partinfo>BBa_K404154 short</partinfo>
 
<br>
 
<br>
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{| style="color:black" cellpadding="6" cellspacing="1" border="2" align="left"
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! colspan="2" style="background:#66bbff;"|[https://parts.igem.org/Part:BBa_K404154 pCMV_Z-EGFR-1907_(AAV2)-VP23 (ViralBrick-587KO-Empty)]
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|-
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|'''BioBrick Nr.'''
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|[https://parts.igem.org/Part:BBa_K404154 BBa_K404154]
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|-
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|'''RFC standard'''
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|[https://parts.igem.org/Help:Assembly_standard_10 RFC 10]
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|-
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|'''Requirement'''
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|pSB1C3<br>
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|-
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|'''Source'''
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|
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|-
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|'''Submitted by'''
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|[http://2010.igem.org/Team:Freiburg_Bioware FreiGEM 2010]
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|}
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<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>
 
<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).  
 
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).
 
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>
 
<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>
 
<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 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.
 
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“.  
+
(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>
 +
 
  
  
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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.<br>
 
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,
 
Walker,
 
R a, and S J Dearing.
 
R a, and S J Dearing.

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


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 665
  • 1000
    INCOMPATIBLE 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, no. 5: 1388-402. doi:10.1016/j.jmb.2007.12.060. http://www.ncbi.nlm.nih.gov/pubmed/18207161.
Göstring, Lovisa, Ming Tsuey Chew, Anna Orlova, Ingmarie Höidén-guthenberg, Anders Wennborg, Jörgen Carlsson, and Fredrik Y Frejd. 2010. Quantification of internalization of EGFR-binding Affibody molecules: Methodological aspects. International Journal of Oncology 36, no. 4 (March): 757-763. doi:10.3892/ijo_00000551. http://www.spandidos-publications.com/ijo/36/4/757.
Hirsch,Fred R, Marileila Varella-Garcia, Paul a Bunn, Michael V Di Maria, Robert Veve, Roy M 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. Journal 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. http://www.ncbi.nlm.nih.gov/pubmed/12953099.
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.
Orlova, Anna, Vladimir Tolmachev, Rikard Pehrson, Malin Lindborg, Thuy Tran, Mattias Sandström, Fredrik Y Nilsson, Anders Wennborg, Lars Abrahmsén, and Joachim Feldwisch. 2007. Synthetic affibody molecules: a novel class of affinity ligands for molecular imaging of HER2-expressing malignant tumors. Cancer research 67, no. 5 (March): 2178-86. doi:10.1158/0008-5472.CAN-06-2887. http://www.ncbi.nlm.nih.gov/pubmed/17332348.
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.
Walker, R a, and S J Dearing. 1999. Expression of epidermal growth factor receptor mRNA and protein in primary breast carcinomas. Breast cancer research and treatment53, no. 2 (January): 167-76. http://www.ncbi.nlm.nih.gov/pubmed/10326794.
Wikman, M, a-C Steffen, E Gunneriusson, V Tolmachev, G P Adams, J Carlsson, and S Ståhl. 2004. Selection and characterization of HER2/neu-binding affibody ligands. Protein engineering, design & selection : PEDS 17, no. 5 (May): 455-62. doi:10.1093/protein/gzh053. http://www.ncbi.nlm.nih.gov/pubmed/15208403.