Difference between revisions of "Part:BBa K2043010"
 
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<b>Table 1</b> Characteristics of Fabric Binding Domain. The numbers next to each fabric means the number of times the sequence was repeated in each fabric<br>
 
<b>Table 1</b> Characteristics of Fabric Binding Domain. The numbers next to each fabric means the number of times the sequence was repeated in each fabric<br>
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     <th style="border: 2px solid black;"> Name </th>
 
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     <th style="border: 2px solid black;"> FBD1 </th>
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     <td style="border: 2px solid black; text-align: center;"> FBD1 </th>
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     <th style="border: 2px solid black;"> MPRLPPA </th>
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     <td style="border: 2px solid black; text-align: center;""> MPRLPPA </th>
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     <th style="border: 2px solid black;"> Non specific - Cotton(2), Linen(25), Polyester(20), Silk(20), Wool(1) </th>
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     <td style="border: 2px solid black; text-align: center;""> Non specific - Cotton(2), Linen(25), Polyester(20), Silk(20), Wool(1) </th>
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     <th style="border: 2px solid black;"> +1 </th>
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     <td style="border: 2px solid black; text-align: center;""> +1 </th>
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     <th style="border: 2px solid black;"> 0.2 </th>
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     <td style="border: 2px solid black; text-align: center;""> 0.2 </th>
 
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<img src="https://static.igem.org/mediawiki/parts/a/a1/2016_paris_bettencourt_FBDs_fig_1.png" width=800><br>
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<img src="https://static.igem.org/mediawiki/parts/a/a1/2016_paris_bettencourt_FBDs_fig_1.png" width=600><br>
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<img src="https://static.igem.org/mediawiki/parts/c/c2/2016_paris_bettencourt_FBDs_fig_2.png" width=800><br>
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<img src="https://static.igem.org/mediawiki/parts/c/c2/2016_paris_bettencourt_FBDs_fig_2.png" width=600><br>
 
<b>Figure 1</b> Fabric binding domain validation by ELISA. Control matrix repeating the procedure of panel A without phage.
 
<b>Figure 1</b> Fabric binding domain validation by ELISA. Control matrix repeating the procedure of panel A without phage.
 
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<h2>References</h2>
 
<h2>References</h2>
  
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General In Vitro Method to Analyze the Interactions of Synthetic Polymers with Human Antibody Repertoires,Anandakumar Soshee, Stefan Zürcher, Nicholas D. Spencer, Avraham Halperin, and Clément Nizak,Biomacromolecules 2014 15 (1), 113-121, DOI: 10.1021/bm401360y
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Berglund, J., Lindbladh, C., Mosbach, K., & Nicholls, I. A. (1998). Selection of phage display combinatorial library peptides with affinity for a yohimbine imprinted methacrylate polymer. Analytical Communications, 35(1), 3-7.
 
<br><br>
 
<br><br>
−
Hierarchy and extremes in selections from pools of randomized proteins,PNAS 2016 113 (13) 3482-3487; published ahead of print March 11, 2016,doi:10.1073/pnas.1517813113
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Boyer, S., Biswas, D., Soshee, A. K., Scaramozzino, N., Nizak, C., & Rivoire, O. (2016). Hierarchy and extremes in selections from pools of randomized proteins. Proceedings of the National Academy of Sciences, 201517813.
 
<br><br>
 
<br><br>
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Identification of Soft Matter Binding Peptide Ligands Using Phage Display Kemal Arda Gü nay and Harm-Anton Klok, Bioconjugate Chem. 2015, 26, 2002−2015, DOI: 10.1021/acs.bioconjchem.5b00377
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Devlin, J. J., Panganiban, L. C., & Devlin, P. E. (1990). Random peptide libraries: a source of specific protein binding molecules. Science, 249(4967), 404-406.
 
<br><br>
 
<br><br>
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Identification of a peptide blocking vascular endothelial growth factor (VEGF)-mediated angiogenesis, Binétruy-Tournaire R1, Demangel C, Malavaud B, Vassy R, Rouyre S, Kraemer M, Plouët J, Derbin C,Perret G, Mazié JC, EMBO J. 2000 Apr 3;19(7):1525-33
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Goncalves, V., Gautier, B., Garbay, C., Vidal, M., & Inguimbert, N. (2007). Development of a chemiluminescent screening assay for detection of vascular endothelial growth factor receptor 1 ligands. Analytical biochemistry, 366(1), 108-110.
 
<br><br>
 
<br><br>
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Multi-subunit proteins on the surface of filamentous phage: methodologies for displaying antibody (Fab) heavy and light chains Hennie R.Hoogenboom1 , Andrew D.Griffiths1 , Kevin S.Johnson2 , David J.Chiswell2 , Peter Hudson4 and Greg Winter, 1991 Nucleic Acids Research, Vol. 19, No. 15 4133-4137.
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Günay, K. A., & Klok, H. A. (2015). Identification of Soft Matter Binding Peptide Ligands Using Phage Display. Bioconjugate chemistry, 26(10), 2002-2015.
 
<br><br>
 
<br><br>
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Random Peptide Libraries: A Source of Specific Protein Binding Molecules , SCIENCE, VOL. 249, JAMES J. DEVLIN,* Lucy C. PANGANIBAN, PATRICIA E. DEVLIN, 1999
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Hoogenboom, H. R., Griffiths, A. D., Johnson, K. S., Chiswell, D. J., Hudson, P., & Winter, G. (1991). Multi-subunit proteins on the surface of filamentous phage: methodologies for displaying antibody (Fab) heavy and light chains. Nucleic acids research, 19(15), 4133-4137.
 
<br><br>
 
<br><br>
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Selection of Arginine-Rich Anti-Gold Antibodies Engineered for Plasmonic Colloid Self-Assembly,Purvi Jain, Anandakumar Soshee, S. Shankara Narayanan, Jadab Sharma, Christian Girard, Erik Dujardin, and Clément Nizak, The Journal of Physical Chemistry C 2014 118 (26), 14502-14510, DOI: 10.1021/jp502118n
+
Jain, P., Soshee, A., Narayanan, S. S., Sharma, J., Girard, C., Dujardin, E., & Nizak, C. (2014). Selection of arginine-rich anti-gold antibodies engineered for plasmonic colloid self-assembly. The Journal of Physical Chemistry C, 118(26), 14502-14510.
 
<br><br>
 
<br><br>
−
Selection of phage display combinatorial library peptides with affinity for a yohimbine imprinted methacrylate polymer, Johanna Berglunda, Christer Lindbladha, Ian A. Nichollsb and Klaus Mosbach, Analytical Communications, January 1998, Vol 35 (3–7)
+
Matsuura, K., Ueno, G., & Fujita, S. (2015). Self-assembled artificial viral capsid decorated with gold nanoparticles. Polymer Journal, 47(2), 146-151.
 
<br><br>
 
<br><br>
−
Self-assembled artificial viral capsid decorated with gold nanoparticles, Kazunori Matsuura, Genki Ueno and Seiya Fujita, Polymer Journal 47, 146-151 (February 2015) | doi:10.1038/pj.2014.99
+
Soshee, A., Zürcher, S., Spencer, N. D., Halperin, A., & Nizak, C. (2013). General in vitro method to analyze the interactions of synthetic polymers with human antibody repertoires. Biomacromolecules, 15(1), 113-121.
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</p>
 
</p>
 
</html>
 
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Latest revision as of 03:39, 28 October 2016


GFP-FBD1

Introduction

This part corresponds to the GFP genes bound to the Fabric Binding Domain 1 (FBD1). In the context of Paris Bettencourt 2016 iGEM project, Frank&Stain, we looked for novel fabric binding domains with phage display technique in order to optimise enzymes by fusing them with different FBD.
Results from our models suggest that the addition of an FBD with optimal affinity can concentrate an enzyme near the fabric surface and therefore increase stain-degrading enzymatic activity. Using the method of phage display, we isolated 40 short peptides with affinity for cotton, linen, wool, polyester or silk. Bioinformatics analysis identified sequence motifs and biophysical features associated with binding to each fabric, or non-specific binding to several fabrics. Several peptides were selected for further analysis by quantitative ELISA. The peptides discovered were used to fuse with GFP and stain-degrading enzymes to target wine-stained fabric samples.
The peptides are identified by in vitro phage-display screening of libraries containing typically 109 distinct, linear 7 amino-acid peptides against our target, in our case different fabrics - cotton, wool, silk, linen, polyester, and the library is enriched with the phages which binds to the fabric over several rounds of panning.

Table 1 Characteristics of Fabric Binding Domain. The numbers next to each fabric means the number of times the sequence was repeated in each fabric
Name Amino Acid Sequence Binding Affinity Charge Hydropathicity
FBD1 MPRLPPA Non specific - Cotton(2), Linen(25), Polyester(20), Silk(20), Wool(1) +1 0.2


Testing the part

ELISA for each FBD incubated with each fabric after two rounds of washing, normalized to the level after a single round. In figure 1 we can see that when it is fused to the phage, the FBD1 binds to all fabrics except wool, but specially to nylon and linen.


Figure 1 Fabric binding domain validation by ELISA. Control matrix repeating the procedure of panel A without phage.

After doing this assay we fuse the FBD with GFP, which is actually the part we are submitting. Then we test the fluorescence of GFP to see if the fusion itself affects the activity or the expression.

Figure 2 Bar plot showing the fluorescence of cell extracts relative to the control (No GFP expressed). Here we compare the fluorescence of different cell extract expressing Fabric Binding Domains (FBDs) with affinity for different fabrics. The part BBa_K1321357 (GFP-CBDex) was used as positive control. The blue bar correspond with the negative control (no GFP in the cell extract) whereas the green ones with those whose fluorescence was higher than the control and in red those which presented no fluorescence, maybe because lacking activity or functionality.

Unfortunately, according with the figure 2 we couldn’t express properly this fusion protein with GFP, or maybe it affects the activity of GFP and therefore we couldn’t see the fluorescence. On the other hand, this FBD was also fused with other proteins and in one it showed activity in CatA, but it caused loss of activity when it was fused with xylE


References

Berglund, J., Lindbladh, C., Mosbach, K., & Nicholls, I. A. (1998). Selection of phage display combinatorial library peptides with affinity for a yohimbine imprinted methacrylate polymer. Analytical Communications, 35(1), 3-7.

Boyer, S., Biswas, D., Soshee, A. K., Scaramozzino, N., Nizak, C., & Rivoire, O. (2016). Hierarchy and extremes in selections from pools of randomized proteins. Proceedings of the National Academy of Sciences, 201517813.

Devlin, J. J., Panganiban, L. C., & Devlin, P. E. (1990). Random peptide libraries: a source of specific protein binding molecules. Science, 249(4967), 404-406.

Goncalves, V., Gautier, B., Garbay, C., Vidal, M., & Inguimbert, N. (2007). Development of a chemiluminescent screening assay for detection of vascular endothelial growth factor receptor 1 ligands. Analytical biochemistry, 366(1), 108-110.

Günay, K. A., & Klok, H. A. (2015). Identification of Soft Matter Binding Peptide Ligands Using Phage Display. Bioconjugate chemistry, 26(10), 2002-2015.

Hoogenboom, H. R., Griffiths, A. D., Johnson, K. S., Chiswell, D. J., Hudson, P., & Winter, G. (1991). Multi-subunit proteins on the surface of filamentous phage: methodologies for displaying antibody (Fab) heavy and light chains. Nucleic acids research, 19(15), 4133-4137.

Jain, P., Soshee, A., Narayanan, S. S., Sharma, J., Girard, C., Dujardin, E., & Nizak, C. (2014). Selection of arginine-rich anti-gold antibodies engineered for plasmonic colloid self-assembly. The Journal of Physical Chemistry C, 118(26), 14502-14510.

Matsuura, K., Ueno, G., & Fujita, S. (2015). Self-assembled artificial viral capsid decorated with gold nanoparticles. Polymer Journal, 47(2), 146-151.

Soshee, A., Zürcher, S., Spencer, N. D., Halperin, A., & Nizak, C. (2013). General in vitro method to analyze the interactions of synthetic polymers with human antibody repertoires. Biomacromolecules, 15(1), 113-121.


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
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]