Difference between revisions of "Part:BBa K4905004"

(The TU-Eindhoven 2023 team used this part in a composite part for the formation of a hydrogel in e.coli. Two different bZIP proteins are made, which will form a heterodimer. This part is one of these bZIP proteins.)
 
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Basic-region Leucine zippers (bZIPs) are alpha-helical domains with a repeating unit “abcdefg”. In this unit, the positions “a” and “d” consist of a hydrophobic residue and the ”e” and “g” positions consist of charged residues. The zippers form an alpha-helix and their charged residues form ion pairs between helices, causing them to associate(Alber, 1992).  
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__NOTOC__
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<partinfo>BBa_K4905004 short</partinfo>
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Individual bZIP proteins can form homodimers or heterodimers with other bZIP proteins with a slightly different sequence(Alber, 1992) Not all bZIP proteins can dimerize with each other, some will only homodimerize with the same bZIP protein. Others will only heterodimerize with specific other bZIP proteins(Hakoshima, n.d.).
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<body>
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In cells, the main function of bZIPs is that they work as transcription factor, where the homodimer or heterodimer will form at the promotor regions of target genes (Seldeen et al., 2010). This makes leucine zippers a large family of transcription factors, where each member has a preference for a specific DNA sequence (Hakoshima, n.d.).
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<h1>Information</h1>
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<p>
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The TU-Eindhoven 2023 team used this part in a composite part for the formation of a hydrogel in e.coli. Two different bZIP proteins are made, which will form a heterodimer. This part is one of these bZIP proteins.  
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Basic-region Leucine zippers (bZIPs) are alpha-helical domains with a repeating unit “abcdefg”. In this unit, the positions “a” and “d” consist of a hydrophobic residue and the ”e” and “g” positions consist of charged residues. The zippers form an alpha-helix and their charged residues form ion pairs between helices, causing them to associate<sup>[1]</sup>.  
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</p>
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<p>
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Individual bZIP proteins can form homodimers or heterodimers with other bZIP proteins with a slightly different sequence<sup>[1]</sup>. Not all bZIP proteins can dimerize with each other, some will only homodimerize with the same bZIP protein. Others will only heterodimerize with specific other bZIP proteins<sup>[2]</sup>.
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</p>
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<p>
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In cells, the main function of bZIPs is that they work as transcription factors, where the homodimer or heterodimer will form at the promotor regions of target genes<sup>[3]</sup>. This makes leucine zippers a large family of transcription factors, where each member has a preference for a specific DNA sequence<sup>[2]</sup>. However, the characteristics of Leucine zippers make them very interesting for many applications.
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</p>
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<p>
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This specific Leucine zipper was designed with inspiration from Gradišar et al.<sup>[4]</sup> where they used it together with a complementary zipper to form heterodimers. Z1 is one of the two complementary Leucine zippers that they used in this research. We wanted to use these zippers in a similar way that Fernández‐Colino et al.<sup>[5]</sup> used leucine zippers together with Elastin-Like Polypeptides (ELPs) to form a reversible, injectable hydrogel. They found that the thermosensitive response of ELPs together with the dimerization of Leucine zippers enables the formation of a thermosensitive hydrogel.
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</p>
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The TU-Eindhoven 2023 team used this part in composite part <a style="color:#F6B227" href="https://parts.igem.org/Part:BBa_K4905006"> BBa_K4905006 </a> for the formation of a hydrogel in <i>E. coli</i>. This composite part consists of ELPs together with two complementary Leucine zippers at their end. This part is one of these bZIP proteins.  
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</p>
  
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Characterization
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<h1>Characterization</h1>
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We ran an electrophoresis gel with the plasmid, digested with enzymes AcuI and BglI. The bands of Z1.1 and Z1.2 is shown in slot 2 and 4 in the gel. A 1 kb ladder (L) was used. The remaining slots were used for different parts. The bands formed as expected.  
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1. A120: BseRI + BglI, with CIP
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We ran an electrophoresis gel with the plasmid, digested with enzymes AcuI and BglI. Slots 2 and 4 were used for different samples of Leucine zipper 1. A 1 kb ladder (L) was used. The remaining slots were used for different parts. The bands formed as expected.  
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2. Z1.1: Acul + BglI, without CIP
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<ol>
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3. A100: BseRI + BglI, with CIP
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<li>A120: BseRI + BglI, with CIP</li>
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4. Z1.2: Acul + BglI, without CIP
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<li>Z1.1: Acul + BglI, without CIP</li>
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5. Z2: Acul + BglI, without CIP
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<li>A100: BseRI + BglI, with CIP</li>
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<li>Z1.2: Acul + BglI, without CIP</li>
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<li>Z2: Acul + BglI, without CIP</li>
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</ol>
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</p>
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<figure><img src="https://static.igem.wiki/teams/4905/wiki/z1-characterization.png" width="300px">
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<figcaption>
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<p><b>Figure 1 | </b>Electrophoresis gel with Z1 in slot 2 and 4</p>
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</figure><be>
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<span class='h3bb'><h1>Sequence and Features</h1></span>
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<partinfo>BBa_K4905004 SequenceAndFeatures</partinfo>
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<body>
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<h1>References</h1>
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<p>
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[1] Alber, T. (1992). Structure of the leucine zipper. Current Opinion in Genetics and Development, 2, 205–210.
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</p>
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<p>
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[2] Hakoshima, T. (n.d.). Leucine Zippers. https://doi.org/10.1038/npg.els.0005049
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</p>
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<p>
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[3] Seldeen, K. L., McDonald, C. B., Deegan, B. J., Bhat, V., & Farooq, A. (2010). Dissecting the Role of Leucine Zippers in the Binding of bZIP Domains of Jun Transcription Factor to DNA. Biochemical and Biophysical Research Communications, 394(4), 1030. https://doi.org/10.1016/J.BBRC.2010.03.116
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</p>
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<p>
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[4] Gradišar, H., & Jerala, R. (2010). De novodesign of orthogonal peptide pairs forming parallel coiled-coil heterodimers. Journal of Peptide Science, 17(2), 100–106. https://doi.org/10.1002/psc.1331
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</p>
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<p>
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[5] Fernández‐Colino, A., Arias, F. J., Alonso, M., & Rodríguez-Cabello, J. C. (2015). Amphiphilic Elastin-Like Block Co-Recombinamers Containing Leucine Zippers: Cooperative Interplay between Both Domains Results in Injectable and Stable Hydrogels. Biomacromolecules, 16(10), 3389–3398. https://doi.org/10.1021/acs.biomac.5b01103
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</p>

Latest revision as of 08:35, 3 October 2023

Leucine zipper Z1

Information

Basic-region Leucine zippers (bZIPs) are alpha-helical domains with a repeating unit “abcdefg”. In this unit, the positions “a” and “d” consist of a hydrophobic residue and the ”e” and “g” positions consist of charged residues. The zippers form an alpha-helix and their charged residues form ion pairs between helices, causing them to associate[1].

Individual bZIP proteins can form homodimers or heterodimers with other bZIP proteins with a slightly different sequence[1]. Not all bZIP proteins can dimerize with each other, some will only homodimerize with the same bZIP protein. Others will only heterodimerize with specific other bZIP proteins[2].

In cells, the main function of bZIPs is that they work as transcription factors, where the homodimer or heterodimer will form at the promotor regions of target genes[3]. This makes leucine zippers a large family of transcription factors, where each member has a preference for a specific DNA sequence[2]. However, the characteristics of Leucine zippers make them very interesting for many applications.

This specific Leucine zipper was designed with inspiration from Gradišar et al.[4] where they used it together with a complementary zipper to form heterodimers. Z1 is one of the two complementary Leucine zippers that they used in this research. We wanted to use these zippers in a similar way that Fernández‐Colino et al.[5] used leucine zippers together with Elastin-Like Polypeptides (ELPs) to form a reversible, injectable hydrogel. They found that the thermosensitive response of ELPs together with the dimerization of Leucine zippers enables the formation of a thermosensitive hydrogel.

The TU-Eindhoven 2023 team used this part in composite part BBa_K4905006 for the formation of a hydrogel in E. coli. This composite part consists of ELPs together with two complementary Leucine zippers at their end. This part is one of these bZIP proteins.

Characterization

We ran an electrophoresis gel with the plasmid, digested with enzymes AcuI and BglI. Slots 2 and 4 were used for different samples of Leucine zipper 1. A 1 kb ladder (L) was used. The remaining slots were used for different parts. The bands formed as expected.

  1. A120: BseRI + BglI, with CIP
  2. Z1.1: Acul + BglI, without CIP
  3. A100: BseRI + BglI, with CIP
  4. Z1.2: Acul + BglI, without CIP
  5. Z2: Acul + BglI, without CIP

Figure 1 | Electrophoresis gel with Z1 in slot 2 and 4

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]

References

[1] Alber, T. (1992). Structure of the leucine zipper. Current Opinion in Genetics and Development, 2, 205–210.

[2] Hakoshima, T. (n.d.). Leucine Zippers. https://doi.org/10.1038/npg.els.0005049

[3] Seldeen, K. L., McDonald, C. B., Deegan, B. J., Bhat, V., & Farooq, A. (2010). Dissecting the Role of Leucine Zippers in the Binding of bZIP Domains of Jun Transcription Factor to DNA. Biochemical and Biophysical Research Communications, 394(4), 1030. https://doi.org/10.1016/J.BBRC.2010.03.116

[4] Gradišar, H., & Jerala, R. (2010). De novodesign of orthogonal peptide pairs forming parallel coiled-coil heterodimers. Journal of Peptide Science, 17(2), 100–106. https://doi.org/10.1002/psc.1331

[5] Fernández‐Colino, A., Arias, F. J., Alonso, M., & Rodríguez-Cabello, J. C. (2015). Amphiphilic Elastin-Like Block Co-Recombinamers Containing Leucine Zippers: Cooperative Interplay between Both Domains Results in Injectable and Stable Hydrogels. Biomacromolecules, 16(10), 3389–3398. https://doi.org/10.1021/acs.biomac.5b01103