Difference between revisions of "Part:BBa K4960028"

 
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A sequence used to encode PVC fiber protein
 
A sequence used to encode PVC fiber protein
  
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===Profile===
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Name:PVC13_NTD-1*EAAAK-CKGGRAKDC-1*EAAAK-PVC13_CTD<br>
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Base Pairs: 1362bp<br>
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Origin:<i> Photorhabdus,</i> Synthetic<br>
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Properties: A sequence used to encode PVC fiber protein
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<!-- Add more about the biology of this part here-->
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===Usage and Biology===
 
===Usage and Biology===
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PVC13 is a sequence that can encode the tail fibre as  the targeting element of the PVC. [1]The PVC fiber protein Pvc13 contains at least 10 repeated motifs resembling the adenovirus fiber and a gp10/gp12 domain, which is probably derived from T4 short tail fiber[2][3]Therefore, it is tempting to speculate that the Pvc13 is another fusion protein derived from the T4 and adenovirus fibers, which may have enabled its recognition of eukaryotic cells.[4]
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Sequence CKGGRAKDC is a peptide motif that homes to white fat vasculature.The in vivo localization studies presented show that CKGGRAKDC targets the white adipose vasculature without a detectable preference for any particular anatomical white fat depot. Meanwhile, the motif is preferentially internalized by a receptor in the adipose vasculature that may serve for targeted delivery of therapeutic compounds to fat.[5]
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The linker 1*EAAAK on both sides of CKGGRAKDC can affect the function and efficiency of bond and recognition by affecting the structure of the tail protein.('''Figure 1''')
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<span class='h3bb'>Sequence and Features</span>
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<p><img src="https://static.igem.wiki/teams/4960/wiki/basic-part/pvc25-26-27-28-29/1.png" alt="" width="900" height="1000" /></p>
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<partinfo>BBa_K4960028 SequenceAndFeatures</partinfo>
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===Functional Parameters===
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'''Figure 1. AlphaFold2-guided Design of Adipose Cell-targeting PVC Coat Expressing Plasmids.'''  AlphaFold2 based prediction of engineered PVC tail fiber trimer structure. Structure of adipose-targeting CKGGRAKDC peptide-presenting PVC tail fiber with indicated linkers were shown.
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<partinfo>BBa_K4960028 parameters</partinfo>
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===Special Design===
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Use the CKGGRAKDC to target fat cells.<br>
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The different linker(1*EAAAK or 3*EAAAK) on both sides of the CKGGRAKDC can affect the structure and function of the tail protein. By altering the linker on both sides of the CKGGRAKDC, we explored the most suitable structure of the tail protein for recognition and bond. At the same time, because of the existence of linker, we can use Golden Gate to replace the sequences in the middle of linker more efficiently than enzyme cutting and enzyme linking.
 
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===Sequence and Features===
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<partinfo>BBa_K4960028 SequenceAndFeatures</partinfo>
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===References===
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[1] Kreitz J, Friedrich MJ, Guru A, Lash B, Saito M, Macrae RK, Zhang F. Programmable protein delivery with a bacterial contractile injection system. Nature. 2023 Apr;616(7956):357-364. doi: 10.1038/s41586-023-05870-7. Epub 2023 Mar 29. <br>
 +
[2] van Raaij, M.J., Mitraki, A., Lavigne, G., and Cusack, S. (1999). A triple beta-
 +
spiral in the adenovirus fibre shaft reveals a new structural motif for a fibrous
 +
protein. Nature 401, 935–938.<br>
 +
[3] Taylor, N.M., Prokhorov, N.S., Guerrero-Ferreira, R.C., Shneider, M.M.,
 +
Browning, C., Goldie, K.N., Stahlberg, H., and Leiman, P.G. (2016). Structure
 +
of the T4 baseplate and its function in triggering sheath contraction. Nature
 +
533, 346–352.<br>
 +
[4]Jiang F, Li N, Wang X, Cheng J, Huang Y, Yang Y, Yang J, Cai B, Wang YP, Jin Q, Gao N. Cryo-EM Structure and Assembly of an Extracellular Contractile Injection System. Cell. 2019 Apr 4;177(2):370-383.e15. doi: 10.1016/j.cell.2019.02.020. Epub 2019 Mar 21. <br>
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[5]Kolonin MG, Saha PK, Chan L, Pasqualini R, Arap W. Reversal of obesity by targeted ablation of adipose tissue. Nat Med. 2004 Jun;10(6):625-32. doi: 10.1038/nm1048. Epub 2004 May 9.<br>

Latest revision as of 14:16, 12 October 2023

PVC13_NTD-1*EAAAK-CKGGRAKDC-1*EAAAK-PVC13_CTD

A sequence used to encode PVC fiber protein

Profile

Name:PVC13_NTD-1*EAAAK-CKGGRAKDC-1*EAAAK-PVC13_CTD
Base Pairs: 1362bp
Origin: Photorhabdus, Synthetic
Properties: A sequence used to encode PVC fiber protein


Usage and Biology

PVC13 is a sequence that can encode the tail fibre as the targeting element of the PVC. [1]The PVC fiber protein Pvc13 contains at least 10 repeated motifs resembling the adenovirus fiber and a gp10/gp12 domain, which is probably derived from T4 short tail fiber[2][3]Therefore, it is tempting to speculate that the Pvc13 is another fusion protein derived from the T4 and adenovirus fibers, which may have enabled its recognition of eukaryotic cells.[4] Sequence CKGGRAKDC is a peptide motif that homes to white fat vasculature.The in vivo localization studies presented show that CKGGRAKDC targets the white adipose vasculature without a detectable preference for any particular anatomical white fat depot. Meanwhile, the motif is preferentially internalized by a receptor in the adipose vasculature that may serve for targeted delivery of therapeutic compounds to fat.[5] The linker 1*EAAAK on both sides of CKGGRAKDC can affect the function and efficiency of bond and recognition by affecting the structure of the tail protein.(Figure 1)

Figure 1. AlphaFold2-guided Design of Adipose Cell-targeting PVC Coat Expressing Plasmids. AlphaFold2 based prediction of engineered PVC tail fiber trimer structure. Structure of adipose-targeting CKGGRAKDC peptide-presenting PVC tail fiber with indicated linkers were shown.

Special Design

Use the CKGGRAKDC to target fat cells.
The different linker(1*EAAAK or 3*EAAAK) on both sides of the CKGGRAKDC can affect the structure and function of the tail protein. By altering the linker on both sides of the CKGGRAKDC, we explored the most suitable structure of the tail protein for recognition and bond. At the same time, because of the existence of linker, we can use Golden Gate to replace the sequences in the middle of linker more efficiently than enzyme cutting and enzyme linking.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 309
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]

References

[1] Kreitz J, Friedrich MJ, Guru A, Lash B, Saito M, Macrae RK, Zhang F. Programmable protein delivery with a bacterial contractile injection system. Nature. 2023 Apr;616(7956):357-364. doi: 10.1038/s41586-023-05870-7. Epub 2023 Mar 29.
[2] van Raaij, M.J., Mitraki, A., Lavigne, G., and Cusack, S. (1999). A triple beta- spiral in the adenovirus fibre shaft reveals a new structural motif for a fibrous protein. Nature 401, 935–938.
[3] Taylor, N.M., Prokhorov, N.S., Guerrero-Ferreira, R.C., Shneider, M.M., Browning, C., Goldie, K.N., Stahlberg, H., and Leiman, P.G. (2016). Structure of the T4 baseplate and its function in triggering sheath contraction. Nature 533, 346–352.
[4]Jiang F, Li N, Wang X, Cheng J, Huang Y, Yang Y, Yang J, Cai B, Wang YP, Jin Q, Gao N. Cryo-EM Structure and Assembly of an Extracellular Contractile Injection System. Cell. 2019 Apr 4;177(2):370-383.e15. doi: 10.1016/j.cell.2019.02.020. Epub 2019 Mar 21.
[5]Kolonin MG, Saha PK, Chan L, Pasqualini R, Arap W. Reversal of obesity by targeted ablation of adipose tissue. Nat Med. 2004 Jun;10(6):625-32. doi: 10.1038/nm1048. Epub 2004 May 9.