Difference between revisions of "Part:BBa K4960037"
 
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<partinfo>BBa_K4960037 short</partinfo>
 
<partinfo>BBa_K4960037 short</partinfo>
  
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A flexible linker which can influence the structure of tail fiber connected to the CKGGRAKDC.<br>
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A flexible linker which can influence the structure of tail fiber connected to the CKGGRAKDC.
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===Profile===
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Name: pvc1-pvc12,pvc13_NTD-3*GGGSG-CKGGRAKDC-3*GGGSG -pvc13_CTD,pvc14-pvc16<br>
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Origin: Synthetic<br>
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Properties: A flexible linker which can influence the structure of tail fiber connected to the CKGGRAKDC.<br>
  
  
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===Usage and Biology===
 
===Usage and Biology===
 
The system is a syringe-like macromolecular complex that inject protein payloads into fat cells by driving a spike through the cellular membrane. Different payloads can be load into the lumen of the inner tube behind the spike, form fusion proteins with the tube, or associate with the spike itself. Studies suggest that the tail fibre is probably involved in target recognition. [1]Our project has enabled the system to target adipocytes by modifying the tail fibre to bind to CKGGRAKDC. CKGGRAKDC is a peptide motif that homes to white fat vasculature. The studies 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.[2] After specific recognition and binding to adipocytes, it can cross the via sheath contraction and inject the desired payloads.
 
The system is a syringe-like macromolecular complex that inject protein payloads into fat cells by driving a spike through the cellular membrane. Different payloads can be load into the lumen of the inner tube behind the spike, form fusion proteins with the tube, or associate with the spike itself. Studies suggest that the tail fibre is probably involved in target recognition. [1]Our project has enabled the system to target adipocytes by modifying the tail fibre to bind to CKGGRAKDC. CKGGRAKDC is a peptide motif that homes to white fat vasculature. The studies 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.[2] After specific recognition and binding to adipocytes, it can cross the via sheath contraction and inject the desired payloads.
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The linker 3*GGGSG on both sides of CKGGRAKDC can affect the function and efficiency of bond and recognition by affecting the structure of the tail protein.(Fig.1)
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The linker 3*GGGSG on both sides of CKGGRAKDC can affect the function and efficiency of bond and recognition by affecting the structure of the tail protein.('''Fig.1''')
 
<html>
 
<html>
  
 
<figure class="figure">
 
<figure class="figure">
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<img src="https://static.igem.wiki/teams/4960/wiki/composite-part/different-linkers.png" class="figure-img img-fluid rounded"  height="400px">
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<img src="https://static.igem.wiki/teams/4960/wiki/composite-part/different-linkers.png" class="figure-img img-fluid rounded"  height="500px">
  
 
</figure>
 
</figure>
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</html>
 
</html>
  
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Figure 1.AlphaFold2 based prediction of engineered PVC tail fiber trimer structure.<br>
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'''Figure 1.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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Structure of adipose-targeting CKGGRAKDC peptide-presenting PVC tail fiber with indicated linkers were shown.
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===Special Design===
 
===Special Design===
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The different linker(1*GGGSG or 3*GGGSG) 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.
 
The different linker(1*GGGSG or 3*GGGSG) 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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<span class='h3bb'>Sequence and Features</span>
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===Sequence and Features===
 
Tube:pvc1, pvc5, pvc7<br>
 
Tube:pvc1, pvc5, pvc7<br>
 
Sheath:pvc2, pvc3, pvc4<br>
 
Sheath:pvc2, pvc3, pvc4<br>
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Tail fbres:pvc13_NTD-3*GGGSG-CKGGRAKDC-3*GGGSG -pvc13_CTD<br>
 
Tail fbres:pvc13_NTD-3*GGGSG-CKGGRAKDC-3*GGGSG -pvc13_CTD<br>
 
Baseplate:pvc9, pvc11, pvc12<br>
 
Baseplate:pvc9, pvc11, pvc12<br>
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Spike:pvc8, pvc10<br>
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Spike:pvc8, pvc10(Fig.2)<br>
 
Assembly method:3A Assembly<br>
 
Assembly method:3A Assembly<br>
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<partinfo>BBa_K4960037 SequenceAndFeatures</partinfo>
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<html>
  
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<figure class="figure">
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<img src="https://static.igem.wiki/teams/4960/wiki/composite-part/bsal-replace/beautiful-pvc.png" class="figure-img img-fluid rounded"  height="100px">
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</figure>
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</html>
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'''Figure 2.PVC composition diagram'''
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<partinfo>BBa_K4960037 SequenceAndFeatures</partinfo>
  
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  
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<partinfo>BBa_K4960037 parameters</partinfo>
 
<partinfo>BBa_K4960037 parameters</partinfo>
 
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===References===
 
===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. PMID: 36991127; PMCID: PMC10097599.<br>
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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.<br>
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[2]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. PMID: 15133506.<br>
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[2]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.<br>

Latest revision as of 10:12, 12 October 2023


pPVC promoter->pvc1-pvc12->pvc13_NTD-3*GGGSG-CKGGRAKDC-3*GGGSG -pvc13_CTD->pvc14-pvc16

A flexible linker which can influence the structure of tail fiber connected to the CKGGRAKDC.

Profile

Name: pvc1-pvc12,pvc13_NTD-3*GGGSG-CKGGRAKDC-3*GGGSG -pvc13_CTD,pvc14-pvc16
Origin: Synthetic
Properties: A flexible linker which can influence the structure of tail fiber connected to the CKGGRAKDC.


Usage and Biology

The system is a syringe-like macromolecular complex that inject protein payloads into fat cells by driving a spike through the cellular membrane. Different payloads can be load into the lumen of the inner tube behind the spike, form fusion proteins with the tube, or associate with the spike itself. Studies suggest that the tail fibre is probably involved in target recognition. [1]Our project has enabled the system to target adipocytes by modifying the tail fibre to bind to CKGGRAKDC. CKGGRAKDC is a peptide motif that homes to white fat vasculature. The studies 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.[2] After specific recognition and binding to adipocytes, it can cross the via sheath contraction and inject the desired payloads. The linker 3*GGGSG on both sides of CKGGRAKDC can affect the function and efficiency of bond and recognition by affecting the structure of the tail protein.(Fig.1)

Figure 1.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*GGGSG or 3*GGGSG) 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

Tube:pvc1, pvc5, pvc7
Sheath:pvc2, pvc3, pvc4
Sheath terminator:pvc15
Tail fbres:pvc13_NTD-3*GGGSG-CKGGRAKDC-3*GGGSG -pvc13_CTD
Baseplate:pvc9, pvc11, pvc12
Spike:pvc8, pvc10(Fig.2)
Assembly method:3A Assembly

Figure 2.PVC composition diagram


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 7406
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 2407
    Illegal BglII site found at 11264
    Illegal BglII site found at 14099
    Illegal BglII site found at 17020
    Illegal XhoI site found at 2691
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 11792
    Illegal NgoMIV site found at 17551
    Illegal NgoMIV site found at 17690
    Illegal AgeI site found at 6704
    Illegal AgeI site found at 9641
    Illegal AgeI site found at 10327
    Illegal AgeI site found at 10468
    Illegal AgeI site found at 11576
    Illegal AgeI site found at 17989
    Illegal AgeI site found at 19677
  • 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.
[2]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.