Difference between revisions of "Part:BBa K5036046"
 
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lang=EN style='font-size:11.0pt;line-height:115%'>this figure illustrates the structure of MCP-MMP9 Nanobody which is attached to our switch
 
lang=EN style='font-size:11.0pt;line-height:115%'>this figure illustrates the structure of MCP-MMP9 Nanobody which is attached to our switch
 
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==Characterization by Mathematical Modeling==
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The model provides the interaction kinetics of MMP-9 to both Nanobody-2 NSP3 from the cap side and Nanobody-2 MCP from MS2 aptamer side to form a binding complex to activate our TID switch. The result shows an increase in the binding complex upon MMP-9 interaction based on parametric values from literature
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<html><div align="center"style="border:solid #17252A; width:100%;float:center;"><img style="                              max-width:850px;
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width:75%;
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height:auto;
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position: relative;
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top: 50%;
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left: 35%;
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transform: translate( -50%);
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padding-top:25px;
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"src="https://static.igem.wiki/teams/5036/parts-modeling/46.png
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<p class=MsoNormal align=center style='text-align:left;border:none;width:98% ;justify-content:center;'><span
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lang=EN style='padding-bottom:30px;font-size:11.0pt;line-height:115%'>Graph(1). Illustrates the relation between decreasing free MMP-9 (Blue line) upon their binding to nanobody-2 NSP3 (orange line) and nanobody-2 MCP (Red line) at the same time, which results in forming a binding complex ( Green line)
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.  </span></p></div></html>
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==Reference==
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Lee DW, Kochenderfer JN, Stetler-Stevenson M, Cui YK, Delbrook C, Feldman SA, Fry TJ, Orentas R, Sabatino M, Shah NN, Steinberg SM. T cells expressing CD19 chimeric antigen receptors for acute lymphoblastic leukaemia in children and young adults: a phase 1 dose-escalation trial. The Lancet. 2015 Feb 7;385(9967):517-28.
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Shin YJ, Park SK, Jung YJ, Kim YN, Kim KS, Park OK, Kwon SH, Jeon SH, Trinh le A, Fraser SE, Kee Y, Hwang BJ. Nanobody-targeted E3-ubiquitin ligase complex degrades nuclear proteins. Sci Rep. 2015 Sep 16;5:14269. doi: 10.1038/srep14269. PMID: 26373678; PMCID: PMC4571616.
  
  

Latest revision as of 15:44, 26 September 2024


MCP-MMP9 Nanobody2

Part Description

Our engineered switch contains a nanobody that recognizes MMP9, an enzyme elevated in injured cells. This nanobody is linked to MCP protein, which is attached to MS2 from the other end because of its high affinity for MS2.

Usage

Our TID device contains MCP protein linked to specific sensors (nanobodies) that detect MMP9, a protein elevated within cells after tissue injury. TID switches from off state to on state when MMP9 is present in the cell cytoplasm. This triggers the circularization of YAP mRNA, which is essential for protein production

this figure illustrates the structure of MCP-MMP9 Nanobody which is attached to our switch .

Characterization by Mathematical Modeling

The model provides the interaction kinetics of MMP-9 to both Nanobody-2 NSP3 from the cap side and Nanobody-2 MCP from MS2 aptamer side to form a binding complex to activate our TID switch. The result shows an increase in the binding complex upon MMP-9 interaction based on parametric values from literature

Graph(1). Illustrates the relation between decreasing free MMP-9 (Blue line) upon their binding to nanobody-2 NSP3 (orange line) and nanobody-2 MCP (Red line) at the same time, which results in forming a binding complex ( Green line) .

Reference

Lee DW, Kochenderfer JN, Stetler-Stevenson M, Cui YK, Delbrook C, Feldman SA, Fry TJ, Orentas R, Sabatino M, Shah NN, Steinberg SM. T cells expressing CD19 chimeric antigen receptors for acute lymphoblastic leukaemia in children and young adults: a phase 1 dose-escalation trial. The Lancet. 2015 Feb 7;385(9967):517-28.

Shin YJ, Park SK, Jung YJ, Kim YN, Kim KS, Park OK, Kwon SH, Jeon SH, Trinh le A, Fraser SE, Kee Y, Hwang BJ. Nanobody-targeted E3-ubiquitin ligase complex degrades nuclear proteins. Sci Rep. 2015 Sep 16;5:14269. doi: 10.1038/srep14269. PMID: 26373678; PMCID: PMC4571616.


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]