Composite

Part:BBa_K5036049

Designed by: Emad hamdy Matter   Group: iGEM24_AFCM-Egypt   (2024-09-21)


MMP9 Nanobody2- NSP3

Part Description

Our engineered switch contains a nanobody that recognizes MMP9, an enzyme elevated in injured cells. This nanobody is linked to NSP3 protein, which is attached to the cap from the other end.

Usage

Our TID device contains NSP3 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 NSP3-MMP9 Nanobody which is attached to the cap of 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
    INCOMPATIBLE WITH RFC[21]
    Illegal XhoI site found at 1660
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


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