Difference between revisions of "Part:BBa K4586024"

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==characterization by mathematical modeling==
 
==characterization by mathematical modeling==
 
This model is to simulate kinetics of the binding between CCP1 of the Syn-Notch on the surface of the stem cell to BCR of autoreactive B-cell. When stem cells are injected into the body, the amount of free CCP1 of the synthetic notch receptor increases, and as BCR binds to it, the amount of free CCP1 portion decreases, forming a binding state of both that activates the internal domain ZF21.16VP64 of the Syn-Notch
 
This model is to simulate kinetics of the binding between CCP1 of the Syn-Notch on the surface of the stem cell to BCR of autoreactive B-cell. When stem cells are injected into the body, the amount of free CCP1 of the synthetic notch receptor increases, and as BCR binds to it, the amount of free CCP1 portion decreases, forming a binding state of both that activates the internal domain ZF21.16VP64 of the Syn-Notch
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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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<p class=MsoNormal align=center style='text-align:left;border:none;width:98% ;justify-content:center;'><span
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lang=EN style='font-size:11.0pt;line-height:115%'>A, Graph(1) shows an increase in the free portion of CCP1 of Syn-Notch (represented as blue line) then decreases as BCR binds to it. As the binding occurs, BCR decreases (represented as orange line) and the binding state increases (represented as green line).
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3)We modeled the kinetics of the CCP1 external domain of the Syn-Notch receptor to explain the binding affinity between it and BCR. Depending on the result of the docking score, It’s concluded that it was stable and reached steady state after binding. Which is the most suitable type in our comparison.
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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:100%;
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height:auto;
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position: relative;
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top: 50%;
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left: 40%;
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transform: translate( -50%);
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padding-bottom:25px;
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padding-top:25px;
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"src="https://static.igem.wiki/teams/4586/wiki/model/pasted-image-0-4.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='font-size:11.0pt;line-height:115%'>Graph(4) shows an increase in the free portion of CCP1 of Syn-Notch (represented as blue line) then decreases as BCR binds to it. As the binding occurs, BCR decreases (represented as orange line) and the binding state increases (represented as green line). that dissociates after binding as it is not stable. </span></p></div></html>
 
<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here
 
===Usage and Biology===
 
===Usage and Biology===

Revision as of 11:56, 12 October 2023


CCP1-Synthetic Notch Receptor

Description and Usage

This composite part codes for a synthetic receptor sensitive to the autoreactive B-cell receptor secreting ACPAs. CCP1 syn notch receptor consists of three main domains, first the extracellular domain represented in tagged citrullinated vimentin conjugated to CD8 alpha signal that mediates the expression of the receptor on the cell membrane, second the transmembrane domain represented in mouse notch core protein that is characterized by mechanosensitive structure that transfer the signal from the extracellular domain to the third intracellular domain that contains our potent transcription module VP64 which trigger the expression of our therapeutic agent (Cas12k\gBAFF-R) as shown in figure 1. and figure 2.

Figure 1 . illustrates the structure of our vimentin synthetic notch receptor, which is formed of 3 components: first, the tagged CCP1 antigen within the extracellular surface of MSCs; second, the mouse notch core protein; and finally, ZF21.16-VP64, representing the internal domain releasing our transcription module VP64





Figure 2. illustrates the design of our genetic circuit coding for the vimentin synthetic notch receptor.






literature characterization

The study used gel electrophoresis to structurally characterize CCP1 compared to other parts. In Addition to studying its presence and association with neural tissues in different cross sections.

A)They observed ccp1 in proteins of brain, spinal cord and peripheral nerves.They confirmed that by detection of extra band in HEK293 transfected with ccp1-YFP fusion proteins and absence of signals in pcd mouse brain B)They found relation of ccp1 with myelinated axons(NF200) but not compact myelin (MBP) C)They found ccp1 in motor neurons( CHAT) in the ventral horn of spinal cord .

characterization by mathematical modeling

This model is to simulate kinetics of the binding between CCP1 of the Syn-Notch on the surface of the stem cell to BCR of autoreactive B-cell. When stem cells are injected into the body, the amount of free CCP1 of the synthetic notch receptor increases, and as BCR binds to it, the amount of free CCP1 portion decreases, forming a binding state of both that activates the internal domain ZF21.16VP64 of the Syn-Notch

A, Graph(1) shows an increase in the free portion of CCP1 of Syn-Notch (represented as blue line) then decreases as BCR binds to it. As the binding occurs, BCR decreases (represented as orange line) and the binding state increases (represented as green line).

3)We modeled the kinetics of the CCP1 external domain of the Syn-Notch receptor to explain the binding affinity between it and BCR. Depending on the result of the docking score, It’s concluded that it was stable and reached steady state after binding. Which is the most suitable type in our comparison.

Graph(4) shows an increase in the free portion of CCP1 of Syn-Notch (represented as blue line) then decreases as BCR binds to it. As the binding occurs, BCR decreases (represented as orange line) and the binding state increases (represented as green line). that dissociates after binding as it is not stable.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NotI site found at 774
    Illegal NotI site found at 783
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 614
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal SapI.rc site found at 1399