Composite

Part:BBa_K5036026

Designed by: Emad hamdy Matter   Group: iGEM24_AFCM-Egypt   (2024-09-21)
Revision as of 07:31, 25 September 2024 by Em100 (Talk | contribs) (→‎Software Characterization)


dCas9(C)_NLS-Syn-VEGFR-1(VEGF-R1, C-TEV, NLS, TCS(Q,G),HA,dCas9(C),VP64,GFP)

Part Description

In our first receptor chain, we've engineered a system that responds to tissue injury. An external domain, VEGF-R1, is attached to an internal domain composed of C terminal domain of TEV protease, a nuclear localization signal (NLS), a TEV cleavage site(TCS(Q,G)), and dCas9(C) which is linked to transcription activator VP64

Usage

this is our receptor's first chain. our receptor is activated after binding of VEGF to the external domain which is designed to attach specifically to it. after activation the two domains of TEV dimerizes forming catalytically active TEV protease which will cleave the two chains at TCS. upon cleavage of the two chains the two domains of dCas9 dimerize and is released attached to transcription activator to be guided to its direction

This figure illustrates our receptor's first chain structure.

Software Characterization

we had the chance to match the external domains with different internal domain components to select single suitable receptor chain. The whole chain affinity is affected by the internal domain, thus we had to try VEGFR1Cdcas with VEGFA:

VEGFR1Cdcas-VEGFA

The interaction between the chain composed of VEGFR1 as an external domain and Cdcas9 as an internal domain with VEGFA yields ΔG of -11.2 kcal mol-1 .


Then we have made a comparison between the four receptor chain variants’ binding stability with VEGFA.

This figure shows that VEGFR2Cdcas-VEGFA complex has the highest stability among other variants and VEGFR1NdCas9-VEGFA complex has the lowest stability among other variants .

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 2173
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 3973
    Illegal NgoMIV site found at 4046
    Illegal NgoMIV site found at 4531
    Illegal NgoMIV site found at 5440
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 6737
    Illegal SapI.rc site found at 3268


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