Composite

Part:BBa_K5036029

Designed by: Emad hamdy Matter   Group: iGEM24_AFCM-Egypt   (2024-09-21)
Revision as of 11:04, 28 September 2024 by Em100 (Talk | contribs)


dCas9(C)_NLS-Syn-VEGFR-1 (VEGF-R1, C-TEV, NLS, TCS(Q,L), 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,L)), 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 variant of our receptor's first chain where TCS (Q, L) is to it.

Dry lab 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 .

The final form of our receptor is composed of two chains, each chain is built of internal and external domains, so we validated these interactions by calculating the binding affinity between the two chains and VEGFA, which simulate the final design of our receptor.

(VEGFR1-Cdcas9 – VEGFR1-Ndcas9) with VEGFA

The figure displays the interaction between two receptor chains and VEGFA, The (VEGFR1-Cdcas9) chain appears in the red colour, and the (VEGFR1-Ndcas9) chain appears in the blue colour. The VEGFA is in green colour. The calculated binding stability (ΔG) of the combination is -12.9 kcal mol-1 .

The final form of our receptor is composed of two chains, each chain is built of internal and external domains, so we validated these interactions by calculating the binding affinity between the two chains and VEGFA, which simulate the final design of our receptor.

(VEGFR1-Cdcas9 – VEGFR2-Ndcas9) with VEGFA

The figure displays the interaction between two receptor chains and VEGFA, The (VEGFR1-Cdcas9) chain appears in the red colour, and the (VEGFR2-Ndcas9) chain appears in the blue colour. The VEGFA is in green colour. The calculated binding stability (ΔG) of the combination is -13.7 kcal mol-1 .


The receptor chains’ affinity could be affected by the internal domains interactions with the external domains, so we compared between the receptors’ variants to choose the best receptor design in our project.

The figure shows that the combination of VEGFR1-Cdcas9 and VEGFR2-Ndcas9 took the upper hand among other variants .

Characterization by Mathematical Modeling

The model provides the interaction kinetics of VEGFR1 receptor upon binding of VEGF to it , the result shows satisfactory binding affinity and stability based on parametric values from literature

Graph (1). Illustrates the decreasing of free VEGFR (Black line) upon binding of VEGF to one of the receptor chains to form (RA) complex (Yellow line), that bind directly to the other chain of the receptor to final form the fitted ligand receptor complex (RAR) to reach 0.2 .


The continuation of the first model provides the activation kinetics of the TEV protease which occurs subsequent to the binding of VEGF to our receptor allowing the dimerization process for the receptor chains to take place. The result shows TEV protease activation based on parametric values from literature

Graph (2). Illustrates the dimerization level (Blue line) that reaches (7.8) upon binding of VEGF to its receptor to activate TEV protease (Red line), The activation level reaches (6.5) to release d-Cas9 system .


The continuation of the second model provides the activation kinetics of the d-Cas9 system which occurs subsequent to cleavage activity of TEV protease after its activation. The result shows increase in d-Cas9 activity which implies successful cleavage of the TEV protease for releasing the N and C terminal of the d-Cas9 system and its assembly based on parametric values from literature

Graph (2). Illustrates the released d-Cas9 system that activation reaches (110), upon activation of TEV protease .

Experimental Characterization

dCas9-VP64-GAL4 expression vector and a UAS-CMV trans-enhancer were constructed to investigate the effectiveness of the GAL4-UAS system for CRISPR-assisted trans-enhancer activation . Both linear (LUAS-CMV) and circular (CUAS-CMV) forms of the UAS-CMV enhancer were successfully recruited to target genes by the dCas9-VP64-fused GAL4 protein.When co-transfected with a reporter gene in 293T cells, both LUAS-CMV and CUAS-CMV significantly activated gene expression on opposite of control conditions.

This figure show Flow cytometry analysis of ZsGreen expression shows very high gene expression with (dCas9-VP64-GAL4/sgRNA-LUAS-CMV) and (dCas9-VP64-GAL4/sgRNA- CUAS-CMV) .

This figure shows graphic illustration of flow cytometry analysis of 293 T cells which shows high gene expression with both LUAS-CMV and CUAS-CMV. These findings highlight the potential of the GAL4-UAS system for efficient CRISPR-mediated trans-enhancer activation .


Also these vectors ( dCas9-VP64-GAL4 with linear (LUAS-CMV) and circular (CUAS-CMV) CMV enhancer) were constructed and co-transfected with a reporter gene(HNF4α gene) in HepG2 cells . then results were illustrated and compared with the results of the same construcrts in 293T cells.

This figure shows graphic illustration of flow cytometry analysis of 293 T cells and HepG2 cells which shows high gene expression with (dCas9-VP64-GAL4/sgRNA-LUAS-CMV) and (dCas9-VP64-GAL4/sgRNA- CUAS-CMV). Gene expression was higher in HepG2 cells. These findings highlight the potential of the GAL4-UAS system for efficient CRISPR-mediated trans-enhancer activation .


Reference

Mac Gabhann F, Popel AS. Dimerization of VEGF receptors and implications for signal transduction: a computational study. Biophys Chem. 2007 Jul;128(2-3):125-39. doi: 10.1016/j.bpc.2007.03.010. Epub 2007 Mar 24. PMID: 17442480; PMCID: PMC2711879.


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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