Difference between revisions of "Part:BBa K5374014"

 
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The Agrin domain plays a role in ECM organization and synapse formation, with collagen-binding capabilities. The fusion with EGFP  
 
The Agrin domain plays a role in ECM organization and synapse formation, with collagen-binding capabilities. The fusion with EGFP  
 
allows for testing of its effect on protein activity, helping determine its suitability as a tag for controlled release systems in tissue engineering.
 
allows for testing of its effect on protein activity, helping determine its suitability as a tag for controlled release systems in tissue engineering.
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<p>The fluorescence data were obtained by expressing various EGFP fusion proteins in E. coli, diluting each culture to an equal cell density. Fluorescence intensity was measured for each group, and the fluorescence ratio relative to EGFP (used as a standard) was calculated. The figure shows these normalized fluorescence values for each fusion protein.</p>
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<img src="https://static.igem.wiki/teams/5374/contribution/fig-1-1.svg" style="width: 300px">
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<p class="img-description">Figure 1.1 The fluorescence activity of each fusion protein</p>
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<p>The fluorescence activity of each fusion protein was tested to evaluate whether the CBDs affected EGFP activity. The relative fluorescence values of the eight CBD-EGFP fusion proteins were measured to assess the impact of the collagen-binding domains (CBDs) on EGFP activity. As shown in the graph:</p>
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<ul>
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<li>SPARC/OD-EGFP, CBD MMPs-EGFP, DB-EGFP, VWF-A Domain-EGFP, and FTD-EGFP exhibited fluorescence values close to or higher than that of the control EGFP, indicating that these CBDs did not significantly affect the bioactivity of EGFP.</li>
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<li>DDR-EGFP, AGR-EGFP and COMP-EGFP showed slightly lower fluorescence values, suggesting some impact on EGFP activity, but still maintaining measurable fluorescence.</li>
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</ul>
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<p>Overall, the majority of CBDs retained sufficient EGFP activity, which confirms that they can be used in further experiments for controlled release without significantly impairing the functionality of the fusion proteins. These results support the selection of CBDs that balance collagen binding with maintaining protein bioactivity.</p>
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<p>Binding affinity tests (via microscale thermophoresis) were also conducted to determine which CBDs had high binding affinity (for BMP-4) and low binding affinity (for VEGF). Based on the binding experiment shown in the graph, the results illustrate the relative binding affinities of different <b>CBD-EGFP fusion proteins</b> to collagen, with the binding affinity represented by the dissociation constant (<b>Kd</b>). The <b>midpoint of each curve</b> on the x-axis corresponds to the Kd value, indicating how tightly the CBDs bind to collagen.</p>
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<img src="https://static.igem.wiki/teams/5374/contribution/fig-1-2.svg" style="width: 500px">
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<p class="img-description">Figure 1.2 Binding energy of each fusion protein</p>
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<ul>
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<li><b>FTD-EGFP</b> shows the strongest binding to collagen, with the lowest Kd value. From the graph, the midpoint of the FTD curve is approximately at <b>8.3*10<sup>-7</sup> M</b>, indicating a high binding affinity.</li>
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<li><b>CBD MMPs-EGFP</b> exhibits the weakest binding to collagen, with the highest Kd value. The midpoint of the CBD MMPs curve is approximately at <b>6.7*10<sup>-6</sup> M</b>, indicating a lower binding affinity compared to the other CBDs.</li>
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<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here

Revision as of 13:32, 22 September 2024


AGR-EGFP (Agrin Domain). A multi-domain proteoglycan that binds collagen, fused with EGFP to determi

The Agrin domain plays a role in ECM organization and synapse formation, with collagen-binding capabilities. The fusion with EGFP allows for testing of its effect on protein activity, helping determine its suitability as a tag for controlled release systems in tissue engineering.

The fluorescence data were obtained by expressing various EGFP fusion proteins in E. coli, diluting each culture to an equal cell density. Fluorescence intensity was measured for each group, and the fluorescence ratio relative to EGFP (used as a standard) was calculated. The figure shows these normalized fluorescence values for each fusion protein.

Figure 1.1 The fluorescence activity of each fusion protein

The fluorescence activity of each fusion protein was tested to evaluate whether the CBDs affected EGFP activity. The relative fluorescence values of the eight CBD-EGFP fusion proteins were measured to assess the impact of the collagen-binding domains (CBDs) on EGFP activity. As shown in the graph:

  • SPARC/OD-EGFP, CBD MMPs-EGFP, DB-EGFP, VWF-A Domain-EGFP, and FTD-EGFP exhibited fluorescence values close to or higher than that of the control EGFP, indicating that these CBDs did not significantly affect the bioactivity of EGFP.
  • DDR-EGFP, AGR-EGFP and COMP-EGFP showed slightly lower fluorescence values, suggesting some impact on EGFP activity, but still maintaining measurable fluorescence.

Overall, the majority of CBDs retained sufficient EGFP activity, which confirms that they can be used in further experiments for controlled release without significantly impairing the functionality of the fusion proteins. These results support the selection of CBDs that balance collagen binding with maintaining protein bioactivity.

Binding affinity tests (via microscale thermophoresis) were also conducted to determine which CBDs had high binding affinity (for BMP-4) and low binding affinity (for VEGF). Based on the binding experiment shown in the graph, the results illustrate the relative binding affinities of different CBD-EGFP fusion proteins to collagen, with the binding affinity represented by the dissociation constant (Kd). The midpoint of each curve on the x-axis corresponds to the Kd value, indicating how tightly the CBDs bind to collagen.

Figure 1.2 Binding energy of each fusion protein

  • FTD-EGFP shows the strongest binding to collagen, with the lowest Kd value. From the graph, the midpoint of the FTD curve is approximately at 8.3*10-7 M, indicating a high binding affinity.
  • CBD MMPs-EGFP exhibits the weakest binding to collagen, with the highest Kd value. The midpoint of the CBD MMPs curve is approximately at 6.7*10-6 M, indicating a lower binding affinity compared to the other CBDs.

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 352
    Illegal PstI site found at 826
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 262
    Illegal NheI site found at 1309
    Illegal PstI site found at 352
    Illegal PstI site found at 826
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 352
    Illegal PstI site found at 826
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 352
    Illegal PstI site found at 826
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 1952