Difference between revisions of "Part:BBa K5374013"

 
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<partinfo>BBa_K5374013 short</partinfo>
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The Discoidin Domain Receptor (DDR) is involved in collagen binding and ECM remodeling. Fusion with EGFP allows evaluation of DDR’s impact on protein bioactivity and provides a screening system for DDR as a potential tag for controlling collagen-based protein release.
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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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<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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<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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<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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===Usage and Biology===
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<span class='h3bb'>Sequence and Features</span>
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<partinfo>BBa_K5374013 SequenceAndFeatures</partinfo>
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<!-- Uncomment this to enable Functional Parameter display
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===Functional Parameters===
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<partinfo>BBa_K5374013 parameters</partinfo>
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Revision as of 13:32, 22 September 2024


DDR-EGFP (Discoidin Domain Receptor). A receptor tyrosine kinase activated by collagen, fused with E

The Discoidin Domain Receptor (DDR) is involved in collagen binding and ECM remodeling. Fusion with EGFP allows evaluation of DDR’s impact on protein bioactivity and provides a screening system for DDR as a potential tag for controlling collagen-based protein release.

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 EcoRI site found at 253
    Illegal EcoRI site found at 337
    Illegal EcoRI site found at 820
    Illegal PstI site found at 259
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 253
    Illegal EcoRI site found at 337
    Illegal EcoRI site found at 820
    Illegal NheI site found at 835
    Illegal PstI site found at 259
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 253
    Illegal EcoRI site found at 337
    Illegal EcoRI site found at 820
    Illegal BglII site found at 459
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 253
    Illegal EcoRI site found at 337
    Illegal EcoRI site found at 820
    Illegal PstI site found at 259
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 253
    Illegal EcoRI site found at 337
    Illegal EcoRI site found at 820
    Illegal PstI site found at 259
    Illegal NgoMIV site found at 588
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 1478