Difference between revisions of "Part:BBa K5322034"

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==Usage and Biology==
 
==Usage and Biology==
 
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<p>The full-length mouse PD-L1 protein has a large molecular weight and a complex structure. Therefore, we referred to the descriptions of mouse PD-L1 in the NCBI database (ADK70951.1, ADK70950.1, Q9NZQ7.1, AAH66841.1) and truncated the Programmed Cell Death 1 Ligand 1 [Mus musculus] (<a href="https://parts.igem.org/Part:BBa_K5322033">BBa_K5322033</a>). The functional domain—the immunoglobulin variable (IgV) domain—corresponds to residues 20 to 130 in the 290 amino acid sequence. To ensure that the functionality of the truncated protein is preserved, we retained the first 19 amino acids and the last 20 amino acids (131-150), aiming to minimize any impact on the IgV structure.
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<p><b>2.1 AlphaFold 2 Prediction Results</b></p>
 
<p><b>2.1 AlphaFold 2 Prediction Results</b></p>
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<p>For the PD-L1 protein, we utilized AlphaFold 2 from Google DeepMind for protein structure prediction, aiming to gain a deeper understanding of PD-L1.</p>
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<p>We used AlphaFold 2 from Google DeepMind to predict the structures of both the full-length and truncated PD-L1 proteins, revealing that the main functional domain of the truncated PD-L1 Functional domainremains unaffected according to the prediction results.</p>
  
 
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<h4>AlphaFold 2 Prediction Results:</h4>
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<h4>AlphaFold 2 Prediction Results of Programmed Cell Death 1 Ligand 1</h4>
 
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   <td><img src="https://static.igem.wiki/teams/5322/wet-lab/alphafold2-all-pd-l1-model5.gif" alt="AlphaFold 2 Prediction Results-model-5" width="300"></td>
 
   <td><img src="https://static.igem.wiki/teams/5322/wet-lab/alphafold2-all-pd-l1-model5.gif" alt="AlphaFold 2 Prediction Results-model-5" width="300"></td>
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<h4>AlphaFold 2 Prediction Results of Programmed Cell Death 1 Ligand 1 Functional Domain:</h4>
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  <td><img src="https://static.igem.wiki/teams/5322/wet-lab/alphafold2-half-pd-l1-model1.gif" alt="alphafold2-half-pd-l1-model1" width="300"></td>
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  <td><img src="https://static.igem.wiki/teams/5322/wet-lab/alphafold2-half-pd-l1-model2.gif" alt="alphafold2-half-pd-l1-model2" width="300"></td>
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  <td rowspan="3" ><img src="https://static.igem.wiki/teams/5322/wet-lab/pd-l1.jpg" alt="AlphaFold 2 Prediction Results-model-1" width="300"></td>
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  <td><img src="https://static.igem.wiki/teams/5322/wet-lab/alphafold2-half-pd-l1-model3.gif" alt="alphafold2-half-pd-l1-model3" width="300"></td>
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  <td><img src="https://static.igem.wiki/teams/5322/wet-lab/alphafold2-half-pd-l1-model4.gif" alt="alphafold2-half-pd-l1-model4" width="300"></td>
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  <td><img src="https://static.igem.wiki/teams/5322/wet-lab/alphafold2-half-pd-l1-model5.gif" alt="alphafold2-half-pd-l1-model5" width="300"></td>
 
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<p><b>2.2 AlphaFold 3 Prediction Results</b></p>
 
<p><b>2.2 AlphaFold 3 Prediction Results</b></p>
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<p>With the release of AlphaFold 3, the accuracy of protein structure prediction has been further improved. Therefore, we conducted another round of protein structure prediction.</p>
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<p>Subsequently, Google released AlphaFold 3, which we utilized to predict the protein structure again. We also performed molecular docking to demonstrate that our truncated PD-L1 can successfully bind to PD-1 and exert its function. The results are illustrated in the following figure.</p>
  
 
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<h4>AlphaFold 3 Prediction Results:</h4>
 
<h4>AlphaFold 3 Prediction Results:</h4>
 
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  <td>Programmed Cell Death 1 Ligand 1</td>
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  <td>Programmed Cell Death 1 Ligand 1 Functional Domain</td>
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   <td><img src="https://static.igem.wiki/teams/5322/wet-lab/all-pd-l1-alpha3-model1.gif" alt="AlphaFold 3 Prediction Results-model-1" width="300"></td>
 
   <td><img src="https://static.igem.wiki/teams/5322/wet-lab/all-pd-l1-alpha3-model1.gif" alt="AlphaFold 3 Prediction Results-model-1" width="300"></td>
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  <td><img src="https://static.igem.wiki/teams/5322/wet-lab/half-pd-l1-alpha3-model1.gif" alt="AlphaFold 3 Prediction Results-model-1" width="300"></td>
 
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   <td><img src="https://static.igem.wiki/teams/5322/wet-lab/all-pd-l1-alpha3-model2.gif" alt="AlphaFold 3 Prediction Results-model-2" width="300"></td>
 
   <td><img src="https://static.igem.wiki/teams/5322/wet-lab/all-pd-l1-alpha3-model2.gif" alt="AlphaFold 3 Prediction Results-model-2" width="300"></td>
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  <td><img src="https://static.igem.wiki/teams/5322/wet-lab/half-pd-l1-alpha3-model2.gif" alt="AlphaFold 3 Prediction Results-model-2" width="300"></td>
 
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   <td><img src="https://static.igem.wiki/teams/5322/wet-lab/all-pd-l1-alpha3-model3.gif" alt="AlphaFold 3 Prediction Results-model-3" width="300"></td>
 
   <td><img src="https://static.igem.wiki/teams/5322/wet-lab/all-pd-l1-alpha3-model3.gif" alt="AlphaFold 3 Prediction Results-model-3" width="300"></td>
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  <td><img src="https://static.igem.wiki/teams/5322/wet-lab/half-pd-l1-alpha3-model3.gif" alt="AlphaFold 3 Prediction Results-model-3" width="300"></td>
 
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   <td><img src="https://static.igem.wiki/teams/5322/wet-lab/all-pd-l1-alpha3-model4.gif" alt="AlphaFold 3 Prediction Results-model-4" width="300"></td>
 
   <td><img src="https://static.igem.wiki/teams/5322/wet-lab/all-pd-l1-alpha3-model4.gif" alt="AlphaFold 3 Prediction Results-model-4" width="300"></td>
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  <td><img src="https://static.igem.wiki/teams/5322/wet-lab/half-pd-l1-alpha3-model4.gif" alt="AlphaFold 3 Prediction Results-model-4" width="300"></td>
 
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   <td><img src="https://static.igem.wiki/teams/5322/wet-lab/all-pd-l1-alpha3-model5.gif" alt="AlphaFold 3 Prediction Results-model-5" width="300"></td>
 
   <td><img src="https://static.igem.wiki/teams/5322/wet-lab/all-pd-l1-alpha3-model5.gif" alt="AlphaFold 3 Prediction Results-model-5" width="300"></td>
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  <td><img src="https://static.igem.wiki/teams/5322/wet-lab/half-pd-l1-alpha3-model5.gif" alt="AlphaFold 3 Prediction Results-model-5" width="300"></td>
 
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<p align="center"><b>Figure 2-2</b> AlphaFold 3 Prediction Results</p>
 
<p align="center"><b>Figure 2-2</b> AlphaFold 3 Prediction Results</p>
 
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                  src="https://static.igem.wiki/teams/5322/half-mouse/pd-l1-pd-1-model1.gif" style="width:100%;"></td>
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                  src="https://static.igem.wiki/teams/5322/half-mouse/pd-l1-pd-1-model2.gif" style="width:100%;"></td>
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                  src="https://static.igem.wiki/teams/5322/half-mouse/pd-l1-pd-1-model3.gif" style="width:100%;"></td>
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              <td><img src="https://static.igem.wiki/teams/5322/whole-mouse/pd-l1-pd-1-model3.gif" style="width:100%;">
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                  src="https://static.igem.wiki/teams/5322/half-mouse/pd-l1-pd-1-model4.gif" style="width:100%;"></td>
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              <td><img src="https://static.igem.wiki/teams/5322/whole-mouse/pd-l1-pd-1-model4.gif" style="width:100%;">
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                  src="https://static.igem.wiki/teams/5322/half-mouse/pd-l1-pd-1-model5.gif" style="width:100%;"></td>
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              <td><img src="https://static.igem.wiki/teams/5322/whole-mouse/pd-l1-pd-1-model5.gif" style="width:100%;">
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Latest revision as of 12:15, 2 October 2024


Programmed Cell Death 1 Ligand 1 Functional Domain [Mus musculus]

Usage and Biology

The full-length mouse PD-L1 protein has a large molecular weight and a complex structure. Therefore, we referred to the descriptions of mouse PD-L1 in the NCBI database (ADK70951.1, ADK70950.1, Q9NZQ7.1, AAH66841.1) and truncated the Programmed Cell Death 1 Ligand 1 [Mus musculus] (BBa_K5322033). The functional domain—the immunoglobulin variable (IgV) domain—corresponds to residues 20 to 130 in the 290 amino acid sequence. To ensure that the functionality of the truncated protein is preserved, we retained the first 19 amino acids and the last 20 amino acids (131-150), aiming to minimize any impact on the IgV structure.

Protein Structure Prediction

2.1 AlphaFold 2 Prediction Results

We used AlphaFold 2 from Google DeepMind to predict the structures of both the full-length and truncated PD-L1 proteins, revealing that the main functional domain of the truncated PD-L1 Functional domainremains unaffected according to the prediction results.

AlphaFold 2 Prediction Results of Programmed Cell Death 1 Ligand 1

AlphaFold 2 Prediction Results-model-1
AlphaFold 2 Prediction Results-model-2 AlphaFold 2 Prediction Results-model-1
AlphaFold 2 Prediction Results-model-3
AlphaFold 2 Prediction Results-model-4
AlphaFold 2 Prediction Results-model-5

AlphaFold 2 Prediction Results of Programmed Cell Death 1 Ligand 1 Functional Domain:

alphafold2-half-pd-l1-model1
alphafold2-half-pd-l1-model2 AlphaFold 2 Prediction Results-model-1
alphafold2-half-pd-l1-model3
alphafold2-half-pd-l1-model4
alphafold2-half-pd-l1-model5

Figure 2-1 AlphaFold 2 Prediction Results

2.2 AlphaFold 3 Prediction Results

Subsequently, Google released AlphaFold 3, which we utilized to predict the protein structure again. We also performed molecular docking to demonstrate that our truncated PD-L1 can successfully bind to PD-1 and exert its function. The results are illustrated in the following figure.

AlphaFold 3 Prediction Results:

Programmed Cell Death 1 Ligand 1 Programmed Cell Death 1 Ligand 1 Functional Domain
AlphaFold 3 Prediction Results-model-1 AlphaFold 3 Prediction Results-model-1
AlphaFold 3 Prediction Results-model-2 AlphaFold 3 Prediction Results-model-2
AlphaFold 3 Prediction Results-model-3 AlphaFold 3 Prediction Results-model-3
AlphaFold 3 Prediction Results-model-4 AlphaFold 3 Prediction Results-model-4
AlphaFold 3 Prediction Results-model-5 AlphaFold 3 Prediction Results-model-5

Figure 2-2 AlphaFold 3 Prediction Results

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 316
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 316
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 216
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 316
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 316
  • 1000
    COMPATIBLE WITH RFC[1000]