Difference between revisions of "Part:BBa K5322033"
 
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Based on the descriptions of the mouse PD-L1 protein structure in the NCBI database (ADK70951.1, ADK70950.1, Q9NZQ7.1, AAH66841.1), as well asprogrammed cell death 1 ligand 1 precursor [Mus musculus](NP_068693.1), we optimized the DNA sequence according to the codon usage table for Escherichia coli. The optimized DNA sequence was obtained accordingly.
 
  
 
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==Usage and Biology==
 
==Usage and Biology==
 
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Plasm12:20, 30 September 2024 (UTC)~
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Based on the descriptions of the mouse PD-L1 protein structure in the NCBI database (ADK70951.1, ADK70950.1, Q9NZQ7.1, AAH66841.1), as well asprogrammed cell death 1 ligand 1 precursor [Mus musculus](NP_068693.1), we optimized the DNA sequence according to the codon usage table for <i>Escherichia coli</i>. The optimized DNA sequence was obtained accordingly.
 
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==Protein Structure Prediction==
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<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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<h4>AlphaFold 2 Prediction Results:</h4>
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  <td><img src="https://static.igem.wiki/teams/5322/wet-lab/alphafold2-all-pd-l1-model1.gif" 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-all-pd-l1-model2.gif" alt="AlphaFold 2 Prediction Results-model-2" width="300"></td>
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  <td rowspan="3" ><img src="https://static.igem.wiki/teams/5322/wet-lab/pd-l1-all.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-all-pd-l1-model3.gif" alt="AlphaFold 2 Prediction Results-model-3" width="300"></td>
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  <td><img src="https://static.igem.wiki/teams/5322/wet-lab/alphafold2-all-pd-l1-model4.gif" alt="AlphaFold 2 Prediction Results-model-4" width="300"></td>
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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>
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<p align="center"><b>Figure 2-1</b> AlphaFold 2 Prediction Results</p>
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<span class='h3bb'>Sequence and Features</span>
 
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<partinfo>BBa_K5322033 SequenceAndFeatures</partinfo>
 
  
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==Functional Parameters==
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<p><b>2.2 AlphaFold 3 Prediction Results</b></p>
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<partinfo>BBa_K5322033 parameters</partinfo>
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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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<style>
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  .center-img {
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        text-align:center;
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    }
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</style>
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<div class="center-img">
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<body>
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<h4>AlphaFold 3 Prediction Results:</h4>
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<table align="center">
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<tr>
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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>
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</tr>
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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>
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</tr>
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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>
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</tr>
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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>
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</tr>
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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>
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</tr>
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</table>
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</body>
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<p align="center"><b>Figure 2-2</b> AlphaFold 3 Prediction Results</p>
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</div>
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</html>
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==Sequence and Features==
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<partinfo>BBa_K5322033 SequenceAndFeatures</partinfo>

Latest revision as of 14:37, 30 September 2024


Programmed Cell Death 1 Ligand 1 [Mus musculus]

Usage and Biology

Based on the descriptions of the mouse PD-L1 protein structure in the NCBI database (ADK70951.1, ADK70950.1, Q9NZQ7.1, AAH66841.1), as well asprogrammed cell death 1 ligand 1 precursor [Mus musculus](NP_068693.1), we optimized the DNA sequence according to the codon usage table for Escherichia coli. The optimized DNA sequence was obtained accordingly.

Protein Structure Prediction

2.1 AlphaFold 2 Prediction Results

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.

AlphaFold 2 Prediction Results:

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

Figure 2-1 AlphaFold 2 Prediction Results

2.2 AlphaFold 3 Prediction Results

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.

AlphaFold 3 Prediction Results:

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

Figure 2-2 AlphaFold 3 Prediction Results

Sequence and Features


Assembly Compatibility:
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    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 295
  • 12
    INCOMPATIBLE WITH RFC[12]
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    Illegal PstI site found at 295
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    Illegal BglII site found at 144
  • 23
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    Illegal PstI site found at 295
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 295
    Illegal NgoMIV site found at 684
    Illegal AgeI site found at 516
  • 1000
    COMPATIBLE WITH RFC[1000]