Difference between revisions of "Part:BBa K5322034"

Revision as of 16:58, 30 September 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 of Programmed Cell Death 1 Ligand 1 Functional Domain:

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

Figure 2-2 AlphaFold 3 Prediction Results

Sequence and Features